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Sample records for benzohydroxamic acid structure

  1. Extractive properties of benzohydroxamic and N-benzoyl-benzohydroxamic acids as analytical reagents towards six transition metal ions

    International Nuclear Information System (INIS)

    Mohamed, Mohamed Rafie Hamid

    1999-06-01

    Two hydroxamic acids were prepared: benzohydroxamic and N-benzoyl benzohydroxamic acids. The former was prepared by coupling the free hydrox amine with benzoyl chloride with the ratio 1:1 in alkaline medium, where as the latter by the same procedure with the ratio 1:2 respectively, they were identified by their melting points, elemental analysis of their nitrogen contents. infra-red spectrophotometry, as well as their nitrogen using elevation of boiling point and the titration method to determine their molecular weights. The two hydroxamic acids were used as analytical reagents for the extraction of the metals Cr(vi), Fe(III), Ti(iv), Co(II) and U(vi). Benzohydroxamic acid has a maximum extraction 99.55% for Cr.(vi) 3M H 2 SO 4 , of 90.16% for Ti(iv) at pH 2.0,of 80.56% for Co(II) at pH 8.0 and 98.01% for U(vi) at pH 6.0. N-benzoyl benzohydroxamic acid has a maximum extraction of 96.45% for Cr(vi) at 3M H 2 So 4 , of 90.82% for Fe(III) at pH 4.0, of 97.02% for V(v) at 3M H 2 So 4 , of 83.56% for Ti(iv) at pH 2.0, of 89.82% for Co(II) at pH 8.0 and of 97.16% for U(vi) at pH 6.0. at the same pH of maximum extraction using heavy matrix, synthetic sea-water, benzohydroxamic acid has maximum values of 91.08%, of 77.99%, of 91.39%, of 87.50 and of 93.17% for Cr(vi), Fe(III), V(v), Ti(iv), Co9II) and U(vi) respectively whereas n-benzoyl benzohydroxamic acid has maximum values of 86.17%, of 77.78%, of 89.61%, of 75.66%, of 79.63% and of 91.18% for Cr(vi), Fe(III), V(v), Ti(iv), Co(II) and U(vi) respectively. The ratio of metal to ligand was determined utilizing the continuous variation method. It was 1 :2, 1: 1, 1 : 1, 1 : 2, 1: 2 and 1 : 2 with respect to Cr(vi), fe(III), Ti(iv), Co(II) and U(vi) respectively.(Author)

  2. Benzohydroxamic acid as a reductometric titrant:determination of manganese, chromium and vanadium in steels

    International Nuclear Information System (INIS)

    Ahmed, M.K.; Subbarao, C.

    1981-01-01

    A method has been developed for the rapid determination of manganese and chromium by direct stepwise reductometric titration with benzohydroxamic acid, and of vanadium by titration with ascorbic acid (with benzohydroxamic acid as indicator) in the same aliquot. The method is free from the interference of common alloying elements present in steels. Some BCS steel samples have been analysed with good precision and accuracy. (author)

  3. Degradation and Mineralization of Benzohydroxamic Acid by Synthesized Mesoporous La/TiO2

    Directory of Open Access Journals (Sweden)

    Xianping Luo

    2016-10-01

    Full Text Available Rare earth element La-doped TiO2 (La/TiO2 was synthesized by the sol-gel method. Benzohydroxamic acid was used as the objective pollutant to investigate the photocatalytic activity of La/TiO2. The physicochemical properties of the prepared materials were characterized by X-ray diffraction, X-ray photoelectron spectroscopy, UV-vis diffuse reflectance spectroscopy, specific surface area and porosity, scanning electron microscopy and transmission electron microscopy. As a result, the doping of La could inhibit the crystal growth of TiO2, increase its specific surface area and expand its response to visible light, thus improving its photocatalytic activity. La/TiO2 with the doping ratio of 0.75% calcined at 500 °C, showing the highest photocatalytic activity to degrade benzohydroxamic acid under the irradiation of 300 W mercury lamp. About 94.1% of benzohydroxamic acid with the original concentration at 30 mg·L−1 was removed after 120 min in a solution of pH 4.4 with an La/TiO2 amount of 0.5 g·L−1. Furthermore, 88.5% of the total organic carbon was eliminated after 120 min irradiation. In addition, after four recycling runs, La/TiO2 still kept high photocatalytic activity on the photodegradation of benzohydroxamic acid. The interfacial charge transfer processes were also hypothesized.

  4. Analytical recovery of Cr (VI), Mo (VI), Ti (IV) and Co (II) by N-phenyl-meta-nitro-benzohydroxamic and N-P-tolyl-meta-nitro-benzohydroxamic acids

    International Nuclear Information System (INIS)

    Ahmed, Abdul Aziz Malik Mohamed

    2000-05-01

    Two hydroxamic acids were prepared; N-phenyl-m-nitro-benzohydroxamic and N-p-tolyl-m-nitro-benzo hydroxamic acids. N-phenyl-m-nitro-benzohydroxamic was prepared by coupling the β-phenyl hydroxylamine with m-nitro-benzoyl chloride in ratio 1:1 in alkaline medium at zero degree centigrade. It recrystallized from a mixture of benzene and petroleum ether (2:1) with the yield of 67%. The product was characterized by: A-nitrogen content which was found to be 10.7% (lit. 10.9%). B-infra-red spectroscopy. C-the molecular weight which was determined by titration, was found to be 257.7 gram (lit. 257 gram). D-the molecular weight which was determined by elevation of the boiling point, was found to be 253.7 gram (lit. 257 gram). E-characteristic violet color reaction with vanadium and blood-red reaction with ferric chloride solutions. F-melting point 117 degree centigrade. N-p-tolyl-m-nitro benzo hydroxamic acid was prepared by coupling the p-tolyl-hydroxylamine with m-nitro benzoyl chloride using the same procedure. It was recrystallized from a mixture of benzene and petroleum ether (2:1) with the yield of 63%. The product was characterized by: A-nitrogen content which was found to be 10.1% (lit. 10.3). B-infra-red spectroscopy. C-the molecular weight which was determined by titration, was found to be 271.6 gram (lit. 272). D-the molecular weight which was determined by elevation of the boiling point, was found to be 269.9 gram (lit. 272 gram). E.characteristic violet color reaction with vanadium and blood-red color with ferric chloride solutions. F-melting point which was found to be 105 degree centigrade (lit. 106 degree c). the two hydroxamic acids were used as analytical reagents for extraction of metal ions Ti (IV), Cr (VI), Mo (VI) and Co (II). With an equal volume of the organic and aqueous phase, and only one extraction, N-phenyl-m-nitro-benzohydroxamic acid was found to have a maximum extraction of 30.18% for Ti (IV) at pH 2.0, of 97.06% for Cr (VI) at 3MH 2 SO 4

  5. Metal complexes of salicylhydroxamic acid (H2Sha), anthranilic hydroxamic acid and benzohydroxamic acid. Crystal and molecular structure of [Cu(phen)2(Cl)]Cl x H2Sha, a model for a peroxidase-inhibitor complex.

    Science.gov (United States)

    O'Brien, E C; Farkas, E; Gil, M J; Fitzgerald, D; Castineras, A; Nolan, K B

    2000-04-01

    Stability constants of iron(III), copper(II), nickel(II) and zinc(II) complexes of salicylhydroxamic acid (H2Sha), anthranilic hydroxamic acid (HAha) and benzohydroxamic acid (HBha) have been determined at 25.0 degrees C, I=0.2 mol dm(-3) KCl in aqueous solution. The complex stability order, iron(III) > copper(II) > nickel(II) approximately = zinc(II) was observed whilst complexes of H2Sha were found to be more stable than those of the other two ligands. In the preparation of ternary metal ion complexes of these ligands and 1,10-phenanthroline (phen) the crystalline complex [Cu(phen)2(Cl)]Cl x H2Sha was obtained and its crystal structure determined. This complex is a model for hydroxamate-peroxidase inhibitor interactions.

  6. Effect of Pb2+ ions on ilmenite flotation and adsorption of benzohydroxamic acid as a collector

    Science.gov (United States)

    Xu, Longhua; Tian, Jia; Wu, Houqin; Lu, Zhongyuan; Yang, Yaohui; Sun, Wei; Hu, Yuehua

    2017-12-01

    The effects of Pb2+ ions on ilmenite flotation and adsorption of benzohydroxamic acid (BHA) as a collector were investigated using microflotation tests, zeta potential measurements, adsorption analysis, Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS). The microflotation results indicate that the addition of Pb2+ significantly improves the recovery of ilmenite using BHA as a collector. A maximum recovery of 88.46% is obtained at pH 8.12 in the presence of Pb2+; a maximum recovery of 45% is obtained at the same pH using BHA alone. At pHs below 8.0, lead nitrate are mainly present in the solution as Pb2+ and PbOH+, while at pHs above 8.0, the predominant components are Pb(OH)2(s) and Pb(OH)3-. The adsorption of these lead species influences the zeta potential of ilmenite and the number of activated sites on the ilmenite surface. FTIR and XPS analyses reveal that lead species and BHA react with the metal sites on the ilmenite surface. The lead species in solution are either adsorbed onto the ilmenite surface, which increases the surface activity of ilmenite, or react with BHA in solution to form complexes of lead and BHA.

  7. Non-aqueous titration of hydroxamic acids.

    Science.gov (United States)

    Stamey, T W; Christian, R

    1966-01-01

    Benzohydroxamic acid is titrated with 0.1M tetrabutyl-anunonium hydroxide in nine non-aqueous solvents with three different indicating electrodes. The best results are obtained using dimethylformamide as solvent and platinum-platinum electrodes. Four monoprotic and three diprotic hydroxamie acids and iron(III) benzohydroxamate have been successfully titrated with this system. The effect of quantitative additions of carbon dioxide to the titrant on its apparent molarity are found to be dependent on the amount added, the strength and sample size of acid titrated and the solvent used.

  8. Characterization and Computation of Yb/TiO2 and Its Photocatalytic Degradation with Benzohydroxamic Acid

    Directory of Open Access Journals (Sweden)

    Xianping Luo

    2017-11-01

    Full Text Available Yb-doped TiO2 (Yb/TiO2 compositions were synthesized by sol-gel method, and the prepared materials were characterized by X-ray Diffraction (XRD, X-ray photoelectron spectroscopy (XPS, UV-visible diffuse-reflectance spectrum (UV-Vis DRS, transmission electron microscope (TEM and high resolution transmission electron microscope (HRTEM, energy dispersive spectrometer (EDS, and N2 adsorption. A beneficiation reagent of benzohydroxamic acid (BHA was used to test the photocatalytic activity of Yb/TiO2. The characterizations indicate that the doping of Yb could inhibit the crystal growth of TiO2, enhance the specific surface area, increase the binding energy of Ti2p, and also slightly expand the adsorption ranges to visible light. Furthermore, the computation of band structure also indicates that Yb-doped TiO2 could make the forbidden band narrower than pure anatase TiO2, which presents a red shift in the absorption spectrum. As a result of the photodegradation experiment on BHA, Yb/TiO2 (0.50% in mass sintered at 450 °C displayed the highest catalytic activity for BHA when compared with pure TiO2 or other doped Yb/TiO2 compositions, and more than 89.2% of the total organic carbon was removed after 120 min. Almost all anions, including Cl−, HCO3−, NO3−, and SO42−, inhibited the degradation of BHA by Yb/TiO2, and their inhibition effects followed the order of HCO3− > NO3− > SO42− > Cl−. Cations of Na+, K+, Ca2+, and Mg2+ displayed a slight suppressing effect due to the impact of Cl− coexisting in the solution. In addition, Yb/TiO2 maintained a high photocatalytic ability with respect to BHA after four runs. It is hypothesized that ·OH is one of the main species involved in the photodegradation of BHA, and the mutual transformation of Yb3+ and Yb2+ could promote the separation of electron-hole pairs.

  9. A comparison study of adsorption of benzohydroxamic acid and amyl xanthate on smithsonite with dodecylamine as co-collector

    Science.gov (United States)

    Wang, Zhen; Xu, Longhua; Wang, Jinming; Wang, Li; Xiao, Junhui

    2017-12-01

    The objective of this paper is to display the results of the flotation and adsorption behaviors of benzohydroxamic acid (BHA), potassium amyl xanthate (KAX), dodecylamine- hydrochloride (DDA), mixed BHA/DDA and KAX/DDA on smithsonite. The flotation results show a collecting ability sequence of BHA > KAX > DDA on smithsonite and the best flotation performance at mixing ratio of 1:4 mol fraction DDA/KAX for mixed collector on smithsonite. The enhancement of smithsonite recovery by co-adsorption of KAX and DDA, while no promotion effect as to mixed BHA/DDA catanionic system, are attributed to the difference in steric effect of absorbed head group. According to the results of zeta potential and contact angle (CA) measurements, a most negative charged and the highest hydrophobic smithsonite surface are attained using KAX with DDA as co-collector, which shows a good agreement with the flotation results. FTIR measurements display the stabilization against oxidation and decomposition of DDA on KAX and the inhibition of preferential adsorbed BHA ions on DDA adsorption. The interaction energies of single and mixed collectors with mineral surface also shows well consistency with experimental results. The adsorption models proposed illustrate the decrease in the electrostatic head-head repulsion and the increase in lateral tail-tail hydrophobic interaction between adjacent KAX anions due to the insertion of DDA cations, while almost no DDA could access to smithsonite surface through adjacent BHA owing to steric effect.

  10. Preparation of N-1 -naphthyl benzo- and N-phenyl benzo hydroxamic acids and study of their extractability towards Fe (III), Cr (VI) and U (VI)

    Energy Technology Data Exchange (ETDEWEB)

    Mohamed, Eltoum Elnour [Department of Chemistry, Faculty of Science, University of Khartoum, Khartoum (Sudan)

    1997-12-01

    Two aryl hydroxamic acids were prepared; The N-phenyl benzo hydroxamic acid and the N-1- naphthyl benzohydroxamic acid the first one was prepared by the partial reduction of nitrobenzene to the {beta}-phenyl hydroxylamine and coupling the latter with benzyl chloride. The reduction was carried out using ammonium chloride and zinc dust; this pair failed after so many attempts to give the N-1- naphthyl hydroxylamine. So the latter was prepared by using a somewhat milder reducing agent; hydrogen sulphide and ammonia gas in absolute alcohol. The two acids were obtained using the modified procedure of Tandon coupling the hydroxylamine with benzoyl chloride. The two acids were characterized by their melting points, elemental analysis, their I.R functional group frequencies and by their characteristic colour tests with vanadium (VI) and Iron (III). The acids were used for the extraction and spectrophotometric determination for iron (III), Chromium (VI), and Uranium (VI) from different molar solution, PH and from synthetic sea water. The maximum recovery of iron (III) occurred at PH 4 and PH 5 giving 92.25 and 91.25% when using N-1-naphthyl benzo hydroxamic acid and a maximum recovery of 100% at PH 5 with other acid. The maximum recovery of Chromium (VI) occurred at 3MH{sup 2}SO{sup 4} of 97.50% when using N-1-naphthyl benzohydroxamic acid and a maximum of 94.25% at the same molar concentration with N-phenyl benzo hydroxamic acid. The maximum recovery for Uranium (VI) was occurred at PH 7 giving 100% when using N-1-naphthyl benzo hydroxamic acid and a maximum recovery of 85% at PH 7 and PH* with the other acid. The two reagents give sharp colour with both iron (III) and chromium (VI), so trials were carried out to compare the curves obtained with that of the original reagent i.e. Thiocynate and diphenylcarbazide, which give a smaller slope.(Author) 121 refs. , 15 tabs. , 13 figs

  11. Preparation of N-1 -naphthyl benzo- and N-phenyl benzo hydroxamic acids and study of their extractability towards Fe (III), Cr (VI) and U (VI)

    International Nuclear Information System (INIS)

    Mohamed, Eltoum Elnour

    1997-12-01

    Two aryl hydroxamic acids were prepared; The N-phenyl benzo hydroxamic acid and the N-1- naphthyl benzohydroxamic acid the first one was prepared by the partial reduction of nitrobenzene to the β-phenyl hydroxylamine and coupling the latter with benzyl chloride. The reduction was carried out using ammonium chloride and zinc dust; this pair failed after so many attempts to give the N-1- naphthyl hydroxylamine. So the latter was prepared by using a somewhat milder reducing agent; hydrogen sulphide and ammonia gas in absolute alcohol. The two acids were obtained using the modified procedure of Tandon coupling the hydroxylamine with benzoyl chloride. The two acids were characterized by their melting points, elemental analysis, their I.R functional group frequencies and by their characteristic colour tests with vanadium (VI) and Iron (III). The acids were used for the extraction and spectrophotometric determination for iron (III), Chromium (VI), and Uranium (VI) from different molar solution, PH and from synthetic sea water. The maximum recovery of iron (III) occurred at PH 4 and PH 5 giving 92.25 and 91.25% when using N-1-naphthyl benzo hydroxamic acid and a maximum recovery of 100% at PH 5 with other acid. The maximum recovery of Chromium (VI) occurred at 3MH 2 SO 4 of 97.50% when using N-1-naphthyl benzohydroxamic acid and a maximum of 94.25% at the same molar concentration with N-phenyl benzo hydroxamic acid. The maximum recovery for Uranium (VI) was occurred at PH 7 giving 100% when using N-1-naphthyl benzo hydroxamic acid and a maximum recovery of 85% at PH 7 and PH* with the other acid. The two reagents give sharp colour with both iron (III) and chromium (VI), so trials were carried out to compare the curves obtained with that of the original reagent i.e. Thiocynate and diphenylcarbazide, which give a smaller slope.(Author)

  12. Flotation performances and adsorption mechanism of α-hydroxyoctyl phosphinic acid to cassiterite

    International Nuclear Information System (INIS)

    Li, Fangxu; Zhong, Hong; Zhao, Gang; Wang, Shuai; Liu, Guangyi

    2015-01-01

    Highlights: • Flotation of cassiterite is carried out using a new collector HPA. • Phosphorous and oxygen of HPA forms chelation with Sn. • HPA exhibits good selectivity to cassiterite against magnetite and hematite. • HPA chemisorbs on cassiterite surface by form of Sn–P and Sn–O–P bond. - Abstract: In this paper, the flotation performances and adsorption mechanism of α-hydroxyoctyl phosphinic acid (HPA) to cassiterite were investigated by adsorption experiments, micro-flotation tests, zeta potential measurements, Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) analyses. The micro-flotation results indicated that compared with styrene phosphonic acid (SPA), diphosphonic acid (DPA), benzohydroxamic acid (BHA) and salicylhydroxamic acid (SHA), HPA exhibited excellent collecting power to cassiterite and superior selectivity against magnetite or hematite over a wide pH range. The results of adsorption experiments and zeta potential deduced that HPA chemisorb on cassiterite surfaces. The results of FTIR inferred HPA chemisorb onto cassiterite surfaces through its P and O atoms with the P–H and O–H bonds broken. XPS analysis further demonstrated HPA react with Sn species by formation of Sn–O–P and Sn–P bond.

  13. Journal of Chemical Sciences | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    In the presence of catechol (H2cat) and benzohydroxamic acid (H2bha), oxovanadium (IV) complexes, [VO (acac)(ONN)] gave mixed-chelate oxovanadium(V) complexes [VO(cat)(ONN)] and [VO(bha)(ONN)] respectively. These complexes are not very stable in solution and slowly convert to the corresponding dioxo species ...

  14. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    Molecular Structure of Nucleic Acids. A Structure for Deoxyribose Nucleic Acid. J. D. Watson and F. H. C. Crick. Medical Research Council Unit for the Study of the Molecular Structure of Biological. Systems, Cavendish Laboratory, Cambridge. April 2. We wish to suggest a structure for the salt of deoxyribose nucleic acid ...

  15. Structure of acid-stable carmine.

    Science.gov (United States)

    Sugimoto, Naoki; Kawasaki, Yoko; Sato, Kyoko; Aoki, Hiromitsu; Ichi, Takahito; Koda, Takatoshi; Yamazaki, Takeshi; Maitani, Tamio

    2002-02-01

    Acid-stable carmine has recently been distributed in the U.S. market because of its good acid stability, but it is not permitted in Japan. We analyzed and determined the structure of the major pigment in acid-stable carmine, in order to establish an analytical method for it. Carminic acid was transformed into a different type of pigment, named acid-stable carmine, through amination when heated in ammonia solution. The features of the structure were clarified using a model compound, purpurin, in which the orientation of hydroxyl groups on the A ring of the anthraquinone skeleton is the same as that of carminic acid. By spectroscopic means and the synthesis of acid-stable carmine and purpurin derivatives, the structure of the major pigment in acid-stable carmine was established as 4-aminocarminic acid, a novel compound.

  16. Effects of nucleotide pool imbalances on the excision repair of ultraviolet-induced damage in the DNA of human diploid fibroblasts

    International Nuclear Information System (INIS)

    Snyder, R.D.

    1985-01-01

    In an attempt to better understand the mechanism of repair inhibition by DNA polymerase inhibitors, and the nature of hydroxyurea enhancement, experiments were initiated in which the effects of a series of ribonucleotide reductase inhibitors on dNTP pools and on the DNA repair process were determined in both quiescent cultures and log-phase cultures of human fibroblasts. It was determined that hydroxyurea, deoxyadenosine, pyridine-2-carboxaldehyde thiosemicarbazone (TSC), pyrozoloimidazole (IMPY), 3,5-diamino-1,2,4-triazole (guanazole), 3,4,5-trihydroxy benzohydroxamic acid (THBA) and 3,4-dihydroxy benzohydroxamic acid (DHBA) are all effective inhibitors of the DNA repair process in confluent cells but not in log-phase cells. Moreover, the effects of these inhibitors can be reversed by the addition of certain combinations of deoxynucleosides. These reversal studies and the direct analysis of dNTP pool modulation by these compounds in log phase and confluent cultures support the notion that specific pool depletions rather than general imbalance of pools gives rise to the inhibition of the DNA excision repair process

  17. Amino acid code of protein secondary structure.

    Science.gov (United States)

    Shestopalov, B V

    2003-01-01

    The calculation of protein three-dimensional structure from the amino acid sequence is a fundamental problem to be solved. This paper presents principles of the code theory of protein secondary structure, and their consequence--the amino acid code of protein secondary structure. The doublet code model of protein secondary structure, developed earlier by the author (Shestopalov, 1990), is part of this theory. The theory basis are: 1) the name secondary structure is assigned to the conformation, stabilized only by the nearest (intraresidual) and middle-range (at a distance no more than that between residues i and i + 5) interactions; 2) the secondary structure consists of regular (alpha-helical and beta-structural) and irregular (coil) segments; 3) the alpha-helices, beta-strands and coil segments are encoded, respectively, by residue pairs (i, i + 4), (i, i + 2), (i, i = 1), according to the numbers of residues per period, 3.6, 2, 1; 4) all such pairs in the amino acid sequence are codons for elementary structural elements, or structurons; 5) the codons are divided into 21 types depending on their strength, i.e. their encoding capability; 6) overlappings of structurons of one and the same structure generate the longer segments of this structure; 7) overlapping of structurons of different structures is forbidden, and therefore selection of codons is required, the codon selection is hierarchic; 8) the code theory of protein secondary structure generates six variants of the amino acid code of protein secondary structure. There are two possible kinds of model construction based on the theory: the physical one using physical properties of amino acid residues, and the statistical one using results of statistical analysis of a great body of structural data. Some evident consequences of the theory are: a) the theory can be used for calculating the secondary structure from the amino acid sequence as a partial solution of the problem of calculation of protein three

  18. Interactive Hangman teaches amino acid structures and abbreviations

    OpenAIRE

    Pennington, BO; Sears, D; Clegg, DO

    2014-01-01

    © 2014 by The International Union of Biochemistry and Molecular Biology, 42(6):495-500, 2014. We developed an interactive exercise to teach students how to draw the structures of the 20 standard amino acids and to identify the one-letter abbreviations by modifying the familiar game of "Hangman." Amino acid structures were used to represent single letters throughout the game. To provide additional practice in identifying structures, hints to the answers were written in "amino acid sentences" f...

  19. Structural transformations on N-acetylneuraminic acid

    International Nuclear Information System (INIS)

    Schmid, W.

    1986-01-01

    Structural transformations on N-Acetylneuraminic acid are of special interest because of the biological importance of this compound. Although many stereo- and regioselective variations (especially for pyranoid derivatives) have been reported, no detailed studies of the furanoid derivatives from N-Acetylneuramino-1, 4-lactone diethyl dithioacetal have been described hitherto. Therefore a series of derivatives of the Neu5Ac-lactone diethyl dithioacetal has been investigated by n.m.r. spectroscopic techniques. The complete assignment of the 1 H and 13 C resonances was achieved by relaxation time measurements, decoupling experiments and 2-D - shiftcorrelation spectroscopy. The influence of different substituents on the conformational behavior is also discussed. For the Tetra-O-Acetyl-N-acetylneuraminic acid-γ-lactone diethyl dithioacetal the conformation in solution could be determined. The observed data were explained by a zigzag conformation of the backbone as described for the acetylated mannose diethyl dithioacetal. The synthesis of the tetrazole-analogue of N-Acetylneuraminic acid is also described. This compound is of special biological interest because there is a similarity in acidity between the carboxyl-group and the tetrazole-function and the metabolic stability of the tetrazole function is enhanced in comparison with the carboxyl-group. Many of the biological functions of N-Acetylneuraminic acid are connected with the presence of the carboxyl-group. It was therefore interesting to transform this group to the bioisostere tetrazole-function to investigate the influence of the tetrazole-group of this compound on biological activity in the future. During the application of protective groups in the field of Neuraminic acid chemistry a new compound, an ortholactone-derivative of Neu5Ac, was discovered. It's structure is similar to an adamantanecage and the chemistry of such an orthoester function opens new possibilities for structural transformations on N

  20. Structural features of lignohumic acids

    Czech Academy of Sciences Publication Activity Database

    Novák, František; Šestauberová, Martina; Hrabal, R.

    2015-01-01

    Roč. 1093, August (2015), s. 179-185 ISSN 0022-2860 Institutional support: RVO:60077344 Keywords : C-13 NMR * FTIR * humic acids * lignohumate * lignosulfonate * structure Subject RIV: DF - Soil Science Impact factor: 1.780, year: 2015

  1. Ambazone-lipoic acid salt: Structural and thermal characterization

    Energy Technology Data Exchange (ETDEWEB)

    Kacso, Irina [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath street, 400293 Cluj-Napoca (Romania); Racz, Csaba-Pal; Santa, Szabolcs [Babes-Bolyai' University, Faculty of Chemistry, 11 Arany Janos street, Cluj-Napoca (Romania); Rus, Lucia [' Iuliu Hatieganu' University of Medicine and Pharmacy, Faculty of Pharmacy, 6 Louis Pasteur street, 400349 Cluj-Napoca (Romania); Dadarlat, Dorin; Borodi, Gheorghe [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath street, 400293 Cluj-Napoca (Romania); Bratu, Ioan, E-mail: ibratu@gmail.com [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath street, 400293 Cluj-Napoca (Romania)

    2012-12-20

    Highlights: Black-Right-Pointing-Pointer Salt of Ambazone with lipoic acid obtained by solvent-drop grinding. Black-Right-Pointing-Pointer Ambazone lipoate salt crystallizes in monoclinic system. Black-Right-Pointing-Pointer FTIR data suggest the deprotonation of the lipoic acid. Black-Right-Pointing-Pointer Thermal behaviour different of ambazone salt as compared to the starting compounds. - Abstract: A suitable method for increasing the solubility, dissolution rate and consequently the bioavailability of poor soluble acidic or basic drugs is their salt formation. The aim of this study is to investigate the structural and thermal properties of the compound obtained by solvent drop grinding (SDG) method at room temperature, starting from the 1:1 molar ratios of ambazone (AMB) and {alpha}-lipoic acid (LA). The structural characterization was performed with X-ray powder diffraction (XRPD) and infrared spectroscopy (FTIR). The thermal behaviour of the obtained compound (AMB{center_dot}LA) was investigated by differential scanning calorimetry (DSC) and thermogravimetry (TG). The photopyroelectric calorimetry, in front detection configuration (FPPE), was applied to measure and compare the room temperature values of one dynamic thermal parameter (thermal effusivity) for starting and resulting compounds. Both structural and supporting calorimetric techniques pointed out a salt structure for AMB{center_dot}LA compound as compared to those of the starting materials.

  2. Effect of acid hydrolysis on starch structure and functionality: a review.

    Science.gov (United States)

    Wang, Shujun; Copeland, Les

    2015-01-01

    Acid hydrolysis is an important chemical modification that can significantly change the structural and functional properties of starch without disrupting its granular morphology. A deep understanding of the effect of acid hydrolysis on starch structure and functionality is of great importance for starch scientific research and its industrial applications. During acid hydrolysis, amorphous regions are hydrolyzed preferentially, which enhances the crystallinity and double helical content of acid hydrolyzed starch. This review discusses current understanding of the effect of acid hydrolysis on starch structure and functionality. The effects of acid hydrolysis on amylose content, chain length distribution of amylopectin molecules, molecular and crystalline organization (including lamellar structure) and granular morphology are considered. Functional properties discussed include swelling power, gelatinization, retrogradation, pasting, gel texture, and in vitro enzyme digestibility. The paper also highlights some promising applications of acid hydrolyzed starch (starch nanocrystals) in the preparation of biodegradable nanocomposites, bio-hydrogen, and slowly digestible starch-based healthy foods.

  3. A Standard Structure for Bile Acids and Derivatives

    Directory of Open Access Journals (Sweden)

    Francisco Meijide

    2018-02-01

    Full Text Available The crystal structures of two ester compounds (a monomer in its methyl ester form, with an amino isophthalic group, and a dimer in which the two steroid units are linked by a urea bridge recrystallized from ethyl acetate/methanol derived from cholic acid are described. Average bond lengths and bond angles from the crystal structures of 26 monomers and four dimers (some of them in several solvents of bile acids and esters (and derivatives are used for proposing a standard steroid nucleus. The hydrogen bond network and conformation of the lateral chain are also discussed. This standard structure was used to compare with the structures of both progesterone and cholesterol.

  4. Interfacial assembly structures and nanotribological properties of saccharic acids.

    Science.gov (United States)

    Shi, Hongyu; Liu, Yuhong; Zeng, Qingdao; Yang, Yanlian; Wang, Chen; Lu, Xinchun

    2017-01-04

    Saccharides have been recognized as potential bio-lubricants because of their good hydration ability. However, the interfacial structures of saccharides and their derivatives are rarely studied and the molecular details of interaction mechanisms have not been well understood. In this paper, the supramolecular assembly structures of saccharic acids (including galactaric acid and lactobionic acid), mediated by hydrogen bonds O-HN and O-HO, were successfully constructed on a highly oriented pyrolytic graphite (HOPG) surface by introducing pyridine modulators and were explicitly revealed by using scanning tunneling microscopy (STM). Furthermore, friction forces were measured in the saccharic acid/pyridine co-assembled system by atomic force microscopy (AFM), revealing a larger value than a pristine saccharic acid system, which could be attributed to the stronger tip-assembled molecule interactions that lead to the higher potential energy barrier needed to overcome. The effort on saccharide-related supramolecular self-assembly and nanotribological behavior could provide a novel and promising pathway to explore the interaction mechanisms underlying friction and reveal the structure-property relationship at the molecular level.

  5. Lymphatic fatty acids in canine with pharmaceutical formulations containing structured triacylglycerols

    DEFF Research Database (Denmark)

    Holm, R.; Porsgaard, Trine; Porter, C.J.H.

    2006-01-01

    The intramolecular structure of dietary triacylglycerols (TAG) influences absorption. In this study, two different pharmaceutical formulations were compared containing TAG differing in fatty acid profiles and intramolecular structures: LML and MLM, where M represented medium-chain fatty acids (MCFA...... was generally higher than from the animals dosed with the MLM vehicle; however, statistically significant differences were only found for 18:0 and 18:3n-3. In conclusion, these results indicated that the fatty acid profile and intramolecular structure of administered TAG influenced the absorption of fatty acids...

  6. Chemical and physical structures of proteinoids and related polyamino acids

    Science.gov (United States)

    Mita, Hajime; Kuwahara, Yusuke; Nomoto, Shinya

    Studies of polyamino acid formation pathways in the prebiotic condition are important for the study of the origins of life. Several pathways of prebiotic polyamino acid formation have been reported. Heating of monoammonium malate [1] and heating of amino acids in molten urea [2] are important pathways of the prebiotic peptide formation. The former case, globular structure called proteinoid microsphere is formed in aqueous conditions. The later case, polyamino acids are formed from unrestricted amino acid species. Heating of aqueous aspargine is also interesting pathway for the prebiotic polyamino acid formation, because polyamino acid formation proceeds in aqueous condition [3]. In this study, we analyzed the chemical structure of the proteinoids and related polyamino acids formed in the above three pathways using with mass spectrometer. In addition, their physical structures are analyzed by the electron and optical microscopes, in order to determine the self-organization abilities. We discuss the relation between the chemical and the physical structures for the origins of life. References [1] Harada, K., J. Org. Chem., 24, 1662 (1959), Fox, S. W., Harada, K., and Kendrick, J., Science, 129, 1221 (1959). [2] Terasaki, M., Nomoto, S., Mita, H., and Shimoyama, A., Chem. Lett., 480 (2002), Mita, H., Nomoto, S., Terasaki, M., Shimoyama, A., and Yamamoto, Y., Int. J. Astrobiol., 4, 145 (2005). [3] Kovacs, K and Nagy, H., Nature, 190, 531 (1961), Munegumi, T., Tanikawa, N., Mita, H. and Harada, K., Viva Origino, 22, 109 (1994).

  7. Nucleic acid secondary structure prediction and display.

    OpenAIRE

    Stüber, K

    1986-01-01

    A set of programs has been developed for the prediction and display of nucleic acid secondary structures. Information from experimental data can be used to restrict or enforce secondary structural elements. The predictions can be displayed either on normal line printers or on graphic devices like plotters or graphic terminals.

  8. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan [Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague (Czech Republic)

    2015-10-27

    The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

  9. Application of GPCR Structures for Modelling of Free Fatty Acid Receptors.

    Science.gov (United States)

    Tikhonova, Irina G

    2017-01-01

    Five G protein-coupled receptors (GPCRs) have been identified to be activated by free fatty acids (FFA). Among them, FFA1 (GPR40) and FFA4 (GPR120) bind long-chain fatty acids, FFA2 (GPR43) and FFA3 (GPR41) bind short-chain fatty acids and GPR84 binds medium-chain fatty acids. Free fatty acid receptors have now emerged as potential targets for the treatment of diabetes, obesity and immune diseases. The recent progress in crystallography of GPCRs has now enabled the elucidation of the structure of FFA1 and provided reliable templates for homology modelling of other FFA receptors. Analysis of the crystal structure and improved homology models, along with mutagenesis data and structure activity, highlighted an unusual arginine charge-pairing interaction in FFA1-3 for receptor modulation, distinct structural features for ligand binding to FFA1 and FFA4 and an arginine of the second extracellular loop as a possible anchoring point for FFA at GPR84. Structural data will be helpful for searching novel small-molecule modulators at the FFA receptors.

  10. Predicting nucleic acid binding interfaces from structural models of proteins.

    Science.gov (United States)

    Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

    2012-02-01

    The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Copyright © 2011 Wiley Periodicals, Inc.

  11. Structural consequences of amino acid substitutions causing Tay-Sachs disease.

    Science.gov (United States)

    Ohno, Kazuki; Saito, Seiji; Sugawara, Kanako; Sakuraba, Hitoshi

    2008-08-01

    To determine the structural changes in the alpha-subunit of beta-hexosaminidase due to amino acid substitutions causing Tay-Sachs disease, we built structural models of mutant alpha-subunits resulting from 33 missense mutations (24 infantile and 9 late-onset), and analyzed the influence of each amino acid replacement on the structure by calculating the number of atoms affected and determining the solvent-accessible surface area of the corresponding amino acid residue in the wild-type alpha-subunit. In the infantile Tay-Sachs group, the number of atoms influenced by a mutation was generally larger than that in the late-onset Tay-Sachs group in both the main chain and the side chain, and residues associated with the mutations found in the infantile Tay-Sachs group tended to be less solvent-accessible than those in the late-onset Tay-Sachs group. Furthermore, color imaging determined the distribution and degree of the structural changes caused by representative amino acid substitutions, and that there were also differences between the infantile and late-onset Tay-Sachs disease groups. Structural study is useful for elucidating the basis of Tay-Sachs disease.

  12. Inhibition of telomerase by linear-chain fatty acids: a structural analysis.

    Science.gov (United States)

    Oda, Masako; Ueno, Takamasa; Kasai, Nobuyuki; Takahashi, Hirotada; Yoshida, Hiromi; Sugawara, Fumio; Sakaguchi, Kengo; Hayashi, Hideya; Mizushina, Yoshiyuki

    2002-01-01

    In the present study, we have found that mono-unsaturated linear-chain fatty acids in the cis configuration with C(18) hydrocarbon chains (i.e. oleic acid) strongly inhibited the activity of human telomerase in a cell-free enzymic assay, with an IC(50) value of 8.6 microM. Interestingly, fatty acids with hydrocarbon chain lengths below 16 or above 20 carbons substantially decreased the potency of inhibition of telomerase. Moreover, the cis-mono-unsaturated C(18) linear-chain fatty acid oleic acid was the strongest inhibitor of all the fatty acids tested. A kinetic study revealed that oleic acid competitively inhibited the activity of telomerase ( K (i)=3.06 microM) with respect to the telomerase substrate primer. The energy-minimized three-dimensional structure of the linear-chain fatty acid was calculated and modelled. A molecule width of 11.53-14.26 A (where 1 A=0.1 nm) in the C(16) to C(20) fatty acid structure was suggested to be important for telomerase inhibition. The three-dimensional structure of the telomerase active site (i.e. the substrate primer-binding site) appears to have a pocket that could bind oleic acid, with the pocket being 8.50 A long and 12.80 A wide. PMID:12121150

  13. The Crystal Structures of Two Novel Cadmium-Picolinic Acid ...

    African Journals Online (AJOL)

    The crystal structures of two novel cadmium-picolinic acid complexes grown in aqueous solutions at selected pH values are reported. The structures are compared to expected solution species under the same conditions. The crystal structure of complex 1 exhibits a seven coordinate structure which contains a protonated ...

  14. Selenium Derivatization of Nucleic Acids for Phase and Structure Determination in Nucleic Acid X-ray Crystallography

    Directory of Open Access Journals (Sweden)

    Zhen Huang

    2008-03-01

    Full Text Available Selenium derivatization (via selenomethionine of proteins for crystal structure determination via MAD phasing has revolutionized protein X-ray crystallography. It is estimated that over two thirds of all new crystal structures of proteins have been determined via Se-Met derivatization. Similarly, selenium functionalities have also been successfully incorporated into nucleic acids to facilitate their structure studies and it has been proved that this Se-derivatization has advantages over halogen strategy, which was usually used as a traditional method in this field. This review reports the development of site-specific selenium derivatization of nucleic acids for phase determination since the year of 2001 (mainly focus on the 2’-position of the ribose. All the synthesis of 2’-SeMe modified phosphoramidite building blocks (U, C, T, A, G and the according oligonucleotides are included. In addition, several structures of selenium contained nucleic acid are also described in this paper.

  15. Structural analysis of Bacillus pumilus phenolic acid decarboxylase, a lipocalin-fold enzyme

    International Nuclear Information System (INIS)

    Matte, Allan; Grosse, Stephan; Bergeron, Hélène; Abokitse, Kofi; Lau, Peter C. K.

    2010-01-01

    The crystal structure of phenolic acid decarboxylase from B. pumilus strain UI-670 has been determined and refined at 1.69 Å resolution. The enzyme is a dimer, with each subunit adopting a β-barrel structure belonging to the lipocalin fold. The decarboxylation of phenolic acids, including ferulic and p-coumaric acids, to their corresponding vinyl derivatives is of importance in the flavouring and polymer industries. Here, the crystal structure of phenolic acid decarboxylase (PAD) from Bacillus pumilus strain UI-670 is reported. The enzyme is a 161-residue polypeptide that forms dimers both in the crystal and in solution. The structure of PAD as determined by X-ray crystallography revealed a β-barrel structure and two α-helices, with a cleft formed at one edge of the barrel. The PAD structure resembles those of the lipocalin-fold proteins, which often bind hydrophobic ligands. Superposition of structurally related proteins bound to their cognate ligands shows that they and PAD bind their ligands in a conserved location within the β-barrel. Analysis of the residue-conservation pattern for PAD-related sequences mapped onto the PAD structure reveals that the conservation mainly includes residues found within the hydrophobic core of the protein, defining a common lipocalin-like fold for this enzyme family. A narrow cleft containing several conserved amino acids was observed as a structural feature and a potential ligand-binding site

  16. Performance of structured lipids incorporating selected phenolic and ascorbic acids.

    Science.gov (United States)

    Gruczynska, Eliza; Przybylski, Roman; Aladedunye, Felix

    2015-04-15

    Conditions applied during frying require antioxidant which is stable at these conditions and provides protection for frying oil and fried food. Novel structured lipids containing nutraceuticals and antioxidants were formed by enzymatic transesterification, exploring canola oil and naturally occurring antioxidants such as ascorbic and selected phenolic acids as substrates. Lipozyme RM IM lipase from Rhizomucor miehei was used as biocatalyst. Frying performance and oxidative stability of the final transesterification products were evaluated. The novel lipids showed significantly improved frying performance compared to canola oil. Oxidative stability assessment of the structured lipids showed significant improvement in resistance to oxidative deterioration compared to original canola oil. Interestingly, the presence of ascorbic acid in an acylglycerol structure protected α-tocopherol against thermal degradation, which was not observed for the phenolic acids. Developed structured lipids containing nutraceuticals and antioxidants may directly affect nutritional properties of lipids also offering nutraceutical ingredients for food formulation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Crystal and molecular structure of eight organic acid-base adducts from 2-methylquinoline and different acids

    Science.gov (United States)

    Zhang, Jing; Jin, Shouwen; Tao, Lin; Liu, Bin; Wang, Daqi

    2014-08-01

    Eight supramolecular complexes with 2-methylquinoline and acidic components as 4-aminobenzoic acid, 2-aminobenzoic acid, salicylic acid, 5-chlorosalicylic acid, 3,5-dinitrosalicylic acid, malic acid, sebacic acid, and 1,5-naphthalenedisulfonic acid were synthesized and characterized by X-ray crystallography, IR, mp, and elemental analysis. All of the complexes are organic salts except compound 2. All supramolecular architectures of 1-8 involve extensive classical hydrogen bonds as well as other noncovalent interactions. The results presented herein indicate that the strength and directionality of the classical hydrogen bonds (ionic or neutral) between acidic components and 2-methylquinoline are sufficient to bring about the formation of binary organic acid-base adducts. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, the complexes 1-8 displayed 2D-3D framework structure.

  18. Structure of polyacrylic acid and polymethacrylic acid solutions: a small angle neutron scattering study

    Energy Technology Data Exchange (ETDEWEB)

    Moussaid, A. (Lab. d' Ultrasons et de Dynamique des Fluides Complexes, Univ. Louis Pasteur, 67 - Strasbourg (France)); Schosseler, F. (Lab. d' Ultrasons et de Dynamique des Fluides Complexes, Univ. Louis Pasteur, 67 - Strasbourg (France)); Munch, J.P. (Lab. d' Ultrasons et de Dynamique des Fluides Complexes, Univ. Louis Pasteur, 67 - Strasbourg (France)); Candau, S.J. (Lab. d' Ultrasons et de Dynamique des Fluides Complexes, Univ. Louis Pasteur, 67 - Strasbourg (France))

    1993-04-01

    The intensity scattered from polyacrylic acid and polymethacrylic acid solutions has been measured by small angle neutron scattering experiments. The influence of polymer concentration, ionization degree, temperature and salt content has been investigated. Results are in qualitative agreement with a model which predicts the existence of microphases in the unstable region of the phase diagram. Quantitative comparison with the theory is performed by fitting the theoretical structure factor to the experimental data. For a narrow range of ionization degrees nearly quantitative agreement with the theory is found for the polyacrylic acid system. (orig.).

  19. Structure of polyacrylic acid and polymethacrylic acid solutions : a small angle neutron scattering study

    Science.gov (United States)

    Moussaid, A.; Schosseler, F.; Munch, J. P.; Candau, S. J.

    1993-04-01

    The intensity scattered from polyacrylic acid and polymethacrylic acid solutions has been measured by small angle neutron scattering experiemnts. The influence of polymer concentration, ionization degree, temperature and salt content has been investigated. Results are in qualitative agreement with a model which predicts the existence of microphases in the unstable region of the phase diagram. Quantitative comparison with the theory is performed by fitting the theoretical structure factor to the experimental data. For a narrow range of ionizaiton degrees nearly quantitative agreement with the theory is found for the polyacrylic acide system.

  20. Adsorption of actinides by chelating agents containing benzene rings, fixed on charcoal

    International Nuclear Information System (INIS)

    Valentini Ganzerli, M.T.; Crespi Caramella, V.; Maggi, L.

    1999-01-01

    The focus of this paper is on the analysis of the actinides in the hydrosphere to study their environmental dispersion. The 8-hydroxyquinoline family and the benzohydroxamic acid have a complexing ability towards the actinides, even if in different oxidation states. Taking advantage of this ability, their salts with some organic acids or bases were prepared. In this way compounds were obtained easily incorporated into active charcoal. Only a small amount of the prepared adsorber may be equilibrated with large sample volumes. Subsequently it can be recovered by filtration. The adsorbed ions may be then re-dissolved with a small volume of the appropriate eluting solution. The 8-hydroxy-quinolines and the 8-hydroxyquinoline produced salts with the benzilic acid. These compounds similarly behave and show wide adsorption coefficients for solutions of pH higher than 3. The adsorption takes place by means of the formation of a complex of the actinide ion with the hydroxyquinoline moiety and also with the benzilic anion. Provided that the active extracting agent is not dissolved in a medium but fixed into a solid phase, the whole adsorption process may be regarded as a solvent extraction reaction. The benzohydroxamic acid was treated with the diphenylamine or with the tribenzylamine to obtain salts, later adsorbed into the charcoal. The adsorption of actinide ions seems to take place by means of a precipitation mechanism of the actinide ions with the hydroxamate ions for solution of pH higher than 3.5. Also in this case high values were obtained for the distribution coefficients. The actinide ions act similarly in the +4 or +6 oxidation state towards the prepared adsorber series. Therefore, it is possible to use only one adsorber to concentrate all actinides. Methods of analysis of actinides in the environment may be suitably set up and the concentration step based on these new prepared adsorber may improve the whole procedure. (authors)

  1. Nucleic acid helix structure determination from NMR proton chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

    2013-06-15

    We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

  2. Structure of polyacrylic acid and polymethacrylic acid solutions : a small angle neutron scattering study

    OpenAIRE

    Moussaid , A.; Schosseler , F.; Munch , J.; Candau , S.

    1993-01-01

    The intensity scattered from polyacrylic acid and polymethacrylic acid solutions has been measured by small angle neutron scattering experiemnts. The influence of polymer concentration, ionization degree, temperature and salt content has been investigated. Results are in qualitative agreement with a model which predicts the existence of microphases in the unstable region of the phase diagram. Quantitative comparison with the theory is performed by fitting the theoretical structure factor to t...

  3. Transcriptome mining and in silico structural and functional analysis of ascorbic acid and tartaric acid biosynthesis pathway enzymes in rose-scanted geranium.

    Science.gov (United States)

    Narnoliya, Lokesh K; Sangwan, Rajender S; Singh, Sudhir P

    2018-06-01

    Rose-scented geranium (Pelargonium sp.) is widely known as aromatic and medicinal herb, accumulating specialized metabolites of high economic importance, such as essential oils, ascorbic acid, and tartaric acid. Ascorbic acid and tartaric acid are multifunctional metabolites of human value to be used as vital antioxidants and flavor enhancing agents in food products. No information is available related to the structural and functional properties of the enzymes involved in ascorbic acid and tartaric acid biosynthesis in rose-scented geranium. In the present study, transcriptome mining was done to identify full-length genes, followed by their bioinformatic and molecular modeling investigations and understanding of in silico structural and functional properties of these enzymes. Evolutionary conserved domains were identified in the pathway enzymes. In silico physicochemical characterization of the catalytic enzymes revealed isoelectric point (pI), instability index, aliphatic index, and grand average hydropathy (GRAVY) values of the enzymes. Secondary structural prediction revealed abundant proportion of alpha helix and random coil confirmations in the pathway enzymes. Three-dimensional homology models were developed for these enzymes. The predicted structures showed significant structural similarity with their respective templates in root mean square deviation analysis. Ramachandran plot analysis of the modeled enzymes revealed that more than 84% of the amino acid residues were within the favored regions. Further, functionally important residues were identified corresponding to catalytic sites located in the enzymes. To, our best knowledge, this is the first report which provides a foundation on functional annotation and structural determination of ascorbic acid and tartaric acid pathway enzymes in rose-scanted geranium.

  4. Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel.

    Science.gov (United States)

    Bera, Asim K; Aukema, Kelly G; Elias, Mikael; Wackett, Lawrence P

    2017-03-27

    Cyanuric acid hydrolases are of industrial importance because of their use in aquatic recreational facilities to remove cyanuric acid, a stabilizer for the chlorine. Degradation of excess cyanuric acid is necessary to maintain chlorine disinfection in the waters. Cyanuric acid hydrolase opens the cyanuric acid ring hydrolytically and subsequent decarboxylation produces carbon dioxide and biuret. In the present study, we report the X-ray structure of TrzD, a cyanuric acid hydrolase from Acidovorax citrulli. The crystal structure at 2.19 Å resolution shows a large displacement of the catalytic lysine (Lys163) in domain 2 away from the active site core, whereas the two other active site lysines from the two other domains are not able to move. The lysine displacement is proposed here to open up a channel for product release. Consistent with that, the structure also showed two molecules of the co-product, carbon dioxide, one in the active site and another trapped in the proposed exit channel. Previous data indicated that the domain 2 lysine residue plays a role in activating an adjacent serine residue carrying out nucleophilic attack, opening the cyanuric acid ring, and the mobile lysine guides products through the exit channel.

  5. Structural analysis of acidic oligosaccharides derived from the methylated, acidic polysaccharide associated with coccoliths of Emiliania huxleyi (lohmann) kamptner

    NARCIS (Netherlands)

    Fichtinger-Schepman, A.M.J.; Kamerling, J.P.; Versluis, C.; Vliegenthart, J.F.G.

    1980-01-01

    A series of acidic oligosaccharides was obtained by graded, acid hydrolysis of the methylated, acidic polysaccharide associated with the coccoliths of the alga Emiliania huxleyi (Lohmann) Kamptner. After fractionation by ion-exchange chromatography, the structures of the oligosaccharides were

  6. Structure-property relationships in halogenbenzoic acids: Thermodynamics of sublimation, fusion, vaporization and solubility.

    Science.gov (United States)

    Zherikova, Kseniya V; Svetlov, Aleksey A; Kuratieva, Natalia V; Verevkin, Sergey P

    2016-10-01

    Temperature dependences of vapor pressures for 2-, 3-, and 4-bromobenzoic acid, as well as for five isomeric bromo-methylbenzoic acids were studied by the transpiration method. Melting temperatures and enthalpies of fusion for all isomeric bromo-methylbenzoic acids and 4-bromobenzoic acid were measured with a DSC. The molar enthalpies of sublimation and vaporization were derived. These data together with results available in the literature were collected and checked for internal consistency using a group-additivity procedure and results from X-ray structural diffraction studies. Specific (hydrogen bonding) interactions in the liquid and in the crystal phase of halogenbenzoic acids were quantified based on experimental values of vaporization and sublimation enthalpies. Structure-property correlations of solubilities of halogenobenzoic acids with sublimation pressures and sublimation enthalpies were developed and solubilities of bromo-benzoic acids were estimated. These new results resolve much of the ambiguity in the available thermochemical and solubility data on bromobenzoic acids. The approach based on structure property correlations can be applied for the assessment of water solubility of sparingly soluble drugs. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    International Nuclear Information System (INIS)

    Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-01-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

  8. Adsorption properties and porous structure of sulfuric acid treated bentonites determined - SHORT COMMUNICATION

    Directory of Open Access Journals (Sweden)

    SNEZANA BREZOVSKA

    2005-02-01

    Full Text Available In a previous paper adsorption isotherms of benzene vapor on natural bentonite from Ginovci, Macedonia, and forms acid activated with 10 % and 15 % solutions of hydrochloric were interpreted by means of the Dubinin–Radushkevich–Stoeckli and Dubinin–Astakhov equations; the investigation has been continued with bentonites acid activated with 10 % and 15 % solutions of sulfuric acid where X-ray analysis indicates smaller structural changes. Using the above equations, the heterogeneity of the micropores and the energetic heterogeneity of the bentonites were determined from the differential distribution of the micropore volume with respect to the structural parameter of the equations characterizing the microporous structure and to the molar free energy of adsorption. Activated bentonites obtain bigger pores but also a certain quantity of new small pores appear during acid activation with the higher concentration of acid. The micropore volumes, determined from the adsorption of benzene vapor, of bentonites activated with 10 % and 15 % solution of hydrochloric acid (144.60 cm3 kg-1 and 110.06 cm3 kg-1, respectively, decrease in comparison with that of natural bentonite (162.55 cm3 kgv.1 In contrast, the values of the micropore volume for bentonities treated with 10 % and 15 % solutions of sulfuric acids increase (169.19 cm3 kg-1 and 227.74 cm3 kg-1. That is due to the difference in the structural changes occurring during activation with hydrochloric and sulfuric acids. The values of the free energy of adsorption of benzene vapor for natural bentonite are higher than those of the acid acitivated bentonities, what is in accordance with the structural and porosity changes.

  9. Structural and morphological changes in supramolecular-structured polymer electrolyte membrane fuel cell on addition of phosphoric acid

    Science.gov (United States)

    Hendrana, S.; Pryliana, R. F.; Natanael, C. L.; Rahayu, I.

    2018-03-01

    Phosphoric acid is one agents used in membrane fuel cell to modify ionic conductivity. Therefore, its distribution in membrane is a key parameter to gain expected conductivity. Efforts have been made to distribute phosphoric acid in a supramolecular-structured membrane prepared with a matrix. To achieve even distribution across bulk of the membrane, the inclusion of the polyacid is carried out under pressurized chamber. Image of scanning electron microscopy (SEM) shows better phosphoric acid distribution for one prepared in pressurized state. It also leads in better performing in ionic conductivity. Moreover, data from differential scanning calorimetry (DSC) indicate that the addition of phosphoric acid is prominent in the change of membrane structure, while morphological changes are captured in SEM images.

  10. Structure and properties of compositions based on petroleum sulfonic acids

    Energy Technology Data Exchange (ETDEWEB)

    Tutorskii, I.A.; Sultanova, A.S.; Belkina, E.V.; Fomin, A.G. [Lomonosov Academy of Fine Chemical Technology, Moscow (Russian Federation)

    1995-03-01

    Colloidal characteristics of compositions based on petroleum sulfonic acids were studied. Neutralized heavy oil residue exhibits surface-active properties and contains an ultradisperse filler. Analysis of the compositions by size-exclusion-chromatography shows deep structural changes in the heavy acid residue upon neutralization with calcium carbonate.

  11. Humic acids: Structural properties and multiple functionalities for novel technological developments.

    Science.gov (United States)

    de Melo, Bruna Alice Gomes; Motta, Fernanda Lopes; Santana, Maria Helena Andrade

    2016-05-01

    Humic acids (HAs) are macromolecules that comprise humic substances (HS), which are organic matter distributed in terrestrial soil, natural water, and sediment. HAs differ from the other HS fractions (fulvic acid and humins) in that they are soluble in alkaline media, partially soluble in water, and insoluble in acidic media. Due to their amphiphilic character, HAs form micelle-like structures in neutral to acidic conditions, which are useful in agriculture, pollution remediation, medicine and pharmaceuticals. HAs have undefined compositions that vary according to the origin, process of obtainment, and functional groups present in their structures, such as quinones, phenols, and carboxylic acids. Quinones are responsible for the formation of reactive oxygen species (ROS) in HAs, which are useful for wound healing and have fungicidal/bactericidal properties. Phenols and carboxylic acids deprotonate in neutral and alkaline media and are responsible for various other functions, such as the antioxidant and anti-inflammatory properties of HAs. In particular, the presence of phenolic groups in HAs provides antioxidant properties due to their free radical scavenging capacity. This paper describes the main multifunctionalities of HAs associated with their structures and properties, focusing on human health applications, and we note perspectives that may lead to novel technological developments. To the best of our knowledge, this is the first review to address this topic from this approach. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Synthesis and structure-activity studies on acidic amino acids and related diacids as NMDA receptor ligands

    DEFF Research Database (Denmark)

    Johansen, T N; Frydenvang, Karla Andrea; Ebert, B

    1994-01-01

    The 3-isoxazolol amino acids (S)-2-amino-3-(3-hydroxy-5-methyl-4- isoxazolyl)propionic acid [(S)-AMPA, 2] and (R,S)-2-amino-2-(3-hydroxy-5-methyl-4-isoxazolyl)acetic acid (AMAA, 5a) (Figure 1) are potent and specific agonists at the AMPA and N-methyl-D-aspartic acid (NMDA) subtypes, respectively......, of (S)-glutamic acid (1) receptors. A number of amino acids and diacids structurally related to AMAA were synthesized and tested electrophysiologically and in receptor-binding assays. The hydroxymethyl analogue 7c of AMAA was an NMDA agonist approximately equipotent with AMAA in the [3H...... by molecular mechanics calculations. Compound 7a possesses extra steric bulk and shows significant restriction of conformational flexibility compared to AMAA and 7c, which may be determining factors for the observed differences in biological activity. Although the nitrogen atom of quinolinic acid (6) has very...

  13. Structural similarity between β(3)-peptides synthesized from β(3)-homo-amino acids and aspartic acid monomers.

    Science.gov (United States)

    Ahmed, Sahar; Sprules, Tara; Kaur, Kamaljit

    2014-07-01

    Formation of stable secondary structures by oligomers that mimic natural peptides is a key asset for enhanced biological response. Here we show that oligomeric β(3)-hexapeptides synthesized from L-aspartic acid monomers (β(3)-peptides 1, 5a, and 6) or homologated β(3)-amino acids (β(3)-peptide 2), fold into similar stable 14-helical secondary structures in solution, except that the former form right-handed 14-helix and the later form left-handed 14-helix. β(3)-Peptides from L-Asp monomers contain an additional amide bond in the side chains that provides opportunities for more hydrogen bonding. However, based on the NMR solution structures, we found that β(3)-peptide from L-Asp monomers (1) and from homologated amino acids (2) form similar structures with no additional side-chain interactions. These results suggest that the β(3)-peptides derived from L-Asp are promising peptide-mimetics that can be readily synthesized using L-Asp monomers as well as the right-handed 14-helical conformation of these β(3)-peptides (such as 1 and 6) may prove beneficial in the design of mimics for right-handed α-helix of α-peptides. © 2014 Wiley Periodicals, Inc.

  14. SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence

    Directory of Open Access Journals (Sweden)

    Zhou Yuan Wu

    2013-07-01

    Full Text Available In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in α-helices, β-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database without considering homologous, and Q3 accuracy is ca. 74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.

  15. Effects of clustering structure on volumetric properties of amino acids in (DMSO + water) mixtures

    International Nuclear Information System (INIS)

    Huang Aimin; Liu Chunli; Ma Lin; Tong Zhangfa; Lin Ruisen

    2012-01-01

    Graphical abstract: Together with static light scattering measurement, volumetric properties of glycine, L-alanine and L-serine were determined and utilized to reveal the microscopic solvent structure of (DMSO + water) mixtures and its influence on the interaction between DMSO and amino acids from a clustering point of view. The results demonstrated that the interaction between amino acids and DMSO was greatly related to the clustering structure of the mixed solvent and that amino acids interacted with already established solvent clusters. Hydrophobic aggregating of DMSO lead to a decrease in the hydrophobic effect of DMSO and the hydrophobic–hydrophilic and hydrophobic–hydrophobic interaction with amino acids, which was reflected by the solvation of proteins. Highlights: ► Determine volumetric properties of three amino acids in aqueous DMSO in details. ► Static light scattering measurement for clustering structure of aqueous DMSO. ► Volumetric behaviour of amino acids depends on clustering structure of aqueous DMSO. ► Clustering structure of aqueous DMSO influences solvation of protein and cellulose. - Abstract: For a better understanding on the functions of DMSO in biological systems at a relatively lower concentration, apparent molar volumes of three typical amino acids, glycine, L-alanine and L-serine in (DMSO + water) mixtures were determined and the transfer volumes from water to the mixtures were evaluated. Together with static light scattering measurement, the results were utilised to reveal the microscopic solvent structure of (DMSO + water) mixtures and its influence on the interaction between DMSO and amino acids from a clustering point of view. The results demonstrate that the interaction between amino acids and DMSO is greatly related to the clustering structure of the mixed solvent and that amino acids interacted with already established solvent clusters. The linear dependence of transfer volume of amino acids on DMSO concentration up to 2

  16. Oxidative stability of structured lipids produced from sunflower oil and caprylic acid

    DEFF Research Database (Denmark)

    Timm Heinrich, Maike; Xu, Xuebing; Nielsen, Nina Skall

    2003-01-01

    Traditional sunflower oil (SO), randomized lipid (RL) and specific structured lipid (SL), both produced from SO and tricaprylin/caprylic acid, respectively, were stored for up to 12 wk to compare their oxidative stabilities by chemical and sensory analyses. Furthermore, the effect of adding...... a commercial antioxidant blend Grindox 117 (propyl gallate/citric acid/ascorbyl palmitate) or gallic acid to the SL was investigated. The lipid type affected the oxidative stability: SL was less stable than SO and RL. The reduced stability was most likely caused by both the structure of the lipid...

  17. Crystal structures of hibiscus acid and hibiscus acid dimethyl ester isolated from Hibiscus sabdariffa (Malvaceae)

    OpenAIRE

    Zheoat, Ahmed M.; Gray, Alexander I.; Igoli, John O.; Kennedy, Alan R.; Ferro, Valerie A.

    2017-01-01

    The biologically active title compounds have been isolated from Hibiscus sabdariffa plants, hibiscus acid as a dimethyl sulfoxide monosolvate [systematic name: (2S,3R)-3-hy?droxy-5-oxo-2,3,4,5-tetra?hydro?furan-2,3-di?carb?oxy?lic acid dimethyl sulfoxide monosolvate], C6H6O7?C2H6OS, (I), and hibiscus acid dimethyl ester [systematic name: dimethyl (2S,3R)-3-hy?droxy-5-oxo-2,3,4,5-tetra?hydro?furan-2,3-di?carboxyl?ate], C8H10O7, (II). Compound (I) forms a layered structure with alternating laye...

  18. Determination of vanadium

    International Nuclear Information System (INIS)

    Stepin, V.V.; Kurbatova, V.I.; Fedorova, N.D.

    1980-01-01

    Techniques of vanadium determination in steels and alloys are developed. Extraction-photometric method with N-phenyl-benzohydroxamic acid when V content is 0.005-0.5% is suggested. Molar coefficient of the complex quenching at lambdasub(max)=530 nm constitutes 5750. Optimum concentration is 15-150 μg per 25 ml of the solution, determination limit is 0.05 μg/ml. Chloroform is an extracting agent. A photometric method with acetohydrazide of anthranilic acid is suggested for the analysis of alloyed steels at V content 0.03-1%. The lower limit of V determination constitutes 0.64 μg/ml. Effect of Fe is removed using phosphoric acid. Amperometric method for steels and alloys at V content from 0.05 to 5% and for steels and alloys containing more than 3% W and Cr is also developed. The method is based on amperometric titration with solution of double sulfuric salt of Fe(2) and ammonium [ru

  19. The primary structure of fatty-acid-binding protein from nurse shark liver. Structural and evolutionary relationship to the mammalian fatty-acid-binding protein family.

    Science.gov (United States)

    Medzihradszky, K F; Gibson, B W; Kaur, S; Yu, Z H; Medzihradszky, D; Burlingame, A L; Bass, N M

    1992-02-01

    The primary structure of a fatty-acid-binding protein (FABP) isolated from the liver of the nurse shark (Ginglymostoma cirratum) was determined by high-performance tandem mass spectrometry (employing multichannel array detection) and Edman degradation. Shark liver FABP consists of 132 amino acids with an acetylated N-terminal valine. The chemical molecular mass of the intact protein determined by electrospray ionization mass spectrometry (Mr = 15124 +/- 2.5) was in good agreement with that calculated from the amino acid sequence (Mr = 15121.3). The amino acid sequence of shark liver FABP displays significantly greater similarity to the FABP expressed in mammalian heart, peripheral nerve myelin and adipose tissue (61-53% sequence similarity) than to the FABP expressed in mammalian liver (22% similarity). Phylogenetic trees derived from the comparison of the shark liver FABP amino acid sequence with the members of the mammalian fatty-acid/retinoid-binding protein gene family indicate the initial divergence of an ancestral gene into two major subfamilies: one comprising the genes for mammalian liver FABP and gastrotropin, the other comprising the genes for mammalian cellular retinol-binding proteins I and II, cellular retinoic-acid-binding protein myelin P2 protein, adipocyte FABP, heart FABP and shark liver FABP, the latter having diverged from the ancestral gene that ultimately gave rise to the present day mammalian heart-FABP, adipocyte FABP and myelin P2 protein sequences. The sequence for intestinal FABP from the rat could be assigned to either subfamily, depending on the approach used for phylogenetic tree construction, but clearly diverged at a relatively early evolutionary time point. Indeed, sequences proximately ancestral or closely related to mammalian intestinal FABP, liver FABP, gastrotropin and the retinoid-binding group of proteins appear to have arisen prior to the divergence of shark liver FABP and should therefore also be present in elasmobranchs

  20. Influence of media with different acidity on structure of FeNi nanotubes

    Science.gov (United States)

    Shumskaya, Alena; Kaniukov, Egor; Kutuzau, Maksim; Bundyukova, Victoria; Tulebayeva, Dinara; Kozlovskiy, Artem; Borgekov, Daryn; Kenzhina, Inesh; Zdorovets, Maxim

    2018-04-01

    A detailed analysis of the structure features of FeNi nanotubes exposed at environment with different acidity is carried out. It is demonstrated that the exposure of the nanostructures in the environment with high acidity causes the structure deformation, leading to sharply increasing of the presents of oxide phases and partial amorphization of nanotubes walls that determined the rate of FeNi nanotubes destruction. It was established that the evolution of the crystal structure parameters concerned with appearance of oxide phases and with formation of disorder regions as a result of oxidation processes.

  1. Spectra-structure correlations of saturated and unsaturated medium-chain fatty acids. Near-infrared and anharmonic DFT study of hexanoic acid and sorbic acid.

    Science.gov (United States)

    Grabska, Justyna; Beć, Krzysztof B; Ishigaki, Mika; Wójcik, Marek J; Ozaki, Yukihiro

    2017-10-05

    Quantum chemical reproduction of entire NIR spectra is a new trend, enabled by contemporary advances in the anharmonic approaches. At the same time, recent increase of the importance of NIR spectroscopy of biological samples raises high demand for gaining deeper understanding of NIR spectra of biomolecules, i.e. fatty acids. In this work we investigate saturated and unsaturated medium-chain fatty acids, hexanoic acid and sorbic acid, in the near-infrared region. By employing fully anharmonic density functional theory (DFT) calculations we reproduce the experimental NIR spectra of these systems, including the highly specific spectral features corresponding to the dimerization of fatty acids. Broad range of concentration levels from 5·10 -4 M in CCl 4 to pure samples are investigated. The major role of cyclic dimers can be evidenced for the vast majority of these samples. A highly specific NIR feature of fatty acids, the elevation of spectral baseline around 6500-4000cm -1 , is being explained by the contributions of combination bands resulting from the vibrations of hydrogen-bonded OH groups in the cyclic dimers. Based on the high agreement between the calculated and experimental NIR spectra, a detailed NIR band assignments are proposed for hexanoic acid and sorbic acid. Subsequently, the correlations between the structure and NIR spectra are elucidated, emphasizing the regions in which clear and universal traces of specific bands corresponding to saturated and unsaturated alkyl chains can be established, thus demonstrating the wavenumber regions highly valuable for structural identifications. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Structure of β- N-dimethylamino-4-dodecyloxypropiophenone complexes with di- and polycarboxylic acids

    Science.gov (United States)

    Lebedeva, Tamara L.; Shandryuk, George A.; Sycheva, Tatyana I.; Bezborodov, Vladimir S.; Talroze, Raissa V.; Platé, Nicolai A.

    1995-07-01

    The type of bonds responsible for the complexation of di- and polyacids with the tertiary amine β- N-dimethylamino-4-dodecyloxypropiophenone is studied by means of FTIR spectroscopy. The complexes are shown to be stable due to strong H-bonding with partial charge transfer. The characteristic composition for complexes of polyacrylic, polymethacrylic and malonic acids is calculated as 2:1 (number of carboxylic groups per number of amine molecules) whereas glutaric acid forms complexes of different composition including 1:1. The characteristic composition results from the structure of the initial acid. The structures of both the characteristic complex and "excess" acid are also discussed.

  3. UPS and DFT investigation of the electronic structure of gas-phase trimesic acid

    Energy Technology Data Exchange (ETDEWEB)

    Reisberg, L., E-mail: rebban@ut.ee [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); Pärna, R. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); MAX IV Laboratory, Lund University, Fotongatan 2, 225 94 Lund (Sweden); Kikas, A.; Kuusik, I.; Kisand, V. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); Hirsimäki, M.; Valden, M. [Surface Science Laboratory, Optoelectronics Research Centre, Tampere University of Technology, FIN-33101 Tampere (Finland); Nõmmiste, E. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia)

    2016-11-15

    Highlights: • In the current study outer valence band electronic structure of benzene-1,3,5-tricarboxylic acid was interpreted. • Experimental and calculated trimesic acid (TMA) spectrum were compared to ones of benzene and benzoic acid. • It is shown that similarities between MO energies and shapes for benzene and TMA exists. • Addition of carboxyl groups to the benzene ring clearly correlates with increasing binding energy of HOMO. - Abstract: Benzene-1,3,5-tricarboxylic acid (trimesic acid, TMA) molecules in gas-phase have been investigated by using valence band photoemission. The photoelectron spectrum in the binding energy region from 9 to 22 eV is interpreted by using density functional theory calculations. The electronic structure of TMA is compared with benzene and benzoic acid in order to demonstrate changes in molecular orbital energies induced by addition of carboxyl groups to benzene ring.

  4. Influence of media with different acidity on structure of FeNi nanotubes

    Directory of Open Access Journals (Sweden)

    Shumskaya Alena

    2018-01-01

    Full Text Available A detailed analysis of the structure features of FeNi nanotubes exposed at environment with different acidity is carried out. It is demonstrated that the exposure of the nanostructures in the environment with high acidity causes the structure deformation, leading to sharply increasing of the presents of oxide phases and partial amorphization of nanotubes walls that determined the rate of FeNi nanotubes destruction. It was established that the evolution of the crystal structure parameters concerned with appearance of oxide phases and with formation of disorder regions as a result of oxidation processes.

  5. Hard and soft acids and bases: structure and process.

    Science.gov (United States)

    Reed, James L

    2012-07-05

    Under investigation is the structure and process that gives rise to hard-soft behavior in simple anionic atomic bases. That for simple atomic bases the chemical hardness is expected to be the only extrinsic component of acid-base strength, has been substantiated in the current study. A thermochemically based operational scale of chemical hardness was used to identify the structure within anionic atomic bases that is responsible for chemical hardness. The base's responding electrons have been identified as the structure, and the relaxation that occurs during charge transfer has been identified as the process giving rise to hard-soft behavior. This is in contrast the commonly accepted explanations that attribute hard-soft behavior to varying degrees of electrostatic and covalent contributions to the acid-base interaction. The ability of the atomic ion's responding electrons to cause hard-soft behavior has been assessed by examining the correlation of the estimated relaxation energies of the responding electrons with the operational chemical hardness. It has been demonstrated that the responding electrons are able to give rise to hard-soft behavior in simple anionic bases.

  6. Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity

    Energy Technology Data Exchange (ETDEWEB)

    Pegan, Scott D., E-mail: pegan@uic.edu [Center of Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago (United States); Serrano, Hector; Whitman, Christian P. [Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin (United States); Mesecar, Andrew D., E-mail: pegan@uic.edu [Center of Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago (United States)

    2008-12-01

    The X-ray structure of a noncovalently modified trans-3-chloroacrylic acid dehalogenase with a substrate-homolog acetate bound in the active site has been determined to 1.7 Å resolution. Elucidation of catalytically important water is reported and multiple conformations of the catalytic residue αGlu52 are observed. Trans-3-chloroacrylic acid dehalogenase (CaaD) is a critical enzyme in the trans-1, 3-dichloropropene (DCP) degradation pathway in Pseudomonas pavonaceae 170. This enzyme allows bacteria to use trans-DCP, a common component in commercially produced fumigants, as a carbon source. CaaD specifically catalyzes the fourth step of the pathway by cofactor-independent dehalogenation of a vinyl carbon–halogen bond. Previous studies have reported an X-ray structure of CaaD under acidic conditions with a covalent modification of the catalytic βPro1 residue. Here, the 1.7 Å resolution X-ray structure of CaaD under neutral (pH 6.5) conditions is reported without the presence of the covalent adduct. In this new structure, a substrate-like acetate molecule is bound within the active site in a position analogous to the putative substrate-binding site. Additionally, a catalytically important water molecule was identified, consistent with previously proposed reaction schemes. Finally, flexibility of the catalytically relevant side chain αGlu52 is observed in the structure, supporting its role in the catalytic mechanism.

  7. Crystal structures of seven molecular salts derived from benzylamine and organic acidic components

    Science.gov (United States)

    Wen, Xianhong; Jin, Xiunan; Lv, Chengcai; Jin, Shouwen; Zheng, Xiuqing; Liu, Bin; Wang, Daqi; Guo, Ming; Xu, Weiqiang

    2017-07-01

    Cocrystallization of the commonly available organic amine, benzylamine, with a series of organic acids gave a total of seven molecular salts with the compositions: (benzylamine): (p-toluenesulfonic acid) (1) [(HL)+ · (tsa-)], (benzylamine): (o-nitrobenzoic acid) (2) [(HL+) · (onba)-], (benzylamine): (3,4-methylenedioxybenzoic acid) (3) [(HL+) · (mdba-)], (benzylamine): (mandelic acid) (4) [(HL+) · (mda-)], (benzylamine): (5-bromosalicylic acid)2(5) [(HL+) · (bsac-) · (Hbsac)], (benzylamine): (m-phthalic acid) (6) [(HL+) · (Hmpta-)], and (benzylamine)2: (trimesic acid) (7) [(HL+)2 · (Htma2-)]. The seven salts have been characterised by X-ray diffraction technique, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the seven investigated crystals the NH2 groups in the benzylamine moieties are protonated when the organic acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted Nsbnd H⋯O hydrogen bond formation between the ammonium and the deprotonated acidic groups. Except the Nsbnd H⋯O hydrogen bond, the Osbnd H⋯O hydrogen bonds (charge assisted or neutral) were also found at the salts 4-7. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O/CH2sbnd O, CHsbnd π/CH2sbnd π, Osbnd O, and Osbnd Cπ associations contribute to the stabilization and expansion of the total high-dimensional (2D-3D) framework structures. For the coexistence of the various weak nonbonding interactions these structures adopted homo or hetero supramolecular synthons or both. Some classical supramolecular synthons, such as R42(8), R43(10) and R44(12), usually observed in organic solids of organic acids with amine, were again shown to be involved in constructing most of these hydrogen bonding networks.

  8. Isolation, structure, and synthesis of viridic acid, a new tetrapeptide mycotoxin of Penicillium viridicatum Westling

    International Nuclear Information System (INIS)

    Holzapfel, C.W.; Koekemoer, J.M.; Van Dyk, M.S.

    1986-01-01

    The isolation of a new toxic metabolite, viridic acid, from Penicillium viridicatum Westling is described. The chemical and spectroscopic properties of the compound are interpreted in terms of the tetrapeptide structure (N,N-dimethyl-o-aminobenzoyl)-glycyl-(N'-methyl-L-valyl)-o-aminobenzoic acid. The structure and chirality of viridic acid were confirmed by total synthesis

  9. Self-assembled structures and pKa value of oleic acid in systems of biological relevance.

    Science.gov (United States)

    Salentinig, Stefan; Sagalowicz, Laurent; Glatter, Otto

    2010-07-20

    In the human digestion process, triglycerides are hydrolyzed by lipases to monoglycerides and the corresponding fatty acids. Here we report the self-assembly of structures in biologically relevant, emulsified oleic acid-monoolein mixtures at various pH values and oleic acid concentrations. Small-angle X-ray scattering, cryogenic transmission electron microscopy, and dynamic light scattering were used to investigate the structures formed, and to follow their transitions while these factors were varied. The addition of oleic acid to monoolein-based cubosomes was found to increase the critical packing parameter in the system. Structural transitions from bicontinuous cubosomes through hexosomes and micellar cubosomes (Fd3m symmetry) to emulsified microemulsions occur with increasing oleic acid concentration. At sufficiently high oleic acid concentration, the internal particle structure was also found to strongly depend on the pH of the aqueous phase: transformations from emulsified microemulsion through micellar cubosomes, hexosomes, and bicontinuous cubosomes to vesicles can be observed as a function of increasing pH. The reversible transition from liquid crystals to vesicles occurs at intestinal pH values (between pH 7 and 8). The hydrodynamic radius of the particles decreases from around 120 nm for internally structured particles to around 60 nm for vesicles. All transitions with pH are reversible. Finally, the apparent pK(a) for oleic acid in monoolein could be determined from the change of structure with pH. This value is within the physiological pH range of the intestine and depends somewhat on composition.

  10. Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids

    Energy Technology Data Exchange (ETDEWEB)

    Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A., E-mail: alashkov83@gmail.com [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2012-05-15

    Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.

  11. Structure, stability and behaviour of nucleic acids in ionic liquids

    Science.gov (United States)

    Tateishi-Karimata, Hisae; Sugimoto, Naoki

    2014-01-01

    Nucleic acids have become a powerful tool in nanotechnology because of their conformational polymorphism. However, lack of a medium in which nucleic acid structures exhibit long-term stability has been a bottleneck. Ionic liquids (ILs) are potential solvents in the nanotechnology field. Hydrated ILs, such as choline dihydrogen phosphate (choline dhp) and deep eutectic solvent (DES) prepared from choline chloride and urea, are ‘green’ solvents that ensure long-term stability of biomolecules. An understanding of the behaviour of nucleic acids in hydrated ILs is necessary for developing DNA materials. We here review current knowledge about the structures and stabilities of nucleic acids in choline dhp and DES. Interestingly, in choline dhp, A–T base pairs are more stable than G–C base pairs, the reverse of the situation in buffered NaCl solution. Moreover, DNA triplex formation is markedly stabilized in hydrated ILs compared with aqueous solution. In choline dhp, the stability of Hoogsteen base pairs is comparable to that of Watson–Crick base pairs. Moreover, the parallel form of the G-quadruplex is stabilized in DES compared with aqueous solution. The behaviours of various DNA molecules in ILs detailed here should be useful for designing oligonucleotides for the development of nanomaterials and nanodevices. PMID:25013178

  12. Structure of eight molecular salts assembled from noncovalent bonding between carboxylic acids, imidazole, and benzimidazole

    Science.gov (United States)

    Jin, Shouwen; Zhang, Huan; Liu, Hui; Wen, Xianhong; Li, Minghui; Wang, Daqi

    2015-09-01

    Eight organic salts of imidazole/benzimidazole have been prepared with carboxylic acids as 2-methyl-2-phenoxypropanoic acid, α-ketoglutaric acid, 5-nitrosalicylic acid, isophthalic acid, 4-nitro-phthalic acid, and 3,5-dinitrosalicylic acid. The eight crystalline forms reported are proton-transfer compounds of which the crystals and compounds were characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. These structures adopted hetero supramolecular synthons, with the most common R22(7) motif observed at salts 2, 3, 5, 6 and 8. Analysis of the crystal packing of 1-8 suggests that there are extensive strong Nsbnd H⋯O, and Osbnd H⋯O hydrogen bonds (charge assisted or neutral) between acid and imidazolyl components in all of the salts. Except the classical hydrogen bonding interactions, the secondary propagating interactions also play important roles in structure extension. This variety, coupled with the varying geometries and number of acidic groups of the acids utilized, has led to the creation of eight supramolecular arrays with 1D-3D structure. The role of weak and strong noncovalent interactions in the crystal packing is analyzed. The results presented herein indicate that the strength and directionality of the Nsbnd H⋯O, and Osbnd H⋯O hydrogen bonds between acids and imidazole/benzimidazole are sufficient to bring about the formation of organic salts.

  13. Structural characteristics and properties of the regenerated silk fibroin prepared from formic acid.

    Science.gov (United States)

    Um, I C; Kweon, H Y; Park, Y H; Hudson, S

    2001-08-20

    Structural characteristics and thermal and solution properties of the regenerated silk fibroin (SF) prepared from formic acid (FU) were compared with those of SF from water (AU). According to the turbidity and shear viscosity measurement, SF formic acid solution was stable and transparent, no molecular aggregations occurred. The sample FU exhibited the beta-sheet structure, while AU random coil conformation using Fourier transform infrared (FTIR), X-ray diffraction (XRD), and differential scanning calorimetry. The effects of methanol treatment on samples were also examined. According to the measurement of crystallinity (XRD) and crystallinity index (FTIR), the concept of long/short-range ordered structure formation was proposed. Long-range ordered crystallites are predominantly formed for methanol treated SF film while SF film cast from formic acid favors the formation of short-range ordered structure. The relaxation temperatures of SF films measured by dynamic thermomechanical analysis supported the above mechanism due to the sensitivity of relaxation temperature on the short-range order.

  14. Hydrogen-bonded co-crystal structure of benzoic acid and zwitterionic l-proline

    Directory of Open Access Journals (Sweden)

    Aaron M. Chesna

    2017-03-01

    Full Text Available The title compound [systematic name: benzoic acid–pyrrolidin-1-ium-2-carboxylate (1/1], C7H6O2·C5H9NO2, is an example of the application of non-centrosymmetric co-crystallization for the growth of a crystal containing a typically centrosymmetric component in a chiral space group. It co-crystallizes in the space group P212121 and contains benzoic acid and l-proline in equal proportions. The crystal structure exhibits chains of l-proline zwitterions capped by benzoic acid molecules which form a C(5[R33(11] hydrogen-bonded network along [100]. The crystal structure is examined and compared to that of a similar co-crystal containing l-proline zwitterions and 4-aminobenzoic acid.

  15. Dioxaphosphorinane-constrained nucleic Acid dinucleotides as tools for structural tuning of nucleic acids.

    Science.gov (United States)

    Catana, Dan-Andrei; Renard, Brice-Loïc; Maturano, Marie; Payrastre, Corinne; Tarrat, Nathalie; Escudier, Jean-Marc

    2012-01-01

    We describe a rational approach devoted to modulate the sugar-phosphate backbone geometry of nucleic acids. Constraints were generated by connecting one oxygen of the phosphate group to a carbon of the sugar moiety. The so-called dioxaphosphorinane rings were introduced at key positions along the sugar-phosphate backbone allowing the control of the six-torsion angles α to ζ defining the polymer structure. The syntheses of all the members of the D-CNA family are described, and we emphasize the effect on secondary structure stabilization of a couple of diastereoisomers of α,β-D-CNA exhibiting wether B-type canonical values or not.

  16. Dioxaphosphorinane-Constrained Nucleic Acid Dinucleotides as Tools for Structural Tuning of Nucleic Acids

    Directory of Open Access Journals (Sweden)

    Dan-Andrei Catana

    2012-01-01

    Full Text Available We describe a rational approach devoted to modulate the sugar-phosphate backbone geometry of nucleic acids. Constraints were generated by connecting one oxygen of the phosphate group to a carbon of the sugar moiety. The so-called dioxaphosphorinane rings were introduced at key positions along the sugar-phosphate backbone allowing the control of the six-torsion angles α to ζ defining the polymer structure. The syntheses of all the members of the D-CNA family are described, and we emphasize the effect on secondary structure stabilization of a couple of diastereoisomers of α,β-D-CNA exhibiting wether B-type canonical values or not.

  17. Structure of the human-heart fatty-acid-binding protein 3 in complex with the fluorescent probe 1-anilinonaphthalene-8-sulphonic acid

    Energy Technology Data Exchange (ETDEWEB)

    Hirose, Mika; Sugiyama, Shigeru, E-mail: sugiyama@chem.eng.osaka-u.ac.jp [Lipid Active Structure Project, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Ishida, Hanako; Niiyama, Mayumi [Lipid Active Structure Project, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Osaka University, 2-1 Yamadaoka, Suita 565-0871 (Japan); Matsuoka, Daisuke; Hara, Toshiaki [Lipid Active Structure Project, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Mizohata, Eiichi [Osaka University, 2-1 Yamadaoka, Suita 565-0871 (Japan); Murakami, Satoshi [Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Kanagaw 226-8501 (Japan); Inoue, Tsuyoshi [Osaka University, 2-1 Yamadaoka, Suita 565-0871 (Japan); Matsuoka, Shigeru; Murata, Michio [Lipid Active Structure Project, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan); Osaka University, 1-1 Machikaneyama-cho, Toyonaka 560-0043 (Japan)

    2013-11-01

    The crystal structure of human-heart-type fatty-acid-binding protein in complex with anilinonaphthalene-8-sulfonate was solved at 2.15 Å resolution revealing the detailed binding mechanism of the fluorescent probe 1-anilinonaphthalene-8-sulfonate. Heart-type fatty-acid-binding protein (FABP3), which is a cytosolic protein abundantly found in cardiomyocytes, plays a role in trafficking fatty acids throughout cellular compartments by reversibly binding intracellular fatty acids with relatively high affinity. The fluorescent probe 1-anilinonaphthalene-8-sulfonate (ANS) is extensively utilized for examining the interaction of ligands with fatty-acid-binding proteins. The X-ray structure of FABP3 was determined in the presence of ANS and revealed the detailed ANS-binding mechanism. Furthermore, four water molecules were clearly identified in the binding cavity. Through these water molecules, the bound ANS molecule forms indirect hydrogen-bond interactions with FABP3. The adipocyte-type fatty-acid-binding protein (FABP4) exhibits 67% sequence identity with FABP3 and its crystal structure is almost the same as that of FABP3. However, FABP4 can bind with a higher affinity to ANS than FABP3. To understand the difference in their ligand specificities, a structural comparison was performed between FABP3–ANS and FABP4–ANS complexes. The result revealed that the orientation of ANS binding to FABP3 is completely opposite to that of ANS binding to FABP4, and the substitution of valine in FABP4 to leucine in FABP3 may result in greater steric hindrance between the side-chain of Leu115 and the aniline ring of ANS.

  18. Structure of the human-heart fatty-acid-binding protein 3 in complex with the fluorescent probe 1-anilinonaphthalene-8-sulphonic acid

    International Nuclear Information System (INIS)

    Hirose, Mika; Sugiyama, Shigeru; Ishida, Hanako; Niiyama, Mayumi; Matsuoka, Daisuke; Hara, Toshiaki; Mizohata, Eiichi; Murakami, Satoshi; Inoue, Tsuyoshi; Matsuoka, Shigeru; Murata, Michio

    2013-01-01

    The crystal structure of human-heart-type fatty-acid-binding protein in complex with anilinonaphthalene-8-sulfonate was solved at 2.15 Å resolution revealing the detailed binding mechanism of the fluorescent probe 1-anilinonaphthalene-8-sulfonate. Heart-type fatty-acid-binding protein (FABP3), which is a cytosolic protein abundantly found in cardiomyocytes, plays a role in trafficking fatty acids throughout cellular compartments by reversibly binding intracellular fatty acids with relatively high affinity. The fluorescent probe 1-anilinonaphthalene-8-sulfonate (ANS) is extensively utilized for examining the interaction of ligands with fatty-acid-binding proteins. The X-ray structure of FABP3 was determined in the presence of ANS and revealed the detailed ANS-binding mechanism. Furthermore, four water molecules were clearly identified in the binding cavity. Through these water molecules, the bound ANS molecule forms indirect hydrogen-bond interactions with FABP3. The adipocyte-type fatty-acid-binding protein (FABP4) exhibits 67% sequence identity with FABP3 and its crystal structure is almost the same as that of FABP3. However, FABP4 can bind with a higher affinity to ANS than FABP3. To understand the difference in their ligand specificities, a structural comparison was performed between FABP3–ANS and FABP4–ANS complexes. The result revealed that the orientation of ANS binding to FABP3 is completely opposite to that of ANS binding to FABP4, and the substitution of valine in FABP4 to leucine in FABP3 may result in greater steric hindrance between the side-chain of Leu115 and the aniline ring of ANS

  19. Attachment of di- and tricarboxylic acids to the starting structure of kukersite kerogen

    Energy Technology Data Exchange (ETDEWEB)

    Pobul, L; Mannik, A

    1974-01-01

    Oxidation of the kerogen of kukersite by alkaline permanganate at 50/sup 0/C gave a product containing straight-chain dicarboxylic acids (up to 80%), among which C/sub 4/-C/sub 10/ acids predominated (over 70%). Tricarboxylic acids (15 to 20%) and ..cap alpha..-methyl dicarboxylic acids (4 to 10%) were present. Straight-chain monocarboxylic acids, their isomers, and phenyl derivatives contributed less than 1%. Probably, ..cap alpha..-methyl dicarboxylic and tricarboxylic acids were original structural units of the kerogen. Similar oxidations of Baltic shale indicated that kerogens of different combustible shales differ in chemical composition, but the content of polymers of fatty acids was characteristic. Oxidation of the polymeric acids gave straight-chain mono- and dicarboxylic acids.

  20. Structural Requirements of Alkylglyceryl-l-Ascorbic Acid Derivatives for Melanogenesis Inhibitory Activity.

    Science.gov (United States)

    Taira, Norihisa; Katsuyama, Yushi; Yoshioka, Masato; Muraoka, Osamu; Morikawa, Toshio

    2018-04-10

    l-Ascorbic acid has multifunctional benefits on skin aesthetics, including inhibition of melanin production, and is widely used in cosmetics. It, however, has low stability and poor skin penetration. We hypothesize that alkylglyceryl-l-ascorbic acid derivatives, highly stable vitamin C-alkylglycerol conjugates, would have similar anti-melanogenic activity with better stability and penetration. We test 28 alkylglyceryl-l-ascorbic acid derivatives ( 1 - 28 ) on theophylline-stimulated B16 melanoma 4A5 cells to determine if they inhibit melanogenesis and establish any structure-function relationships. Although not the most potent inhibitors, 3- O -(2,3-dihydroxypropyl)-2- O -hexyl-l-ascorbic acid ( 6 , IC 50 = 81.4 µM) and 2- O -(2,3-dihydroxypropyl)-3- O -hexyl-l-ascorbic acid ( 20 , IC 50 = 117 µM) are deemed the best candidate derivatives based on their inhibitory activities and low toxicities. These derivatives are also found to be more stable than l-ascorbic acid and to have favorable characteristics for skin penetration. The following structural requirements for inhibitory activity of alkylglyceryl-l-ascorbic acid derivatives are also determined: (i) alkylation of glyceryl-l-ascorbic acid is essential for inhibitory activity; (ii) the 3- O -alkyl-derivatives ( 2 - 14 ) exhibit stronger inhibitory activity than the corresponding 2- O -alkyl-derivatives ( 16 - 28 ); and (iii) derivatives with longer alkyl chains have stronger inhibitory activities. Mechanistically, our studies suggest that l-ascorbic acid derivatives exert their effects by suppressing the mRNA expression of tyrosinase and tyrosine-related protein-1.

  1. Salinomycin Hydroxamic Acids: Synthesis, Structure, and Biological Activity of Polyether Ionophore Hybrids.

    Science.gov (United States)

    Borgström, Björn; Huang, Xiaoli; Chygorin, Eduard; Oredsson, Stina; Strand, Daniel

    2016-06-09

    The polyether ionophore salinomycin has recently gained attention due to its exceptional ability to selectively reduce the proportion of cancer stem cells within a number of cancer cell lines. Efficient single step strategies for the preparation of hydroxamic acid hybrids of this compound varying in N- and O-alkylation are presented. The parent hydroxamic acid, salinomycin-NHOH, forms both inclusion complexes and well-defined electroneutral complexes with potassium and sodium cations via 1,3-coordination by the hydroxamic acid moiety to the metal ion. A crystal structure of an cationic sodium complex with a noncoordinating anion corroborates this finding and, moreover, reveals a novel type of hydrogen bond network that stabilizes the head-to-tail conformation that encapsulates the cation analogously to the native structure. The hydroxamic acid derivatives display down to single digit micromolar activity against cancer cells but unlike salinomycin selective reduction of ALDH(+) cells, a phenotype associated with cancer stem cells was not observed. Mechanistic implications are discussed.

  2. 7.5-Å cryo-em structure of the mycobacterial fatty acid synthase.

    Science.gov (United States)

    Boehringer, Daniel; Ban, Nenad; Leibundgut, Marc

    2013-03-11

    The mycobacterial fatty acid synthase (FAS) complex is a giant 2.0-MDa α(6) homohexameric multifunctional enzyme that catalyzes synthesis of fatty acid precursors of mycolic acids, which are major components of the cell wall in Mycobacteria and play an important role in pathogenicity. Here, we present a three-dimensional reconstruction of the Mycobacterium smegmatis FAS complex at 7.5Å, highly homologous to the Mycobacterium tuberculosis multienzyme, by cryo-electron microscopy. Based on the obtained structural data, which allowed us to identify secondary-structure elements, and sequence homology with the fungal FAS, we generated an accurate architectural model of the complex. The FAS system from Mycobacteria resembles a minimized version of the fungal FAS with much larger openings in the reaction chambers. These architectural features of the mycobacterial FAS may be important for the interaction with mycolic acid processing and condensing enzymes that further modify the precursors produced by FAS and for autoactivation of the FAS complex. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. The construction of an amino acid network for understanding protein structure and function.

    Science.gov (United States)

    Yan, Wenying; Zhou, Jianhong; Sun, Maomin; Chen, Jiajia; Hu, Guang; Shen, Bairong

    2014-06-01

    Amino acid networks (AANs) are undirected networks consisting of amino acid residues and their interactions in three-dimensional protein structures. The analysis of AANs provides novel insight into protein science, and several common amino acid network properties have revealed diverse classes of proteins. In this review, we first summarize methods for the construction and characterization of AANs. We then compare software tools for the construction and analysis of AANs. Finally, we review the application of AANs for understanding protein structure and function, including the identification of functional residues, the prediction of protein folding, analyzing protein stability and protein-protein interactions, and for understanding communication within and between proteins.

  4. Amino acid size, charge, hydropathy indices and matrices for protein structure analysis

    Directory of Open Access Journals (Sweden)

    Biro JC

    2006-03-01

    Full Text Available Abstract Background Prediction of protein folding and specific interactions from only the sequence (ab initio is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynamic principle is correct for all kinds of proteins, and all the information necessary to form a concrete 3D structure is indeed present in the sequence. Results We indexed the 200 possible amino acid pairs for their compatibility regarding the three major physicochemical properties – size, charge and hydrophobicity – and constructed Size, Charge and Hydropathy Compatibility Indices and Matrices (SCI & SCM, CCI & CCM, and HCI & HCM. Each index characterized the expected strength of interaction (compatibility of two amino acids by numbers from 1 (not compatible to 20 (highly compatible. We found statistically significant positive correlations between these indices and the propensity for amino acid co-locations in real protein structures (a sample containing total 34630 co-locations in 80 different protein structures: for HCI: p We tried to predict or reconstruct simple 2D representations of 3D structures from the sequence using these matrices by applying a dot plot-like method. The location and pattern of the most compatible subsequences was very similar or identical when the three fundamentally different matrices were used, which indicates the consistency of physicochemical compatibility. However, it was not sufficient to choose one preferred configuration between the many possible predicted options. Conclusion Indexing of amino acids for major physico-chemical properties is a powerful approach to understanding and assisting protein design. However, it is probably insufficient itself for complete ab initio structure prediction.

  5. Enzymatic synthesis of capric acid-rich structured lipids (MUM type) using Candida antarctica lipase.

    Science.gov (United States)

    SilRoy, Sumita; Ghosh, Mahua

    2011-01-01

    The objective of the work was to produce capric acid rich structured lipids starting from various Indian indigenous vegetable oils, such as rice bran, ground nut and mustard oils. Acidolysis reaction between individual vegetable oils and capric acid in one is to three molar ratios at 45 degree centigrade temperature was carried out using position specific Candida antarctica lipase so as to protect the Sn-2 position of the oils which are rich in unsaturated fatty acids. The incorporation of capric acid depended on the reaction time showing 6 % within 6 h and 30.8 % in 72 h with rice bran oil. Similarly, in ground nut oil incorporation of capric acid was 34.2 % in 72 h compared to 5.3 % in 6 h. Thus mustard oil showed much lower incorporation than the other two oils, with 3.3 % and 19.5 % in 6 and 72 h respectively. The incorporation of capric acid was influenced by the nature of the fatty acids present in the original oil. The fatty acid composition of Sn-2 position of the structured triacylglycerols of the three oils revealed that capric acid was mainly replacing the fatty acids occupying the Sn-1 and 3 positions of the triglyceride molecule.

  6. ReaxFF molecular dynamics simulation of intermolecular structure formation in acetic acid-water mixtures at elevated temperatures and pressures

    Science.gov (United States)

    Sengul, Mert Y.; Randall, Clive A.; van Duin, Adri C. T.

    2018-04-01

    The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was investigated using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ xHAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ xHAc), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental results. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations indicate that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.

  7. Molecular structure and interactions of nucleic acid components in nanoparticles: ab initio calculations

    International Nuclear Information System (INIS)

    Rubin, Yu.V.; Belous, L.F.

    2012-01-01

    Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150-200 atoms with enough large basis sets (for example, 6-31G * ). The aim of this work is to reveal the peculiarities of molecular and electronic structures, as well as the energy features of nanoparticles of nucleic acid components. We had carried out ab initio calculations of the molecular structure and interactions in the stacking dimer, trimer, and tetramer of nucleic base pairs and in the stacking (TpG)(ApC) dimer and (TpGpC) (ApCpG) trimer of nucleotides, which are small DNA fragments. The performed calculations of molecular structures of dimers and trimers of nucleotide pairs showed that the interplanar distance in the structures studied is equal to 3.2 A on average, and the helical angle in a trimer is approximately equal to 30 o : The distance between phosphor atoms in neighboring chains is 13.1 A. For dimers and trimers under study, we calculated the horizontal interaction energies. The analysis of interplanar distances and angles between nucleic bases and their pairs in the calculated short oligomers of nucleic acid base pairs (stacking dimer, trimer, and tetramer) has been carried out. Studies of interactions in the calculated short oligomers showed a considerable role of the cross interaction in the stabilization of the structures. The contribution of cross interactions to the horizontal interactions grows with the length of an oligomer. Nanoparticle components get electric charges in nanoparticles. Longwave low-intensity bands can appear in the electron spectra of nanoparticles.

  8. Crystal structures of hibiscus acid and hibiscus acid dimethyl ester isolated from Hibiscus sabdariffa (Malvaceae).

    Science.gov (United States)

    Zheoat, Ahmed M; Gray, Alexander I; Igoli, John O; Kennedy, Alan R; Ferro, Valerie A

    2017-09-01

    The biologically active title compounds have been isolated from Hibiscus sabdariffa plants, hibiscus acid as a dimethyl sulfoxide monosolvate [systematic name: (2 S ,3 R )-3-hy-droxy-5-oxo-2,3,4,5-tetra-hydro-furan-2,3-di-carb-oxy-lic acid dimethyl sulfoxide monosolvate], C 6 H 6 O 7 ·C 2 H 6 OS, (I), and hibiscus acid dimethyl ester [systematic name: dimethyl (2 S ,3 R )-3-hy-droxy-5-oxo-2,3,4,5-tetra-hydro-furan-2,3-di-carboxyl-ate], C 8 H 10 O 7 , (II). Compound (I) forms a layered structure with alternating layers of lactone and solvent mol-ecules, that include a two-dimensional hydrogen-bonding construct. Compound (II) has two crystallographically independent and conformationally similar mol-ecules per asymmetric unit and forms a one-dimensional hydrogen-bonding construct. The known absolute configuration for both compounds has been confirmed.

  9. Design, synthesis and structure of new potential electrochemically active boronic acid-based glucose sensors

    DEFF Research Database (Denmark)

    Norrild, Jens Chr.; Søtofte, Inger

    2002-01-01

    In the course of our investigations on new boronic acid based carbohydrate sensors three new boronic acids 3, 7 and 11 containing a ferrocene moiety were synthesised. Their design includes an intramolecular B-N bonding motif in order to facilitate binding at physiological pH. We report the synthe......In the course of our investigations on new boronic acid based carbohydrate sensors three new boronic acids 3, 7 and 11 containing a ferrocene moiety were synthesised. Their design includes an intramolecular B-N bonding motif in order to facilitate binding at physiological pH. We report...... the synthesis of the compounds and our investigations on glucose complexation as studied by C-13 NMR spectroscopy. The crystal structure of 2,4,6-tris[2-(N-ferrocenylmethyl-N-methylaminomethyl) phenyl] boroxin (13) (boroxin of boronic acid 3) (boroxin = cyclotriboroxane) was obtained and compared...... with structures obtained of 2,4,6-tris[2-(N,N-dimethylaminomethyl)phenyl]boroxin (14) and 2,2-dimethyl-1,3-diyl[2-(N,N-dimethylaminomethyl)phenyl]boronate (15). The structure of 13 shows the existence of intramolecular B-N bonds in the solid phase....

  10. Investigation of supramolecular synthons and structural characterisation of aminopyridine-carboxylic acid derivatives.

    Science.gov (United States)

    Hemamalini, Madhukar; Loh, Wan-Sin; Quah, Ching Kheng; Fun, Hoong-Kun

    2014-01-01

    Co-crystal is a structurally homogeneous crystalline material that contains two or more neutral building blocks that are present in definite stoichiometric amounts. The main advantage of co-crystals is their ability to generate a variety of solid forms of a drug that have distinct physicochemical properties from the solid co-crystal components. In the present investigation, five co-crystals containing 2-amino-6-chloropyridine (AMPY) moiety were synthesized and characterized. The crystal structure of 2-amino-6-chloropyridine (AMPY) (I), and the robustness of pyridine-acid supramolecular synthon were discussed in four stoichiometry co-crystals of AMPY…BA (II), AMPY…2ABA (III), AMPY…3CLBA (IV) and AMPY…4NBA (V). The abbreviated designations used are benzoic acid (BA), 2-aminobenzoic acid (2ABA), 3-chlorobenzoic acid (3CLBA) and 4-nitrobenzoic acid (4NBA). All the crystalline materials have been characterized by (1)HNMR, (13)CNMR, IR, photoluminescence, TEM analysis and X-ray diffraction. The supramolecular assembly of each co-crystal is analyzed and discussed. Extensive N---H · · · N/N---H · · · O/O---H · · · N hydrogen bonds are found in (I-V), featuring different supramolecular synthons. In the crystal structure, for compound (I), the 2-amino-6-chloropyridine molecules are linked together into centrosymmetric dimers by hydrogen bonds to form homosynthon, whereas for compounds (II-V), the carboxylic group of the respective acids (benzoic acid, 2-aminobenzoic acid, 3-chlorobenzoic acid and 4-nitrobenzoic acid) interacts with pyridine molecule in a linear fashion through a pair of N---H · · · O and O---H · · · N hydrogen bonds, generating cyclic hydrogen-bonded motifs with the graph-set notation [Formula: see text] , to form heterosynthon. In compound (II), another intermolecular N---H · · · O hydrogen bonds further link these heterosynthons into zig-zag chains. Whereas in compounds (IV) and (V

  11. Optical Absorption, Stability and Structure of NpO2+ Complexes with Dicarboxylic Acids

    International Nuclear Information System (INIS)

    Guoxin Tian; Linfeng Rao

    2006-01-01

    Complexation of NpO2+ with oxalic acid (OX),2,2'-oxydiacetic acid (ODA), 2,2'-iminodiacetic acid (IDA) and 2,2'-thiodiacetic acid (TDA), has been studied using spectrophotometry in1 M NaClO4. Both the position and the intensity of the absorption band of NpO2+ at 980 nm are affected by the formation of NpO2+/dicarboxylate complexes, providing useful information on the complexation strength, the coordination mode and the structure of the complexes

  12. Two-dimensional hydrogen-bonded polymers in the crystal structures of the ammonium salts of phenoxyacetic acid, (4-fluorophenoxyacetic acid and (4-chloro-2-methylphenoxyacetic acid

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2014-12-01

    Full Text Available The structures of the ammonium salts of phenoxyacetic acid, NH4+·C8H6O3−, (I, (4-fluorophenoxyacetic acid, NH4+·C8H5FO3−, (II, and the herbicidally active (4-chloro-2-methylphenoxyacetic acid (MCPA, NH4+·C9H8ClO3−·0.5H2O, (III have been determined. All have two-dimensional layered structures based on inter-species ammonium N—H...O hydrogen-bonding associations, which give core substructures consisting primarily of conjoined cyclic motifs. The crystals of (I and (II are isomorphous with the core comprising R12(5, R12(4 and centrosymmetric R42(8 ring motifs, giving two-dimensional layers lying parallel to (100. In (III, the water molecule of solvation lies on a crystallographic twofold rotation axis and bridges two carboxyl O atoms in an R44(12 hydrogen-bonded motif, creating two R43(10 rings, which together with a conjoined centrosymmetric R42(8 ring incorporating both ammonium cations, generate two-dimensional layers lying parallel to (100. No π–π ring associations are present in any of the structures.

  13. Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.

    Science.gov (United States)

    Sales, Mark; Plecs, Joseph J; Holton, James M; Alber, Tom

    2007-10-01

    The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Angstrom resolution using a designed metal binding site to coordinate a single Yb(2+) ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Angstrom. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures.

  14. A family of uranium-carboxylic acid hybrid materials: synthesis, structure and mixed-dye selective adsorption

    International Nuclear Information System (INIS)

    Xue Gao; Jian Song; Yong Heng Xing; Feng Ying Bai; Li Xian Sun; Zhan Shi

    2016-01-01

    Four uranyl complexes (UO_2)_2(pht)_2(Hpac)_2(H_2O)_2 (pht = phthalic acid and Hpac = nicotinic acid) (1), (UO_2)(pac)_2(H_2O)_2 (2), [(UO_2)(CMA)_3][H_2N(CH_3)_2] (CMA = cinnamic acid) (3) and (UO_2)_2(C_2O_4)(μ_2- OH)_2(H_2O)_2H_2O (4) were synthesized by the reaction of UO_2(CH_3COO)_2.2H_2O as the metal source with phthalic acid, nicotinic acid, cinnamic acid or oxalic acid as the ligand. They were characterized by elemental analysis, IR, UV-vis, XRD, single crystal X-ray diffraction and thermal gravimetric analysis. The structural analysis showed that complexes 1, 2 and 3 were discrete structures, and by hydrogen bonding interactions, the adjacent molecular units are connected to form a three-dimensional (3D) supramolecular network structure for complex 1 and one-dimensional (1D) chains for complexes 2 and 3. Meanwhile, in the structure of complex 4, a tetrameric SBU (UO_2)_4(μ_2-OH)_4(H_2O)_4 is linked to a 2D layer through a bridging oxalic acid ligand, and furthermore extends the 2D layer into a 3D supramolecular architecture by hydrogen bonding interactions. In order to extend their functional properties, their photoluminescence, surface photovoltage and mixed-dye selective adsorption properties have been studied for the first time. Through experiments, we found that the adsorption performance of complex 3 was better than others, and the amount of adsorbed RhB was 4.22 mg.g"-"1. (authors)

  15. Oxidative stability during storage of structured lipids produced from fish oil and caprylic acid

    DEFF Research Database (Denmark)

    Nielsen, Nina Skall; Xu, Xuebing; Timm Heinrich, Maike

    2004-01-01

    Structured lipids produced by enzymatic or chemical methods for different applications have been receiving considerable attention. The oxidative stability of a randomized structured lipid (RFO), produced by chemical interesterification from fish oil (FO) and tricaprylin, and a specific structured...... lipid (SFO), produced by enzymatic interesterification from the same oil and caprylic acid, was compared with the stability of FO. Oils were stored at 2degreesC for 11 wk followed by storage at 20degreesC for 6 wk. In addition, the antioxidative effect of adding the metal chelators EDTA or citric acid...

  16. Hydroxycinnamic acid bound arabinoxylans from millet brans-structural features and antioxidant activity.

    Science.gov (United States)

    Bijalwan, Vandana; Ali, Usman; Kesarwani, Atul Kumar; Yadav, Kamalendra; Mazumder, Koushik

    2016-07-01

    Hydroxycinnamic acid bound arabinoxylans (HCA-AXs) were extracted from brans of five Indian millet varieties and response surface methodology was used to optimize the extraction conditions. The optimal condition to obtain highest yield of millet HCA-AXs was determined as follows: time 61min, temperature 66°C, ratio of solvent to sample 12ml/g. Linkage analysis indicated that hydroxycinnamic acid bound arabinoxylan from kodo millet (KM-HCA-AX) contained comparatively low branched arabinoxylan consisting of 14.6% mono-substituted, 1.2% di-substituted and 41.2% un-substituted Xylp residues. The HPLC analysis of millet HCA-AXs showed significant variation in the content of three major bound hydroxycinnamic acids (caffeic, p-coumaric and ferulic acid). The antioxidant activity of millet HCA-AXs were evaluated using three in vitro assay methods (DPPH, FRAP and β-carotene linoleate emulsion assays) which suggested both phenolic acid composition and structural characteristics of arabinoxylans could be correlated to their antioxidant potential, the detailed structural analysis revealed that low substituted KM-HCA-AX exhibited relatively higher antioxidant activity compared to other medium and highly substituted HCA-AXs from finger (FM), proso (PM), barnyard (BM) and foxtail (FOXM) millet. Copyright © 2016. Published by Elsevier B.V.

  17. Anthropogenic and natural sources of acidity and metals and their influence on the structure of stream food webs

    International Nuclear Information System (INIS)

    Hogsden, Kristy L.; Harding, Jon S.

    2012-01-01

    We compared food web structure in 20 streams with either anthropogenic or natural sources of acidity and metals or circumneutral water chemistry in New Zealand. Community and diet analysis indicated that mining streams receiving anthropogenic inputs of acidic and metal-rich drainage had much simpler food webs (fewer species, shorter food chains, less links) than those in naturally acidic, naturally high metal, and circumneutral streams. Food webs of naturally high metal streams were structurally similar to those in mining streams, lacking fish predators and having few species. Whereas, webs in naturally acidic streams differed very little from those in circumneutral streams due to strong similarities in community composition and diets of secondary and top consumers. The combined negative effects of acidity and metals on stream food webs are clear. However, elevated metal concentrations, regardless of source, appear to play a more important role than acidity in driving food web structure. - Highlights: ► Food webs in acid mine drainage impacted streams are small and extremely simplified. ► Conductivity explained differences in food web properties between streams. ► Number of links and web size accounted for much dissimilarity between food webs. ► Food web structure was comparable in naturally acidic and circumneutral streams. - Food web structure differs in streams with anthropogenic and natural sources of acidity and metals.

  18. Synthesis of structured triacylglycerols containing caproic acid by lipase-catalyzed acidolysis: Optimization by response surface methodology

    DEFF Research Database (Denmark)

    Zhou, D.Q.; Xu, Xuebing; Mu, Huiling

    2001-01-01

    Production in a batch reactor with a solvent-free system of structured triacylglycerols containing short-chain fatty acids by Lipozyme RM IM-catalyzed acidolysis between rapeseed oil and caproic acid was optimized using response surface methodology (RSM). Reaction time (t(r)), substrate ratio (S......-r = 2-6 mol/mol; and W-c = 2-12 wt %. The biocatalyst was Lipozyme RM IM, in which Rhizomucor miehei lipase is immobilized on a resin. The incorporation of caproic acid into rapeseed oil was the main monitoring response. In addition, the contents of mono-incorporated structured triacylglycerols and di......-incorporated structured triacylglycerols were also evaluated. The optimal reaction conditions for the incorporation of caproic acid and the content of di-incorporated structured triacylglycerols were as follows: t(r) = 17 h; 8, = 5; E-1 = 14 wt %; W-c = 10 wt %; T-e = 65 degreesC. At these conditions, products with 55...

  19. Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to cholic and oleic acid.

    Science.gov (United States)

    Capaldi, Stefano; Guariento, Mara; Perduca, Massimiliano; Di Pietro, Santiago M; Santomé, José A; Monaco, Hugo L

    2006-07-01

    The family of the liver bile acid-binding proteins (L-BABPs), formerly called liver basic fatty acid-binding proteins (Lb-FABPs) shares fold and sequence similarity with the paralogous liver fatty acid-binding proteins (L-FABPs) but has a different stoichiometry and specificity of ligand binding. This article describes the first X-ray structure of a member of the L-BABP family, axolotl (Ambystoma mexicanum) L-BABP, bound to two different ligands: cholic and oleic acid. The protein binds one molecule of oleic acid in a position that is significantly different from that of either of the two molecules that bind to rat liver FABP. The stoichiometry of binding of cholate is of two ligands per protein molecule, as observed in chicken L-BABP. The cholate molecule that binds buried most deeply into the internal cavity overlaps well with the analogous bound to chicken L-BABP, whereas the second molecule, which interacts with the first only through hydrophobic contacts, is more external and exposed to the solvent. (c) 2006 Wiley-Liss, Inc.

  20. Probing the molecular and electronic structure of the lichen metabolite usnic acid: A DFT study

    International Nuclear Information System (INIS)

    Galasso, V.

    2010-01-01

    Graphical abstract: DFT calculations of structural preferences, acidic properties, carbonyl vibrations, 13 C NMR chemical shifts, and absorption spectrum account for the unique structural backbone, chemical behaviour, and spectroscopic properties of usnic acid, the cortical pigment and potent reactive of lichens. - Abstract: The molecular structure of usnic acid was investigated by the density functional theory (DFT). Two keto-enol tautomers are nearly isoenergetic and more stable than other tautomers. Noteworthy is the energy difference among the three intramolecular O-H...O hydrogen bonds. The DFT/PCM calculated dissociation constants account for the acidic sequence of the three OH-groups. The electronic structure was also studied by calculating IR/Raman, NMR, and absorption features. A reliable assignment of the 'fingerprint' carbonyl stretching modes was supported by calculations on related molecules. The calculated NMR chemical shifts fit expectation in terms of a fast interconversion between the two most preferred tautomers. A variety of π → π* and n → π* excitations, localized on a single ring or involving a charge-transfer between the two lateral rings of the molecule, gives rise to the broad UV-absorption bands. This property accounts for the efficient protection against damaging solar radiation provided by usnic acid for lichens.

  1. Probing the molecular and electronic structure of the lichen metabolite usnic acid: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Galasso, V., E-mail: galasso@univ.trieste.it [Dipartimento di Scienze Chimiche, Universita di Trieste, I-34127 Trieste (Italy)

    2010-08-23

    Graphical abstract: DFT calculations of structural preferences, acidic properties, carbonyl vibrations, {sup 13}C NMR chemical shifts, and absorption spectrum account for the unique structural backbone, chemical behaviour, and spectroscopic properties of usnic acid, the cortical pigment and potent reactive of lichens. - Abstract: The molecular structure of usnic acid was investigated by the density functional theory (DFT). Two keto-enol tautomers are nearly isoenergetic and more stable than other tautomers. Noteworthy is the energy difference among the three intramolecular O-H...O hydrogen bonds. The DFT/PCM calculated dissociation constants account for the acidic sequence of the three OH-groups. The electronic structure was also studied by calculating IR/Raman, NMR, and absorption features. A reliable assignment of the 'fingerprint' carbonyl stretching modes was supported by calculations on related molecules. The calculated NMR chemical shifts fit expectation in terms of a fast interconversion between the two most preferred tautomers. A variety of {pi} {yields} {pi}* and n {yields} {pi}* excitations, localized on a single ring or involving a charge-transfer between the two lateral rings of the molecule, gives rise to the broad UV-absorption bands. This property accounts for the efficient protection against damaging solar radiation provided by usnic acid for lichens.

  2. New insights into structure and function of the different types of fatty acid-binding protein

    NARCIS (Netherlands)

    Zimmerman, Augusta Wilhelmina

    2002-01-01

    Fatty acid binding proteins (FABPs) are small cytosolic proteins with virtually identical backbone structures that facilitate the solubility and intracellular transport of fatty acids. They may also modulate the effect of fatty acids on various metabolic enzymes and receptors and on cellular

  3. Effect of synthesis parameters on polymethacrylic acid xerogel structures and equilibrium swelling

    Science.gov (United States)

    Panić, V.; Jovanović, J.; Adnadjević, B.; Velicković, S.

    2009-09-01

    Hydrogels based on crosslinked polymethacrylic acid were synthesized via free-radical polymerization in aqueous solution, using N,N'-methylene bisacrylamide as a crosslinking agent and 2,2'-azobis-[2-(2-imidazolin-2-yl)propane] dihydrochloride as an initiator. The influence of the reaction parameters (the neutralization degree of methacrylic acid and the initial monomer concentration) on the equilibrium swelling degree, the swelling kinetic parameters and the basic structural properties of xerogels was investigated. The change of synthesis parameters leads to the change of the basic structural parameters of xerogel, as well as the equilibrium swelling degree and the initial swelling rate of the hydrogels. It is found that there are power form relationships between the equilibrium swelling degree, the initial swelling rate and the structural xerogel’s properties and the change of the neutralization degree of monomer, i.e. the monomer concentration. The examined correlations proved that the crosslinking density is the crucial parameter which determines all the other investigated structural and swelling parameters.

  4. Noncoded amino acids in protein engineering: Structure-activity relationship studies of hirudin-thrombin interaction.

    Science.gov (United States)

    De Filippis, Vincenzo; Acquasaliente, Laura; Pontarollo, Giulia; Peterle, Daniele

    2018-01-01

    The advent of recombinant DNA technology allowed to site-specifically insert, delete, or mutate almost any amino acid in a given protein, significantly improving our knowledge of protein structure, stability, and function. Nevertheless, a quantitative description of the physical and chemical basis that makes a polypeptide chain to efficiently fold into a stable and functionally active conformation is still elusive. This mainly originates from the fact that nature combined, in a yet unknown manner, different properties (i.e., hydrophobicity, conformational propensity, polarizability, and hydrogen bonding capability) into the 20 standard natural amino acids, thus making difficult, if not impossible, to univocally relate the change in protein stability or function to the alteration of physicochemical properties caused by amino acid exchange(s). In this view, incorporation of noncoded amino acids with tailored side chains, allowing to finely tune the structure at a protein site, would facilitate to dissect the effects of a given mutation in terms of one or a few physicochemical properties, thus much expanding the scope of physical organic chemistry in the study of proteins. In this review, relevant applications from our laboratory will be presented on the use of noncoded amino acids in structure-activity relationships studies of hirudin binding to thrombin. © 2017 International Union of Biochemistry and Molecular Biology, Inc.

  5. Steric structure and thermodynamic aspects of Dy3+ complexes with aminobenzoic acids in aqueous solutions

    International Nuclear Information System (INIS)

    Kondrashina, Yu.G.; Mustafina, A.R.; Vul'fson, S.G.

    1994-01-01

    Stability and structure of dysprosium(3) aminobenzoate complexes with molar ratios Dy:L 1:1 and 1:2 (HL-aminobenzoic acid) in aqueous solutions are determined on the basis of pH-metric and paramagnetic birefringence data. The increase of conjugation effect in the series of benzoic, meta- ortho-, and para-aminobenzoic acid results in the increase of stability of 1:1 and 1:2 complexes. Features of the structure and coordination of ligands in dysprosium complexes with meta-, ortho-, and para-aminobenzoic acid are considered. 11 refs.; 4 figs.; 2 tabs

  6. Surface Patterning of Benzene Carboxylic Acids on Graphite: Influence of structure, solvent, and concentration on molecular self-assembly

    Science.gov (United States)

    Florio, Gina; Stiso, Kimberly; Campanelli, Joseph; Dessources, Kimberly; Folkes, Trudi

    2012-02-01

    Scanning tunneling microscopy (STM) was used to investigate the molecular self-assembly of four different benzene carboxylic acid derivatives at the liquid/graphite interface: pyromellitic acid (1,2,4,5-benzenetetracarboxylic acid), trimellitic acid (1,2,4-benzenetricarboxylic acid), trimesic acid (1,3,5-benzenetricarboxylic acid), and 1,3,5-benzenetriacetic acid. A range of two dimensional networks are observed that depend sensitively on the number of carboxylic acids present, the nature of the solvent, and the solution concentration. We will describe our recent efforts to determine (a) the preferential two-dimensional structure(s) for each benzene carboxylic acid at the liquid/graphite interface, (b) the thermodynamic and kinetic factors influencing self-assembly (or lack thereof), (c) the role solvent plays in the assembly, (e) the effect of in situ versus ex situ dilution on surface packing density, and (f) the temporal evolution of the self-assembled monolayer. Results of computational analysis of analog molecules and model monolayer films will also be presented to aid assignment of network structures and to provide a qualitative picture of surface adsorption and network formation.

  7. Evaluation of structure effects on the pharmacological behavior of radioiodinated phenylpentadecanoic acids

    Energy Technology Data Exchange (ETDEWEB)

    Knapp, F.F. Jr.; Goodman, M.M.; Machulla, H.J.; Knust, E.J.; Kartje, M.; Vyska, K.

    1986-01-01

    For studying the pharmacokinetic behaviour of fatty acids with different chemical structures four STI-labelled compounds, i.e., the ortho and para STI-isomers of 15-phenylpentadecanoic acid (IPPA) and 3-methyl-15-phenylpentadecanoic acid were prepared and the organ distribution determined in mice. The results show a significant decrease of the maximal heart uptake for the two ortho compounds. Further, the hypothesis of a blocked metabolism as an effect of the US -methylation could not be confirmed. Both US -methylated compounds show a biexponential elimination behavior from the heart. 5 refs., 2 figs.

  8. Lymphatic recovery of exogenous oleic acid in rats on long chain or specific structured triacylglycerol diets

    DEFF Research Database (Denmark)

    Vistisen, Bodil; Mu, Huiling; Høy, Carl-Erik

    2006-01-01

    Specific structured triacylglycerols, MLM (M = medium-chain fatty acid, L = long-chain fatty acid), rapidly deliver energy and long-chain fatty acids to the body and are used for longer periods in human enteral feeding. In the present study rats were fed diets of 10 wt% MLM or LLL (L = oleic acid......% and 45%, respectively). However, the recovery of exogenous 18:1 n-9 was higher after a single bolus of MLM compared with a bolus of LLL in rats on the MLM diet (40% and 24%, respectively, P = 0.009). The recovery of lymphatic 18:1 n-9 of the LLL bolus tended to depend on the diet triacylglycerol...... structure and composition (P = 0.07). This study demonstrated that with a diet containing specific structured triacylglycerol, the lymphatic recovery of 18:1 n-9 after a single bolus of fat was dependent on the triacylglycerol structure of the bolus. This indicates that the lymphatic recovery of long...

  9. Thermodynamics and Structure of Actinide(IV) Complexes with Nitrilotriacetic Acid

    Energy Technology Data Exchange (ETDEWEB)

    Bonin, L.; Guillaumont, D.; Jeanson, A.; Den Auwer, C.; Moisy, Ph. [CEA Marcoule, DEN, DRCP, SCPS, F-30207 Bagnols Sur Ceze (France); Grigoriev, M. [RAS, AN Frumkin Inst Phys Chem and Electrochem, Moscow 119991 (Russian Federation); Berthet, J.C. [CEA Saclay, DSM, IRAMIS, URA 331, Serv Chim Mol, CNRS, F-91191 Gif Sur Yvette (France); Hennig, C.; Scheinost, A. [Forschungszentrum Dresden Rossendorf, Inst Radiochem, D-01314 Dresden (Germany)

    2009-05-15

    Nitrilotriacetic acid, commonly known as NITA (N(CH{sub 2}CO{sub 2}H){sub 3}), can be considered a representative of the polyamino-carboxylic family. The results presented in this paper describe the thermodynamical complexation and structural investigation of An(IV) complexes with NTA in aqueous solution. In the first part, the stability constants of the An(IV) complexes (An = Pu, Np, U, and Th) have been determined by spectrophotometry. In the second part, the coordination spheres of the actinide cation in these complexes have been described using extended X-ray absorption fine structure spectroscopy and compared to the solid-state structure of (Hpy){sub 2}[U(NTA){sub 2}].H{sub 2}O. These data are further compared to quantum chemical calculations, and their evolution across the actinide series is discussed. In particular, an interpretation of the role of the nitrogen atom in the coordination mode is proposed. These results are considered to be model behavior of polyamino-carboxylic ligands such as diethylenetriamine pentaacetic acid, which is nowadays the best candidate for a chelating agent in the framework of actinide decorporation for the human body. (authors)

  10. Structural and electronic properties of L-amino acids

    Science.gov (United States)

    Tulip, P. R.; Clark, S. J.

    2005-05-01

    The structural and electronic properties of four L-amino acids alanine, leucine, isoleucine, and valine have been investigated using density functional theory (DFT) and the generalized gradient approximation. Within the crystals, it is found that the constituent molecules adopt zwitterionic configurations, in agreement with experimental work. Lattice constants are found to be in good agreement with experimentally determined values, although certain discrepancies do exist due to the description of van der Waals interactions. We find that these materials possess wide DFT band gaps in the region of 5 eV, with electrons highly localized to the constituent molecules. It is found that the main mechanisms behind crystal formation are dipolar interactions and hydrogen bonding of a primarily electrostatic character, in agreement with current biochemical understanding of these systems. The electronic structure suggests that the amine and carboxy functional groups are dominant in determining band structure.

  11. Crystal and molecular structure of adduct of 6-benzylaminopurine and 5-sulfosalicylic acid

    Energy Technology Data Exchange (ETDEWEB)

    Xia Min, E-mail: xiamin@hytc.edu.cn; Ma Kuirong [Huaiyin Normal University, Jiangsu Key Laboratory for Chemistry of Low-Dimensional Materials, School of Chemistry and Chemical Engineering (China)

    2010-12-15

    The crystal structure of adduct of 6-benzylaminopurine and 5-sulfosalicylic acid C{sub 19}H{sub 25}N{sub 5}O{sub 10}S 1 is studied using single-crystal diffraction (R = 0.0482 for 2852 reflections with I > 2{sigma}(I)). The asymmetric unit of 1 contains one 6-benzylaminopurine molecule and one 5-sulfosalicylic acid molecule, as well as four lattice water molecules. Hydrogen bonds, formed by 6-benzylaminopurine and 5-sulfosalicylic acid, link the two molecules into one-dimensional chain (omitting four water molecules), further joined to two-dimensional layer network. Short ring-interactions with intra-chain {pi}-{pi} stacking are observed. The data of IR spectroscopy confirm the formation of the two-dimensional supramolecular layer structure. At last, a 3D supramolecular network constructs via hydrogen bonds.

  12. Genomes in Turmoil: Frugality Drives Microbial Community Structure in Extremely Acidic Environments

    Science.gov (United States)

    Holmes, D. S.

    2016-12-01

    Extremely acidic environments (To gain insight into these issues, we have conducted deep bioinformatic analyses, including metabolic reconstruction of key assimilatory pathways, phylogenomics and network scrutiny of >160 genomes of acidophiles, including representatives from Archaea, Bacteria and Eukarya and at least ten metagenomes of acidic environments [Cardenas JP, et al. pp 179-197 in Acidophiles, eds R. Quatrini and D. B. Johnson, Caister Academic Press, UK (2016)]. Results yielded valuable insights into cellular processes, including carbon and nitrogen management and energy production, linking biogeochemical processes to organismal physiology. They also provided insight into the evolutionary forces that shape the genomic structure of members of acidophile communities. Niche partitioning can explain diversity patterns in rapidly changing acidic environments such as bioleaching heaps. However, in spatially and temporally homogeneous acidic environments genome flux appears to provide deeper insight into the composition and evolution of acidic consortia. Acidophiles have undergone genome streamlining by gene loss promoting mutual coexistence of species that exploit complementarity use of scarce resources consistent with the Black Queen hypothesis [Morris JJ et al. mBio 3: e00036-12 (2012)]. Acidophiles also have a large pool of accessory genes (the microbial super-genome) that can be accessed by horizontal gene transfer. This further promotes dependency relationships as drivers of community structure and the evolution of keystone species. Acknowledgements: Fondecyt 1130683; Basal CCTE PFB16

  13. Synthesis and conductivity of heptadecatungstovanadodiphosphoric heteropoly acid with Dawson structure

    Energy Technology Data Exchange (ETDEWEB)

    Tong Xia; Zhu Weiming [Department of Chemistry, Zhejiang University, Hangzhou 310027 (China); Wu Qingyin, E-mail: qywu@zju.edu.cn [Department of Chemistry, Zhejiang University, Hangzhou 310027 (China); Qian Xueyu; Liu Zhen [Department of Chemistry, Zhejiang University, Hangzhou 310027 (China); Yan Wenfu [State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Changchun 130012 (China); Gong Jian [Key Lab of Polyoxometalate Science, the Ministry of Education, Northeast Normal University, Changchun 130024 (China)

    2011-07-21

    A new solid high-proton conductor, heptadecatungstovanadodiphosphoric heteropoly acid H{sub 7}P{sub 2}W{sub 17}VO{sub 62}.28H{sub 2}O with Dawson structure was synthesized by the stepwise acidification and the stepwise addition of element solutions. The optimal proportion of component compounds in the synthesis reaction was given. The product was characterized by chemical analysis, potentiometric titration, IR, UV, XRD, {sup 31}P NMR, TG-DTA and electrochemical impedance spectroscopy (EIS). The results indicate that H{sub 7}P{sub 2}W{sub 17}VO{sub 62}.28H{sub 2}O possesses the Dawson structure. EIS measurements show a high conductivity (3.10 x 10{sup -2} S cm{sup -1} at 26 deg. C and 75% relative humidity), with an activation energy of 32.23 kJ mol{sup -1} for proton conduction. The mechanism of proton conduction for this heteropoly acid is Vehicle mechanism.

  14. Copper coordination polymers constructed from thiazole-5-carboxylic acid: Synthesis, crystal structures, and structural transformation

    Energy Technology Data Exchange (ETDEWEB)

    Meundaeng, Natthaya; Rujiwatra, Apinpus [Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Prior, Timothy J., E-mail: t.prior@hull.ac.uk [Chemistry, University of Hull, Kingston upon Hull HU6 7RX (United Kingdom)

    2017-01-15

    We have successfully prepared crystals of thiazole-5-carboxylic acid (5-Htza) (L) and three new thiazole-5-carboxylate-based Cu{sup 2+} coordination polymers with different dimensionality, namely, 1D [Cu{sub 2}(5-tza){sub 2}(1,10-phenanthroline){sub 2}(NO{sub 3}){sub 2}] (1), 2D [Cu(5-tza){sub 2}(MeOH){sub 2}] (2), and 3D [Cu(5-tza){sub 2}]·H{sub 2}O (3). These have been characterized by single crystal X-ray diffraction and thermogravimetry. Interestingly, the 2D network structure of 2 can directly transform into the 3D framework of 3 upon removal of methanol molecules at room temperature. 2 can also undergo structural transformation to produce the same 2D network present in the known [Cu(5-tza){sub 2}]·1.5H{sub 2}O upon heat treatment for 2 h. This 2D network can adsorb water and convert to 3 upon exposure to air. - Highlights: • Rare examples of coordination polymers of thiazole-5-carboxylic acid were prepared. • Non-covalent interactions play a key role on the assembly of the complexes in solid state. • Structural transformation of a 2D framework to a 3D upon removal of methanol is observed.

  15. Quantitative structure-property relationship (correlation analysis) of phosphonic acid-based chelates in design of MRI contrast agent.

    Science.gov (United States)

    Tiwari, Anjani K; Ojha, Himanshu; Kaul, Ankur; Dutta, Anupama; Srivastava, Pooja; Shukla, Gauri; Srivastava, Rakesh; Mishra, Anil K

    2009-07-01

    Nuclear magnetic resonance imaging is a very useful tool in modern medical diagnostics, especially when gadolinium (III)-based contrast agents are administered to the patient with the aim of increasing the image contrast between normal and diseased tissues. With the use of soft modelling techniques such as quantitative structure-activity relationship/quantitative structure-property relationship after a suitable description of their molecular structure, we have studied a series of phosphonic acid for designing new MRI contrast agent. Quantitative structure-property relationship studies with multiple linear regression analysis were applied to find correlation between different calculated molecular descriptors of the phosphonic acid-based chelating agent and their stability constants. The final quantitative structure-property relationship mathematical models were found as--quantitative structure-property relationship Model for phosphonic acid series (Model 1)--log K(ML) = {5.00243(+/-0.7102)}- MR {0.0263(+/-0.540)}n = 12 l r l = 0.942 s = 0.183 F = 99.165 quantitative structure-property relationship Model for phosphonic acid series (Model 2)--log K(ML) = {5.06280(+/-0.3418)}- MR {0.0252(+/- .198)}n = 12 l r l = 0.956 s = 0.186 F = 99.256.

  16. Adsorption and photodegradation of methylene blue by iron oxide impregnated on granular activated carbons in an oxalate solution

    International Nuclear Information System (INIS)

    Kadirova, Zukhra C.; Katsumata, Ken-ichi; Isobe, Toshihiro; Matsushita, Nobuhiro; Nakajima, Akira; Okada, Kiyoshi

    2013-01-01

    The photocatalytic adsorbents BAU-OA, BAU-CL and BAU-HA with varying iron oxide content (9–10 mass%) were prepared by heat treatment at 250 °C from commercial activated carbon (BAU) impregnated with iron oxalate, chloride, tris-benzohydroxamate, respectively. The XRD patterns showed amorphous structure in the BAU-CL sample (S BET 50 m 2 /g) and low crystallinity (as FeOOH and Fe 2 O 3 phases) in the BAU-HA and BAU-OA samples (S BET 4 and 111 m 2 /g, respectively). The methylene blue adsorption capacities was decreased in order of BAU-OA app ) was increased in same order BAU-HA < BAU-CL < BAU-OA under the standard experimental conditions (initial MB concentrations 0.015–0.025 mM; sample content – 10 mg/l; initial oxalic acid concentration – 0.43 mM; pH 3–4; UV illumination). The process included high efficiency combination of adsorption, heterogeneous and homogeneous catalysis under UV and solar lights illumination without addition of hydrogen peroxide. The detoxification of water sample containing organic dyes was confirmed after combined sorption-photocatalytic treatment.

  17. Porous structure and surface chemistry of phosphoric acid activated carbon from corncob

    Science.gov (United States)

    Sych, N. V.; Trofymenko, S. I.; Poddubnaya, O. I.; Tsyba, M. M.; Sapsay, V. I.; Klymchuk, D. O.; Puziy, A. M.

    2012-11-01

    Active carbons have been prepared from corncob using chemical activation with phosphoric acid at 400 °C using varied ratio of impregnation (RI). Porous structure of carbons was characterized by nitrogen adsorption and scanning electron microscopy. Surface chemistry was studied by IR and potentiometric titration method. It has been shown that porosity development was peaked at RI = 1.0 (SBET = 2081 m2/g, Vtot = 1.1 cm3/g), while maximum amount of acid surface groups was observed at RI = 1.25. Acid surface groups of phosphoric acid activated carbons from corncob includes phosphate and strongly acidic carboxylic (pK = 2.0-2.6), weakly acidic carboxylic (pK = 4.7-5.0), enol/lactone (pK = 6.7-7.4; 8.8-9.4) and phenol (pK = 10.1-10.7). Corncob derived carbons showed high adsorption capacity to copper, especially at low pH. Maximum adsorption of methylene blue and iodine was observed for carbon with most developed porosity (RI = 1.0).

  18. Evaluation of structure effects on the pharmacological behavior of radioiodinated phenylpentadecanoic acids

    International Nuclear Information System (INIS)

    Knapp, F.F. Jr.; Goodman, M.M.; Machulla, H.J.; Knust, E.J.; Kartje, M.; Vyska, K.

    1986-01-01

    For studying the pharmacokinetic behaviour of fatty acids with different chemical structures four 123 I-labelled compounds, i.e., the ortho and para 123 I-isomers of 15-phenylpentadecanoic acid (IPPA) and 3-methyl-15-phenylpentadecanoic acid were prepared and the organ distribution determined in mice. The results show a significant decrease of the maximal heart uptake for the two ortho compounds. Further, the hypothesis of a blocked metabolism as an effect of the β-methylation could not be confirmed. Both β-methylated compounds show a biexponential elimination behavior from the heart. 5 refs., 2 figs

  19. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    Science.gov (United States)

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

  20. Quantitative structure-cytotoxicity relationship of piperic acid amides.

    Science.gov (United States)

    Shimada, Chiyako; Uesawa, Yoshihiro; Ishihara, Mariko; Kagaya, Hajime; Kanamoto, Taisei; Terakubo, Shigemi; Nakashima, Hideki; Takao, Koichi; Miyashiro, Takaki; Sugita, Yoshiaki; Sakagami, Hiroshi

    2014-09-01

    A total of 12 piperic acid amides, including piperine, were subjected to quantitative structure-activity relationship (QSAR) analysis, based on their cytotoxicity, tumor selectivity and anti-HIV activity, in order to find new biological activities. Cytotoxicity against four human oral squamous cell carcinoma (OSCC) cell lines and three human oral normal cells was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Tumor selectivity was evaluated by the ratio of the mean 50% cytotoxic concentration (CC50) against normal oral cells to that against OSCC cell lines. Anti-HIV activity was evaluated by the ratio of the CC50 to 50% HIV infection-cytoprotective concentration (EC50). Physicochemical, structural, and quantum-chemical parameters were calculated based on the conformations optimized by LowModeMD method followed by density functional theory method. All compounds showed low-to-moderate tumor selectivity, but no anti-HIV activity. N-Piperoyldopamine ( 8: ) which has a catechol moiety, showed the highest tumor selectivity, possibly due to its unique molecular shape and electrostatic interaction, especially its largest partial equalization of orbital electronegativities and vsurf descriptors. The present study suggests that molecular shape and ability for electrostatic interaction are useful parameters for estimating the tumor selectivity of piperic acid amides. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  1. Structure and functioning of the acid-base system in the Baltic Sea

    Science.gov (United States)

    Kuliński, Karol; Schneider, Bernd; Szymczycha, Beata; Stokowski, Marcin

    2017-12-01

    The marine acid-base system is relatively well understood for oceanic waters. Its structure and functioning is less obvious for the coastal and shelf seas due to a number of regionally specific anomalies. In this review article we collect and integrate existing knowledge of the acid-base system in the Baltic Sea. Hydrographical and biogeochemical characteristics of the Baltic Sea, as manifested in horizontal and vertical salinity gradients, permanent stratification of the water column, eutrophication, high organic-matter concentrations and high anthropogenic pressure, make the acid-base system complex. In this study, we summarize the general knowledge of the marine acid-base system as well as describe the peculiarities identified and reported for the Baltic Sea specifically. In this context we discuss issues such as dissociation constants in brackish water, different chemical alkalinity models including contributions by organic acid-base systems, long-term changes in total alkalinity, anomalies of borate alkalinity, and the acid-base effects of biomass production and mineralization. Finally, we identify research gaps and specify limitations concerning the Baltic Sea acid-base system.

  2. [Teichoic acids from lactic acid bacteria].

    Science.gov (United States)

    Livins'ka, O P; Harmasheva, I L; Kovalenko, N K

    2012-01-01

    The current view of the structural diversity of teichoic acids and their involvement in the biological activity of lactobacilli has been reviewed. The mechanisms of effects of probiotic lactic acid bacteria, in particular adhesive and immunostimulating functions have been described. The prospects of the use of structure data of teichoic acid in the assessment of intraspecific diversity of lactic acid bacteria have been also reflected.

  3. Structural basis for olivetolic acid formation by a polyketide cyclase from Cannabis sativa.

    Science.gov (United States)

    Yang, Xinmei; Matsui, Takashi; Kodama, Takeshi; Mori, Takahiro; Zhou, Xiaoxi; Taura, Futoshi; Noguchi, Hiroshi; Abe, Ikuro; Morita, Hiroyuki

    2016-03-01

    In polyketide biosynthesis, ring formation is one of the key diversification steps. Olivetolic acid cyclase (OAC) from Cannabis sativa, involved in cannabinoid biosynthesis, is the only known plant polyketide cyclase. In addition, it is the only functionally characterized plant α+β barrel (DABB) protein that catalyzes the C2-C7 aldol cyclization of the linear pentyl tetra-β-ketide CoA as the substrate, to generate olivetolic acid (OA). Herein, we solved the OAC apo and OAC-OA complex binary crystal structures at 1.32 and 1.70 Å resolutions, respectively. The crystal structures revealed that the enzyme indeed belongs to the DABB superfamily, as previously proposed, and possesses a unique active-site cavity containing the pentyl-binding hydrophobic pocket and the polyketide binding site, which have never been observed among the functionally and structurally characterized bacterial polyketide cyclases. Furthermore, site-directed mutagenesis studies indicated that Tyr72 and His78 function as acid/base catalysts at the catalytic center. Structural and/or functional studies of OAC suggested that the enzyme lacks thioesterase and aromatase activities. These observations demonstrated that OAC employs unique catalytic machinery utilizing acid/base catalytic chemistry for the formation of the precursor of OA. The structural and functional insights obtained in this work thus provide the foundation for analyses of the plant polyketide cyclases that will be discovered in the future. Structural data reported in this paper are available in the Protein Data Bank under the accession numbers 5B08 for the OAC apo, 5B09 for the OAC-OA binary complex and 5B0A, 5B0B, 5B0C, 5B0D, 5B0E, 5B0F and 5B0G for the OAC His5Q, Ile7F, Tyr27F, Tyr27W, Val59M, Tyr72F and His78S mutant enzymes, respectively. © 2016 Federation of European Biochemical Societies.

  4. Crystal structure of a bacterial homologue of the bile acid sodium symporter ASBT

    Science.gov (United States)

    Hu, Nien-Jen; Iwata, So; Cameron, Alexander D.; Drew, David

    2011-01-01

    High cholesterol levels greatly increase the risk of cardiovascular disease. By its conversion into bile acids, about 50% of cholesterol is eliminated from the body. However bile acids released from the bile duct are constantly recycled, being reabsorbed in the intestine via the Apical Sodium dependent Bile acid Transporter (ASBT). It has been shown in animal models that plasma cholesterol levels are significantly lowered by specific inhibitors of ASBT1,2, thus ASBT is a target for hypercholesterolemia drugs. Here, we describe the crystal structure of a bacterial homologue of ASBT from Neisseria meningitidis (ASBTNM) at 2.2Å. ASBTNM contains two inverted structural repeats of five transmembrane helices. A Core domain of six helices harbours two sodium ions while the remaining helices form a Panel-like domain. Overall the architecture of the protein is remarkably similar to the sodium-proton antiporter NhaA3 despite no detectable sequence homology. A bile acid molecule is situated between the Core and Panel domains in a large hydrophobic cavity. Residues near to this cavity have been shown to affect the binding of specific inhibitors of human ASBT4. The position of the bile acid together with the molecular architecture suggests the rudiments of a possible transport mechanism. PMID:21976025

  5. Facile synthesis of graphene hybrid tube-like structure for simultaneous detection of ascorbic acid, dopamine, uric acid and tryptophan

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Wen [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Chai Yaqin, E-mail: yqchai@swu.edu.cn [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Yuan Ruo, E-mail: yuanruo@swu.edu.cn [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Chen Shihong; Han Jing; Yuan Dehua [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China)

    2012-12-05

    Graphical abstract: A tube-like structure of graphene hybrid (GS-PTCA) was synthesized via {pi}-{pi} stacking interaction, and was used as modifier to fabricate electrode for simultaneous detection of ascorbic acid (AA), dopamine (DA), uric acid (UA) and tryptophan (Trp). SEM images of GS, PTCA and GS-PTCA were presented. Under the synergistic effects between GS and PTCA, the modified electrode displayed high catalytic activity and selectivity toward the oxidation of AA, DA, UA, and Trp. Highlights: Black-Right-Pointing-Pointer A simple strategy for simultaneous detection of AA, DA, UA and Trp has been constructed. Black-Right-Pointing-Pointer The tube-like structure of graphene hybrid (GS-PTCA) was synthesized. Black-Right-Pointing-Pointer The GS-PTCA provided a selective interface for discrimination of AA, DA, UA and Trp. - Abstract: In the present work, a tube-like structure of graphene hybrid as modifier to fabricate electrode for simultaneous detection of ascorbic acid (AA), dopamine (DA), uric acid (UA) and tryptophan (Trp) was reported. The hybrid was synthesized by a simple method based on graphene sheets (GS) and 3,4,9,10-perylenetetracarboxylic acid (PTCA) via {pi}-{pi} stacking interaction under ultrasonic condition. The combination of GS and PTCA could effectively improve the dispersion of GS, owing to PTCA with the carboxylic-functionalized interface. Comparing with pure GS or PTCA modified electrode, GS-PTCA displayed high catalytic activity and selectivity toward the oxidation of AA, DA, UA, and Trp. Moreover, cyclic voltammetry, different pulse voltammetry and scanning electron microscopy were employed to characterize the sensors. The experiment results showed that the linear response range for simultaneous detection of AA, DA, UA, and Trp were 20-420 {mu}M, 0.40-374 {mu}M, 4-544 {mu}M and 0.40-138 {mu}M, respectively, and the detection limits were 5.60 {mu}M, 0.13 {mu}M, 0.92 {mu}M and 0.06 {mu}M (S/N = 3). Importantly, the proposed method offers

  6. Nutritional evaluation of structured lipid containing omega 6 fatty acid synthesized from coconut oil in rats.

    Science.gov (United States)

    Rao, Reena; Lokesh, Belur R

    2003-06-01

    Coconut oil is rich in medium chain fatty acids, but deficient in polyunsaturated fatty acids (PUFA). Structured lipids (SL) enriched with omega 6 PUFA were synthesized from coconut oil triglycerides by employing enzymatic acidolysis with free fatty acids obtained from safflower oil. Rats were fed a diet containing coconut oil, coconut oil-safflower oil blend (1:0.7 w/ w) or structured lipid at 10% levels for a period of 60 days. The SL lowered serum cholesterol levels by 10.3 and 10.5% respectively in comparison with those fed coconut oil and blended oil. Similarly the liver cholesterol levels were also decreased by 35.9 and 26.6% respectively in animals fed structured lipids when compared to those fed on coconut oil or the blended oil. Most of the decrease observed in serum cholesterol levels of animals fed structured lipids was found in LDL fraction. The triglyceride levels in serum showed a decrease by 17.5 and 17.4% while in the liver it was reduced by 45.8 and 23.5% in the structured lipids fed animals as compared to those fed coconut oil or blended oil respectively. Differential scanning calorimetric studies indicated that structured lipids had lower melting points and solid fat content when compared to coconut oil or blended oils. These studies indicated that enrichment of coconut oil triglycerides with omega 6 fatty acids lowers its solid fat content. The omega 6 PUFA enriched structured lipids also exhibited hypolipidemic activity.

  7. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  8. Improvement of surface acidity and structural regularity of Zr-modified mesoporous MCM-41

    Energy Technology Data Exchange (ETDEWEB)

    Chen, L.F. [Departamento de Ciencias Basicas, Universidad Autonoma Metropolitana-A, Av. San Pablo 180, Col. Reynosa-Tamaulipas, 02200 Mexico D.F. (Mexico)]. E-mail: chenlf2001@yahoo.com; Norena, L.E. [Departamento de Ciencias Basicas, Universidad Autonoma Metropolitana-A, Av. San Pablo 180, Col. Reynosa-Tamaulipas, 02200 Mexico D.F. (Mexico); Navarrete, J. [Grupo de Molecular Ingenieria, Instituto Mexicano del Petroleo, Eje Lazaro Cardenas 152, 07730 Mexico D.F. (Mexico); Wang, J.A. [Laboratorio de Catalisis y Materiales, SEPI-ESIQIE, Instituto Politecnico Nacional, Av. Politecnico S/N, Col. Zacatenco, 07738 Mexico D.F. (Mexico)

    2006-06-10

    This work reports the synthesis and surface characterization of a Zr-modified mesoporous MCM-41 solid with an ordered hexagonal arrangement, prepared through a templated synthesis route, using cetyltrimethylammonium chloride as the template. The surface features, crystalline structure, textural properties and surface acidity of the materials were characterized by in situ Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), N{sub 2} physisorption isotherms, {sup 29}Si MAS-NMR and in situ FT-IR of pyridine adsorption. It is evident that the surfactant cations inserted into the network of the solids during the preparation could be removed by calcination of the sample above 500 deg. C. The resultant material showed a large surface area of 680.6 m{sup 2} g{sup -1} with a uniform pore diameter distribution in a very narrow range centered at approximately 2.5 nm. Zirconium incorporation into the Si-MCM-41 framework, confirmed by {sup 29}Si MAS-NMR analysis, increased not only the wall thickness of the mesopores but also the long-range order of the periodically hexagonal structure. Both, Lewis and Broensted acid sites, were formed on the surface of the Zr-modified MCM-41 solid. Compared to Si-MCM-41 on which only very weak Lewis acid sites were formed, the densities of both Lewis and Broensted acid sites and the strength of the acidity on the Zr-modified sample were significantly increased, indicating that the incorporation of zirconium greatly enhances the acidity of the material.

  9. The effect of natural and synthetic fatty acids on membrane structure, microdomain organization, cellular functions and human health.

    Science.gov (United States)

    Ibarguren, Maitane; López, David J; Escribá, Pablo V

    2014-06-01

    This review deals with the effects of synthetic and natural fatty acids on the biophysical properties of membranes, and on their implication on cell function. Natural fatty acids are constituents of more complex lipids, like triacylglycerides or phospholipids, which are used by cells to store and obtain energy, as well as for structural purposes. Accordingly, natural and synthetic fatty acids may modify the structure of the lipid membrane, altering its microdomain organization and other physical properties, and provoking changes in cell signaling. Therefore, by modulating fatty acids it is possible to regulate the structure of the membrane, influencing the cell processes that are reliant on this structure and potentially reverting pathological cell dysfunctions that may provoke cancer, diabetes, hypertension, Alzheimer's and Parkinson's disease. The so-called Membrane Lipid Therapy offers a strategy to regulate the membrane composition through drug administration, potentially reverting pathological processes by re-adapting cell membrane structure. Certain fatty acids and their synthetic derivatives are described here that may potentially be used in such therapies, where the cell membrane itself can be considered as a target to combat disease. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Efficacy of Folic Acid Supplementation in Autistic Children Participating in Structured Teaching: An Open-Label Trial.

    Science.gov (United States)

    Sun, Caihong; Zou, Mingyang; Zhao, Dong; Xia, Wei; Wu, Lijie

    2016-06-07

    Autism spectrum disorders (ASD) are recognized as a major public health issue. Here, we evaluated the effects of folic acid intervention on methylation cycles and oxidative stress in autistic children enrolled in structured teaching. Sixty-six autistic children enrolled in this open-label trial and participated in three months of structured teaching. Forty-four children were treated with 400 μg folic acid (two times/daily) for a period of three months during their structured teaching (intervention group), while the remaining 22 children were not given any supplement for the duration of the study (control group). The Autism Treatment Evaluation Checklist (ATEC) and Psychoeducational Profile-third edition (PEP-3) were measured at the beginning and end of the treatment period. Folic acid, homocysteine, and glutathione metabolism in plasma were measured before and after treatment in 29 autistic children randomly selected from the intervention group and were compared with 29 age-matched unaffected children (typical developmental group). The results illustrated folic acid intervention improved autism symptoms towards sociability, cognitive verbal/preverbal, receptive language, and affective expression and communication. Furthermore, this treatment also improved the concentrations of folic acid, homocysteine, and normalized glutathione redox metabolism. Folic acid supplementation may have a certain role in the treatment of children with autism.

  11. Structure and behaviour of proteins, nucleic acids and viruses from vibrational Raman optical activity

    DEFF Research Database (Denmark)

    Barron, L.D.; Blanch, E.W.; McColl, I.H.

    2003-01-01

    stacking arrangement and the mutual orientation of the sugar and base rings around the C-N glycosidic link. The ROA spectra of intact viruses provide information on the folds of the coat proteins and the nucleic acid structure. The large number of structure-sensitive bands in protein ROA spectra...... is especially favourable for fold determination using pattern recognition techniques. This article gives a brief account of the ROA technique and presents the ROA spectra of a selection of proteins, nucleic acids and viruses that illustrate the applications of ROA spectroscopy in biomolecular research....

  12. Anthropogenic and natural sources of acidity and metals and their influence on the structure of stream food webs.

    Science.gov (United States)

    Hogsden, Kristy L; Harding, Jon S

    2012-03-01

    We compared food web structure in 20 streams with either anthropogenic or natural sources of acidity and metals or circumneutral water chemistry in New Zealand. Community and diet analysis indicated that mining streams receiving anthropogenic inputs of acidic and metal-rich drainage had much simpler food webs (fewer species, shorter food chains, less links) than those in naturally acidic, naturally high metal, and circumneutral streams. Food webs of naturally high metal streams were structurally similar to those in mining streams, lacking fish predators and having few species. Whereas, webs in naturally acidic streams differed very little from those in circumneutral streams due to strong similarities in community composition and diets of secondary and top consumers. The combined negative effects of acidity and metals on stream food webs are clear. However, elevated metal concentrations, regardless of source, appear to play a more important role than acidity in driving food web structure. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

    Directory of Open Access Journals (Sweden)

    Andreas Martin Lisewski

    2008-09-01

    Full Text Available The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is transmitted with limited error probability, additional random errors in sequence (amino acid substitutions and in structure (structural defects trigger a decrease in communication capacity toward a Shannon limit at 0.010 bits per amino acid symbol at which communication breaks down. In several controls, simulated error rates above a critical threshold and models of unfolded structures always produce capacities below this limiting value. Thus an essential biological system can be realistically modeled as a digital communication channel that is (a sensitive to random errors and (b restricted by a Shannon error limit. This forms a novel basis for predictions consistent with observed rates of defective ribosomal products during protein synthesis, and with the estimated excess of mutual information in protein contact potentials.

  14. Secondary structure classification of amino-acid sequences using state-space modeling

    OpenAIRE

    Brunnert, Marcus; Krahnke, Tillmann; Urfer, Wolfgang

    2001-01-01

    The secondary structure classification of amino acid sequences can be carried out by a statistical analysis of sequence and structure data using state-space models. Aiming at this classification, a modified filter algorithm programmed in S is applied to data of three proteins. The application leads to correct classifications of two proteins even when using relatively simple estimation methods for the parameters of the state-space models. Furthermore, it has been shown that the assumed initial...

  15. Hydrogen bonded 1D-3D supramolecular structures from Benzylamine and organic acidic components

    Science.gov (United States)

    Gao, Xingjun; Li, XiaoLiang; Jin, Shouwen; Hu, Kaikai; Guo, Jianzhong; Guo, Ming; Xu, Weiqiang; Wang, Daqi

    2018-03-01

    Cocrystallization of the commonly available organic amine, benzylamine, with a series of organic acids afforded a total of seven organic salts with the compositions: (benzylamine)2: (p-nitrophenol)2: (H2O) (1) [(HL)2+⋯(npl-)2⋯(H2O), npl- = p-nitrophenolate], (benzylamine): (4-tert-butylbenzoic acid) (2) [(HL+)⋯(tba-), tba- = 4-tert-butylbenzoate], (benzylamine): (3,4-dichlorobenzoic acid) (3) [(HL+)⋯dcba-), dcba- = 3,4-dichlorobenzoate], (benzylamine): (2,5-dihydroxybenzoic acid) (4) [(HL+)⋯(dhba-), dhba- = 2,5-dihydroxybenzoate], (benzylamine): (2-bromo-but-2-enedioic acid) (5) [(HL+)⋯(Hbba-), Hbba- = 2-bromo-hydrogenbut-2-enedioate], (benzylamine): (2,6-pyridinedicarboxylic acid) (6) [(HL+)⋯(Hpdc-), Hpdc- = 2,6-pyridine hydrogendicarboxylate], and (benzylamine)2: (3-nitrophthalic acid): 2(H2O) (7) [(HL+)2⋯(npa2-)⋯(H2O)2, npa2- = 3-nitrophthalate]. The seven salts have been characterised by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The results reveal that among the seven investigated crystals the NH2 in the benzylamine are protonated when the organic acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted Nsbnd H⋯O hydrogen bond between the NH3+ and deprotonated acidic groups. Except the Nsbnd H⋯O hydrogen bond, the Osbnd H⋯O hydrogen bonds (charge assisted or neutral) were also found at the salts 1, 4, 5, 6, and 7. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O/CH2sbnd O, CH-π/CH2-π, Cπ-Cπ, Osbnd O, O-Cπ, O-π, and Cl-π associations also contribute to the stabilization and expansion of the total high-dimensional framework structures. For the coexistence of the various weak nonbonding interactions, these structures adopted a variety of

  16. Crystal structures of two 1:2 dihydrate compounds of chloranilic acid with 2-carboxypyridine and 2-carboxyquinoline

    Directory of Open Access Journals (Sweden)

    Kazuma Gotoh

    2017-12-01

    Full Text Available The crystal structure of the 1:2 dihydrate compound of chloranilic acid (systematic name: 2,5-dichloro-3,6-dihydroxy-1,4-benzoquinone with 2-carboxypyridine (another common name: picolinic acid; systematic name: pyridine-2-carboxylic acid, namely, 2C6H5.5NO20.5+·C6HCl2O4−·2H2O, (I, has been determined at 180 K, and the structure of the 1:2 dihydrate compound of chloranilic acid with 2-carboxyquinoline (another common name: quinaldic acid; systematic name: quinoline-2-carboxylic acid, namely, 2C10H7NO2·C6H2Cl2O4·2H2O, (II, has been redetermined at 200 K. This determination presents a higher precision crystal structure than the previously published structure [Marfo-Owusu & Thompson (2014. X-ray Struct. Anal. Online, 30, 55–56]. Compound (I was analysed as a disordered structure over two states, viz. salt and co-crystal. The salt is bis(2-carboxypyridinium chloranilate dihydrate, 2C6H6NO2+·C6Cl2O42−·2H2O, and the co-crystal is bis(pyridinium-2-carboxylate chloranilic acid dihydrate, 2C6H5NO2·C6H2Cl2O4·2H2O, including zwitterionic 2-carboxypyridine. In both salt and co-crystal, the water molecule links the chloranilic acid and 2-carboxypyridine molecules through O—H...O and N—H...O hydrogen bonds. The 2-carboxypyridine molecules are connected into a head-to-head inversion dimer by a short O—H...O hydrogen bond, in which the H atom is disordered over two positions. Compound (II is a 1:2 dihydrate co-crystal of chloranilic acid and zwitterionic 2-carboxyquinoline. The water molecule links the chloranilic acid and 2-carboxyquinoline molecules through O—H...O hydrogen bonds. The 2-carboxyquinoline molecules are connected into a head-to-tail inversion dimer by a pair of N—H...O hydrogen bonds.

  17. α,β-Unsaturated monoterpene acid glucose esters: structural diversity, bioactivities and functional roles.

    Science.gov (United States)

    Goodger, Jason Q D; Woodrow, Ian E

    2011-12-01

    The glycosylation of lipophilic small molecules produces many important plant secondary metabolites. The majority of these are O-glycosides with relatively fewer occurring as glucose esters of aromatic or aliphatic acids. In particular, monoterpene acid glucose esters have much lower structural diversity and distribution compared to monoterpene glycosides. Nevertheless, there have been over 20 monoterpene acid glucose esters described from trees in the genus Eucalyptus (Myrtaceae) in recent years, all based on oleuropeic acid, menthiafolic acid or both. Here we review all of the glucose esters containing these monoterpenoids identified in plants to date. Many of the compounds contain phenolic aglycones and all contain at least one α,β-unsaturated carbonyl, affording a number of important potential therapeutic reactivities such as anti-tumor promotion, carcinogenesis suppression, and anti-oxidant and anti-inflammatory activities. Additional properties such as cytotoxicity, bitterness, and repellency are suggestive of a role in plant defence, but we also discuss their localization to the exterior of foliar secretory cavity lumina, and suggest they may also protect secretory cells from toxic terpenes housed within these structures. Finally we discuss how the use of a recently developed protocol to isolate secretory cavities in a functional state could be used in conjunction with systems biology approaches to help characterize their biosynthesis and roles in plants. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. Structural analysis and taste evaluation of γ-glutamyl peptides comprising sulfur-containing amino acids.

    Science.gov (United States)

    Amino, Yusuke; Wakabayashi, Hidehiko; Akashi, Satoko; Ishiwatari, Yutaka

    2018-03-01

    The structures, flavor-modifying effects, and CaSR activities of γ-glutamyl peptides comprising sulfur-containing amino acids were investigated. The chemical structures, including the linkage mode of the N-terminal glutamic acid, of γ-L-glutamyl-S-(2-propenyl)-L-cysteine (γ-L-glutamyl-S-allyl-L-cysteine) and its sulfoxide isolated from garlic were established by comparing their NMR spectra with those of authentic peptides prepared using chemical methods. Mass spectrometric analysis also enabled determination of the linkage modes in the glutamyl dipeptides by their characteristic fragmentation. In sensory evaluation, these peptides exhibited flavor-modifying effects (continuity) in umami solutions less pronounced but similar to that of glutathione. Furthermore, the peptides exhibited intrinsic flavor due to the sulfur-containing structure, which may be partially responsible for their flavor-modifying effects. In CaSR assays, γ-L-glutamyl-S-methyl-L-cysteinylglycine was most active, which indicates that the presence of a medium-sized aliphatic substituent at the second amino acid residue in γ-glutamyl peptides enhances CaSR activity.

  19. Regioisomers of octanoic acid-containing structured triacylglycerols analyzed by tandem mass spectrometry using ammonia negative ion chemical ionization

    DEFF Research Database (Denmark)

    Kurvinen, J.P.; Mu, Huiling; Kallio, H.

    2001-01-01

    Tandem mass spectrometry based on ammonia negative ion chemical ionization and sample introduction via direct exposure probe was applied to analysis of regioisomeric structures of octanoic acid containing structured triacylglycerols (TAG) of type MML, MLM, MLL, and LML (M, medium-chain fatty acid...

  20. Porous structure and surface chemistry of phosphoric acid activated carbon from corncob

    International Nuclear Information System (INIS)

    Sych, N.V.; Trofymenko, S.I.; Poddubnaya, O.I.; Tsyba, M.M.; Sapsay, V.I.; Klymchuk, D.O.; Puziy, A.M.

    2012-01-01

    Highlights: ► Phosphoric acid activation results in formation of carbons with acidic surface groups. ► Maximum amount of surface groups is introduced at impregnation ratio 1.25. ► Phosphoric acid activated carbons show high capacity to copper. ► Phosphoric acid activated carbons are predominantly microporous. ► Maximum surface area and pore volume achieved at impregnation ratio 1.0. - Abstract: Active carbons have been prepared from corncob using chemical activation with phosphoric acid at 400 °C using varied ratio of impregnation (RI). Porous structure of carbons was characterized by nitrogen adsorption and scanning electron microscopy. Surface chemistry was studied by IR and potentiometric titration method. It has been shown that porosity development was peaked at RI = 1.0 (S BET = 2081 m 2 /g, V tot = 1.1 cm 3 /g), while maximum amount of acid surface groups was observed at RI = 1.25. Acid surface groups of phosphoric acid activated carbons from corncob includes phosphate and strongly acidic carboxylic (pK = 2.0–2.6), weakly acidic carboxylic (pK = 4.7–5.0), enol/lactone (pK = 6.7–7.4; 8.8–9.4) and phenol (pK = 10.1–10.7). Corncob derived carbons showed high adsorption capacity to copper, especially at low pH. Maximum adsorption of methylene blue and iodine was observed for carbon with most developed porosity (RI = 1.0).

  1. Porous structure and surface chemistry of phosphoric acid activated carbon from corncob

    Energy Technology Data Exchange (ETDEWEB)

    Sych, N.V.; Trofymenko, S.I.; Poddubnaya, O.I.; Tsyba, M.M. [Institute for Sorption and Endoecology Problems, National Academy of Sciences of Ukraine, 13 General Naumov St., 03164 Kyiv (Ukraine); Sapsay, V.I.; Klymchuk, D.O. [M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, 2 Tereshchenkivska St., 01601 Kyiv (Ukraine); Puziy, A.M., E-mail: alexander.puziy@ispe.kiev.ua [Institute for Sorption and Endoecology Problems, National Academy of Sciences of Ukraine, 13 General Naumov St., 03164 Kyiv (Ukraine)

    2012-11-15

    Highlights: Black-Right-Pointing-Pointer Phosphoric acid activation results in formation of carbons with acidic surface groups. Black-Right-Pointing-Pointer Maximum amount of surface groups is introduced at impregnation ratio 1.25. Black-Right-Pointing-Pointer Phosphoric acid activated carbons show high capacity to copper. Black-Right-Pointing-Pointer Phosphoric acid activated carbons are predominantly microporous. Black-Right-Pointing-Pointer Maximum surface area and pore volume achieved at impregnation ratio 1.0. - Abstract: Active carbons have been prepared from corncob using chemical activation with phosphoric acid at 400 Degree-Sign C using varied ratio of impregnation (RI). Porous structure of carbons was characterized by nitrogen adsorption and scanning electron microscopy. Surface chemistry was studied by IR and potentiometric titration method. It has been shown that porosity development was peaked at RI = 1.0 (S{sub BET} = 2081 m{sup 2}/g, V{sub tot} = 1.1 cm{sup 3}/g), while maximum amount of acid surface groups was observed at RI = 1.25. Acid surface groups of phosphoric acid activated carbons from corncob includes phosphate and strongly acidic carboxylic (pK = 2.0-2.6), weakly acidic carboxylic (pK = 4.7-5.0), enol/lactone (pK = 6.7-7.4; 8.8-9.4) and phenol (pK = 10.1-10.7). Corncob derived carbons showed high adsorption capacity to copper, especially at low pH. Maximum adsorption of methylene blue and iodine was observed for carbon with most developed porosity (RI = 1.0).

  2. Antioxidant activity of amino acids in soybean oil at frying temperature: Structural effects and synergism with tocopherols

    Science.gov (United States)

    The purpose of this study was to evaluate amino acids as natural antioxidants for frying. Twenty amino acids were added to soybean oil heated to 180 ºC, and the effects of amino acid structure on the antioxidant activity were investigated. Amino acids containing a thiol, a thioether, or an extra ami...

  3. Novel Mechanism of Fatty Acid Sensing in Enteroendocrine Cells: Specific Structures in Oxo-Fatty Acids Produced by Gut Bacteria are Responsible for CCK Secretion in STC-1 Cells via GPR40.

    Science.gov (United States)

    Hira, Tohru; Ogasawara, Shono; Yahagi, Asuka; Kamachi, Minami; Li, Jiaxin; Nishimura, Saki; Sakaino, Masayoshi; Yamashita, Takatoshi; Kishino, Shigenobu; Ogawa, Jun; Hara, Hiroshi

    2018-06-25

    The secretion of gut hormones, such as cholecystokinin (CCK) is stimulated by fatty acids. Although a chain length-dependent mechanism has been proposed, other structural relationships to releasing activity remain unclear. We aimed to elucidate specific structures in fatty acids that are responsible for their CCK-releasing activity, and related sensing mechanisms in enteroendocrine cells. We examined CCK secretory activities in a murine CCK-producing cell line STC-1 by exposing the cells to various modified fatty acids produced by gut lactic acid bacteria. The effects of fatty acids on gastric emptying rate as a CCK-mediated function were examined using acetaminophen- and phenol red-methods in rats. Out of more than thirty octadecanoic (C18)-derived fatty acids tested, five oxo-fatty acids potently stimulated CCK secretion without cytotoxic effects in STC-1 cells. Three fatty acids had a distinct specific structure containing one double-bond, whereas the other two had two double-bonds, nearby an oxo residue. CCK secretion induced by representative fatty acids (10-oxo-trans-11-18:1 and 13-oxo-cis-9,cis-15-18:2) was attenuated by a fatty acid-receptor GPR40 antagonist. Oral administration of 13-oxo-cis-9,cis-15-18:2 lowered the gastric emptying rate in rats in a dose- and structure-dependent manner. These results revealed a novel fatty acid-sensing mechanism in enteroendocrine cells. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  4. Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

    Science.gov (United States)

    Jelínek, Jan; Škoda, Petr; Hoksza, David

    2017-12-06

    Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank. All proteins involved in PPIs were converted into labeled graphs with nodes corresponding to amino acids and edges to pairs of neighboring amino acids. A structural neighborhood of each node was then encoded into a bit string and stored in the knowledge base. When predicting PPIs, INSPiRE labels amino acids of unknown proteins as interface or non-interface based on how often their structural neighborhood appears as interface or non-interface in the knowledge base. We evaluated INSPiRE's behavior with respect to different types and sizes of the structural neighborhood. Furthermore, we examined the suitability of several different features for labeling the nodes. Our evaluations showed that INSPiRE clearly outperforms existing methods with respect to Matthews correlation coefficient. In this paper we introduce a new knowledge-based method for identification of protein-protein interaction sites called INSPiRE. Its knowledge base utilizes structural patterns of known interaction sites in the Protein Data Bank which are then used for PPI prediction. Extensive experiments on several well-established datasets show that INSPiRE significantly surpasses existing PPI approaches.

  5. Structure of rat acidic fibroblast growth factor at 1.4 Å resolution

    International Nuclear Information System (INIS)

    Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Arthur; Kristensen, Ole; Kastrup, Jette Sandholm; Berezin, Vladimir; Bock, Elisabeth; Gajhede, Michael

    2007-01-01

    The structure of rat acidic fibroblast growth factor was determined and compared with those of human, bovine and newt origin. The rat and human structures were found to be very similar. Fibroblast growth factors (FGFs) constitute a family of 22 structurally related heparin-binding polypeptides that are involved in the regulation of cell growth, survival, differentiation and migration. Here, a 1.4 Å resolution X-ray structure of rat FGF1 is presented. Two molecules are present in the asymmetric unit of the crystal and they coordinate a total of five sulfate ions. The structures of human, bovine and newt FGF1 have been published previously. Human and rat FGF1 are found to have very similar structures

  6. Crystal structures of thiosemicarbazide diacetic acid and coordination compounds on its basis

    International Nuclear Information System (INIS)

    Burshtejn, I.F.; Petukhov, L.I.; Gehrbehlehu, N.V.; Volodina, G.F.; Bologa, O.A.

    1985-01-01

    Results of X-ray structure investigation of thiosemicarbazide diacetic acid (H 2 tscda) and its complex derivatives of the composition Mtscda (M=Cd, Co, Cu) have been reviewed. Structure characteristics of Cdtscdax4H 2 O are as follows: a=14.513, b=8.648, c=9.871 A, γ=98.46 deg, sp.gr. P2 1 /a, z=4. Cadmium complex structure represents a centrosymmetrical dimer with bridge oxygen atom of carboxylic group. Cd-Cd distance is 3.815 A. Cd atom has coordination number 7. Coordination Cd-polyhedron in the structure has configuration of trigonal one-cap prism

  7. Structure Properties and Mechanisms of Action of Naturally Originated Phenolic Acids and Their Derivatives against Human Viral Infections.

    Science.gov (United States)

    Wu, Yi-Hang; Zhang, Bing-Yi; Qiu, Li-Peng; Guan, Rong-Fa; Ye, Zi-Hong; Yu, Xiao-Ping

    2017-01-01

    A great effort has been made to develop efficacious antiviral drugs, but many viral infections are still lack of efficient antiviral therapies so far. The related exploration of natural products to fight viruses has been raised in recent years. Natural compounds with structural diversity and complexity offer a great chance to find new antiviral agents. Particularly, phenolic acids have attracted considerable attention owing to their potent antiviral abilities and unique mechanisms. The aim of this review is to report new discoveries and updates pertaining to antiviral phenolic acids. The relevant references on natural phenolic acids were searched. The antiviral phenolic acids were classified according to their structural properties and antiviral types. Meanwhile, the antiviral characteristics and structure-activity relationships of phenolic acids and their derivatives were summarized. The review finds that natural phenolic acids and their derivatives possessed potent inhibitory effects on multiple virus in humans such as human immunodeficiency virus, hepatitis C virus, hepatitis B virus, herpes simplex virus, influenza virus and respiratory syncytial virus. In particular, caffeic acid/gallic acid and their derivatives exhibited outstanding antiviral properties by a variety of modes of action. Naturally derived phenolic acids especially caffeic acid/gallic acid and their derivatives may be regarded as novel promising antiviral leads or candidates. Additionally, scarcely any of these compounds has been used as antiviral treatment in clinical practice. Therefore, these phenolic acids with diverse skeletons and mechanisms provide us an excellent resource for finding novel antiviral drugs. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  8. A new planetary structure fabrication process using phosphoric acid

    Science.gov (United States)

    Buchner, Christoph; Pawelke, Roland H.; Schlauf, Thomas; Reissner, Alexander; Makaya, Advenit

    2018-02-01

    Minimising the launch mass is an important aspect of exploration mission planning. In-situ resource utilisation (ISRU) can improve this by reducing the amount of terrestrial materials needed for planetary exploration activities. We report on a recently concluded investigation into the requirements and available technologies for creating hardware on extra-terrestrial bodies, using the limited resources available on site. A trade-off of ISRU technologies for hardware manufacturing was conducted. A new additive manufacturing process suitable for fabricating structures on the Moon or Mars was developed. The process uses planetary regolith as the base material and concentrated phosphoric acid as the liquid binder. Mixing the reagents creates a sticky construction paste that slowly solidifies into a hard, rock-like material. Prior to solidification, the paste is extruded in layers, creating the desired structures in a 3D printing process. We used Martian regolith simulant JSC-Mars-1A, but the process is not selective towards regolith composition. Samples were exposed to thermal cycles and were mechanically characterised. Reduced-scale demonstrator structures were printed to demonstrate structure fabrication using the developed process.

  9. Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus

    International Nuclear Information System (INIS)

    Pereira, Jose H.; Goh, Ee-Been; Keasling, Jay D.; Beller, Harry R.; Adams, Paul D.

    2012-01-01

    In an effort to better understand the control of the formation of branched fatty acids in Micrococcus luteus, the structure of β-ketoacyl-ACP synthase III, which catalyzes the initial step of fatty-acid biosynthesis, has been determined. Micrococcus luteus is a Gram-positive bacterium that produces iso- and anteiso-branched alkenes by the head-to-head condensation of fatty-acid thioesters [coenzyme A (CoA) or acyl carrier protein (ACP)]; this activity is of interest for the production of advanced biofuels. In an effort to better understand the control of the formation of branched fatty acids in M. luteus, the structure of FabH (MlFabH) was determined. FabH, or β-ketoacyl-ACP synthase III, catalyzes the initial step of fatty-acid biosynthesis: the condensation of malonyl-ACP with an acyl-CoA. Analysis of the MlFabH structure provides insights into its substrate selectivity with regard to length and branching of the acyl-CoA. The most structurally divergent region of FabH is the L9 loop region located at the dimer interface, which is involved in the formation of the acyl-binding channel and thus limits the substrate-channel size. The residue Phe336, which is positioned near the catalytic triad, appears to play a major role in branched-substrate selectivity. In addition to structural studies of MlFabH, transcriptional studies of M. luteus were also performed, focusing on the increase in the ratio of anteiso:iso-branched alkenes that was observed during the transition from early to late stationary phase. Gene-expression microarray analysis identified two genes involved in leucine and isoleucine metabolism that may explain this transition

  10. Significance of Nanoparticles and the Role of Amino Acids in Structuring Them-A Review.

    Science.gov (United States)

    Kulandaisamy, Arockia Jayalatha; Rayappan, John Bosco Balaguru

    2018-08-01

    Nanoparticles has occupied an eminent place in our tech-facilitated society. The processes involved in synthesizing nanoparticles are important not only to find their applications, but also to make them eco-friendly. Attempts are being made to replace the use of harmful surfactants/reagents by amino acids, in the due course of nanoparticle synthesis. Especially in synthesizing the multifunctional metal and metal oxide nanoparticles the use of amino acids as surfactant/as catalyst, helps to obtain required size and shape. Amino acids have the inherent property in directing and assembling the superstructures. They have the tendency to act as a capping agent and their presence during the synthesis processes alters the synthesized particles' morphology. Review has been made to study the role of amino acids like histidine, lysine, arginine in structuring ZnO, FeO, Au and Ag nanoparticles. The change in their morphology that resulted due to the addition of amino acids has been compared. It is important to understand the role of amino acids in synthesizing the nanoparticles, and so it is more important to understand the internal energy variation of the same. To achieve this, the interaction between the bio (amino acids) and non-bio (metal and metal oxide) nanoparticles are to be discussed both experimentally and theoretically. At times the theoretical characterization, especially at low dimensions, help us to understand inter-particle interaction and intra-particle interaction by determining their chemical potential and Lennard-Jones potential. This review has been concluded with a model to characterize the precursor solution (amino acids and inorganic materials) by considering the Equation of State for liquids, which could also be extended to determine the structure factor of nanoparticles.

  11. Effect of the structure of gallic acid and its derivatives on their interaction with plant ferritin.

    Science.gov (United States)

    Wang, Qunqun; Zhou, Kai; Ning, Yong; Zhao, Guanghua

    2016-12-15

    Gallic acid and its derivatives co-exist with protein components in foodstuffs, but there is few report on their interaction with proteins. On the other hand, plant ferritin represents not only a novel class of iron supplement, but also a new nanocarrier for encapsulation of bioactive nutrients. However, plant ferritin is easy to be degraded by pepsin in the stomach, thereby limiting its application. Herein, we investigated the interaction of gallic acid and its derivatives with recombinant soybean seed H-2 ferritin (rH-2). We found that these phenolic acids interacted with rH-2 in a structure-dependent manner; namely, gallic acid (GA), methyl gallate (MEGA) and propyl gallate (PG) having three HO groups can bind to rH-2, while their analogues with two HO groups cannot. Consequently, such binding largely inhibited ferritin degradation by pepsin. These findings advance our understanding of the relationship between the structure and function of phenolic acids. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Effect of a Long Chain Carboxylate Acid on Sodium Dodecyl Sulfate Micelle Structure: A Small-angle Neutron Scattering Study

    International Nuclear Information System (INIS)

    Arum Patriati; Edy Giri Rachman Putra

    2009-01-01

    The effect of different hydrocarbon chain length of carboxylate acid, i.e. dodecanoic acid, CH 3 (CH 2 ) 10 COOH and hexadecanoic acid, CH 3 (CH 2 ) 14 COOH as a co-surfactant in the 0.3M SDS micellar solution has been studied using small angle neutron scattering (SANS). Here, the present of dodecanoic acid has induced the SDS structural micelles. The ellipsoid micelles structures changed significantly in length (major axis) from 21.7 Armstrong to 35.5 Armstrong at a fixed minor axis of 16.7 Armstrong in the present of 0.005M to 0.1M dodecanoic acid. Nevertheless, this effect was not shown in the present of hexadecanoic acid with the same concentration range. The present of hexadecanoic acid molecules gave a small effect on growth of SDS micelles where the major axis of the micelle was simply elongated from 21.5 Armstrong to 23.5 Armstrong. It showed that the appropriate hydrocarbon chain length between surfactant and co-surfactant molecules is one of the determining factors in forming a mixed micelles structure. (author)

  13. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    Science.gov (United States)

    Xie, Jianming [San Diego, CA; Wang, Lei [San Diego, CA; Wu, Ning [Boston, MA; Schultz, Peter G [La Jolla, CA

    2008-07-15

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  14. Interaction between metals and nucleic acids. Part 3. Synthesis and structural studies of copper(II) complexes with Schiff base ligands derived from barbituric acid

    Energy Technology Data Exchange (ETDEWEB)

    Sasaki, I.; Gaudemer, A.; Chiaroni, A.; Riche, C.

    1986-02-17

    Schiff bases have been prepared from 5-formylbarbituric acid and 5-formyl-1,3-dimethyl-barbituric acid and various di- or tri-amines. The structure of the corresponding copper(II) complexes have been established by elemental analysis and spectroscopic methods. The molecular structure of one of the complexes, Cu(DiMeBardpt), was determined by X-ray diffraction. Electrochemical study shows that these complexes are reduced at slightly more negative potentials than the corresponding complexes obtained from uracil, which suggests that these new ligands are better electron-donors.

  15. Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation

    Science.gov (United States)

    Li, Jiang; Green, Alexander A.; Yan, Hao; Fan, Chunhai

    2017-11-01

    Nucleic acids have attracted widespread attention due to the simplicity with which they can be designed to form discrete structures and programmed to perform specific functions at the nanoscale. The advantages of DNA/RNA nanotechnology offer numerous opportunities for in-cell and in-vivo applications, and the technology holds great promise to advance the growing field of synthetic biology. Many elegant examples have revealed the potential in integrating nucleic acid nanostructures in cells and in vivo where they can perform important physiological functions. In this Review, we summarize the current abilities of DNA/RNA nanotechnology to realize applications in live cells and then discuss the key problems that must be solved to fully exploit the useful properties of nanostructures. Finally, we provide viewpoints on how to integrate the tools provided by DNA/RNA nanotechnology and related new technologies to construct nucleic acid nanostructure-based molecular circuitry for synthetic biology.

  16. DSSR-enhanced visualization of nucleic acid structures in Jmol.

    Science.gov (United States)

    Hanson, Robert M; Lu, Xiang-Jun

    2017-07-03

    Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Syntheses and structure characterization of ten acid-base hybrid crystals based on N-containing aromatic brønsted bases and mineral acids

    Science.gov (United States)

    Lin, Zhihao; Jin, Shouwen; Li, Xiaoliang; Xiao, Xiao; Hu, Kaikai; Guo, Ming; Chi, Xinchen; Liu, Hui; Wang, Daqi

    2017-10-01

    Cocrystallization of the aromatic brønsted bases with a series of mineral acids gave a total of ten hybrid salts with the compositions: (2-methylquinoline)2: (hydrochloride acid): 3H2O [(HL1)+. (L1)·· (Cl-) · (H2O)3] (1), (6-bromobenzo[d]thiazol-2-amine): (hydrochloride acid) [(HL2)+. (Cl-)] (2), (6-bromobenzo[d]thiazol-2-amine): (nitric acid) [(HL2)+. (NO3-)] (3), (6-bromobenzo[d]thiazol-2-amine): (sulfuric acid) [(HL2)+ · (HSO4)-] (4), (6-bromobenzo[d]thiazol-2-amine): (phosphoric acid) [(HL2)+ · (H2PO4)-] (5), (5,7-dimethyl-1,8-naphthyridine-2-amine): (hydrochloride acid): 3H2O [(HL3)+ · (Cl-) (H2O)3] (6), (5,7-dimethyl-1,8-naphthyridine-2-amine): (hydrobromic acid): CH3OH [(HL3)+ · (Br)- · CH3OH] (7), (5,7-dimethyl-1,8-naphthyridine-2-amine): (sulfuric acid): H2O [(HL3)+ · (HSO4)- · H2O] (8), (2-aminophenol): (phosphoric acid) [(HL4)+ · (H2PO4)-] (9), and (2-amino-4-chlorophenol): (phosphoric acid) [(HL5)+ · (H2PO4)-] (10). The ten salts have been characterized by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the ten investigated crystals the ring N of the heterocycle or the NH2 in the aminophenol are protonated when the acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted classical hydrogen bonds between the NH+/NH3+ and deprotonated acidic groups. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O, CHsbnd Cl, CH3sbnd N, CH3sbnd O, CHsbnd Br, CH3sbnd Br, Brsbnd Cl, Clsbnd S, Osbnd S, Osbnd O, Brsbnd S, Hsbnd H, and π-π associations contribute to the stabilization and expansion of the total high-dimensional frameworks. For the coexistence of the various weak nonbonding interactions these structures adopted homo or hetero supramolecular synthons or both. Some classical

  18. Solution structure of human intestinal fatty acid binding protein: Implications for ligand entry and exit

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Fengli [Boston University School of Medicine, Department of Biophysics (United States); Luecke, Christian [Johann Wolfgang Goethe-Universitaet (Germany); Baier, Leslie J. [NIDDK, NIH, Phoenix Epidemiology and Clinical Research Branch (United States); Sacchettini, James C. [Texas A and M University, Department of Biochemistry and Biophysics (United States); Hamilton, James A. [Boston University School of Medicine, Department of Biophysics (United States)

    1997-04-15

    The human intestinal fatty acid binding protein (I-FABP) is a small (131 amino acids) protein which binds dietary long-chain fatty acids in the cytosol of enterocytes. Recently, an alanine to threonine substitution at position 54 in I-FABP has been identified which affects fatty acid binding and transport, and is associated with the development of insulin resistance in several populations including Mexican-Americans and Pima Indians. To investigate the molecular basis of the binding properties of I-FABP, the 3D solution structure of the more common form of human I-FABP (Ala54) was studied by multidimensional NMR spectroscopy.Recombinant I-FABP was expressed from E. coli in the presence and absence of 15N-enriched media. The sequential assignments for non-delipidated I-FABP were completed by using 2D homonuclear spectra (COSY, TOCSY and NOESY) and 3D heteronuclear spectra(NOESY-HMQC and TOCSY-HMQC). The tertiary structure of human I-FABP was calculated by using the distance geometry program DIANA based on 2519 distance constraints obtained from the NMR data. Subsequent energy minimization was carried out by using the program SYBYL in the presence of distance constraints. The conformation of human I-FABP consists of 10 antiparallel {beta}-strands which form two nearly orthogonal {beta}-sheets of five strands each, and two short {alpha}-helices that connect the {beta}-strands A and B. The interior of the protein consists of a water-filled cavity between the two {beta}-sheets. The NMR solution structure of human I-FABP is similar to the crystal structure of rat I-FABP.The NMR results show significant conformational variability of certain backbone segments around the postulated portal region for the entry and exit of fatty acid ligand.

  19. Solution structure of human intestinal fatty acid binding protein: Implications for ligand entry and exit

    International Nuclear Information System (INIS)

    Zhang Fengli; Luecke, Christian; Baier, Leslie J.; Sacchettini, James C.; Hamilton, James A.

    1997-01-01

    The human intestinal fatty acid binding protein (I-FABP) is a small (131 amino acids) protein which binds dietary long-chain fatty acids in the cytosol of enterocytes. Recently, an alanine to threonine substitution at position 54 in I-FABP has been identified which affects fatty acid binding and transport, and is associated with the development of insulin resistance in several populations including Mexican-Americans and Pima Indians. To investigate the molecular basis of the binding properties of I-FABP, the 3D solution structure of the more common form of human I-FABP (Ala54) was studied by multidimensional NMR spectroscopy.Recombinant I-FABP was expressed from E. coli in the presence and absence of 15N-enriched media. The sequential assignments for non-delipidated I-FABP were completed by using 2D homonuclear spectra (COSY, TOCSY and NOESY) and 3D heteronuclear spectra(NOESY-HMQC and TOCSY-HMQC). The tertiary structure of human I-FABP was calculated by using the distance geometry program DIANA based on 2519 distance constraints obtained from the NMR data. Subsequent energy minimization was carried out by using the program SYBYL in the presence of distance constraints. The conformation of human I-FABP consists of 10 antiparallel β-strands which form two nearly orthogonal β-sheets of five strands each, and two short α-helices that connect the β-strands A and B. The interior of the protein consists of a water-filled cavity between the two β-sheets. The NMR solution structure of human I-FABP is similar to the crystal structure of rat I-FABP.The NMR results show significant conformational variability of certain backbone segments around the postulated portal region for the entry and exit of fatty acid ligand

  20. Structures of metal complexes with anions of di(hydroxymethyl)phosphinic and di(chloromethyl)phosphinic acids

    International Nuclear Information System (INIS)

    Sergienko, V.S.; Aleksandrov, G.G.

    2001-01-01

    The structural peculiarities of the different metals [Cu, Ni, rare earths (La, Nd, Er, Lu), Ag, Li, Na, Sr] with anions of di-substituted monophosphonic acids - di(hydroxymethyl) phosphonic acid (HOCH 2 ) 2 PO 2 - (L 1 ) and di(chloromethyl) phosphonic acid (ClCH 2 ) 2 PO 2 - (L 2 ), and the methods of coordinating ligands L 1 and L 2 with these metals were viewed. Coordination number of metal decreases from eight in the case of La, Nd to seven for Er, and further to six for Lu with decreasing size of rare earth element. M-O bond lengths decrease the same way. The LiL 2 · H 2 O structure was determined, Li atom shows tetrahedron coordination by three oxygen atoms of the three ligands L 2 and atom O(ω) of water molecule. The ligand L 1 are acting as a tetradentate chelate μ 3 -bridge function in the structure of the Sr(L 1 ) 2 compound. The interval of Sr-O distances comprises 2.521 - 2.683 A [ru

  1. Effects of citric acid esterification on digestibility, structural and physicochemical properties of cassava starch.

    Science.gov (United States)

    Mei, Ji-Qiang; Zhou, Da-Nian; Jin, Zheng-Yu; Xu, Xue-Ming; Chen, Han-Qing

    2015-11-15

    In this study, citric acid was used to react with cassava starch in order to compare the digestibility, structural and physicochemical properties of citrate starch samples. The results indicated that citric acid esterification treatment significantly increased the content of resistant starch (RS) in starch samples. The swelling power and solubility of citrate starch samples were lower than those of native starch. Compared with native starch, a new peak at 1724 cm(-1) was appeared in all citrate starch samples, and crystalline peaks of all starch citrates became much smaller or even disappeared. Differential scanning calorimetry results indicated that the endothermic peak of citrate starches gradually shrank or even disappeared. Moreover, the citrate starch gels exhibited better freeze-thaw stability. These results suggested that citric acid esterification induced structural changes in cassava starch significantly affected its digestibility and it could be a potential method for the preparation of RS with thermal stability. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Syntheses and structure characterization of ten acid-base hybrid crystals based on imidazole derivatives and mineral acids

    Science.gov (United States)

    Hu, Kaikai; Deng, Bowen; Jin, Shouwen; Ding, Aihua; Jin, Shide; Zhu, Jin; Zhang, Huan; Wang, Daqi

    2018-04-01

    Cocrystallization of the imidazole derivatives with a series of mineral acids gave a total of ten hybrid salts with the compositions: [(H2bzm)(Cl)2·3H2O] (1), [(H2bzm)(ClO4)2] (2), [(H2bze)(Cl)2·2H2O] (3), [(H2bze)(Br)2·2H2O] (4), [(H2bzp)(Cl)2·4H2O] (5), [(H2bzp)(Br)2·4H2O] (6), (2-(imidazol-1-yl)-1-phenylethanone): (phosphoric acid) [(Himpeta)+(H2PO4)-] (7), [(H2impd)(Br)2] (8), [(H2impd)(ClO4)2] (9), and [(Hbzml)(Cl)] (10). The ten salts have been characterised by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the ten investigated crystals the ring N atoms of the imidazole are protonated when the acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted classical H-bonds between the NH+ and deprotonated acidic groups. Further analysis of the crystal packing of the salts indicated that a different set of additional CHsbnd O, CH2sbnd O, CHsbnd Cl, CH2sbnd Cl, CHsbnd N, CHsbnd Br, CH2sbnd Br, Osbnd O, O-π, Br-π, CH-π, and π-π associations contribute to the stabilization and expansion of the total high-dimensional frameworks. For the coexistence of the various weak nonbonding interactions these structures adopted homo or hetero supramolecular synthons or both. Some classical supramolecular synthons, such as R21(7), R22(7), R22(8), and R42(8), usually observed in the organic solids, were again shown to be involved in constructing some of these H-bonding networks.

  3. Physical and structural characterisation of starch/polyester blends with tartaric acid

    International Nuclear Information System (INIS)

    Olivato, J.B.; Müller, C.M.O.; Carvalho, G.M.; Yamashita, F.; Grossmann, M.V.E.

    2014-01-01

    Starch/PBAT blends were produced by reactive extrusion with tartaric acid (TA) as an additive. The effects of TA, glycerol and starch + PBAT on the mechanical, optical and structural properties of the films were evaluated, with formulations based in a constrained mixture design. Tartaric acid acts as a compatibiliser and promotes the acid hydrolysis of starch chains. These two functions explain the observed film resistance and opacity. TA reduced the weight loss in water. Scanning electron microscopy (SEM) images showed that TA reduces the interfacial tension between the polymeric phases, resulting in more homogeneous films. Nuclear magnetic resonance ( 13 C CPMAS) and Fourier transform infrared spectroscopy (FT-IR) suggest that tartaric acid is able to react with the hydroxyl groups of the starch by esterification/transesterification reactions, confirming its role as a compatibiliser. The addition of TA results in materials with better properties that are suitable for use in food packaging. - Highlights: • Tartaric acid (TA) was efficient as compatibiliser of starch/PBAT blends. • Film properties were analysed based on the modelling of the mixture design. • Greater proportions of TA resulted in more opaque and less soluble materials. • Esterification reactions promoted by TA were characterised by FT-IR and 13 C CPMAS NMR. • Compatibilised blends with TA showed better morphological and mechanical properties

  4. Physical and structural characterisation of starch/polyester blends with tartaric acid

    Energy Technology Data Exchange (ETDEWEB)

    Olivato, J.B., E-mail: jubonametti@uel.br [Departamento de Ciência e Tecnologia de Alimentos, Centro de Ciências Agrárias, Universidade Estadual de Londrina, PO Box 6001, 86051-980 Londrina, PR (Brazil); Müller, C.M.O. [Departamento de Ciência e Tecnologia de Alimentos, Centro de Ciências Agrárias, Universidade Estadual de Londrina, PO Box 6001, 86051-980 Londrina, PR (Brazil); Carvalho, G.M. [Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, PO Box 6001, 86051-980 Londrina, PR (Brazil); Yamashita, F.; Grossmann, M.V.E. [Departamento de Ciência e Tecnologia de Alimentos, Centro de Ciências Agrárias, Universidade Estadual de Londrina, PO Box 6001, 86051-980 Londrina, PR (Brazil)

    2014-06-01

    Starch/PBAT blends were produced by reactive extrusion with tartaric acid (TA) as an additive. The effects of TA, glycerol and starch + PBAT on the mechanical, optical and structural properties of the films were evaluated, with formulations based in a constrained mixture design. Tartaric acid acts as a compatibiliser and promotes the acid hydrolysis of starch chains. These two functions explain the observed film resistance and opacity. TA reduced the weight loss in water. Scanning electron microscopy (SEM) images showed that TA reduces the interfacial tension between the polymeric phases, resulting in more homogeneous films. Nuclear magnetic resonance ({sup 13}C CPMAS) and Fourier transform infrared spectroscopy (FT-IR) suggest that tartaric acid is able to react with the hydroxyl groups of the starch by esterification/transesterification reactions, confirming its role as a compatibiliser. The addition of TA results in materials with better properties that are suitable for use in food packaging. - Highlights: • Tartaric acid (TA) was efficient as compatibiliser of starch/PBAT blends. • Film properties were analysed based on the modelling of the mixture design. • Greater proportions of TA resulted in more opaque and less soluble materials. • Esterification reactions promoted by TA were characterised by FT-IR and {sup 13}C CPMAS NMR. • Compatibilised blends with TA showed better morphological and mechanical properties.

  5. The acidic pH-induced structural changes in apo-CP43 by spectral methodologies and molecular dynamics simulations

    Science.gov (United States)

    Wang, Wang; Li, Xue; Wang, Qiuying; Zhu, Xixi; Zhang, Qingyan; Du, Linfang

    2018-01-01

    CP43 is closely associated with the photosystem II and exists the plant thylakoid membranes. The acidic pH-induced structural changes had been investigated by fluorescence spectrum, ANS spectrum, RLS spectrum, energy transfer experiment, acrylamide fluorescence quenching assay and MD simulation. The fluorescence spectrum indicated that the structural changes in acidic pH-induced process were a four-state model, which was nature state (N), partial unfolding state (PU), refolding state (R), and molten-globule state (M), respectively. Analysis of ANS spectrum illustrated that inner hydrophobic core exposed partially to surface below pH 2.0 and inferred also that the molten-globule state existed. The RLS spectrum showed the aggregation of apo-CP43 around the pI (pH 4.5-4.0). The alterations of apo-CP43 secondary structure with different acidic treatments were confirmed by FTIR spectrum. The energy transfer experiment and quenching research demonstrated structural change at pH 4.0 was loosest. The RMSF suggested two terminals played an important function in acidic denaturation process. The distance of two terminals shown slight difference in acidic pH-induced process during the unfolding process, both N-terminal and C-terminal occupied the dominant role. However, the N-terminal accounted for the main part in the refolding process. All kinds of SASA values corresponded to spectral results. The tertiary and secondary structure by MD simulation indicated that the part transmembrane α-helix was destroyed at low pH.

  6. Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding

    International Nuclear Information System (INIS)

    Vaezeslami, Soheila; Jia, Xiaofei; Vasileiou, Chrysoula; Borhan, Babak; Geiger, James H.

    2008-01-01

    A water network stabilizes the structure of cellular retionic acid binding protein II. The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple different mutations. A water-mediated network is found to be present across the large binding cavity, extending from Arg111 deep inside the cavity to the α2 helix at its entrance. This chain of interactions acts as a ‘pillar’ that maintains the integrity of the protein. The disruption of the water network upon loss of Arg111 leads to decreased structural integrity of the protein. A water-mediated network can be re-established by introducing the hydrophilic Glu121 inside the cavity, which results in a rigid protein with the α2 helix adopting an altered conformation compared with wild-type CRABPII

  7. Microscale and nanoscale hierarchical structured mesh films with superhydrophobic and superoleophilic properties induced by long-chain fatty acids

    International Nuclear Information System (INIS)

    Wang Shutao; Song Yanlin; Jiang Lei

    2007-01-01

    Inspired by the lotus effect, we fabricate new microscale and nanoscale hierarchical structured copper mesh films by a simple electrochemical deposition. After modification of the long-chain fatty acid monolayer, these films show superhydrophobic and superoleophilic properties, which could be used for the effective separation of oil and water. The length of the fatty acid chain strongly influences the surface wettability of as-prepared films. It is confirmed that the cooperative effect of the hierarchical structure of the copper film and the nature of the long-chain fatty acid contribute to this unique surface wettability

  8. Structural basis of enzymatic activity for the ferulic acid decarboxylase (FADase from Enterobacter sp. Px6-4.

    Directory of Open Access Journals (Sweden)

    Wen Gu

    Full Text Available Microbial ferulic acid decarboxylase (FADase catalyzes the transformation of ferulic acid to 4-hydroxy-3-methoxystyrene (4-vinylguaiacol via non-oxidative decarboxylation. Here we report the crystal structures of the Enterobacter sp. Px6-4 FADase and the enzyme in complex with substrate analogues. Our analyses revealed that FADase possessed a half-opened bottom β-barrel with the catalytic pocket located between the middle of the core β-barrel and the helical bottom. Its structure shared a high degree of similarity with members of the phenolic acid decarboxylase (PAD superfamily. Structural analysis revealed that FADase catalyzed reactions by an "open-closed" mechanism involving a pocket of 8 × 8 × 15 Å dimension on the surface of the enzyme. The active pocket could directly contact the solvent and allow the substrate to enter when induced by substrate analogues. Site-directed mutagenesis showed that the E134A mutation decreased the enzyme activity by more than 60%, and Y21A and Y27A mutations abolished the enzyme activity completely. The combined structural and mutagenesis results suggest that during decarboxylation of ferulic acid by FADase, Trp25 and Tyr27 are required for the entering and proper orientation of the substrate while Glu134 and Asn23 participate in proton transfer.

  9. Synthesis and Molecular Structures of (E-non-2-enoic Acid and (E-dec-2-enoic Acid

    Directory of Open Access Journals (Sweden)

    Marcel Sonneck

    2015-10-01

    Full Text Available The molecular structures of (E-non-2-enoic acid (C9 and (E-dec-2-enoic acid (C10 are reported. The title compounds were crystallized by slow evaporation of ethanolic solutions at −30 °C. C9 crystallizes in the monoclinic space group P21/c and C10 in the triclinic space group P-1, each with 4 molecules in the unit cell. The unit cell parameters for C9 are: a = 10.6473(4 Å, b = 5.2855(2 Å, c = 17.0313(7 Å; β = 106.0985(10° and V = 920.87(6 Å3. The unit cell parameters for C10 are: a = 4.1405(2 Å, b = 15.2839(6 Å, c = 17.7089(7 Å; α = 68.3291(11°, β = 83.3850(13°, γ = 85.0779(12° and V = 1033.39(8 Å3.

  10. C9/12 Ribbon-Like Structures in Hybrid Peptides Alternating α- and Thiazole-Based γ-Amino Acids.

    Science.gov (United States)

    Bonnel, Clément; Legrand, Baptiste; Simon, Matthieu; Martinez, Jean; Bantignies, Jean-Louis; Kang, Young Kee; Wenger, Emmanuel; Hoh, Francois; Masurier, Nicolas; Maillard, Ludovic T

    2017-12-11

    According to their restricted conformational freedom, heterocyclic γ-amino acids are usually considered to be related to Z-vinylogous γ-amino acids. In this context, oligomers alternating α-amino acids and thiazole-based γ-amino acids (ATCs) were expected to fold into a canonical 12-helical shape as described for α/γ-hybrid peptides composed of cis-α/β-unsaturated γ-amino acids. However, through a combination of X-ray crystallography, NMR spectroscopy, FTIR experiments, and DFT calculations, it was determined that the folding behavior of ATC-containing hybrid peptides is much more complex. The homochiral α/(S)-ATC sequences were unable to adopt a stable conformation, whereas the heterochiral α/(R)-ATC peptides displayed novel ribbon structures stabilized by unusual C 9/12 -bifurcated hydrogen bonds. These ribbon structures could be considered as a succession of pre-organized γ/α dipeptides and may provide the basis for designing original α-helix mimics. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Ligand complex structures of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 and its conformational change.

    Science.gov (United States)

    Im, Dohyun; Matsui, Daisuke; Arakawa, Takatoshi; Isobe, Kimiyasu; Asano, Yasuhisa; Fushinobu, Shinya

    2018-03-01

    l-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 (l-AAO/MOG) catalyzes both the oxidative deamination and oxidative decarboxylation of the α-group of l-Lys to produce a keto acid and amide, respectively. l-AAO/MOG exhibits limited specificity for l-amino acid substrates with a basic side chain. We previously determined its ligand-free crystal structure and identified a key residue for maintaining the dual activities. Here, we determined the structures of l-AAO/MOG complexed with l-Lys, l-ornithine, and l-Arg and revealed its substrate recognition. Asp238 is located at the ceiling of a long hydrophobic pocket and forms a strong interaction with the terminal, positively charged group of the substrates. A mutational analysis on the D238A mutant indicated that the interaction is critical for substrate binding but not for catalytic control between the oxidase/monooxygenase activities. The catalytic activities of the D238E mutant unexpectedly increased, while the D238F mutant exhibited altered substrate specificity to long hydrophobic substrates. In the ligand-free structure, there are two channels connecting the active site and solvent, and a short region located at the dimer interface is disordered. In the l-Lys complex structure, a loop region is displaced to plug the channels. Moreover, the disordered region in the ligand-free structure forms a short helix in the substrate complex structures and creates the second binding site for the substrate. It is assumed that the amino acid substrate enters the active site of l-AAO/MOG through this route. The atomic coordinates and structure factors (codes 5YB6, 5YB7, and 5YB8) have been deposited in the Protein Data Bank (http://wwpdb.org/). 1.4.3.2 (l-amino acid oxidase), 1.13.12.2 (lysine 2-monooxygenase).

  12. A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures

    International Nuclear Information System (INIS)

    Rovira, Carme; Alfonso-Prieto, Mercedes; Biarnes, Xevi; Carpena, Xavi; Fita, Ignacio; Loewen, Peter C.

    2006-01-01

    Density functional molecular dynamics simulations using a QM/MM approach are used to get insight into the binding modes of formic acid in catalase. Two ligand binding sites are found, named A and B, in agreement with recent high resolution structures of catalase with bound formic acid. In addition, the calculations show that the His56 residue is protonated and the ligand is present as a formate anion. The lowest energy minimum structure (A) corresponds to the ligand interacting with both the heme iron and the catalytic residues (His56 and Asn129). The second minimum energy structure (B) corresponds to the situation in which the ligand interacts solely with the catalytic residues. A mechanism for the process of formic acid binding in catalase is suggested

  13. A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures

    Energy Technology Data Exchange (ETDEWEB)

    Rovira, Carme [Centre especial de Recerca en Quimica Teorica, Parc Cientific de Barcelona, Josep Samitier 1-5, 08028 Barcelona (Spain)], E-mail: crovira@pcb.ub.es; Alfonso-Prieto, Mercedes [Centre especial de Recerca en Quimica Teorica, Parc Cientific de Barcelona, Josep Samitier 1-5, 08028 Barcelona (Spain); Biarnes, Xevi [Centre especial de Recerca en Quimica Teorica, Parc Cientific de Barcelona, Josep Samitier 1-5, 08028 Barcelona (Spain); Carpena, Xavi [Consejo Superior de Investigaciones Cientificas y Parc Cientific de Barcelona (CSIC-PCB), Josep Samitier 1-5, 08028 Barcelona (Spain); Fita, Ignacio [Consejo Superior de Investigaciones Cientificas y Parc Cientific de Barcelona (CSIC-PCB), Josep Samitier 1-5, 08028 Barcelona (Spain); Loewen, Peter C. [Department of Microbiology, University of Manitoba, Winnipeg, Canada MB R3T 2N2 (Canada)

    2006-03-31

    Density functional molecular dynamics simulations using a QM/MM approach are used to get insight into the binding modes of formic acid in catalase. Two ligand binding sites are found, named A and B, in agreement with recent high resolution structures of catalase with bound formic acid. In addition, the calculations show that the His56 residue is protonated and the ligand is present as a formate anion. The lowest energy minimum structure (A) corresponds to the ligand interacting with both the heme iron and the catalytic residues (His56 and Asn129). The second minimum energy structure (B) corresponds to the situation in which the ligand interacts solely with the catalytic residues. A mechanism for the process of formic acid binding in catalase is suggested.

  14. Biophysical study of resin acid effects on phospholipid membrane structure and properties

    DEFF Research Database (Denmark)

    Jagalski, Vivien; Barker, Robert; Topgaard, Daniel

    2016-01-01

    Hydrophobic resin acids (RAs) are synthesized by conifer trees as part of their defense mechanisms. One of the functions of RAs in plant defense is suggested to be the perturbation of the cellular membrane. However, there is a vast diversity of chemical structures within this class of molecules, ...

  15. Adsorption and photodegradation of methylene blue by iron oxide impregnated on granular activated carbons in an oxalate solution

    Energy Technology Data Exchange (ETDEWEB)

    Kadirova, Zukhra C., E-mail: zuhra_kadirova@yahoo.com [Institute of General and Inorganic Chemistry, Academy of Sciences of the Republic of Uzbekistan, Mirzo Ulugbek Str. 77a, Tashkent 100170 (Uzbekistan); Materials and Structures Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama 226-8503 (Japan); Katsumata, Ken-ichi [Materials and Structures Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama 226-8503 (Japan); Isobe, Toshihiro [Department of Metallurgy and Ceramics Science, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro, Tokyo 152-8552 (Japan); Matsushita, Nobuhiro [Materials and Structures Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama 226-8503 (Japan); Nakajima, Akira [Department of Metallurgy and Ceramics Science, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro, Tokyo 152-8552 (Japan); Okada, Kiyoshi [Materials and Structures Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori, Yokohama 226-8503 (Japan)

    2013-11-01

    The photocatalytic adsorbents BAU-OA, BAU-CL and BAU-HA with varying iron oxide content (9–10 mass%) were prepared by heat treatment at 250 °C from commercial activated carbon (BAU) impregnated with iron oxalate, chloride, tris-benzohydroxamate, respectively. The XRD patterns showed amorphous structure in the BAU-CL sample (S{sub BET} 50 m{sup 2}/g) and low crystallinity (as FeOOH and Fe{sub 2}O{sub 3} phases) in the BAU-HA and BAU-OA samples (S{sub BET} 4 and 111 m{sup 2}/g, respectively). The methylene blue adsorption capacities was decreased in order of BAU-OA < BAU-CL < BAU-HA sample and the adsorption followed Langmuir model. The apparent MB photodegradation rate constant (k{sub app}) was increased in same order BAU-HA < BAU-CL < BAU-OA under the standard experimental conditions (initial MB concentrations 0.015–0.025 mM; sample content – 10 mg/l; initial oxalic acid concentration – 0.43 mM; pH 3–4; UV illumination). The process included high efficiency combination of adsorption, heterogeneous and homogeneous catalysis under UV and solar lights illumination without addition of hydrogen peroxide. The detoxification of water sample containing organic dyes was confirmed after combined sorption-photocatalytic treatment.

  16. In silico discovery of novel Retinoic Acid Receptor agonist structures

    Directory of Open Access Journals (Sweden)

    Samuels Herbert H

    2001-06-01

    Full Text Available Abstract Background Several Retinoic Acid Receptors (RAR agonists have therapeutic activity against a variety of cancer types; however, unacceptable toxicity profiles have hindered the development of drugs. RAR agonists presenting novel structural and chemical features could therefore open new avenues for the discovery of leads against breast, lung and prostate cancer or leukemia. Results We have analysed the induced fit of the active site residues upon binding of a known ligand. The derived binding site models were used to dock over 150,000 molecules in silico (or virtually to the structure of the receptor with the Internal Coordinates Mechanics (ICM program. Thirty ligand candidates were tested in vitro. Conclusions Two novel agonists resulting from the predicted receptor model were active at 50 nM. One of them displays novel structural features which may translate into the development of new ligands for cancer therapy.

  17. Gas Phase Structure of Amino Acids: La-Mb Studies

    Science.gov (United States)

    Mata, I. Pena S.; Sanz, M. E.; Vaquero, V.; Cabezas, C.; Perez, C.; Blanco, S.; López, J. C.; Alonso, J. L.

    2009-06-01

    Recent improvements in our laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectrometer such as using Laval-type nozzles and picoseconds Nd:YAG lasers (30 to 150 ps) have allowed a major step forward in the capabilities of this experimental technique as demonstrated by the last results in serine cysteine and threonine^a for which seven, six and seven conformers have been respectively identified. Taking advantage of these improvements we have investigated the natural amino acids metionine, aspartic and glutamic acids and the γ-aminobutyric acid (GABA) with the aim of identify and characterize their lower energy conformers. Searches in the rotational spectra have lead to the identification of seven conformers of metionine, six and five of aspartic and glutamic acids, respectively, and seven for the γ-aminobutyric. These conformers have been unambiguously identified by their spectroscopic constants. In particular the ^{14}N nuclear quadrupole coupling constants, that depend heavily on the orientation of the amino group with respect to the principal inertial axes of the molecule, prove to be a unique tool to distinguish unambigously between conformations with similar rotational constants. For the γ-aminobutyric acid two of the seven observed structures are stablized by an intramolecular interaction n-π*. Two new conformers of proline have been identified together with the two previously observed. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys.Chem.Chem.Phys., 2009, 11, 617. D. B. Atkinson, M. A. Smith, Rev. Sci. Instrum. 1995, 66, 4434 S. Blanco, M. E. Sanz, J. C. López, J. L. Alonso, Proc. Natl. Acad. Sci. USA2007, 104, 20183. M. E. Sanz, S. Blanco, J. C. López, J. L. Alonso, Angew. Chem. Int. Ed.,2008, 120, 6312. A. Lesarri, S. Mata, E. J. Cocinero, S. Blanco, J.C. López, J. L. Alonso, Angew. Chem. Int. Ed. , 2002, 41, 4673

  18. Oxidative stability of milk drinks containing structured lipids produced from sunflower oil and caprylic acid

    DEFF Research Database (Denmark)

    Timm Heinrich, Maike; Xu, Xuebing; Nielsen, Nina Skall

    2003-01-01

    Milk drinks containing 5% traditional sunflower oil (SO), randomized lipid (RL) or specific structured lipid (SL) (both produced from SO and tricaprylin/caprylic acid) were compared with respect to their particle size, viscosity and oxidative stability during storage. Furthermore, the effect...... drink could not be ascribed was most likely influenced by the structure of the lipid and to a single factor, differences in the process applied to produce and purify the lipids. EDTA was a strong antioxidant, while gallic acid did not exert a distinct antioxidative effect in the milk drink based on SL....... of adding potential antioxidants EDTA or gallic acid to the milk drink based on SL was investigated. The lipid type significantly affected the oxidative stability of the milk drinks: Milk drink based on SL oxidized faster than milk drink based on RL or SO. The reduced oxidative stability in the SL milk...

  19. Characterization of lignocellulosic biomass thermal degradation and physiochemical structure: Effects of demineralization by diverse acid solutions

    International Nuclear Information System (INIS)

    Asadieraghi, Masoud; Wan Daud, Wan Mohd Ashri

    2014-01-01

    Highlights: • HF showed interesting results on EFB (empty fruit bunches) and PMF (palm mesocarp fibre) deashing. • HCl indicated maximum ash removal from PKS (palm kernel shell). • Significant pyrolysis reactions took place at ∼250 °C to ∼400 °C. • Inorganics played a considerable catalytic role during the biomasses pyrolysis. • Acid pretreatment introduced some impacts on the biomasses structure. - Abstract: To eliminate the negative impacts of inorganic constituents during biomass thermochemical processes, leaching method by different diluted acid solutions was chosen. The different palm oil biomass samples (palm kernel shell (PKS), empty fruit bunches (EFB) and palm mesocarp fiber (PMF)) were pretreated by various diluted acid solutions (H 2 SO 4 , HClO 4 , HF, HNO 3 , HCl). Acids with the highest degrees of demineralization were selected to investigate the dematerialization impacts on the biomass thermal characteristics and physiochemical structure. Thermogravimetric analysis coupled with mass spectroscopy (TGA-MS) and Fourier transform infrared spectroscopy (TGA-FTIR) were employed to examine the biomass thermal degradation. TGA and DTG (Derivative thermogravimetry) indicated that the maximum degradation temperatures increased after acid pretreatment due to the minerals catalytic effects. The main permanent evolved gases comprising H 2 , CO 2 , CO were detected online during analysis. The major permanent gases produced at the temperature range of 250–750 °C were attributed to the condensable vapors cracking and probably some secondary reactions. The physiochemical structure change of the acid-treated biomass samples was examined by using Brunauer Emmett Teller (BET) method, Scanning Electron Microscope (SEM) and FTIR. The pyrolysis kinetics of the different palm oil biomasses were investigated using first order reaction model

  20. Fast computational methods for predicting protein structure from primary amino acid sequence

    Science.gov (United States)

    Agarwal, Pratul Kumar [Knoxville, TN

    2011-07-19

    The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

  1. Structural analysis and binding domain of albumin complexes with natural dietary supplement humic acid

    International Nuclear Information System (INIS)

    Ding Fei; Diao Jianxiong; Yang Xinling; Sun Ying

    2011-01-01

    Humic acid, a natural ionic molecule, is rapidly being recognized as one of the crucial elements in our modern diets of the new century. A biophysical protocol utilizing circular dichroism (CD), steady state and time-resolved fluorescence for the investigation of the complexation of the humic acid to the staple in vivo transporter, human serum albumin (HSA), as a model for protein-humic substances, is proclaimed. The alterations of CD and three-dimensional fluorescence suggest that the polypeptide chain of HSA partially folded after complexation with humic acid. The data of fluorescence emission displayed that the binding of humic acid to HSA is the formation of HSA-humic acid complex with an association constant of 10 4 M -1 ; this corroborates the fluorescence lifetime measurements that the static mechanism was operated. The precise binding domain of humic acid in HSA has been verified from the denaturation of albumin, hydrophobic ANS displacement, and site-specific ligands; subdomain IIA (Sudlow's site I) was earmarked to possess high-affinity for humic acid. The observations are relevant for other albumin-humic substance systems when the ligands have analogous configuration with humic acid. - Highlights: → Albumin structure partially folds upon humic acid complexation. → Static type is dominance for the diminution in the Trp-214 fluorescence.→ Subdomain IIA is designate to possess high-affinity site for humic acid.

  2. Alcohol-induced structural transitions in the acid-denatured Bacillus licheniformis α-amylase

    Directory of Open Access Journals (Sweden)

    Adyani Azizah Abd Halim

    2017-01-01

    Full Text Available Alcohol-induced structural changes in the acid-denatured Bacillus licheniformis α-amylase (BLA at pH 2.0 were studied by far-ultra violet circular dichroism, intrinsic, three-dimensional and 8-anilino-1-naphthalene sulfonic acid (ANS fluorescence, acrylamide quenching and thermal denaturation. All the alcohols used in this study produced partial refolding in the acid-denatured BLA as evident from the increased mean residue ellipticity at 222 nm, increased intrinsic fluorescence and decreased ANS fluorescence. The order of effectiveness of these alcohols to induce a partially folded state of BLA was found to be: 2,2,2-trifluoroethanol/tert-butanol > 1-propanol/2-propanol > 2-chloroethanol > ethanol > methanol. Three-dimensional fluorescence and acrylamide quenching results obtained in the presence of 5.5 M tert-butanol also suggested formation of a partially folded state in the acid-denatured BLA. However, 5.5 M tert-butanol-induced state of BLA showed a non-cooperative thermal transition. All these results suggested formation of a partially folded state of the acid-denatured BLA in the presence of these alcohols. Furthermore, their effectiveness was found to be guided by their chain length, position of methyl groups and presence of the substituents.

  3. Structures and energetics of hydrated deprotonated cis-pinonic acid anion clusters and their atmospheric relevance

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Gao-Lei; Zhang, Jun; Valiev, Marat; Wang, Xue-Bin

    2017-01-01

    Pinonic acid, a C10-monocarboxylic acid with a hydrophilic –CO2H group and a hydrophobic hydrocarbon backbone, is a key intermediate oxidation product of α-pinene – an important monoterpene compound in biogenic emission processes that influences the atmosphere. Molecular interaction between cis-pinonic acid and water is essential for understanding its role in the formation and growth of pinene-derived secondary organic aerosols. In this work, we studied the structures, energetics, and optical properties of hydrated clusters of cis-pinonate anion (cPA–), the deprotonated form of cis-pinonic acid, by negative ion photoelectron spectroscopy and ab initio theoretical calculations. Our results show that cPA– can adopt two different structural configurations – open and folded. In the absence of waters, the open configuration has the lowest energy and provides the best agreement with the experiment. The addition waters, which mainly interact with the negatively charged -CO2– group, gradually stabilize the folded configuration and lower its energy difference relative to the most stable open-configured structure. Thermochemical and equilibrium hydrate distribution analysis suggests that the mono- and di- hydrates are likely to exist in humid atmospheric environment with high populations. The detailed molecular description of cPA– hydrated clusters unraveled in this study provides a valuable reference for understanding the initial nucleation process and aerosol formation involving organics containing both hydrophilic and hydrophobic groups, as well as for analyzing the optical properties of those organic aerosols.

  4. Drug-drug cocrystals of antituberculous 4-aminosalicylic acid: Screening, crystal structures, thermochemical and solubility studies.

    Science.gov (United States)

    Drozd, Ksenia V; Manin, Alex N; Churakov, Andrei V; Perlovich, German L

    2017-03-01

    Experimental multistage cocrystal screening of the antituberculous drug 4-aminosalicylic acid (PASA) has been conducted with a number of coformers (pyrazinamide (PYR), nicotinamide (NAM), isonicotinamide (iNAM), isoniazid (INH), caffeine (CAF) and theophylline (TPH)). The crystal structures of 4-aminosalicylic acid cocrystals with isonicotinamide ([PASA+iNAM] (2:1)) and methanol solvate with caffeine ([PASA+CAF+MeOH] (1:1:1)) have been determined by single X-ray diffraction experiments. For the first time for PASA cocrystals it has been found that the structural unit of the [PASA+iNAM] cocrystal (2:1) is formed by 2 types of heterosynthons: acid-pyridine and acid-amide. The desolvation study of the [PASA+CAF+MeOH] cocrystal solvate (1:1:1) has been conducted. The correlation models linking the melting points of the cocrystals with the melting points of the coformers used in this paper have been developed. The thermochemical and solubility properties for all the obtained cocrystals have been studied. Cocrystallization has been shown to lead not only to PASA solubility improving but also to its higher stability against the chemical decomposition. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. New Insights into the Role of Pb-BHA Complexes in the Flotation of Tungsten Minerals

    Science.gov (United States)

    Yue, Tong; Han, Haisheng; Hu, Yuehua; Sun, Wei; Li, Xiaodong; Liu, Runqing; Gao, Zhiyong; Wang, Li; Chen, Pan; Zhang, Chenyang; Tian, Mengjie

    2017-11-01

    Lead ions (lead nitrate) were introduced to modify the surface properties of tungsten minerals, effectively improving the floatability, with benzohydroxamic acid (BHA) serving as the collector. Flotation tests indicated that Pb-BHA complexes were the active species responsible for flotation of the tungsten minerals. The developed Pb-BHA complexes and the novel flotation process effectively increased the recovery of scheelite and wolframite, simplified the technological process, and led to reduced costs. Fourier transform infrared spectra data showed the presence of adsorbed Pb-BHA complexes on the surface of the minerals. The characteristic peaks of BHA shifted by a considerable extent, indicating that chemical adsorption plays an important role in the flotation process. Zeta potential results confirmed physical adsorption of the positively charged Pb-BHA complexes on the mineral surfaces. The synergistic effect between chemical and physical adsorption facilitated the maximum flotation recovery of scheelite and wolframite.

  6. Protein and energy metabolism of young male Wistar rats fed conjugated linoleic acid as structured triacylglycerol

    DEFF Research Database (Denmark)

    Jørgensen, H.; Hansen, C. H.; Mu, Huiling

    2010-01-01

    Twelve 4-week-old male Wistar rats weighing 100 g were fed diets semi-ad libitum for 22 d containing either 1.5% conjugated linoleic acid (CLA-diet) or high oleic sunflower oil (Control-diet). The CLA was structured triacylglycerol with predominantly cis-9, trans-11 and trans-10, cis-12 fatty acid...

  7. Structure, function, and regulation of enzymes involved in amino acid metabolism of bacteria and archaea.

    Science.gov (United States)

    Tomita, Takeo

    2017-11-01

    Amino acids are essential components in all organisms because they are building blocks of proteins. They are also produced industrially and used for various purposes. For example, L-glutamate is used as the component of "umami" taste and lysine has been used as livestock feed. Recently, many kinds of amino acids have attracted attention as biological regulators and are used for a healthy life. Thus, to clarify the mechanism of how amino acids are biosynthesized and how they work as biological regulators will lead to further effective utilization of them. Here, I review the leucine-induced-allosteric activation of glutamate dehydrogenase (GDH) from Thermus thermophilus and the relationship with the allosteric regulation of GDH from mammals. Next, I describe structural insights into the efficient production of L-glutamate by GDH from an excellent L-glutamate producer, Corynebacterium glutamicum. Finally, I review the structural biology of lysine biosynthesis of thermophilic bacterium and archaea.

  8. Synthesis, characterization and crystal structures of new organic compounds containing cyanoacrylic acid

    Czech Academy of Sciences Publication Activity Database

    Khalaji, A.D.; Mogheiseh, M.; Eigner, Václav; Dušek, Michal; Chow, T.J.; Maddahi, E.

    2015-01-01

    Roč. 1098, Oct (2015), s. 318-323 ISSN 0022-2860 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : organic compounds * cyanoacrylic acid * single-crystal structure analysis * dye-sensitized solar cells * density functional theory Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.780, year: 2015

  9. Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes.

    Science.gov (United States)

    Wang, Yongxiang; Li, Jishan; Wang, Hao; Jin, Jianyu; Liu, Jinhua; Wang, Kemin; Tan, Weihong; Yang, Ronghua

    2010-08-01

    Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

  10. Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase.

    Science.gov (United States)

    Min, Kyungjin; Yoon, Hye-Jin; Matsuura, Atsushi; Kim, Yong Hwan; Lee, Hyung Ho

    2018-04-30

    L-pipecolic acid is a non-protein amino acid commonly found in plants, animals, and microorganisms. It is a well-known precursor to numerous microbial secondary metabolites and pharmaceuticals, including anticancer agents, immunosuppressants, and several antibiotics. Lysine cyclodeaminase (LCD) catalyzes β-deamination of L-lysine into L-pipecolic acid using β-nicotinamide adenine dinucleotide as a cofactor. Expression of a human homolog of LCD, μ-crystallin, is elevated in prostate cancer patients. To understand the structural features and catalytic mechanisms of LCD, we determined the crystal structures of Streptomyces pristinaespiralis LCD (SpLCD) in (i) a binary complex with NAD + , (ii) a ternary complex with NAD + and L-pipecolic acid, (iii) a ternary complex with NAD + and L-proline, and (iv) a ternary complex with NAD + and L-2,4-diamino butyric acid. The overall structure of SpLCD was similar to that of ornithine cyclodeaminase from Pseudomonas putida . In addition, SpLCD recognized L-lysine, L-ornithine, and L-2,4-diamino butyric acid despite differences in the active site, including differences in hydrogen bonding by Asp236, which corresponds with Asp228 from Pseudomonas putida ornithine cyclodeaminase. The substrate binding pocket of SpLCD allowed substrates smaller than lysine to bind, thus enabling binding to ornithine and L-2,4-diamino butyric acid. Our structural and biochemical data facilitate a detailed understanding of substrate and product recognition, thus providing evidence for a reaction mechanism for SpLCD. The proposed mechanism is unusual in that NAD + is initially converted into NADH and then reverted back into NAD + at a late stage of the reaction.

  11. Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

    Science.gov (United States)

    Teschke, Omar; Soares, David Mendez

    2016-03-29

    Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

  12. Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

    Science.gov (United States)

    Shieh, H S; Ghisla, S; Hanson, L K; Ludwig, M L; Nordman, C E

    1981-08-04

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

  13. Glycerol oxidehydration into acrolein and acrylic acid over W/V/Nb bronzes with hexagonal structure

    Energy Technology Data Exchange (ETDEWEB)

    Basile, F.; Cavani, F.; Chieregato, A. [Bologna Univ. (Italy). Dipt. di Chimica Industriale e dei Materiali; CIRI Energia e Ambiente, Bologna (Italy); Concepcion, P.; Lopez Nieto, J.M.; Soriano, M.D. [Univ. Politecnica de Valencia (Spain). Inst. de Tecnologia Quimica; Liosi, G.; Trevisanut, C. [Bologna Univ. (Italy). Dipt. di Chimica Industriale e dei Materiali

    2012-07-01

    This paper deals with an investigation of hexagonal W-V-Nb-O and W-V-Mo-O bronzes as catalysts for the one-pot oxidehydration of glycerol into acrylic acid. In a previous work, we reported a study on a bi-component bronze W-V-O that allowed us to obtain a 25% acrylic acid selectivity; in the current work, the incorporation of either Nb or Mo in a tri-component bronze structure allowed us to tune the acid and redox properties of the catalyst, so as to study their influence on the overall reaction scheme. (orig.)

  14. Insights into cadmium induced physiological and ultra-structural disorders in Juncus effusus L. and its remediation through exogenous citric acid

    International Nuclear Information System (INIS)

    Najeeb, Ullah; Jilani, Ghulam; Ali, Shafaqat; Sarwar, Muhammad; Xu Ling; Zhou, Weijun

    2011-01-01

    This study appraised cadmium (Cd) toxicity stress in wetland plant Juncus effusus, and explored its potential for Cd phytoextraction through chelators (citric acid and EDTA). Cadmium altered morphological and physiological attributes of J. effusus as reflected by growth retardation. Citric acid in the presence of 100 μM Cd significantly countered Cd toxicity by improving plant growth. Elevated Cd concentrations reduced translocation factor that was increased under application of both chelators. Citric acid enhanced Cd accumulation, while EDTA reduced its uptake. Cadmium induced oxidative stress modified the antioxidative enzyme activity. Both levels of citric acid (2.5 and 5.0 mM) and lower EDTA concentration (2.5 mM) helped plants to overcome oxidative stress by enhancing their antioxidative enzyme activities. Cadmium damaged the root cells through cytoplasmic shrinkage and metal deposition. Citric acid restored structure and shape of root cells and eliminated plasmolysis; whereas, EDTA exhibited no positive effect on it. Shoot cells remained unaffected under Cd treatment alone or with citric acid except for chloroplast swelling. Only EDTA promoted starch accumulation in chloroplast reflecting its negative impact on cellular structure. It concludes that Cd and EDTA induce structural and morphological damage in J. effusus; while, citric acid ameliorates Cd toxicity stress.

  15. Insights into cadmium induced physiological and ultra-structural disorders in Juncus effusus L. and its remediation through exogenous citric acid

    Energy Technology Data Exchange (ETDEWEB)

    Najeeb, Ullah [Institute of Crop Science, Zhejiang University, Hangzhou 310029 (China); Crop Sciences Institute, National Agriculture Research Centre, Islamabad 45500 (Pakistan); Jilani, Ghulam, E-mail: jilani@uaar.edu.pk [Department of Soil Science, PMAS Arid Agriculture University, Rawalpindi, Punjab 46300 (Pakistan); Ali, Shafaqat [Institute of Crop Science, Zhejiang University, Hangzhou 310029 (China); Sarwar, Muhammad [Land Resources Research Institute, National Agriculture Research Centre, Islamabad 45500 (Pakistan); Xu Ling [Institute of Crop Science, Zhejiang University, Hangzhou 310029 (China); Zhou, Weijun, E-mail: wjzhou@zju.edu.cn [Institute of Crop Science, Zhejiang University, Hangzhou 310029 (China)

    2011-02-15

    This study appraised cadmium (Cd) toxicity stress in wetland plant Juncus effusus, and explored its potential for Cd phytoextraction through chelators (citric acid and EDTA). Cadmium altered morphological and physiological attributes of J. effusus as reflected by growth retardation. Citric acid in the presence of 100 {mu}M Cd significantly countered Cd toxicity by improving plant growth. Elevated Cd concentrations reduced translocation factor that was increased under application of both chelators. Citric acid enhanced Cd accumulation, while EDTA reduced its uptake. Cadmium induced oxidative stress modified the antioxidative enzyme activity. Both levels of citric acid (2.5 and 5.0 mM) and lower EDTA concentration (2.5 mM) helped plants to overcome oxidative stress by enhancing their antioxidative enzyme activities. Cadmium damaged the root cells through cytoplasmic shrinkage and metal deposition. Citric acid restored structure and shape of root cells and eliminated plasmolysis; whereas, EDTA exhibited no positive effect on it. Shoot cells remained unaffected under Cd treatment alone or with citric acid except for chloroplast swelling. Only EDTA promoted starch accumulation in chloroplast reflecting its negative impact on cellular structure. It concludes that Cd and EDTA induce structural and morphological damage in J. effusus; while, citric acid ameliorates Cd toxicity stress.

  16. Synthesis, structural characterization and quantum chemical studies of silicon-containing benzoic acid derivatives

    Science.gov (United States)

    Zaltariov, Mirela-Fernanda; Cojocaru, Corneliu; Shova, Sergiu; Sacarescu, Liviu; Cazacu, Maria

    2016-09-01

    The present paper is concerned with the synthesis and molecular structure investigation of two new benzoic acid derivatives having trimethylsilyl tails, 4-((trimethylsilyl)methoxy) and 4-(3-(trimethylsilyl)propoxy)benzoic acids. The structures of the novel compounds have been confirmed by X-ray crystallography, Fourier-transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (1H and 13C NMR). The theoretical studies of molecules were conducted by using the quantum chemical methods, such as Density Functional Theory (DFT B3LYP/6-31 + G**), Hartree-Fock (HF/6-31 + G**) and semiempirical computations (PM3, PM6 and PM7). The optimized molecular geometries have been found to be in good agreement with experimental structures resulted from the X-ray diffraction. The maximum electronic absorption bands observed at 272-287 nm (UV-vis spectra) have been assigned to π → π* transitions, which were in reasonable agreement with the time dependent density functional theory (TD-DFT) calculations. The computed vibrational frequencies by DFT method were assigned and compared with the experimental FTIR spectra. The mapped electrostatic potentials revealed the reactive sites, which corroborated the observation of the dimer supramolecular structures formed in the crystals by hydrogen-bonding. The energies of frontier molecular orbitals (HOMO and LUMO), energy gap, dipole moment and molecular descriptors for the new compounds were calculated and discussed.

  17. Amino acid and structural variability of Yersinia pestis LcrV protein

    Energy Technology Data Exchange (ETDEWEB)

    Anisimov, A P; Dentovskaya, S V; Panfertsev, E A; Svetoch, T E; Kopylov, P K; Segelke, B W; Zemla, A; Telepnev, M V; Motin, V L

    2009-11-09

    The LcrV protein is a multifunctional virulence factor and protective antigen of the plague bacterium which is generally conserved between the epidemic strains of Yersinia pestis. They investigated the diversity in the LcrV sequences among non-epidemic Y. pestis strains which have a limited virulence in selected animal models and for humans. Sequencing of lcrV genes from ten Y. pestis strains belonging to different phylogenetic groups (subspecies) showed that the LcrV proteins possess four major variable hotspots at positions 18, 72, 273, and 324-326. These major variations, together with other minor substitutions in amino acid sequences, allowed them to classify the LcrV alleles into five sequence types (A-E). They observed that the strains of different Y. pestis subspecies can have the same typ of LcrV, and different types of LcrV can exist within the same natural plague focus. The LcrV polymorphisms were structurally analyzed by comparing the modeled structures of LcrV from all available strains. All changes except one occurred either in flexible regions or on the surface of the protein, but local chemical properties (i.e. those of a hydrophobic, hydrophilic, amphipathic, or charged nature) were conserved across all of the strains. Polymorphisms in flexible and surface regions are likely subject to less selective pressure, and have a limited impact on the structure. In contrast, the substitution of tryptophan at position 113 with either glutamic acid or glycine likely has a serious influence on the regional structure of the protein, and these mutations might have an effect on the function of LcrV. The polymorphisms at positions 18, 72 and 273 were accountable for differences in oligomerization of LcrV. The importance of the latter property in emergence of epidemic strains of Y. pestis during evolution of this pathogen will need to be further investigated.

  18. Lipase-catalyzed acidolysis of canola oil with caprylic acid to produce medium-, long- and medium-chain-type structured lipids

    DEFF Research Database (Denmark)

    Wang, Yingyao; Xia, Luan; Xu, Xuebing

    2012-01-01

    Lipase-catalyzed acidolysis of canola oil with caprylic acid was performed to produce structured lipids (SLs) containing medium-chain fatty acid (M) at position sn-1,3 and long-chain fatty acid (L) at the sn-2 position in a solvent-free system. Six commercial lipases from different sources were...

  19. [Structural characterization of Astragalus polysaccharides using partial acid hydrolysis-hydrophilic interaction liquid chromatography-mass spectrometry].

    Science.gov (United States)

    Liang, Tu; Fu, Qing; Xin, Huaxia; Li, Fangbing; Jin, Yu; Liang, Xinmiao

    2014-12-01

    Water-soluble polysaccharides from traditional Chinese medicine (TCM) have properties of broad-spectrum treatment and low toxicity, making them as important components in natural medicines and health products. In order to solve the problem of polysaccharides characterization caused by their complex structures, a "bottom-up" approach was developed to complete the characterization of polysaccharides from Astragalus. Firstly, Astragalus pieces were extracted with hot water and then were precipitated by ethanol to obtain Astragalus polysaccharides. Secondly, a partial acid hydrolysis method was carried out and the effects of time, acid concentration and temperature on hydrolysis were investigated. The degree of hydrolysis increased along with the increase of hydrolysis time and acid concentration. The temperature played a great role in the hydrolysis process. No hydrolysis of the polysaccharides occurred at low temperature, while the polysaccharides were almost hydrolyzed to monosaccharide at high temperature. Under the optimum hydrolysis conditions (4 h, 1.5 mol/L trifluoroacetic acid, and 80 °C), Astragalus polysaccharides were hydrolyzed to characteristic oligosaccharide fragments. At last, a hydrophilic liquid chromatography-mass spectrometry method was used for the separation and structural characterization of the polysaccharide hydrolysates. The results showed that the resulting polysaccharides were mainly 1--> 4 linear glucan, and gluco-oligosaccharides with the degrees of polymerization (DP) of 4 - 11 were obtained after partial acid hydrolysis. The significance of this study is that it is the guidance for the characterization of other TCM polysaccharides.

  20. Structural Characterisation of FabG from Yersinia pestis, a Key Component of Bacterial Fatty Acid Synthesis.

    Science.gov (United States)

    Nanson, Jeffrey D; Forwood, Jade K

    2015-01-01

    Ketoacyl-acyl carrier protein reductases (FabG) are ubiquitously expressed enzymes that catalyse the reduction of acyl carrier protein (ACP) linked thioesters within the bacterial type II fatty acid synthesis (FASII) pathway. The products of these enzymes, saturated and unsaturated fatty acids, are essential components of the bacterial cell envelope. The FASII reductase enoyl-ACP reductase (FabI) has been the focus of numerous drug discovery efforts, some of which have led to clinical trials, yet few studies have focused on FabG. Like FabI, FabG appears to be essential for survival in many bacteria, similarly indicating the potential of this enzyme as a drug target. FabG enzymes are members of the short-chain alcohol dehydrogenase/reductase (SDR) family, and like other SDRs, exhibit highly conserved secondary and tertiary structures, and contain a number of conserved sequence motifs. Here we describe the crystal structures of FabG from Yersinia pestis (YpFabG), the causative agent of bubonic, pneumonic, and septicaemic plague, and three human pandemics. Y. pestis remains endemic in many parts of North America, South America, Southeast Asia, and Africa, and a threat to human health. YpFabG shares a high degree of structural similarity with bacterial homologues, and the ketoreductase domain of the mammalian fatty acid synthase from both Homo sapiens and Sus scrofa. Structural characterisation of YpFabG, and comparison with other bacterial FabGs and the mammalian fatty acid synthase, provides a strong platform for virtual screening of potential inhibitors, rational drug design, and the development of new antimicrobial agents to combat Y. pestis infections.

  1. Structural Characterisation of FabG from Yersinia pestis, a Key Component of Bacterial Fatty Acid Synthesis.

    Directory of Open Access Journals (Sweden)

    Jeffrey D Nanson

    Full Text Available Ketoacyl-acyl carrier protein reductases (FabG are ubiquitously expressed enzymes that catalyse the reduction of acyl carrier protein (ACP linked thioesters within the bacterial type II fatty acid synthesis (FASII pathway. The products of these enzymes, saturated and unsaturated fatty acids, are essential components of the bacterial cell envelope. The FASII reductase enoyl-ACP reductase (FabI has been the focus of numerous drug discovery efforts, some of which have led to clinical trials, yet few studies have focused on FabG. Like FabI, FabG appears to be essential for survival in many bacteria, similarly indicating the potential of this enzyme as a drug target. FabG enzymes are members of the short-chain alcohol dehydrogenase/reductase (SDR family, and like other SDRs, exhibit highly conserved secondary and tertiary structures, and contain a number of conserved sequence motifs. Here we describe the crystal structures of FabG from Yersinia pestis (YpFabG, the causative agent of bubonic, pneumonic, and septicaemic plague, and three human pandemics. Y. pestis remains endemic in many parts of North America, South America, Southeast Asia, and Africa, and a threat to human health. YpFabG shares a high degree of structural similarity with bacterial homologues, and the ketoreductase domain of the mammalian fatty acid synthase from both Homo sapiens and Sus scrofa. Structural characterisation of YpFabG, and comparison with other bacterial FabGs and the mammalian fatty acid synthase, provides a strong platform for virtual screening of potential inhibitors, rational drug design, and the development of new antimicrobial agents to combat Y. pestis infections.

  2. An additional role for the Brønsted acid-base catalysts of mandelate racemase in transition state stabilization.

    Science.gov (United States)

    Nagar, Mitesh; Bearne, Stephen L

    2015-11-10

    Mandelate racemase (MR) catalyzes the interconversion of the enantiomers of mandelate and serves as a paradigm for understanding the enzyme-catalyzed abstraction of an α-proton from a carbon acid substrate with a high pKa. The enzyme utilizes a two-base mechanism with Lys 166 and His 297 acting as Brønsted acid and base catalysts, respectively, in the R → S reaction direction. In the S → R reaction direction, their roles are reversed. Using isothermal titration calorimetry (ITC), MR is shown to bind the intermediate/transition state (TS) analogue inhibitor benzohydroxamate (BzH) in an entropy-driven process with a value of ΔCp equal to -358 ± 3 cal mol(-1) K(-1), consistent with an increased number of hydrophobic interactions. However, MR binds BzH with an affinity that is ∼2 orders of magnitude greater than that predicted solely on the basis of hydrophobic interactions [St. Maurice, M., and Bearne, S. L. (2004) Biochemistry 43, 2524], suggesting that additional specific interactions contribute to binding. To test the hypothesis that cation-π/NH-π interactions between the side chains of Lys 166 and His 297 and the aromatic ring and/or the hydroxamate/hydroximate moiety of BzH contribute to the binding of BzH, site-directed mutagenesis was used to generate the MR variants K166M, K166C, H297N, and K166M/H297N and their binding affinity for various ligands determined using ITC. Comparison of the binding affinities of these MR variants with the intermediate/TS analogues BzH and cyclohexanecarbohydroxamate revealed that cation-π/NH-π interactions between His 297 and the hydroxamate/hydroximate moiety and the phenyl ring of BzH contribute approximately 0.26 and 0.91 kcal/mol to binding, respectively, while interactions with Lys 166 contribute approximately 1.74 and 1.74 kcal/mol, respectively. Similarly, comparison of the binding affinities of these mutants with substrate analogues revealed that Lys 166 contributes >2.93 kcal/mol to the binding of (R

  3. The shikimate pathway: review of amino acid sequence, function and three-dimensional structures of the enzymes.

    Science.gov (United States)

    Mir, Rafia; Jallu, Shais; Singh, T P

    2015-06-01

    The aromatic compounds such as aromatic amino acids, vitamin K and ubiquinone are important prerequisites for the metabolism of an organism. All organisms can synthesize these aromatic metabolites through shikimate pathway, except for mammals which are dependent on their diet for these compounds. The pathway converts phosphoenolpyruvate and erythrose 4-phosphate to chorismate through seven enzymatically catalyzed steps and chorismate serves as a precursor for the synthesis of variety of aromatic compounds. These enzymes have shown to play a vital role for the viability of microorganisms and thus are suggested to present attractive molecular targets for the design of novel antimicrobial drugs. This review focuses on the seven enzymes of the shikimate pathway, highlighting their primary sequences, functions and three-dimensional structures. The understanding of their active site amino acid maps, functions and three-dimensional structures will provide a framework on which the rational design of antimicrobial drugs would be based. Comparing the full length amino acid sequences and the X-ray crystal structures of these enzymes from bacteria, fungi and plant sources would contribute in designing a specific drug and/or in developing broad-spectrum compounds with efficacy against a variety of pathogens.

  4. Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST

    Directory of Open Access Journals (Sweden)

    Nalin CW Goonesekere

    2009-06-01

    Full Text Available Nalin CW GoonesekereDepartment of Chemistry and Biochemistry, University of Northern iowa, Cedar Falls, IA, USAAbstract: The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the complex evolutionary and functional relationships that exist between proteins. Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. The substitution matrices in common use today are constructed using sequences aligned without reference to protein structure. Here we present amino acid substitution matrices constructed from the alignment of a large number of protein domain structures from the structural classification of proteins (SCOP database. We show that when incorporated into the homology search algorithms BLAST and PSI-blaST, the structure-based substitution matrices enhance the efficacy of detecting remote homologs. Keywords: computational biology, protein homology, amino acid substitution matrix, protein structure

  5. Effects of nanorod structure and conformation of fatty acid self-assembled layers on superhydrophobicity of zinc oxide surface.

    Science.gov (United States)

    Badre, Chantal; Dubot, P; Lincot, Daniel; Pauporte, Thierry; Turmine, Mireille

    2007-12-15

    Superhydrophobic surfaces have been prepared from nanostructured zinc oxide layers by a treatment with fatty acid molecules. The layers are electrochemically deposited from an oxygenated aqueous zinc chloride solution. The effects of the layer's structure, from a dense film to that of a nanorod array, as well as that of the properties of the fatty acid molecules based on C18 chains are described. A contact angle (CA) as high as 167 degrees is obtained with the nanorod structure and the linear saturated molecule (stearic acid). Lower values are found with molecules having an unsaturated bond on C9, in particular with a cis conformation (140 degrees ). These results, supplemented by infrared spectroscopy, indicate an enhancement of the sensitivity to the properties of the fatty acid molecules (conformation, flexibility, saturated or not) when moving from the flat surface to the nanostructured surface. This is attributed to a specific influence of the structure of the tops of the rods and lateral wall properties on the adsorption and organization of the molecules. CA measurements show a very good stability of the surface in time if stored in an environment protected from UV radiations.

  6. Effect of fatty acids on functional properties of normal wheat and waxy wheat starches: A structural basis.

    Science.gov (United States)

    Wang, Shujun; Wang, Jinrong; Yu, Jinglin; Wang, Shuo

    2016-01-01

    The effects of three saturated fatty acids on functional properties of normal wheat and waxy wheat starches were investigated. The complexing index (CI) of normal wheat starch-fatty acid complexes decreased with increasing carbon chain length. In contrast, waxy wheat starch-fatty acid complexes presented much lower CI. V-type crystalline polymorphs were formed between normal wheat starch and three fatty acids, with shorter chain fatty acids producing more crystalline structure. FTIR and Raman spectroscopy presented the similar results with XRD. The formation of amylose-fatty acid complex inhibited granule swelling, gelatinization progression, retrogradation and pasting development of normal wheat starch, with longer chain fatty acids showing greater inhibition. Amylopectin can also form complexes with fatty acids, but the amount of complex was too little to be detected by XRD, FTIR, Raman and DSC. As a consequence, small changes were observed in the functional properties of waxy wheat starch with the addition of fatty acids. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Quantitative structure-activity relationship study of antioxidative peptide by using different sets of amino acids descriptors

    Science.gov (United States)

    Li, Yao-Wang; Li, Bo; He, Jiguo; Qian, Ping

    2011-07-01

    A database consisting of 214 tripeptides which contain either His or Tyr residue was applied to study quantitative structure-activity relationships (QSAR) of antioxidative tripeptides. Partial Least-Squares Regression analysis (PLSR) was conducted using parameters individually of each amino acid descriptor, including Divided Physico-chemical Property Scores (DPPS), Hydrophobic, Electronic, Steric, and Hydrogen (HESH), Vectors of Hydrophobic, Steric, and Electronic properties (VHSE), Molecular Surface-Weighted Holistic Invariant Molecular (MS-WHIM), isotropic surface area-electronic charge index (ISA-ECI) and Z-scale, to describe antioxidative tripeptides as X-variables and antioxidant activities measured with ferric thiocyanate methods were as Y-variable. After elimination of outliers by Hotelling's T 2 method and residual analysis, six significant models were obtained describing the entire data set. According to cumulative squared multiple correlation coefficients ( R2), cumulative cross-validation coefficients ( Q2) and relative standard deviation for calibration set (RSD c), the qualities of models using DPPS, HESH, ISA-ECI, and VHSE descriptors are better ( R2 > 0.6, Q2 > 0.5, RSD c 0.44). Furthermore, the predictive ability of models using DPPS descriptor is best among the six descriptors systems (cumulative multiple correlation coefficient for predict set ( Rext2) > 0.7). It was concluded that the DPPS is better to describe the amino acid of antioxidative tripeptides. The results of DPPS descriptor reveal that the importance of the center amino acid and the N-terminal amino acid are far more than the importance of the C-terminal amino acid for antioxidative tripeptides. The hydrophobic (positively to activity) and electronic (negatively to activity) properties of the N-terminal amino acid are suggested to play the most important significance to activity, followed by the hydrogen bond (positively to activity) of the center amino acid. The N-terminal amino acid

  8. Absorbability, Mechanism and Structure-Property Relationship of Three Phenolic Acids from the Flowers of Trollius chinensis

    Directory of Open Access Journals (Sweden)

    Xiu-Wen Wu

    2014-11-01

    Full Text Available The absorption properties, mechanism of action, and structure-property relationship of three phenolic acids isolated from the flowers of Trollius chinensis Bunge, namely, proglobeflowery acid (PA, globeflowery acid (GA and trolloside (TS, were investigated using the human Caco-2 cell monolayer model. The results showed that these three phenolic acids were transported across the Caco-2 cell monolayer in a time and concentration dependent manner at the Papp level of 10−5 cm/s, and their extent of absorption correlated with their polarity and molecular weight. In conclusion, all three of these compounds were easily absorbed through passive diffusion, which implied their high bioavailability and significant contribution to the effectiveness of T. chinensis.

  9. Choline-amino acid ionic liquids: past and recent achievements about the structure and properties of these really "green" chemicals.

    Science.gov (United States)

    Gontrani, Lorenzo

    2018-06-01

    The structure of choline-amino acid ionic liquids, atoxic task-specific solvents composed of materials originated from renewable feedstocks, is reviewed in this letter. The varied and strong interactions that these liquids are capable of establishing are largely dependent on their structure and confer them outstanding solvating properties with respect to a large number of different solutes. Among the experimental methods capable of yielding structural insight, the energy-dispersive version of X-Ray diffraction, that uses the Bremsstrahlung radiation of the X-Ray tube, is a technique very well suited to investigate these liquid systems. The diffraction spectra of five choline-amino acid ionic liquids, recently measured, are reported and discussed; in particular, the presence or absence of the medium-range order pre-peak is related to the presence of polar groups within the amino acid side chain that destroys the hydrophobic interactions between aliphatic chains. In the final section, a recent example of choline-amino acid ionic liquids as for ancient paper preservation and two other interesting results are discussed at the end.

  10. Development of a C3-symmetric benzohydroxamate tripod: Trimetallic complexation with Fe(III), Cr(III) and Al(III)

    Science.gov (United States)

    Baral, Minati; Gupta, Amit; Kanungo, B. K.

    2016-06-01

    The design, synthesis and physicochemical characterization of a C3-symmetry Benzene-1,3,5-tricarbonylhydroxamate tripod, noted here as BTHA, are described. The chelator was built from a benzene as an anchor, symmetrically extended by three hydroxamate as ligating moieties, each bearing O, O donor sites. A combination of absorption spectrophotometry, potentiometry and theoretical investigations are used to explore the complexation behavior of the ligand with some trivalent metal ions: Fe(III), Cr(III), and Al(III). Three protonation constants were calculated for the ligand in a pH range of 2-11 in a highly aqueous medium (9:1 H2O: DMSO). A high rigidity in the molecular structure restricts the formation of 1:1 (M/L) metal encapsulation but shows a high binding efficiency for a 3:1 metal ligand stoichiometry giving formation constant (in β unit) 28.73, 26.13 and 19.69 for [M3L]; Mdbnd Fe(III), Al(III) and Cr(III) respectively, and may be considered as an efficient Fe-carrier. The spectrophotometric study reveals of interesting electronic transitions occurred during the complexation. BTHA exhibits a peak at 238 nm in acidic pH and with the increase of pH, a new peak appeared at 270 nm. A substantial shifting in both of the peaks in presence of the metal ions implicates a s coordination between ligand and metal ions. Moreover, complexation of BTHA with iron shows three distinct colors, violet, reddish orange and yellow in different pH, enables the ligand to be considered for the use as colorimetric sensor.

  11. Oriented gold ripple-like structures on poly-L-lactic acid

    Energy Technology Data Exchange (ETDEWEB)

    Juřík, Petr, E-mail: petr.jurik@gmail.com [Department of Solid State Engineering, Institute of Chemical Technology, Prague (Czech Republic); Slepička, Petr [Department of Solid State Engineering, Institute of Chemical Technology, Prague (Czech Republic); Mistrík, Jan; Janíček, Petr [Department of Applied Physics and Mathematics, University of Pardubice (Czech Republic); Rimpelová, Silvie [Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague (Czech Republic); Kolská, Zdeňka [Faculty of Science, University of J. E. Purkyně, Ústí nad Labem (Czech Republic); Švorčík, Václav [Department of Solid State Engineering, Institute of Chemical Technology, Prague (Czech Republic)

    2014-12-01

    Highlights: • We prepared oriented ripple-like structures on polymer surface with thin gold layer. • These structures show preferential orientation over large areas which is unusual for heat induced wrinkling. • Significant electrical and optical anisotropy was observed. • Zeta-potential, XPS, goniometry and ellipsometry suggest formation of gold lines separated by polymer gaps. • Increase in cell growth in comparison with poly-styrene mock was observed. - Abstract: In this paper chemical, morphological, electrical and biological properties of poly-L-lactic acid thin films with gold nanolayers were studied. These samples were examined as-sputtered and annealed at glass transition temperature. Morphological changes of poly-L-lactic films introduced by annealing were studied by means of atomic force microscopy. This method showed formation of oriented ripple-like structures on the surface of the film. X-ray photoelectron spectroscopy, goniometry, ellipsometry, sheet resistance measurement and electrokinetic analysis were used to determine distribution of gold on the surface. Combined data suggests that these ripple-like structures were formed by gold lines with insulating polymer gaps in between. These lines show preferential orientation over large areas and under proper conditions offer simple way to form electrically anisotropic material on large scale. Also cytocompatibility was studied showing increased cell adhesion and proliferation of mouse embryonic fibroblasts offering another use for these easily formed structures.

  12. Oriented gold ripple-like structures on poly-L-lactic acid

    International Nuclear Information System (INIS)

    Juřík, Petr; Slepička, Petr; Mistrík, Jan; Janíček, Petr; Rimpelová, Silvie; Kolská, Zdeňka; Švorčík, Václav

    2014-01-01

    Highlights: • We prepared oriented ripple-like structures on polymer surface with thin gold layer. • These structures show preferential orientation over large areas which is unusual for heat induced wrinkling. • Significant electrical and optical anisotropy was observed. • Zeta-potential, XPS, goniometry and ellipsometry suggest formation of gold lines separated by polymer gaps. • Increase in cell growth in comparison with poly-styrene mock was observed. - Abstract: In this paper chemical, morphological, electrical and biological properties of poly-L-lactic acid thin films with gold nanolayers were studied. These samples were examined as-sputtered and annealed at glass transition temperature. Morphological changes of poly-L-lactic films introduced by annealing were studied by means of atomic force microscopy. This method showed formation of oriented ripple-like structures on the surface of the film. X-ray photoelectron spectroscopy, goniometry, ellipsometry, sheet resistance measurement and electrokinetic analysis were used to determine distribution of gold on the surface. Combined data suggests that these ripple-like structures were formed by gold lines with insulating polymer gaps in between. These lines show preferential orientation over large areas and under proper conditions offer simple way to form electrically anisotropic material on large scale. Also cytocompatibility was studied showing increased cell adhesion and proliferation of mouse embryonic fibroblasts offering another use for these easily formed structures

  13. Crystal structures of carbamate kinase from Giardia lamblia bound with citric acid and AMP-PNP.

    Directory of Open Access Journals (Sweden)

    Kap Lim

    Full Text Available The parasite Giardia lamblia utilizes the L-arginine dihydrolase pathway to generate ATP from L-arginine. Carbamate kinase (CK catalyzes the last step in this pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate. Because the L-arginine pathway is essential for G. lamblia survival and absent in high eukaryotes including humans, the enzyme is a potential target for drug development. We have determined two crystal structures of G. lamblia CK (glCK with bound ligands. One structure, in complex with a nonhydrolyzable ATP analog, adenosine 5'-adenylyl-β,γ-imidodiphosphate (AMP-PNP, was determined at 2.6 Å resolution. The second structure, in complex with citric acid bound in the postulated carbamoyl phosphate binding site, was determined in two slightly different states at 2.1 and 2.4 Å resolution. These structures reveal conformational flexibility of an auxiliary domain (amino acid residues 123-170, which exhibits open or closed conformations or structural disorder, depending on the bound ligand. The structures also reveal a smaller conformational change in a region associated the AMP-PNP adenine binding site. The protein residues involved in binding, together with a model of the transition state, suggest that catalysis follows an in-line, predominantly dissociative, phosphotransfer reaction mechanism, and that closure of the flexible auxiliary domain is required to protect the transition state from bulk solvent.

  14. [Studies on interaction of acid-treated nanotube titanic acid and amino acids].

    Science.gov (United States)

    Zhang, Huqin; Chen, Xuemei; Jin, Zhensheng; Liao, Guangxi; Wu, Xiaoming; Du, Jianqiang; Cao, Xiang

    2010-06-01

    Nanotube titanic acid (NTA) has distinct optical and electrical character, and has photocatalysis character. In accordance with these qualities, NTA was treated with acid so as to enhance its surface activity. Surface structures and surface groups of acid-treated NTA were characterized and analyzed by Transmission Electron Microscope (TEM) and Fourier Transform Infrared Spectrometry (FT-IR). The interaction between acid-treated NTA and amino acids was investigated. Analysis results showed that the lengths of acid-treated NTA became obviously shorter. The diameters of nanotube bundles did not change obviously with acid-treating. Meanwhile, the surface of acid-treated NTA was cross-linked with carboxyl or esterfunction. In addition, acid-treated NTA can catch amino acid residues easily, and then form close combination.

  15. Spectroscopic and structural studies on some divalent metal salt of p-aminobenzoic acid (ABA(MG)) tetracyanonickelate complexes

    International Nuclear Information System (INIS)

    Atalay, Y.

    2004-01-01

    Infrared spectra of MLNi (CN) 4 [ M=Mn, Fe, Co, Ni, Zn or Cd and LDivalent metal salt of p- Aminobenzoic Acid or ABA (Mg) ] are reported. Their structure consists of polymeric layers of [M-Ni(CN) 4 ] α with the divalent metal salt of p-aminobenzoic acid [ABA(Mg)] molecules bound directly to the metal (M). These spectra were comparewith powder the Xray diffraction pattern of complexes. It is show that proposed structures for these complexes derived from Mattson 1000 FTIR spectra are consistent with the X-ray powder diffraction measurements and elemental analysis result

  16. Dietary structured lipids for post-weaning piglets: fat digestibility, nitrogen retention and fatty acid profiles of tissues

    DEFF Research Database (Denmark)

    Straarup, Ellen Marie; Danielsen, V.; Høy, Carl-Erik

    2006-01-01

    In four groups of post-weaning piglets the effects of triacylglycerol structure and fatty acid profiles of four dietary fats on apparent faecal nutrient digestibility, nitrogen retention and fatty acid profiles of platelet and erythrocyte membranes, liver, adipose tissue and skeletal muscle were...... examined. Dietary fats included as 10% (w/w) of the diets were two structured fats of rapeseed oil interesterified with tridecanoin (R1) or coconut oil (R2), respectively, one mixture of rapeseed oil and coconut oil (R3) and rapeseed oil as control (R4). Faeces and urine from piglets weaned at 28 days...

  17. Dietary structured triacylglycerols containing docosahexaenoic acid given from birth affect visual and auditory performance and tissue fatty acid profiles of rats

    DEFF Research Database (Denmark)

    Christensen, M. M.; Lund, S. P.; Simonsen, L.

    1998-01-01

    To examine whether it is possible to enhance the level of 22:6(n-3) in the central nervous system, newborn rats were fed dietary supplements containing oils with either specific or random triacylglycerol structure, but similar concentrations of polyunsaturated fatty acids. In the specific structu...... in differences in learning ability, but caused changes in visual function, evidenced by higher latency of the b-wave and lower oscillatory potential, and in auditory brainstem response, evidenced by generally greater amplitude of wave la in the group fed specific structured oil....

  18. Establishment of novel meniscal scaffold structures using polyglycolic and poly-l-lactic acids.

    Science.gov (United States)

    Murakami, Tomohiko; Otsuki, Shuhei; Nakagawa, Kosuke; Okamoto, Yoshinori; Inoue, Tae; Sakamoto, Yuki; Sato, Hideki; Neo, Masashi

    2017-08-01

    The purpose of this study was to evaluate various types of meniscus scaffolds that mimic the meniscus structure, and to establish a novel cell-free meniscus scaffold with polyglycolic acid or poly-l-lactic acid. Four types of scaffolds were implanted into Japanese white rabbits: poly-l-lactic acid sponge poly-l-lactic acid, PGA-coated PLLA sponge, PGA lamination, and film-coated PGA lamination. Samples were harvested at 8 and 12 weeks after implantation, and a compression stress test was performed. The meniscus size and Ishida scores were evaluated for regenerated tissue. Immunohistochemistry was analyzed by anti-type I, II and X collagen antibodies to investigate the structure of the regenerated tissue, and by anti-iNOS antibody to investigate the inflammatory tissue of the meniscus. The cell nuclei of lymphocytes and foreign body multinucleated giant cells were counted in hematoxylin and eosin staining. Modified Mankin scores for cartilage degeneration were used for assessment after Safranin-O/Fast Green staining. The biomechanical test showed that l- and film-coated PGA lamination exhibited greater strength than s- and PGA-coated PLLA sponge. At 12 weeks, the size of meniscus and the Ishida score in implanted film-coated PGA lamination were improved significantly compared with the defect groups. The type II collagen staining intensity in the PGA lamination lamination is significantly higher than the defect at eight weeks. The staining intensity of iNOS and number of lymphocytes significantly increased in sponge poly-l-lactic acid at eight weeks, and increased in p-PLLA at 12 weeks. Foreign body multinucleated giant cells in implantation groups appeared, especially at eight weeks. The Mankin score for film-coated PGA lamination was significantly lower than for the defect at 12 weeks. Novel meniscal scaffolds especially PGA should possess not only biological but also biomechanical functions. In conclusions, film-coated PGA lamination was the beneficial property

  19. A Conductive Porous Structured Chitosan-grafted Polyaniline Cryogel for use as a Sialic Acid Biosensor

    International Nuclear Information System (INIS)

    Fatoni, Amin; Numnuam, Apon; Kanatharana, Proespichaya; Limbut, Warakorn; Thavarungkul, Panote

    2014-01-01

    Highlights: • A novel chitosan grafted polyaniline cryogel was used as support for a highly stable and sensitive biosensor. • The use of two enzymes mediated with ferrocene showed a high selectivity for sialic acid. • The biosensor provided a rapid sialic acid detection in blood. - Abstract: A porous conductive supporting material base on chitosan grafted polyaniline (CPANI) cryogel was developed for the fabrication of a sialic acid biosensor. Two enzymes, N-acetylneuraminic acid aldolase (NAL) and pyruvate oxidase (PYO), were employed together with an electrochemical detector. The electron transfer was further enhanced by using multiwalled carbon nanotubes (MWCNTs) and mediated by ferrocene (Fc) entrapped in the cryogel pores wall. A sialic acid derived electroactive product was detected amperometrically in a flow injection system. The fabricated sialic acid biosensor provided excellent analytical performances with a wide linear range of 0.025 to 15.0 mM and a limit of detection of 18 μM. Under the low applied potential of 0.20 V versus a Ag/AgCl, common electroactive interfering compounds such as ascorbic acid, uric acid and pyruvic acid were not detected and they have no effect on the analysis of sialic acid. The fabricated sialic acid biosensor also demonstrated a high stability after up to 100 injections. The reliability of the biosensor to detect sialic acid in blood plasma was in good agreement (P > 0.05) with a standard periodic-resorcinol spectrophotometric method. This easy to prepare conductive and biocompatible porous structure should be a prospective supporting material for biosensor development

  20. Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals

    DEFF Research Database (Denmark)

    Campbell, Meghan A; Wengel, Jesper

    2011-01-01

    Oligonucleotide chemistry has been developed greatly over the past three decades, with many advances in increasing nuclease resistance, enhancing duplex stability and assisting with cellular uptake. Locked nucleic acid (LNA) is a structurally rigid modification that increases the binding affinity...... of a modified-oligonucleotide. In contrast, unlocked nucleic acid (UNA) is a highly flexible modification, which can be used to modulate duplex characteristics. In this tutorial review, we will compare the synthetic routes to both of these modifications, contrast the structural features, examine...... the hybridization properties of LNA and UNA modified duplexes, and discuss how they have been applied within biotechnology and drug research. LNA has found widespread use in antisense oligonucleotide technology, where it can stabilize interactions with target RNA and protect from cellular nucleases. The newly...

  1. Impact of amylosucrase modification on the structural and physicochemical properties of native and acid-thinned waxy corn starch.

    Science.gov (United States)

    Zhang, Hao; Zhou, Xing; He, Jian; Wang, Tao; Luo, Xiaohu; Wang, Li; Wang, Ren; Chen, Zhengxing

    2017-04-01

    Recombinant amylosucrase from Neisseria polysaccharea was utilized to modify native and acid-thinned starches. The molecular structures and physicochemical properties of modified starches were investigated. Acid-thinned starch displayed much lower viscosity after gelatinization than did the native starch. However, the enzyme exhibited similar catalytic efficiency for both forms of starch. The modified starches had higher proportions of long (DP>33) and intermediate chains (DP 13-33), and X-ray diffraction showed a B-type crystalline structure for all modified starches. With increasing reaction time, the relative crystallinity and endothermic enthalpy of the modified starches gradually decreased, whereas the melting peak temperatures and resistant starch contents increased. Slight differences were observed in thermal parameters, relative crystallinity, and branch chain length distribution between the modified native and acid-thinned starches. Moreover, the digestibility of the modified starches was not affected by acid hydrolysis pretreatment, but was affected by the percentage of intermediate and long chains. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Structural evidence for solvent-stabilisation by aspartic acid as a mechanism for halophilic protein stability in high salt concentrations.

    Science.gov (United States)

    Lenton, Samuel; Walsh, Danielle L; Rhys, Natasha H; Soper, Alan K; Dougan, Lorna

    2016-07-21

    Halophilic organisms have adapted to survive in high salt environments, where mesophilic organisms would perish. One of the biggest challenges faced by halophilic proteins is the ability to maintain both the structure and function at molar concentrations of salt. A distinct adaptation of halophilic proteins, compared to mesophilic homologues, is the abundance of aspartic acid on the protein surface. Mutagenesis and crystallographic studies of halophilic proteins suggest an important role for solvent interactions with the surface aspartic acid residues. This interaction, between the regions of the acidic protein surface and the solvent, is thought to maintain a hydration layer around the protein at molar salt concentrations thereby allowing halophilic proteins to retain their functional state. Here we present neutron diffraction data of the monomeric zwitterionic form of aspartic acid solutions at physiological pH in 0.25 M and 2.5 M concentration of potassium chloride, to mimic mesophilic and halophilic-like environmental conditions. We have used isotopic substitution in combination with empirical potential structure refinement to extract atomic-scale information from the data. Our study provides structural insights that support the hypothesis that carboxyl groups on acidic residues bind water more tightly under high salt conditions, in support of the residue-ion interaction model of halophilic protein stabilisation. Furthermore our data show that in the presence of high salt the self-association between the zwitterionic form of aspartic acid molecules is reduced, suggesting a possible mechanism through which protein aggregation is prevented.

  3. Varic acid analogues from fungus as PTP1B inhibitors: Biological evaluation and structure-activity relationships.

    Science.gov (United States)

    Sun, Wenlong; Zhuang, Chunlin; Li, Xia; Zhang, Bowei; Lu, Xinhua; Zheng, Zhihui; Dong, Yuesheng

    2017-08-01

    Protein tyrosine phosphatase 1B (PTP1B) inhibitors as potential therapies for diabetes and obesity have attracted much attention in recent years. Six varic acid analogues were isolated from two strains of fungi and evaluated for PTP1B inhibition activities. The structure-activity relationships were also characterized and predicted by molecular modeling. Further kinetic studies indicated the reversible and competitive inhibition manner of varic acid analogues. Trivaric acid showed insulin-sensitizing effect not only in vitro but also in vivo, representing a promising lead compound for further optimization. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Synthesis and crystal structure of acid indium phosphite In(H3PO3)3

    International Nuclear Information System (INIS)

    Zakharova, B.S.; Chudinova, N.N.; Ilyhkhin, A.B.

    1996-01-01

    A group of isostructural acid phosphites of trivalent metals M(H 2 PO 3 ) 3 , where M 3 =V, Fe, Ga, In, was synthesized. Crystal structure of In(H 2 PO 3 ) 3 was determined. The compound crystallizes in hexagonal syngony, a = 8.414(2), c = 7.069(2) A, V = 433.3(2) A 3 , Z = 2, sp.gr. P6 3 . In (H 2 PO 3 ) 3 structure is of frame type. 9 refs.; 3 tabs

  5. Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus.

    Science.gov (United States)

    Pereira, Jose H; Goh, Ee-Been; Keasling, Jay D; Beller, Harry R; Adams, Paul D

    2012-10-01

    Micrococcus luteus is a Gram-positive bacterium that produces iso- and anteiso-branched alkenes by the head-to-head condensation of fatty-acid thioesters [coenzyme A (CoA) or acyl carrier protein (ACP)]; this activity is of interest for the production of advanced biofuels. In an effort to better understand the control of the formation of branched fatty acids in M. luteus, the structure of FabH (MlFabH) was determined. FabH, or β-ketoacyl-ACP synthase III, catalyzes the initial step of fatty-acid biosynthesis: the condensation of malonyl-ACP with an acyl-CoA. Analysis of the MlFabH structure provides insights into its substrate selectivity with regard to length and branching of the acyl-CoA. The most structurally divergent region of FabH is the L9 loop region located at the dimer interface, which is involved in the formation of the acyl-binding channel and thus limits the substrate-channel size. The residue Phe336, which is positioned near the catalytic triad, appears to play a major role in branched-substrate selectivity. In addition to structural studies of MlFabH, transcriptional studies of M. luteus were also performed, focusing on the increase in the ratio of anteiso:iso-branched alkenes that was observed during the transition from early to late stationary phase. Gene-expression microarray analysis identified two genes involved in leucine and isoleucine metabolism that may explain this transition.

  6. Thermodynamic Characterization of Humic Acid-surfactant Interaction: New Insights into the Characteristics and Structure of Humic Acids

    Directory of Open Access Journals (Sweden)

    Leonardus Vergütz

    2015-12-01

    Full Text Available ABSTRACT Humic acids (HA are a component of humic substances (HS, which are found in nearly all soils, sediments, and waters. They play a key role in many, if not most, chemical and physical properties in their environment. Despite the importance of HA, their high complexity makes them a poorly understood system. Therefore, understanding the physicochemical properties and interactions of HA is crucial for determining their fundamental role and obtaining structural details. Cationic surfactants are known to interact electrostatically and hydrophobically with HA. Because they are a very well-known and characterized system, they offer a good choice as molecular probes for studying HA. The objective of this study was to evaluate the interaction between cationic surfactants and HA through isothermal titration calorimetry in a thermodynamic manner, aiming to obtain information about the basic structure of HA, the nature of this interaction, and if HA from different origins show different basic structures. Contrary to what the supramolecular model asserts, HA structure is not loosely held, though it may separate depending on the conditions the HA are subjected to in their milieu. It did not show any division or conformational change when interacting with surfactants. The basic structure of the HA remains virtually the same regardless of the different sources and compositions of these HA.

  7. Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase .

    Science.gov (United States)

    Dey, Sanghamitra; Lane, James M; Lee, Richard E; Rubin, Eric J; Sacchettini, James C

    2010-08-10

    Mycobacterium tuberculosis (Mtb) depends on biotin synthesis for survival during infection. In the absence of biotin, disruption of the biotin biosynthesis pathway results in cell death rather than growth arrest, an unusual phenotype for an Mtb auxotroph. Humans lack the enzymes for biotin production, making the proteins of this essential Mtb pathway promising drug targets. To this end, we have determined the crystal structures of the second and third enzymes of the Mtb biotin biosynthetic pathway, 7,8-diaminopelargonic acid synthase (DAPAS) and dethiobiotin synthetase (DTBS), at respective resolutions of 2.2 and 1.85 A. Superimposition of the DAPAS structures bound either to the SAM analogue sinefungin or to 7-keto-8-aminopelargonic acid (KAPA) allowed us to map the putative binding site for the substrates and to propose a mechanism by which the enzyme accommodates their disparate structures. Comparison of the DTBS structures bound to the substrate 7,8-diaminopelargonic acid (DAPA) or to ADP and the product dethiobiotin (DTB) permitted derivation of an enzyme mechanism. There are significant differences between the Mtb enzymes and those of other organisms; the Bacillus subtilis DAPAS, presented here at a high resolution of 2.2 A, has active site variations and the Escherichia coli and Helicobacter pylori DTBS have alterations in their overall folds. We have begun to exploit the unique characteristics of the Mtb structures to design specific inhibitors against the biotin biosynthesis pathway in Mtb.

  8. Oxidizability of unsaturated fatty acids and of a non-phenolic lignin structure in the manganese peroxidase-dependent lipid peroxidation system

    Science.gov (United States)

    Alexander N. Kapich; Tatyana V. Korneichik; Annele Hatakka; Kenneth E. Hammel

    2010-01-01

    Unsaturated fatty acids have been proposed to mediate the oxidation of recalcitrant, non-phenolic lignin structures by fungal manganese peroxidases (MnP), but their precise role remains unknown. We investigated the oxidizability of three fatty acids with varying degrees of polyunsaturation (linoleic, linolenic, and arachidonic acids) by measuring conjugated dienes...

  9. Enamel proteins mitigate mechanical and structural degradations in mature human enamel during acid attack

    Science.gov (United States)

    Lubarsky, Gennady V.; Lemoine, Patrick; Meenan, Brian J.; Deb, Sanjukta; Mutreja, Isha; Carolan, Patrick; Petkov, Nikolay

    2014-04-01

    A hydrazine deproteination process was used to investigate the role of enamel proteins in the acid erosion of mature human dental enamel. Bright field high resolution transmission electron micrographs and x-ray diffraction analysis show no crystallographic changes after the hydrazine treatment with similar nanoscale hydroxyapatite crystallite size and orientation for sound and de-proteinated enamel. However, the presence of enamel proteins reduces the erosion depth, the loss of hardness and the loss of structural order in enamel, following exposure to citric acid. Nanoindentation creep is larger for sound enamel than for deproteinated enamel but it reduces in sound enamel after acid attack. These novel results are consistent with calcium ion-mediated visco-elasticty in enamel matrix proteins as described previously for nacre, bone and dental proteins. They are also in good agreement with a previous double layer force spectroscopy study by the authors which found that the proteins electrochemically buffer enamel against acid attack. Finally, this suggests that acid attack, and more specifically dental erosion, is influenced by ionic permeation through the enamel layer and that it is mitigated by the enamel protein matrix.

  10. Investigation into structure and dehydration dynamic of gallic acid monohydrate: A Raman spectroscopic study.

    Science.gov (United States)

    Cai, Qiang; Xue, Jiadan; Wang, Qiqi; Du, Yong

    2018-05-02

    The dehydration process of gallic acid monohydrate was carried out by heating method and characterized using Raman spectroscopic technique. Density functional theory calculation with B3LYP function is applied to simulate optimized structures and vibrational frequencies of anhydrous gallic acid and its corresponding monohydrated form. Different vibrational modes are assigned by comparison between experimental and theoretical Raman spectra of above two polymorphs. Raman spectra show that vibrational modes of the monohydrate are distinctively different from those of anhydrous one. Meanwhile, the dynamic information about dehydration process of gallic acid monohydrate could also be observed and monitored directly with the help of Raman spectral analysis. The decay rate of the characteristic band from gallic acid monohydrate and the growth rate of anhydrous one are pretty consistent with each other. It indicates that there is no intermediate present during the dehydration process of gallic acid monohydrate. The results could offer us benchmark works for identifying both anhydrous and hydrated pharmaceutical compounds, characterizing their corresponding molecular conformation within various crystalline forms, and also providing useful information about the process of dehydration dynamic at the microscopic molecular level. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Enamel proteins mitigate mechanical and structural degradations in mature human enamel during acid attack

    International Nuclear Information System (INIS)

    Lubarsky, Gennady V; Lemoine, Patrick; Meenan, Brian J; Deb, Sanjukta; Mutreja, Isha; Carolan, Patrick; Petkov, Nikolay

    2014-01-01

    A hydrazine deproteination process was used to investigate the role of enamel proteins in the acid erosion of mature human dental enamel. Bright field high resolution transmission electron micrographs and x-ray diffraction analysis show no crystallographic changes after the hydrazine treatment with similar nanoscale hydroxyapatite crystallite size and orientation for sound and de-proteinated enamel. However, the presence of enamel proteins reduces the erosion depth, the loss of hardness and the loss of structural order in enamel, following exposure to citric acid. Nanoindentation creep is larger for sound enamel than for deproteinated enamel but it reduces in sound enamel after acid attack. These novel results are consistent with calcium ion-mediated visco-elasticty in enamel matrix proteins as described previously for nacre, bone and dental proteins. They are also in good agreement with a previous double layer force spectroscopy study by the authors which found that the proteins electrochemically buffer enamel against acid attack. Finally, this suggests that acid attack, and more specifically dental erosion, is influenced by ionic permeation through the enamel layer and that it is mitigated by the enamel protein matrix. (papers)

  12. Cyanuric acid hydrolase from Azorhizobium caulinodans ORS 571: crystal structure and insights into a new class of Ser-Lys dyad proteins.

    Directory of Open Access Journals (Sweden)

    Seunghee Cho

    Full Text Available Cyanuric acid hydrolase (CAH catalyzes the hydrolytic ring-opening of cyanuric acid (2,4,6-trihydroxy-1,3,5-triazine, an intermediate in s-triazine bacterial degradation and a by-product from disinfection with trichloroisocyanuric acid. In the present study, an X-ray crystal structure of the CAH-barbituric acid inhibitor complex from Azorhizobium caulinodans ORS 571 has been determined at 2.7 Å resolution. The CAH protein fold consists of three structurally homologous domains forming a β-barrel-like structure with external α-helices that result in a three-fold symmetry, a dominant feature of the structure and active site that mirrors the three-fold symmetrical shape of the substrate cyanuric acid. The active site structure of CAH is similar to that of the recently determined AtzD with three pairs of active site Ser-Lys dyads. In order to determine the role of each Ser-Lys dyad in catalysis, a mutational study using a highly sensitive, enzyme-coupled assay was conducted. The 10⁹-fold loss of activity by the S226A mutant was at least ten times lower than that of the S79A and S333A mutants. In addition, bioinformatics analysis revealed the Ser226/Lys156 dyad as the only absolutely conserved dyad in the CAH/barbiturase family. These data suggest that Lys156 activates the Ser226 nucleophile which can then attack the substrate carbonyl. Our combination of structural, mutational, and bioinformatics analyses differentiates this study and provides experimental data for mechanistic insights into this unique protein family.

  13. Structure, Morphology and Optical Properties of TiO2 Films Formed by Anodizing in a Mixed Solution of Citric Acid and Sulfamic Acid

    Science.gov (United States)

    Choudhary, R. K.; Sarkar, P.; Biswas, A.; Mishra, P.; Abraham, G. J.; Sastry, P. U.; Kain, V.

    2017-08-01

    TiO2 films of 50-180 nm thickness were formed at room temperature by anodization of titanium metal in a mixture of citric acid and sulfamic acid in the potential range of 5-30 V. The films so obtained were characterized for their crystal structure, surface morphology, chemical composition and optical properties. Grazing incidence x-ray diffraction and micro-laser Raman spectroscopy measurements of the anodic films confirmed the formation of brookite phase of TiO2 at anodizing potentials of 15, 20, 25 and 30 V and amorphous structure at 5 and 10 V. Field emission scanning electron microscopy revealed non-porous microstructure of the films. Spectroscopic ellipsometry measurements evaluated the band gap of TiO2 at around 3.3 eV, whereas the refractive index of the films was found to be in the range of 2-2.35, in the visible range of spectrum.

  14. A structural insight into the P1S1 binding mode of diaminoethylphosphonic and phosphinic acids, selective inhibitors of alanine aminopeptidases

    Energy Technology Data Exchange (ETDEWEB)

    Węglarz-Tomczak, Ewelina; Berlicki, Łukasz; Pawełczak, Małgorzata; Nocek, Bogusław; Joachimiak, Andrzej; Mucha, Artur

    2016-07-01

    N0 -substituted 1,2-diaminoethylphosphonic acids and 1,2-diaminoethylphosphinic dipeptides were explored to unveil the structural context of the unexpected selectivity of these inhibitors of M1 alanine aminopeptidases (APNs) versus M17 leucine aminopeptidase (LAP). The diaminophosphonic acids were obtained via aziridines in an improved synthetic procedure that was further expanded for the phosphinic pseudodipeptide system. The inhibitory activity, measured for three M1 and one M17 metalloaminopeptidases of different sources (bacterial, human and porcine), revealed several potent compounds (e.g., Ki ¼ 65 nM of 1u for HsAPN). Two structures of an M1 representative (APN from Neisseria meningitidis) in complex with N-benzyl-1,2-diaminoethylphosphonic acid and N-cyclohexyl-1,2- diaminoethylphosphonic acid were determined by the X-ray crystallography. The analysis of these structures and the models of the phosphonic acid complexes of the human ortholog provided an insight into the role of the additional amino group and the hydrophobic substituents of the ligands within the S1 active site region.

  15. Effect of poly and mono-unsaturated fatty acids on stability and structure of recombinant S100A8/A9.

    Science.gov (United States)

    Asghari, Hamideh; Chegini, Koorosh Goodarzvand; Amini, Abbas; Gheibi, Nematollah

    2016-03-01

    Recombinant pET 15b vectors containing the coding sequences S100A8 and S100A9 are expressed in Escherichia coli BL21 (DE3) and purified using Ni-NTA affinity chromatography. The structural changes of S100A8/A9 complex are analyzed upon interaction with poly/mono-unsaturated fatty acids (UFAs). The thermodynamic values, Gibbs free energy and the protein melting point, are obtained through thermal denaturation of protein both with and without UFAs by thermal scanning of protein emission using the fluorescence spectroscopy technique. The far-ultraviolet circular dichroism spectra show that all studied unsaturated fatty acids, including arachidonic, linoleic, alpha-linolenic and oleic acids, induce changes in the secondary structure of S100A8/A9 by reducing the α-helix and β-sheet structures. The tertiary structure of S100A8/A9 has fluctuations in the fluorescence emission spectra after the incubation of protein with UFAs. The blue-shift of emission maximum wavelength and the increase in fluorescence intensity of anilino naphthalene-8-sulfonic acid confirm that the partial unfolding is caused by the conformational changes in the tertiary structure in the presence of UFAs. The structural changes in S100A8/A9 and its lower stability in the presence of UFAs may be necessary for S100A8/A9 to play a biological role in the inflammatory milieu. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Investigation of rare earth complexes with pyridoxalydenamino acids by optical methods. Structure of complexes on basis of hydrophobic amino acids

    International Nuclear Information System (INIS)

    Zolin, V.F.; Koreneva, L.G.; Serbinova, T.A.; Tsaryuk, V.I.

    1975-01-01

    The structure of pyridoxalidene amino acid complexes was studied by circular dichroism, magnetic circular dichroism and luminescence spectroscopy. It was shown that these are two-ligand complexes, whereby in the case of those based on valine, leucine and isoleucine the chromophores are almost perpendicular to one another. In the case of complexes based on glycine and alanine the co-ordination sphere is strongly deformed. (author)

  17. Structure of the Mitochondrial Aminolevulinic Acid Synthase, a Key Heme Biosynthetic Enzyme.

    Science.gov (United States)

    Brown, Breann L; Kardon, Julia R; Sauer, Robert T; Baker, Tania A

    2018-04-03

    5-Aminolevulinic acid synthase (ALAS) catalyzes the first step in heme biosynthesis. We present the crystal structure of a eukaryotic ALAS from Saccharomyces cerevisiae. In this homodimeric structure, one ALAS subunit contains covalently bound cofactor, pyridoxal 5'-phosphate (PLP), whereas the second is PLP free. Comparison between the subunits reveals PLP-coupled reordering of the active site and of additional regions to achieve the active conformation of the enzyme. The eukaryotic C-terminal extension, a region altered in multiple human disease alleles, wraps around the dimer and contacts active-site-proximal residues. Mutational analysis demonstrates that this C-terminal region that engages the active site is important for ALAS activity. Our discovery of structural elements that change conformation upon PLP binding and of direct contact between the C-terminal extension and the active site thus provides a structural basis for investigation of disruptions in the first step of heme biosynthesis and resulting human disorders. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. Structural and thermal properties of carboxylic acid functionalized polythiophenes

    Directory of Open Access Journals (Sweden)

    Ariane de França Mescoloto

    2014-01-01

    Full Text Available Polythiophenes functionalized with polar groups at the end of side-chain have emerged as an alternative method to obtain good compatibility between this class of conjugated polymers and electron acceptor compounds. The aim is to prevent phase segregation and to improve the efficiency of the polythiophene technological devices. However, homopolymers synthesized from thiophene rings with high polar groups at the end of the side-chain, such as hydroxyl and carboxylic acid groups, are poorly soluble in common volatile organic solvents. We report on a systematic preparation of copolymers of 3-hexylthiophene (HT and thiophene-3-acetic acid (TAA, using different feed ratios. The chemical structures of the copolymers were confirmed by FTIR and ¹H-NMR. The TAA content in these copolymers were 33, 38 and 54 mol %. HPSEC results did not show any remarkable correlation with TAA contents in the copolymers. In contrast, the thermal analyses showed a decrease in the thermal stability and an increase in rigidity of their backbones, for the copolymers with high amounts of TAA. The solubility and optical property of copolymers were also related to the TAA contents. Thus, the properties of these copolymers can be modulated by a simple control of feed ratio of TAA in the copolymerization.

  19. Rational identification of aggregation hotspots based on secondary structure and amino acid hydrophobicity.

    Science.gov (United States)

    Matsui, Daisuke; Nakano, Shogo; Dadashipour, Mohammad; Asano, Yasuhisa

    2017-08-25

    Insolubility of proteins expressed in the Escherichia coli expression system hinders the progress of both basic and applied research. Insoluble proteins contain residues that decrease their solubility (aggregation hotspots). Mutating these hotspots to optimal amino acids is expected to improve protein solubility. To date, however, the identification of these hotspots has proven difficult. In this study, using a combination of approaches involving directed evolution and primary sequence analysis, we found two rules to help inductively identify hotspots: the α-helix rule, which focuses on the hydrophobicity of amino acids in the α-helix structure, and the hydropathy contradiction rule, which focuses on the difference in hydrophobicity relative to the corresponding amino acid in the consensus protein. By properly applying these two rules, we succeeded in improving the probability that expressed proteins would be soluble. Our methods should facilitate research on various insoluble proteins that were previously difficult to study due to their low solubility.

  20. Structural and Functional Analysis of Campylobacter jejuni PseG: a Udp-sugarhydrolase from the Pseudaminic Acid Biosynthetic Pathway

    Energy Technology Data Exchange (ETDEWEB)

    E Rangarajan; A Proteau; Q Cui; S Logan; Z Potetinova; D Whitfield; E Purisima; M Cygler; A Matte; et al.

    2011-12-31

    Flagella of the bacteria Helicobacter pylori and Campylobacter jejuni are important virulence determinants, whose proper assembly and function are dependent upon glycosylation at multiple positions by sialic acid-like sugars, such as 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-nonulosonic acid (pseudaminic acid (Pse)). The fourth enzymatic step in the pseudaminic acid pathway, the hydrolysis of UDP-2,4-diacetamido-2,4,6-trideoxy-{beta}-l-altropyranose to generate 2,4-diacetamido-2,4,6-trideoxy-l-altropyranose, is performed by the nucleotide sugar hydrolase PseG. To better understand the molecular basis of the PseG catalytic reaction, we have determined the crystal structures of C. jejuni PseG in apo-form and as a complex with its UDP product at 1.8 and 1.85 {angstrom} resolution, respectively. In addition, molecular modeling was utilized to provide insight into the structure of the PseG-substrate complex. This modeling identifies a His{sup 17}-coordinated water molecule as the putative nucleophile and suggests the UDP-sugar substrate adopts a twist-boat conformation upon binding to PseG, enhancing the exposure of the anomeric bond cleaved and favoring inversion at C-1. Furthermore, based on these structures a series of amino acid substitution derivatives were constructed, altering residues within the active site, and each was kinetically characterized to examine its contribution to PseG catalysis. In conjunction with structural comparisons, the almost complete inactivation of the PseG H17F and H17L derivatives suggests that His{sup 17} functions as an active site base, thereby activating the nucleophilic water molecule for attack of the anomeric C-O bond of the UDP-sugar. As the PseG structure reveals similarity to those of glycosyltransferase family-28 members, in particular that of Escherichia coli MurG, these findings may also be of relevance for the mechanistic understanding of this important enzyme family.

  1. Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid.

    Science.gov (United States)

    Guimarães, Samuel L; Coitinho, Juliana B; Costa, Débora M A; Araújo, Simara S; Whitman, Christian P; Nagem, Ronaldo A P

    2016-05-10

    The enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. In a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria Pseudomonas putida G7. In this organism, the 83 kb NAH7 plasmid carries several genes involved in this biotransformation process. One enzyme in this route, NahK, a 4-oxalocrotonate decarboxylase (4-OD), converts 2-oxo-3-hexenedioate to 2-hydroxy-2,4-pentadienoate using Mg(2+) as a cofactor. Efforts to study how 4-OD catalyzes this decarboxylation have been hampered because 4-OD is present in a complex with vinylpyruvate hydratase (VPH), which is the next enzyme in the same pathway. For the first time, a monomeric, stable, and active 4-OD has been expressed and purified in the absence of VPH. Crystal structures for NahK in the apo form and bonded with five substrate analogues were obtained using two distinct crystallization conditions. Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for specific residues in a proposed reaction mechanism. In addition, we assign a possible function for the NahK N-terminal domain, which differs from most of the other members of the fumarylacetoacetate hydrolase superfamily. Although the structural basis for metal-dependent β-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous β-keto acid decarboxylase and the first crystal structure of a 4-OD.

  2. The stereospecific triacylglycerol structures and fatty acid profiles of human milk and infant formulas

    DEFF Research Database (Denmark)

    Straarup, Ellen Marie; Lauritzen, L.; Færk, Jan

    2006-01-01

    Background: The stereospecific structures of the triacylglycerol molecules in human milk differ from that of cow's milk and vegetable oils, which are the fat sources used in infant formula. In human milk, palmitic acid (16:0) is predominantly esterified in the sn2 position, whereas vegetable oils...

  3. Ring-Substituted Benzohydroxamic Acids: 1H, 13C and 15N NMR Spectra and NHOH Proton Exchange

    Czech Academy of Sciences Publication Activity Database

    Schraml, Jan; Tkadlecová, M.; Pataridis, S.; Soukupová, Ludmila; Blechta, Vratislav; Roithová, Jana; Exner, Otto

    2005-01-01

    Roč. 43, č. 7 (2005), s. 535-542 ISSN 0749-1581 R&D Projects: GA ČR(CZ) GA203/03/1566; GA AV ČR(CZ) IAA4072605; GA AV ČR(CZ) IAA4072005; GA MŠk(CZ) LB98233 Institutional research plan: CEZ:AV0Z40720504 Keywords : proton exchange * substituent effects * chemical shifts Subject RIV: CC - Organic Chemistry Impact factor: 1.553, year: 2005

  4. Structure-thermodynamics-antioxidant activity relationships of selected natural phenolic acids and derivatives: an experimental and theoretical evaluation.

    Science.gov (United States)

    Chen, Yuzhen; Xiao, Huizhi; Zheng, Jie; Liang, Guizhao

    2015-01-01

    Phenolic acids and derivatives have potential biological functions, however, little is known about the structure-activity relationships and the underlying action mechanisms of these phenolic acids to date. Herein we investigate the structure-thermodynamics-antioxidant relationships of 20 natural phenolic acids and derivatives using DPPH• scavenging assay, density functional theory calculations at the B3LYP/6-311++G(d,p) levels of theory, and quantitative structure-activity relationship (QSAR) modeling. Three main working mechanisms (HAT, SETPT and SPLET) are explored in four micro-environments (gas-phase, benzene, water and ethanol). Computed thermodynamics parameters (BDE, IP, PDE, PA and ETE) are compared with the experimental radical scavenging activities against DPPH•. Available theoretical and experimental investigations have demonstrated that the extended delocalization and intra-molecular hydrogen bonds are the two main contributions to the stability of the radicals. The C = O or C = C in COOH, COOR, C = CCOOH and C = CCOOR groups, and orthodiphenolic functionalities are shown to favorably stabilize the specific radical species to enhance the radical scavenging activities, while the presence of the single OH in the ortho position of the COOH group disfavors the activities. HAT is the thermodynamically preferred mechanism in the gas phase and benzene, whereas SPLET in water and ethanol. Furthermore, our QSAR models robustly represent the structure-activity relationships of these explored compounds in polar media.

  5. Ibotenic acid and thioibotenic acid

    DEFF Research Database (Denmark)

    Hermit, Mette B; Greenwood, Jeremy R; Nielsen, Birgitte

    2004-01-01

    In this study, we have determined and compared the pharmacological profiles of ibotenic acid and its isothiazole analogue thioibotenic acid at native rat ionotropic glutamate (iGlu) receptors and at recombinant rat metabotropic glutamate (mGlu) receptors expressed in mammalian cell lines....... Thioibotenic acid has a distinct pharmacological profile at group III mGlu receptors compared with the closely structurally related ibotenic acid; the former is a potent (low microm) agonist, whereas the latter is inactive. By comparing the conformational energy profiles of ibotenic and thioibotenic acid...... with the conformations preferred by the ligands upon docking to mGlu1 and models of the other mGlu subtypes, we propose that unlike other subtypes, group III mGlu receptor binding sites require a ligand conformation at an energy level which is prohibitively expensive for ibotenic acid, but not for thioibotenic acid...

  6. Encapsulating fly ash and acidic process waste water in brick structure

    International Nuclear Information System (INIS)

    Koseoglu, K.; Polat, M.; Polat, H.

    2010-01-01

    Fly ash contains metals such as cadmium, iron, lead, aluminum and zinc in its structure in appreciable amounts. These metals can leach out into surface and ground waters if fly ash is not properly disposed of. A similar problem also exists for acidic process waste waters discharged by numerous industries. The purpose of this study was to utilize such wastes as additives in the production of construction quality bricks for the purpose of waste elimination. The bricks produced were subjected to flexural strength and water retention capacity tests along with heavy metal leaching experiments in order to determine the applicability of the procedure and the best possible recipes. This paper summarizes the results obtained in these tests along with the possible mechanisms involved in stabilizing the two wastes in the brick structure.

  7. Structure and polymer form of poly-3-hydroxyalkanoates produced by Pseudomonas oleovorans grown with mixture of sodium octanoate/undecylenic acid and sodium octanoate/5-phenylvaleric acid.

    Science.gov (United States)

    Ho, I-Ching; Yang, Sheng-Pin; Chiu, Wen-Yen; Huang, Shih-Yow

    2007-01-30

    PHAs (poly-3-hydroxyalkanoates) obtained by Pseudomonas oleovorans grown with mixed carbon sources were investigated. Mixed carbon sources were sodium octanoate/undecylenic acid and sodium octanoate/5-phenylvaleric acid. Effect of carbon source in pre-culture on PHAs structure was investigated. Main fermentation was conducted with mixture of sodium octanoate/undecylenic acid, and PHA contained both saturated and unsaturated units. When more undecylenic acid was used in the medium, the ratio of unsaturated unit increased and the T(g) of the products also changed. The PHA grown with mixture of sodium octanoate and undecylenic acid was a random copolymer, which was determined by DSC analysis. Using mixed carbon sources of sodium octanoate and 5-phenylvaleric acid, highest dry cell weight and PHA concentration were obtained when 0.02g or 0.04g of 5-phenylvaleric acid were added in 50mL medium. Cultured with sodium octanoate and 5-phenylvaleric acid, PHA containing HO (3-hydroxyoctanoate) unit and HPV (3-hydroxy-5-phenylvalerate) unit was produced. T(g) of the products fell between those of pure PHO and pure PHPV. By means of DSC analysis and fractionation method, the PHA obtained was regarded as a random copolymer.

  8. Crystal structures of three anhydrous salts of the Lewis base 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU with the ring-substituted benzoic acid analogues 4-aminobenzoic acid, 3,5-dinitrobenzoic acid and 3,5-dinitrosalicylic acid

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2016-03-01

    Full Text Available The anhydrous salts of the Lewis base 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU with 4-aminobenzoic acid [1-aza-8-azoniabicyclo[5.4.0]undec-7-ene 4-aminobenzoate, C9H17N2+·C7H6NO2− (I], 3,5-dinitrobenzoic acid [1-aza-8-azoniabicyclo[5.4.0]undec-7-ene 3,5-dinitrobenzoate, C9H17N2+·C7H3N2O6−, (II] and 3,5-dinitrosalicylic acid (DNSA [1-aza-8-azoniabicyclo[5.4.0]undec-7-ene 2-hydroxy-3,5-dinitrobenzoate, C9H17N2+·C7H3N2O7−, (III] have been determined and their hydrogen-bonded structures are described. In both (II and (III, the DBU cations have a common disorder in three of the C atoms of the six-membered ring moieties [site-occupancy factors (SOF = 0.735 (3/0.265 (3 and 0.686 (4/0.314 (4, respectively], while in (III, there is additional rotational disorder in the DNSA anion, giving two sites (SOF = 0.72/0.28, values fixed for the phenol group. In the crystals of (I and (III, the cation–anion pairs are linked through a primary N—H...Ocarboxyl hydrogen bond [2.665 (2 and 2.869 (3 Å, respectively]. In (II, the ion pairs are linked through an asymmetric three-centre R12(4, N—H...O,O′ chelate association. In (I, structure extension is through amine N—H...Ocarboxyl hydrogen bonds between the PABA anions, giving a three-dimensional structure. The crystal structures of (II and (III are very similar, the cation–anion pairs being associated only through weak C—H...O hydrogen bonds, giving in both overall two-dimensional layered structures lying parallel to (001. No π–π ring associations are present in any of the structures.

  9. Composition, structure and electrical properties of alumina barrier layers grown in fluoride-containing oxalic acid solutions

    Energy Technology Data Exchange (ETDEWEB)

    Jagminas, A. [Institute of Chemistry, A. Gostauto 9, LT-01108 Vilnius (Lithuania)], E-mail: jagmin@ktl.mii.lt; Vrublevsky, I. [Department of Microelectricals, Belarusian State University of Informatics and Radioelectricals, 6 Brovka Street, Minsk 220013 (Belarus); Kuzmarskyte, J.; Jasulaitiene, V. [Institute of Chemistry, A. Gostauto 9, LT-01108 Vilnius (Lithuania)

    2008-04-15

    The composition, structure and electrical properties of alumina barrier layers grown by anodic oxidation in F{sup -}-containing (FC) and F{sup -}-free (FF) oxalic acid solutions were studied using the re-anodizing/dissolution technique, Fourier-transformed infrared and X-ray photoelectron spectroscopy. These results confirmed formation in FC anodizing solutions of films structurally different from ones grown in FF oxalic acid baths. It was found that the barrier layer of FC alumina films is composed of two layers differing in the dissolution rate. These differences are related to the formation in the FC electrolyte of a barrier layer composed of a more microporous outer part and a thin, non-porous and non-scalloped inner part consisting of aluminum oxide and aluminum fluoride.

  10. Far-red fluorescent probes for canonical and non-canonical nucleic acid structures: current progress and future implications.

    Science.gov (United States)

    Suseela, Y V; Narayanaswamy, Nagarjun; Pratihar, Sumon; Govindaraju, Thimmaiah

    2018-02-05

    The structural diversity and functional relevance of nucleic acids (NAs), mainly deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are indispensable for almost all living organisms, with minute aberrations in their structure and function becoming causative factors in numerous human diseases. The standard structures of NAs, termed canonical structures, are supported by Watson-Crick hydrogen bonding. Under special physiological conditions, NAs adopt distinct spatial organisations, giving rise to non-canonical conformations supported by hydrogen bonding other than the Watson-Crick type; such non-canonical structures have a definite function in controlling gene expression and are considered as novel diagnostic and therapeutic targets. Development of molecular probes for these canonical and non-canonical DNA/RNA structures has been an active field of research. Among the numerous probes studied, probes with turn-on fluorescence in the far-red (600-750 nm) region are highly sought-after due to minimal autofluorescence and cellular damage. Far-red fluorescent probes are vital for real-time imaging of NAs in live cells as they provide good resolution and minimal perturbation of the cell under investigation. In this review, we present recent advances in the area of far-red fluorescent probes of DNA/RNA and non-canonical G-quadruplex structures. For the sake of continuity and completeness, we provide a brief overview of visible fluorescent probes. Utmost importance is given to design criteria, characteristic properties and biological applications, including in cellulo imaging, apart from critical discussion on limitations of the far-red fluorescent probes. Finally, we offer current and future prospects in targeting canonical and non-canonical NAs specific to cellular organelles, through sequence- and conformation-specific far-red fluorescent probes. We also cover their implications in chemical and molecular biology, with particular focus on decoding various disease

  11. Structural Basis for Catalysis by the Mono and Dimetalated forms of the dapE-encoded N-succinyl-L,L-Diaminopimelic Acid Desuccinylase

    Science.gov (United States)

    Nocek, Boguslaw P.; Gillner, Danuta M.; Fan, Yao; Holz, Richard C.; Joachimiak, Andrzej

    2010-01-01

    Biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. The dapE operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent a potential targets for novel antibacterials. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts N-succinyl-L,L-diaminopimelic acid (L,L-SDAP) to L,L-diaminopimelic acid and succinate. Deletion of the dapE gene is lethal to Helicobacter pylori and Mycobacterium smegmatis indicating that DapE’s are essential for cell growth and proliferation. Since there are no similar pathways in humans, inhibitors that target DapE may have selective toxicity against only bacteria. A major limitation in developing antimicrobial agents that target DapE has been the lack of structural information. Herein we report the high-resolution X-ray crystal structures of the DapE from Haemophilus influenzae with one and two zinc ions bound in the active site, respectively. These two forms show different activity. Based on these newly determined structures we propose a revised catalytic mechanism of peptide bond cleavage by DapE enzymes. These structures provide important insight into catalytic mechanism of DapE enzymes as well as a structural foundation that is critical for the rational design of DapE inhibitors. PMID:20138056

  12. Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.

    Science.gov (United States)

    Nocek, Boguslaw P; Gillner, Danuta M; Fan, Yao; Holz, Richard C; Joachimiak, Andrzej

    2010-04-02

    Biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. The dapE operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts N-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. Deletion of the dapE gene is lethal to Helicobacter pylori and Mycobacterium smegmatis, indicating that DapE's are essential for cell growth and proliferation. Since there are no similar pathways in humans, inhibitors that target DapE may have selective toxicity against only bacteria. A major limitation in developing antimicrobial agents that target DapE has been the lack of structural information. Herein, we report the high-resolution X-ray crystal structures of the DapE from Haemophilus influenzae with one and two zinc ions bound in the active site, respectively. These two forms show different activity. Based on these newly determined structures, we propose a revised catalytic mechanism of peptide bond cleavage by DapE enzymes. These structures provide important insight into catalytic mechanism of DapE enzymes as well as a structural foundation that is critical for the rational design of DapE inhibitors. Copyright 2010 Elsevier Ltd. All rights reserved.

  13. Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Pabit, Suzette A.; Katz, Andrea M.; Pollack, Lois [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 (United States); Tolokh, Igor S. [Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061 (United States); Drozdetski, Aleksander [Department of Physics, Virginia Tech, Blacksburg, Virginia 24061 (United States); Baker, Nathan [Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Onufriev, Alexey V. [Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061 (United States); Department of Physics, Virginia Tech, Blacksburg, Virginia 24061 (United States)

    2016-05-28

    Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.

  14. Crystal structure and hydrogen bonding in N-(1-deoxy-β-d-fructopyranos-1-yl-2-aminoisobutyric acid

    Directory of Open Access Journals (Sweden)

    Valeri V. Mossine

    2018-01-01

    Full Text Available The title compound, alternatively called d-fructose-2-aminoisobutyric acid (FruAib, C10H19NO7, (I, crystallizes exclusively in the β-pyranose form, with two conformationally non-equivalent molecules [(IA and (IB] in the asymmetric unit. In solution, FruAib establishes an equilibrium, with 75.6% of the population consisting of β-pyranose, 10.4% β-furanose, 10.1% α-furanose, 3.0% α-pyranose and <0.7% the acyclic forms. The carbohydrate ring in (I has the normal 2C5 chair conformation and the amino acid portion is in the zwitterion form. Bond lengths and valence angles compare well with the average values from related pyranose structures. All carboxyl, hydroxy and ammonium groups are involved in hydrogen bonding and form a three-dimensional network of infinite chains that are connected through homodromic rings and short chains. Intramolecular hydrogen bonds bridge the amino acid and sugar portions in both molecules. A comparative Hirshfeld surfaces analysis of FruAib and four other sugar–amino acids suggests an increasing role of intramolecular heteroatom interactions in crystal structures with an increasing proportion of C—H bonds.

  15. Nephrotoxicity of mercapturic acids of three structurally related 2,2-difluoroethylenes in the rat. Indications for different bioactivation mechanisms.

    NARCIS (Netherlands)

    Commandeur, J.N.M.; Brakenhoff, J.P.G.; de Kanter, F.J.J.; Vermeulen, N.P.E.

    1988-01-01

    The biotransformation and the hepato- and nephrotoxicity of the mercapturic acids (N-acetyl-1-cysteine S-conjugates) of three structurally related 2,2-difluoroethylenes were investigated in vivo in the rat. All mercapturic acids appeared to cause nephrotoxicity, without any measureable effect on the

  16. Overexpression, purification, crystallization and preliminary structural studies of p-coumaric acid decarboxylase from Lactobacillus plantarum

    International Nuclear Information System (INIS)

    Rodríguez, Héctor; Rivas, Blanca de las; Muñoz, Rosario; Mancheño, José M.

    2007-01-01

    The enzyme p-coumaric acid decarboxylase (PDC) from L. plantarum has been recombinantly expressed, purified and crystallized. The structure has been solved at 2.04 Å resolution by the molecular-replacement method. The substrate-inducible p-coumaric acid decarboxylase (PDC) from Lactobacillus plantarum has been overexpressed in Escherichia coli, purified and confirmed to possess decarboxylase activity. The recombinant His 6 -tagged enzyme was crystallized using the hanging-drop vapour-diffusion method from a solution containing 20%(w/v) PEG 4000, 12%(w/v) 2-propanol, 0.2 M sodium acetate, 0.1 M Tris–HCl pH 8.0 with 0.1 M barium chloride as an additive. Diffraction data were collected in-house to 2.04 Å resolution. Crystals belonged to the tetragonal space group P4 3 , with unit-cell parameters a = b = 43.15, c = 231.86 Å. The estimated Matthews coefficient was 2.36 Å 3 Da −1 , corresponding to 48% solvent content, which is consistent with the presence of two protein molecules in the asymmetric unit. The structure of PDC has been determined by the molecular-replacement method. Currently, the structure of PDC complexed with substrate analogues is in progress, with the aim of elucidating the structural basis of the catalytic mechanism

  17. Overexpression, purification, crystallization and preliminary structural studies of p-coumaric acid decarboxylase from Lactobacillus plantarum

    Energy Technology Data Exchange (ETDEWEB)

    Rodríguez, Héctor; Rivas, Blanca de las; Muñoz, Rosario [Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain); Mancheño, José M., E-mail: xjosemi@iqfr.csic.es [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain); Instituto de Fermentaciones Industriales, CSIC, Juan de la Cierva 3, 28006 Madrid (Spain)

    2007-04-01

    The enzyme p-coumaric acid decarboxylase (PDC) from L. plantarum has been recombinantly expressed, purified and crystallized. The structure has been solved at 2.04 Å resolution by the molecular-replacement method. The substrate-inducible p-coumaric acid decarboxylase (PDC) from Lactobacillus plantarum has been overexpressed in Escherichia coli, purified and confirmed to possess decarboxylase activity. The recombinant His{sub 6}-tagged enzyme was crystallized using the hanging-drop vapour-diffusion method from a solution containing 20%(w/v) PEG 4000, 12%(w/v) 2-propanol, 0.2 M sodium acetate, 0.1 M Tris–HCl pH 8.0 with 0.1 M barium chloride as an additive. Diffraction data were collected in-house to 2.04 Å resolution. Crystals belonged to the tetragonal space group P4{sub 3}, with unit-cell parameters a = b = 43.15, c = 231.86 Å. The estimated Matthews coefficient was 2.36 Å{sup 3} Da{sup −1}, corresponding to 48% solvent content, which is consistent with the presence of two protein molecules in the asymmetric unit. The structure of PDC has been determined by the molecular-replacement method. Currently, the structure of PDC complexed with substrate analogues is in progress, with the aim of elucidating the structural basis of the catalytic mechanism.

  18. Structure of a Bacterial ABC Transporter Involved in the Import of an Acidic Polysaccharide Alginate.

    Science.gov (United States)

    Maruyama, Yukie; Itoh, Takafumi; Kaneko, Ai; Nishitani, Yu; Mikami, Bunzo; Hashimoto, Wataru; Murata, Kousaku

    2015-09-01

    The acidic polysaccharide alginate represents a promising marine biomass for the microbial production of biofuels, although the molecular and structural characteristics of alginate transporters remain to be clarified. In Sphingomonas sp. A1, the ATP-binding cassette transporter AlgM1M2SS is responsible for the import of alginate across the cytoplasmic membrane. Here, we present the substrate-transport characteristics and quaternary structure of AlgM1M2SS. The addition of poly- or oligoalginate enhanced the ATPase activity of reconstituted AlgM1M2SS coupled with one of the periplasmic solute-binding proteins, AlgQ1 or AlgQ2. External fluorescence-labeled oligoalginates were specifically imported into AlgM1M2SS-containing proteoliposomes in the presence of AlgQ2, ATP, and Mg(2+). The crystal structure of AlgQ2-bound AlgM1M2SS adopts an inward-facing conformation. The interaction between AlgQ2 and AlgM1M2SS induces the formation of an alginate-binding tunnel-like structure accessible to the solvent. The translocation route inside the transmembrane domains contains charged residues suitable for the import of acidic saccharides. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Small-angle X-ray-scattering investigation and structural-model study of the fatty-acid synthetase from pig liver

    International Nuclear Information System (INIS)

    Folkhard, W.; Felser, B.; Pilz, I.; Kratky, O.; Dutler, H.; Vogel, H.

    1977-01-01

    The structure of the fatty acid synthetase from pig liver was studied on models based upon structural and functional properties selected from pertinent results available from numerous investigations carried out with fatty acid synthetase from this and other sources. When comparing small-angle X-ray-scattering curves calculated with these models and curves obtained from small-angle X-ray-scattering experiments carried out with the pig-liver enzyme, we tried to select a model which would lead to an acceptable correlation between the calculated and the experimental curves and at the same time fulfil the known structural and the functional requirements. The comparison of the curves was started with a model of low complexity. The observed discrepancy, together with arguments from the structural and the functional properties, helped decide which is the next most reasonable model to be considered. This procedure was repeated for five models of increasing complexity. In the model which led to the best fit the multienzyme complex is composed of two halves in an asymmetric conformation including hollow spaces. This highly anisotropic model would imply that the two halves change their conformation each time a synthetic cycle is completed and that the growing fatty acid is handed over from one half to the other. (orig.) [de

  20. Structure characteristics of an acidic polysaccharide purified from banana (Musa nana Lour.) pulp and its enzymatic degradation.

    Science.gov (United States)

    Liu, Huiling; Jiang, Yueming; Yang, Hongshun; Yang, Bao

    2017-08-01

    Banana is one of the most important fruits over the world. The chemical composition is critical for the organoleptic properties and health benefits. As one of the leading bioactive components in banana pulp, the polysaccharides may contribute to the beneficial health effects. However, their precise structure information remains unknown. A leading acidic polysaccharide (ABPP) of banana pulp was purified and identified by nuclear magnetic resonnance spectroscopy (NMR) and gas chromatography-mass spectrometry (GC-MS). →4-α-d-GalpA-1→ and →4-α-d-GalpAMe-1→ constituted the backbone. No branch chains were detected. The molecular weight was determined to be 8.9kDa by gel permeation chromatography, which was smaller than previously reported fruit-derived polygalacturonic acids. The precise structure was identified as below. Digestion by enzyme would lead to production of oligogalacturonic acids and quick accumulation of 5000-7000Da fraction. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Structure Determination of Cisplatin-Amino Acid Analogues by Infrared Multiple Photon Dissociation Action Spectroscopy

    Science.gov (United States)

    He, Chenchen; Bao, Xun; Zhu, Yanlong; Strobehn, Stephen; Kimutai, Bett; Nei, Y.-W.; Chow, C. S.; Rodgers, M. T.; Gao, Juehan; Oomens, J.

    2015-06-01

    To gain a better understanding of the binding mechanism and assist in the optimization of relevant drug and chemical probe design, both experimental and theoretical studies were performed on a series of amino acid-linked cisplatin derivatives, including glycine-, lysine-, and ornithine-linked cisplatin, Gplatin, Kplatin, and Oplatin, respectively. Cisplatin, the first FDA-approved platinum-based anticancer drug, has been widely used in cancer chemotherapy. Its pharmacological mechanism has been identified as its ability to coordinate to genomic DNA, and guanine is its major target. In previous reports, cisplatin was successfully utilized as a chemical probe to detect solvent accessible sites in ribosomal RNA (rRNA). Among the amino-acid-linked cisplatin derivatives, Oplatin exhibits preference for adenine over guanine. The mechanism behind its different selectivity compared to cisplatin may relate to its potential of forming a hydrogen bond between the carboxylate group in Pt (II) complex and the 6-amino moiety of adenosine stabilizes A-Oplatin products. Tandem mass spectrometry analysis also indicates that different coordination sites of Oplatin on adenosine affect glycosidic bond stability. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on all three amino acid-linked cisplatin to characterize their structures. An extensive theoretical study has been performed on Gplatin to guide the selection of the most effective theory and basis set based on its geometric information. The results for Gplatin provide the foundation for characterization of the more complex amino acid-linked cisplatin derivatives, Oplatin and Kplatin. Structural and energetic information elucidated for these compounds, particularly Oplatin reveal the reason for its alternative selectivity compared to cisplatin.

  2. Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure

    Directory of Open Access Journals (Sweden)

    Giovanni N. Roviello

    2015-06-01

    Full Text Available The employment of molecular tools with nucleic acid binding ability to specifically control crucial cellular functions represents an important scientific area at the border between biochemistry and pharmaceutical chemistry. In this review we describe several molecular systems of natural or artificial origin, which are able to bind polyriboadenylic acid (poly(rA both in its single-stranded or structured forms. Due to the fundamental role played by the poly(rA tail in the maturation and stability of mRNA, as well as in the initiation of the translation process, compounds able to bind this RNA tract, influencing the mRNA fate, are of special interest for developing innovative biomedical strategies mainly in the field of anticancer therapy.

  3. Synthesis and Structural Characterization of 1- and 2-Substituted Indazoles: Ester and Carboxylic Acid Derivatives

    Directory of Open Access Journals (Sweden)

    Isabel Bento

    2006-11-01

    Full Text Available A series of indazoles substituted at the N-1 and N-2 positions with ester-containing side chains -(CH2nCO2R of different lengths (n = 0-6, 9, 10 are described.Nucleophilic substitution reactions on halo esters (X(CH2nCO2R by 1H-indazole inalkaline solution lead to mixtures of N-1 and N-2 isomers, in which the N-1 isomerpredominates. Basic hydrolysis of the ester derivatives allowed the synthesis of thecorresponding indazole carboxylic acids. All compounds were fully characterised bymultinuclear NMR and IR spectroscopies, MS spectrometry and elemental analysis; theNMR spectroscopic data were used for structural assignment of the N-1 and N-2 isomers.The molecular structure of indazol-2-yl-acetic acid (5b was determined by X-raydiffraction, which shows a supramolecular architecture involving O2-H...N1intermolecular hydrogen bonds.

  4. Effect of acid hydrolysis on morphology, structure and digestion property of starch from Cynanchum auriculatum Royle ex Wight.

    Science.gov (United States)

    Wang, Xingchi; Wen, Fanting; Zhang, Shurong; Shen, Ruru; Jiang, Wei; Liu, Jun

    2017-03-01

    Effect of acid hydrolysis on the morphology, structure and digestion property of starch from Cynanchum auriculatum Royle ex Wight was investigated in this study. The hydrolysis degree of C. auriculatum starch rapidly increased to 63.69% after 4days and reached 78.67% at the end of 9days. Morphology observation showed that the starch granules remained intact during the first 4days of hydrolysis. However, serious erosion phenomenon was observed after 5days and starch granules completely fell into pieces after 7days. During acid hydrolysis process, the crystal type of hydrolyzed starch changed from original C B -type to final A-type. Small-angle X-ray scattering patterns showed the semi-crystalline growth rings started to be hydrolyzed after 4days. The proportions of single helix and amorphous components as well as amylose content in starch gradually decreased, whereas the proportion of double helix components continuously increased during acid hydrolysis. However, the contents of rapidly digestible starch, slowly digestible starch and resistant starch were almost constant during acid hydrolysis process, indicating the in vitro digestion property of C. auriculatum starch was not affected by acid hydrolysis. Our results provided novel information on the inner structure of C. auriculatum starch granules. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. SHEETSPAIR: A Database of Amino Acid Pairs in Protein Sheet Structures

    Directory of Open Access Journals (Sweden)

    Ning Zhang

    2007-10-01

    Full Text Available Within folded strands of a protein, amino acids (AAs on every adjacent two strands form a pair of AAs. To explore the interactions between strands in a protein sheet structure, we have established an Internet-accessible relational database named SheetsPairs based on SQL Server 2000. The database has collected AAs pairs in proteins with detailed information. Furthermore, it utilizes a non-freetext database structure to store protein sequences and a specific database table with a unique number to store strands, which provides more searching options and rapid and accurate access to data queries. An IIS web server has been set up for data retrieval through a custom web interface, which enables complex data queries. Also searchable are parallel or anti-parallel folded strands and the list of strands in a specified protein.

  6. The structures of three metabolites of the algal hepatotoxin okadaic acid produced by oxidation with human cytochrome P450

    Science.gov (United States)

    Liu, Li; Guoa, Fujiang; Crain, Sheila; Quilliam, Michael A.; Wang, Xiaotang; Rein, Kathleen S.

    2012-01-01

    Four metabolites of okadaic acid were generated by incubation with human recombinant cytochrome P450 3A4. The structures of two of the four metabolites have been determined by MS/MS experiments and 1D and 2D NMR methods using 94 and 133 μg of each metabolite. The structure of a third metabolite was determined by oxidation to a metabolite of known structure. Like okadaic acid, the metabolites are inhibitors of protein phosphatase PP2A. Although one of the metabolites does have an α,β unsaturated carbonyl with the potential to form adducts with an active site cysteine, all of the metabolites are reversible inhibitors of PP2A. PMID:22608922

  7. The solid-state structures of organic salts formed by calix[4]arene dihydroxyphosphonic acid with nucleic bases cations: adeninium, cytosinium, guaninium and uracilium

    KAUST Repository

    Shkurenko, Aleksander

    2018-02-19

    Calix[4]arene dihydroxyphosphonic acid has been demonstrated to possess an interesting range of biological properties, including atypical anti-cancer activity. The robustness of calix[4]arene dihydroxyphosphonic acid and its ubiquitous dimeric motif offers perspectives for pre-defined solid state complexation with small molecules. In the current article we describe co-crystals (organic salts) of calix[4]arene dihydroxyphosphonic acid with four nucleic base cations: adeninium, cytosinium, guaninium and uracilium. A number of characteristic interactions between the components in the four co-crystals are pointed out also using the Hirshfeld surface analysis. All the four co-crystals are based on layers of calix[4]arene dimers, alternating with layers of nucleic acid molecules. Two of the reported crystal structures (cytosinium and guaninium) are 1D channel-type structures, while the two others (adeninium and uracilium) represent 2D channel-type structures. In three out of four reported structures, interactions between the cations of nucleic bases are present generating 1D chains of cations. A constant motif is that the nucleic base is present in a type of cavity formed by one aromatic ring and a phosphonic acid moiety.

  8. Effect of pore structure on the removal of clofibric acid by magnetic anion exchange resin.

    Science.gov (United States)

    Tan, Liang; Shuang, Chendong; Wang, Yunshu; Wang, Jun; Su, Yihong; Li, Aimin

    2018-01-01

    The effect of pore structure of resin on clofibric acid (CA) adsorption behavior was investigated by using magnetic anion exchange resins (ND-1, ND-2, ND-3) with increasing pore diameter by 11.68, 15.37, 24.94 nm. Resin with larger pores showed faster adsorption rates and a higher adsorption capacity because the more opened tunnels provided by larger pores benefit the CA diffusion into the resin matrix. The ion exchange by the electrostatic interactions between Cl-type resin and CA resulted in chloride releasing to the solution, and the ratio of released chloride to CA adsorption amount decreased from 0.90 to 0.65 for ND-1, ND-2 and ND-3, indicating that non-electrostatic interactions obtain a larger proportional part of the adsorption into the pores. Co-existing inorganic anions and organic acids reduced the CA adsorption amounts by the competition effect of electrostatic interaction, whereas resins with more opened pore structures weakened the negative influence on CA adsorption because of the existence of non-electrostatic interactions. 85.2% and 65.1% adsorption amounts decrease are calculated for resin ND-1 and ND-3 by the negative influence of 1 mmol L -1 NaCl. This weaken effect of organic acid is generally depends on its hydrophobicity (Log Kow) for carboxylic acid and its ionization degree (pKb) for sulfonic acid. The resins could be reused with the slightly decreases by 1.9%, 3.2% and 5.4% after 7 cycles of regeneration, respectively for ND-1, ND-2 and ND-3, suggesting the ion exchange resin with larger pores are against its reuse by the brine solution regeneration. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Structural and solubility parameter correlations of gelation abilities for dihydroxylated derivatives of long-chain, naturally occurring fatty acids.

    Science.gov (United States)

    Zhang, Mohan; Selvakumar, Sermadurai; Zhang, Xinran; Sibi, Mukund P; Weiss, Richard G

    2015-06-01

    Creating structure-property correlations at different distance scales is one of the important challenges to the rational design of molecular gelators. Here, a series of dihydroxylated derivatives of long-chain fatty acids, derived from three naturally occurring molecules-oleic, erucic and ricinoleic acids-are investigated as gelators of a wide variety of liquids. Conclusions about what constitutes a more (or less!) efficient gelator are based upon analyses of a variety of thermal, structural, molecular modeling, and rheological results. Correlations between the manner of molecular packing in the neat solid or gel states of the gelators and Hansen solubility data from the liquids leads to the conclusion that diol stereochemistry, the number of carbon atoms separating the two hydroxyl groups, and the length of the alkanoic chains are the most important structural parameters controlling efficiency of gel formation for these gelators. Some of the diol gelators are as efficient or even more efficient than the well-known, excellent gelator, (R)-12-hydroxystearic acid; others are much worse. The ability to form extensive intermolecular H-bonding networks along the alkyl chains appears to play a key role in promoting fiber growth and, thus, gelation. In toto, the results demonstrate how the efficiency of gelation can be modulated by very small structural changes and also suggest how other structural modifications may be exploited to create efficient gelators. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Production of structured lipid with a low omega-6/omega-3 fatty acids ratio by enzymatic interesterification

    International Nuclear Information System (INIS)

    Ilyasoglu, H.

    2017-01-01

    A structured lipid (SL) constituting omega fatty acids was synthesized by using linseed and grape seed oils as substrates via a lipase-catalyzed reaction. Lipozyme® TL IM was used as a biocatalyst. Good quadratic models predicting the incorporation of omega fatty acids were achieved via the Response surface methodology (RSM). The optimal conditions for targeted omega-6/omega-3 fatty acid ratio (2:1) were obtained at a substrate molar ratio 1.4, time 8.4 h, and enzyme amount 6.4%. The SL contained linoleic acid (43 g 100g-1), which was mainly located in the sn-2 position (40 g 100g-1). α-Linoleic acid, and α-linolenic acid at the sn-2 position were 22 g 100g-1, and 11 g 100g-1, respectively. The oxidative stability of the SL, and SL with antioxidants was also investigated. The produced SL may be proposed as a source of a balanced intake of omega fatty acids and an ingredient in functional food formulations. [es

  11. Oxidative stability of mayonnaise containing structured lipids produced from sunflower oil and caprylic acid

    DEFF Research Database (Denmark)

    Jacobsen, Charlotte; Xu, Xuebing; Nielsen, Nina Skall

    2003-01-01

    Mayonnaise based on enzymatically produced specific structured lipid (SL) from sunflower oil and caprylic acid was compared with mayonnaise based on traditional sunflower oil (SO) or chemically randomized lipid (RL) with respect to their oxidative stability, sensory and rheological properties......, but was most likely influenced by the structure of the lipid, the lower tocopherol content and the higher initial levels of lipid hydroperoxides and secondary volatile oxidation compounds in the SL itself compared with the RL and traditional sunflower oil employed. EDTA was a strong antioxidant, while propyl...

  12. Catalytic biofilms on structured packing for the production of glycolic acid.

    Science.gov (United States)

    Li, Xuan Zhong; Hauer, Bernhard; Rosche, Bettina

    2013-02-01

    While structured packing modules are known to be efficient for surface wetting and gas-liquid exchange in abiotic surface catalysis, this model study explores structured packing as a growth surface for catalytic biofilms. Microbial biofilms have been proposed as self-immobilized and self-regenerating catalysts for the production of chemicals. A concern is that the complex and dynamic nature of biofilms may cause fluctuations in their catalytic performance over time or may affect process reproducibility. An aerated continuous trickle-bed biofilm reactor system was designed with a 3 L structured packing, liquid recycling and pH control. Pseudomonas diminuta established a biofilm on the stainless steel structured packing with a specific surface area of 500 m2 m-3 and catalyzed the oxidation of ethylene glycol to glycolic acid for over two months of continuous operation. A steady-state productivity of up to 1.6 gl-1h-1 was achieved at a dilution rate of 0.33 h-1. Process reproducibility between three independent runs was excellent, despite process interruptions and activity variations in cultures grown from biofilm effluent cells. The results demonstrate the robustness of a catalytic biofilm on structured packing, despite its dynamic nature. Implementation is recommended for whole-cell processes that require efficient gas-liquid exchange, catalyst retention for continuous operation, or improved catalyst stability.

  13. Acid indium strontium phosphate SrIn2[PO3(OH)]4: synthesis and crystal structure

    International Nuclear Information System (INIS)

    Rusakov, D.A.; Bobylev, A.P.; Komissarova, L.N.; Filaretov, A.A.; Danilov, V.P.

    2007-01-01

    Acid indium-strontium phosphate SrIn 2 [PO 3 (OH)] 4 is synthesized and characterized. Crystal structure and lattice parameters ate determined. In atoms in SrIn 2 [PO 3 (OH)] 4 structure are in distorted InO 6 octahedrons and form with PO 3 (OH) tetrahedrons mixed paraskeleton {In 2 [PO 3 (OH)] 4 } 3∞ 2- with emptinesses occupied by big Sr 2+ cations. The compound is thermally stable up to 400 Deg C [ru

  14. Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST.

    Science.gov (United States)

    Goonesekere, Nalin Cw

    2009-01-01

    The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the complex evolutionary and functional relationships that exist between proteins. Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. The substitution matrices in common use today are constructed using sequences aligned without reference to protein structure. Here we present amino acid substitution matrices constructed from the alignment of a large number of protein domain structures from the structural classification of proteins (SCOP) database. We show that when incorporated into the homology search algorithms BLAST and PSI-blast, the structure-based substitution matrices enhance the efficacy of detecting remote homologs.

  15. Molecular interaction of pinic acid with sulfuric acid

    DEFF Research Database (Denmark)

    Elm, Jonas; Kurtén, Theo; Bilde, Merete

    2014-01-01

    We investigate the molecular interactions between the semivolatile α-pinene oxidation product pinic acid and sulfuric acid using computational methods. The stepwise Gibbs free energies of formation have been calculated utilizing the M06-2X functional, and the stability of the clusters is evaluated...... cluster. The involvement of more than one pinic acid molecule in a single cluster is observed to lead to the formation of favorable (pinic acid)2(H2SO4) and (pinic acid)2(H2SO4)2 clusters. The identified most favorable growth paths starting from a single pinic acid molecule lead to closed structures...

  16. Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.

    Science.gov (United States)

    Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

    2014-09-18

    Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.

  17. Phenylacetic acids and the structurally related non-steroidal anti-inflammatory drug diclofenac bind to specific gamma-hydroxybutyric acid sites in rat brain

    DEFF Research Database (Denmark)

    Wellendorph, Petrine; Høg, Signe; Skonberg, Christian

    2009-01-01

    with a twofold higher affinity than GHB. Measuring the affinities of structurally related NSAIDs for the [(3)H]NCS-382 site identified diclofenac, a clinically relevant NSAID (Voltaren, Diclon) of the phenylacetic acid (PAA) type, as a GHB ligand (K(i) value of 5.1 microM). Other non-NSAID PAAs also exhibited...... affinities similar to GHB. Our data raise the interesting possibility that the widely used over-the-counter drug compound, diclofenac, might affect GHB binding at relevant clinical dosages. Furthermore, the identification of PAAs as GHB ligands supplies new information about the structural preferences...

  18. Structures, Energetics, and IR Spectra of Monohydrated Inorganic Acids: Ab initio and DFT Study.

    Science.gov (United States)

    Kołaski, Maciej; Zakharenko, Aleksey A; Karthikeyan, S; Kim, Kwang S

    2011-10-11

    We carried out extensive calculations of diverse inorganic acids interacting with a single water molecule, through a detailed analysis of many possible conformations. The optimized structures were obtained by using density functional theory (DFT) and the second order Møller-Plesset perturbation theory (MP2). For the most stable conformers, we calculated the interaction energies at the complete basis set (CBS) limit using coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The -OH stretching harmonic and anharmonic frequencies are provided as fingerprints of characteristic conformers. The zero-point energy (ZPE) uncorrected/corrected (ΔEe/ΔE0) interaction energies and the enthalpies/free energies (ΔHr/ΔGr at room temperature and 1 bar) are reported. Various comparisons are made between many diverse inorganic acids (HmXOn where X = B/N/P/Cl/Br/I, m = 1-3, and n = 0-4) as well as other simple inorganic acids. In many cases, we find that the dispersion-driven van der Waals interactions between X in inorganic acid molecules and O in water molecules as well as the X(+)···O(-) electrostatic interactions are important.

  19. Uptake and metabolism of structured triglyceride by Caco-2 cells: reversal of essential fatty acid deficiency.

    Science.gov (United States)

    Spalinger, J H; Seidman, E G; Lepage, G; Ménard, D; Gavino, V; Levy, E

    1998-10-01

    Structured lipids have been proposed as efficient vehicles for the supplementation of essential fatty acids (EFA) to patients with malabsorption. We investigated how a novel structured triglyceride (STG), containing purely octanoic acid in the sn-1/sn-3 and [14C]linoleic acid in the sn-2 positions, was incorporated into different lipid classes in Caco-2 cells. We also evaluated the contribution of gastric lipase in the uptake and metabolism of [14C]linoleic acid from the STG. We furthermore determined the potential of the STG to correct EFA deficiency induced in Caco-2 cells. The absorption of STG by Caco-2 cells was significantly greater compared with that of triolein. The addition of human gastric lipase significantly enhanced cellular uptake of the labeled substrate, reflecting the stereoselectivity of gastric lipase to hydrolyze medium chain FA. Analysis of the intracellular lipids synthesized revealed a predominance of phospholipids-monoglycerides. Most of the radioactivity in the lipoproteins isolated from Caco-2 cells was recovered in TG-rich lipoproteins (45%) and to a lesser extent in the high-density lipoprotein (36%) and low-density lipoprotein (17%) fractions. The administration of STG to Caco-2 cells rendered EFA deficient produced a marked increase of the cellular level of linoleic and arachidonic acids. This resulted in a lower ratio of 20:3(n-9) to 20:4(n-6), reflecting the correction of EFA deficiency in Caco-2 cells. Our data demonstrate that STG, in the presence of gastric lipase, have beneficial effects on lipid incorporation, lipoprotein production, and EFA status, utilizing Caco-2 cells as a model of EFA deficiency.

  20. Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

    Science.gov (United States)

    Kinjo, Akira R; Nakamura, Haruki

    2013-01-01

    Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

  1. Effects of electron beam irradiation on the structural properties of polylactic acid/polyethylene blends

    Energy Technology Data Exchange (ETDEWEB)

    Bee, Soo-Tueen, E-mail: direct.beest@gmail.com [Department of Chemical Engineering, Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Jalan Genting Kelang, 53300 Setapak, Kuala Lumpur (Malaysia); Ratnam, C.T. [Radiation Processing Technology Division, Malaysian Nuclear Agency, Bangi, 43000 Kajang, Selangor (Malaysia); Sin, Lee Tin, E-mail: direct.tinsin@gmail.com [Department of Chemical Engineering, Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Jalan Genting Kelang, 53300 Setapak, Kuala Lumpur (Malaysia); Tee, Tiam-Ting; Wong, Wai-Kien; Lee, Jiuun-Xiang [Department of Chemical Engineering, Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Jalan Genting Kelang, 53300 Setapak, Kuala Lumpur (Malaysia); Rahmat, A.R. [Department of Polymer Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor (Malaysia)

    2014-09-01

    Highlights: •Electron beam irradiation on polyethylene (LDPE) and polylactic acid (PLA) blends. •Irradiated PLA/LDPE blends exhibit structural rearrangement to highly ordered structure. •Irradiated PLA/LDPE matrix extends continuity of polymer matrix with larger fibrils diameter. -- Abstract: The purpose of this research was to investigate the effects of electron beam irradiation on the properties of polylactic acid (PLA) and low density polyethylene (LDPE) blends. The PLA were compounded with 20–80% LDPE and were exposed to electron beam irradiation dosages of 20–120 kGy. The results from gel content and X-ray diffraction analyses showed that the addition of LDPE to PLA effectively increased the gel content and crystallinity. However, an increasing percentage of LDPE reduced the tensile strength and Young’s modulus of the PLA/LDPE samples due to the lower intermolecular bonding of LDPE than of PLA. Moreover, an increase in irradiation dosages gradually decreased the mechanical properties of low-LDPE PLA/LDPE. In contrast, the increasing irradiation dosage enhanced the mechanical properties of higher-LDPE PLA/LDPE. These results indicate that higher amounts of LDPE effectively react with the release of free radicals within the amorphous phase if the blends are subjected to irradiation. The higher amounts of free radicals induce the formation of three-dimensional cross-linked networks in the polymer matrix and thus increase the gel content. The irradiation-induced cross-linking in PLA/LDPE samples improves the mechanical properties and crystallinity by promoting a structural rearrangement of the polymer matrix into a highly ordered structure.

  2. Effects of electron beam irradiation on the structural properties of polylactic acid/polyethylene blends

    International Nuclear Information System (INIS)

    Bee, Soo-Tueen; Ratnam, C.T.; Sin, Lee Tin; Tee, Tiam-Ting; Wong, Wai-Kien; Lee, Jiuun-Xiang; Rahmat, A.R.

    2014-01-01

    Highlights: •Electron beam irradiation on polyethylene (LDPE) and polylactic acid (PLA) blends. •Irradiated PLA/LDPE blends exhibit structural rearrangement to highly ordered structure. •Irradiated PLA/LDPE matrix extends continuity of polymer matrix with larger fibrils diameter. -- Abstract: The purpose of this research was to investigate the effects of electron beam irradiation on the properties of polylactic acid (PLA) and low density polyethylene (LDPE) blends. The PLA were compounded with 20–80% LDPE and were exposed to electron beam irradiation dosages of 20–120 kGy. The results from gel content and X-ray diffraction analyses showed that the addition of LDPE to PLA effectively increased the gel content and crystallinity. However, an increasing percentage of LDPE reduced the tensile strength and Young’s modulus of the PLA/LDPE samples due to the lower intermolecular bonding of LDPE than of PLA. Moreover, an increase in irradiation dosages gradually decreased the mechanical properties of low-LDPE PLA/LDPE. In contrast, the increasing irradiation dosage enhanced the mechanical properties of higher-LDPE PLA/LDPE. These results indicate that higher amounts of LDPE effectively react with the release of free radicals within the amorphous phase if the blends are subjected to irradiation. The higher amounts of free radicals induce the formation of three-dimensional cross-linked networks in the polymer matrix and thus increase the gel content. The irradiation-induced cross-linking in PLA/LDPE samples improves the mechanical properties and crystallinity by promoting a structural rearrangement of the polymer matrix into a highly ordered structure

  3. The effect of different clays on the structure, morphology and degradation behavior of poly(lactic acid)

    CSIR Research Space (South Africa)

    Neppalli, R

    2014-01-01

    Full Text Available In this work, polylactic acid (PLA)-based nanocomposites filled with different kinds of clay were prepared and their structure, morphology and degradation behavior were compared. A similar degree of dispersion was achieved in the case of cationic...

  4. Bamboo-Polylactic Acid (PLA) Composite Material for Structural Applications.

    Science.gov (United States)

    Pozo Morales, Angel; Güemes, Alfredo; Fernandez-Lopez, Antonio; Carcelen Valero, Veronica; De La Rosa Llano, Sonia

    2017-11-09

    Developing an eco-friendly industry based on green materials, sustainable technologies, and optimum processes with low environmental impact is a general societal goal, but this remains a considerable challenge to achieve. Despite the large number of research on green structural composites, limited investigation into the most appropriate manufacturing methodology to develop a structural material at industrial level has taken place. Laboratory panels have been manufactured with different natural fibers but the methodologies and values obtained could not be extrapolated at industrial level. Bamboo industry panels have increased in the secondary structural sector such as building application, flooring and sport device, because it is one of the cheapest raw materials. At industrial level, the panels are manufactured with only the inner and intermediate region of the bamboo culm. However, it has been found that the mechanical properties of the external shells of bamboo culm are much better than the average cross-sectional properties. Thin strips of bamboo (1.5 mm thick and 1500 mm long) were machined and arranged with the desired lay-up and shape to obtain laminates with specific properties better than those of conventional E-Glass/Epoxy laminates in terms of both strength and stiffness. The strips of bamboo were bonded together by a natural thermoplastic polylactic acid (PLA) matrix to meet biodegradability requirements. The innovative mechanical extraction process developed in this study can extract natural strip reinforcements with high performance, low cost, and high rate, with no negative environmental impact, as no chemical treatments are used. The process can be performed at the industrial level. Furthermore, in order to validate the structural applications of the composite, the mechanical properties were analyzed under ageing conditions. This material could satisfy the requirements for adequate mechanical properties and life cycle costs at industrial sectors such

  5. Bamboo–Polylactic Acid (PLA Composite Material for Structural Applications

    Directory of Open Access Journals (Sweden)

    Angel Pozo Morales

    2017-11-01

    Full Text Available Developing an eco-friendly industry based on green materials, sustainable technologies, and optimum processes with low environmental impact is a general societal goal, but this remains a considerable challenge to achieve. Despite the large number of research on green structural composites, limited investigation into the most appropriate manufacturing methodology to develop a structural material at industrial level has taken place. Laboratory panels have been manufactured with different natural fibers but the methodologies and values obtained could not be extrapolated at industrial level. Bamboo industry panels have increased in the secondary structural sector such as building application, flooring and sport device, because it is one of the cheapest raw materials. At industrial level, the panels are manufactured with only the inner and intermediate region of the bamboo culm. However, it has been found that the mechanical properties of the external shells of bamboo culm are much better than the average cross-sectional properties. Thin strips of bamboo (1.5 mm thick and 1500 mm long were machined and arranged with the desired lay-up and shape to obtain laminates with specific properties better than those of conventional E-Glass/Epoxy laminates in terms of both strength and stiffness. The strips of bamboo were bonded together by a natural thermoplastic polylactic acid (PLA matrix to meet biodegradability requirements. The innovative mechanical extraction process developed in this study can extract natural strip reinforcements with high performance, low cost, and high rate, with no negative environmental impact, as no chemical treatments are used. The process can be performed at the industrial level. Furthermore, in order to validate the structural applications of the composite, the mechanical properties were analyzed under ageing conditions. This material could satisfy the requirements for adequate mechanical properties and life cycle costs at

  6. Bamboo–Polylactic Acid (PLA) Composite Material for Structural Applications

    Science.gov (United States)

    Pozo Morales, Angel; Güemes, Alfredo; Fernandez-Lopez, Antonio; Carcelen Valero, Veronica; De La Rosa Llano, Sonia

    2017-01-01

    Developing an eco-friendly industry based on green materials, sustainable technologies, and optimum processes with low environmental impact is a general societal goal, but this remains a considerable challenge to achieve. Despite the large number of research on green structural composites, limited investigation into the most appropriate manufacturing methodology to develop a structural material at industrial level has taken place. Laboratory panels have been manufactured with different natural fibers but the methodologies and values obtained could not be extrapolated at industrial level. Bamboo industry panels have increased in the secondary structural sector such as building application, flooring and sport device, because it is one of the cheapest raw materials. At industrial level, the panels are manufactured with only the inner and intermediate region of the bamboo culm. However, it has been found that the mechanical properties of the external shells of bamboo culm are much better than the average cross-sectional properties. Thin strips of bamboo (1.5 mm thick and 1500 mm long) were machined and arranged with the desired lay-up and shape to obtain laminates with specific properties better than those of conventional E-Glass/Epoxy laminates in terms of both strength and stiffness. The strips of bamboo were bonded together by a natural thermoplastic polylactic acid (PLA) matrix to meet biodegradability requirements. The innovative mechanical extraction process developed in this study can extract natural strip reinforcements with high performance, low cost, and high rate, with no negative environmental impact, as no chemical treatments are used. The process can be performed at the industrial level. Furthermore, in order to validate the structural applications of the composite, the mechanical properties were analyzed under ageing conditions. This material could satisfy the requirements for adequate mechanical properties and life cycle costs at industrial sectors such

  7. Tip-induced domain structures and polarization switching in ferroelectric amino acid glycine

    Energy Technology Data Exchange (ETDEWEB)

    Seyedhosseini, E., E-mail: Seyedhosseini@ua.pt; Ivanov, M. [CICECO-Aveiro Institute of Materials and Department of Physics, University of Aveiro, 3810-193 Aveiro (Portugal); Bdikin, I. [TEMA and Department of Mechanical Engineering, University of Aveiro, 3810-193 Aveiro (Portugal); Vasileva, D. [Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg (Russian Federation); Kudryavtsev, A. [Moscow State Institute of Radioengineering, Electronics and Automation, 119454 Moscow (Russian Federation); Rodriguez, B. J. [Conway Institute of Biomolecular and Biomedical Research and School of Physics, University College Dublin, Dublin (Ireland); Kholkin, A. L. [CICECO-Aveiro Institute of Materials and Department of Physics, University of Aveiro, 3810-193 Aveiro (Portugal); Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg (Russian Federation)

    2015-08-21

    Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and a switchable polarization at room temperature. Here, we study tip-induced domain structures and polarization switching in the smallest amino acid β-glycine, representing a broad class of non-centrosymmetric amino acids. We show that β-glycine is indeed a room-temperature ferroelectric and polarization can be switched by applying a bias to non-polar cuts via a conducting tip of atomic force microscope (AFM). Dynamics of these in-plane domains is studied as a function of an applied voltage and pulse duration. The domain shape is dictated by polarization screening at the domain boundaries and mediated by growth defects. Thermodynamic theory is applied to explain the domain propagation induced by the AFM tip. Our findings suggest that the properties of β-glycine are controlled by the charged domain walls which in turn can be manipulated by an external bias.

  8. Crystal structure of ethylenedioxytetrathiafulvalene-4,5-bis(thiolbenzoic acid 0.25-hydrate

    Directory of Open Access Journals (Sweden)

    Yuanyuan Zhang

    2017-09-01

    Full Text Available In the title compound (systematic name: 4,4′-{[2-(5,6-dihydro-[1,3]dithiolo[4,5-b][1,4]dioxin-2-ylidene-1,3-dithiole-4,5-diyl]bis(sulfanediyl}dibenzoic acid 0.25-hydrate, C22H14O6S6·0.25H2O, the tetrathiafulvalene (TTF core adopts a boat conformation, where the central S2C=CS2 plane makes dihedral angles of 31.34 (4 and 26.83 (6°, respectively, with the peripheral S2C=CS2 and S2C2O2 planes. In the crystal, the benzoic acid molecules are linked via O—H...O hydrogen bonds, forming inversion dimers with R22(8 motifs. The dimers are linked through weak C—H...O hydrogen bonds into a chain structure along [-101]. The chains stack along the a axis through S...S and S...C short contacts, forming layers parallel to the ac plane.

  9. Wafer Cakes of Improved Amino Acid Structure

    Directory of Open Access Journals (Sweden)

    Roksolana Boidunyk

    2017-11-01

    Full Text Available The article presents the results of the study of the amino acid composition of newly developed wafer cakes with adipose fillings combined with natural additives. The appropriateness of the using non-traditional raw materials (powder of willow herb, poppy oilcake, carob, as well as skimmed milk powder in order to increase the biological value of wafer cakes and improve their amino acid composition is proven.

  10. Polymorphism in Self-Assembled Structures of 9-Anthracene Carboxylic Acid on Ag(111

    Directory of Open Access Journals (Sweden)

    Bo Xu

    2012-06-01

    Full Text Available Surface self-assembly process of 9-anthracene carboxylic acid (AnCA on Ag(111 was investigated using STM. Depending on the molecular surface density, four spontaneously formed and one annealed AnCA ordered phases were observed, namely a straight belt phase, a zigzag double-belt phase, two simpler dimer phases, and a kagome phase. The two high-density belt phases possess large unit cells on the scale length of 10 nm, which are seldom observed in molecular self-assembled structures. This structural diversity stems from a complicated competition of different interactions of AnCA molecules on metal surface, including intermolecular and molecular-substrate interactions, as well as the steric demand from high molecular surface density.

  11. Structure of Quinolinate Synthase from Pyrococcus horikoshii in the Presence of Its Product, Quinolinic Acid.

    Science.gov (United States)

    Esakova, Olga A; Silakov, Alexey; Grove, Tyler L; Saunders, Allison H; McLaughlin, Martin I; Yennawar, Neela H; Booker, Squire J

    2016-06-15

    Quinolinic acid (QA) is a common intermediate in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) and its derivatives in all organisms that synthesize the molecule de novo. In most prokaryotes, it is formed from the condensation of dihydroxyacetone phosphate (DHAP) and aspartate-enamine by the action of quinolinate synthase (NadA). NadA contains a [4Fe-4S] cluster cofactor with a unique, non-cysteinyl-ligated, iron ion (Fea), which is proposed to bind the hydroxyl group of a postulated intermediate in the last step of the reaction to facilitate a dehydration. However, direct evidence for this role in catalysis has yet to be provided. Herein, we present the structure of NadA in the presence of the product of its reaction, QA. We find that N1 and the C7 carboxylate group of QA ligate to Fea in a bidentate fashion, which is confirmed by Hyperfine Sublevel Correlation (HYSCORE) spectroscopy. This binding mode would place the C5 hydroxyl group of the postulated final intermediate distal to Fea and virtually incapable of coordinating to it. The structure shows that three strictly conserved amino acids, Glu198, Tyr109, and Tyr23, are in close proximity to the bound product. Substitution of these amino acids with Gln, Phe, and Phe, respectively, leads to complete loss of activity.

  12. The Structure of p-Aminobenzoic Acid in Water: Studies Combining UV-Vis, NEXAFS and RIXS Spectroscopies

    International Nuclear Information System (INIS)

    Gainar, A; Stevens, J S; Schroeder, S L M; Suljoti, E; Xiao, J; Golnak, R; Aziz, E F

    2016-01-01

    NEXAFS-RIXS and home laboratory-based UV-Vis absorption spectroscopy are combined to examine the speciation and electronic structure of para -aminobenzoic acid (PABA) in aqueous solution as a function of pH. DFT and TD-DFT electronic structure calculations reproduce the experimental trends and provide a correlation between the experimental HOMO↔LUMO gap as well as the electronic transitions between molecular orbitals in the non-ionic, anionic and cationic forms of PABA. (paper)

  13. Precise equilibrium structure determination of hydrazoic acid (HN3) by millimeter-wave spectroscopy

    International Nuclear Information System (INIS)

    Amberger, Brent K.; Esselman, Brian J.; Woods, R. Claude; McMahon, Robert J.; Stanton, John F.

    2015-01-01

    The millimeter-wave spectrum of hydrazoic acid (HN 3 ) was analyzed in the frequency region of 235-450 GHz. Transitions from a total of 14 isotopologues were observed and fit using the A-reduced or S-reduced Hamiltonian. Coupled-cluster calculations were performed to obtain a theoretical geometry, as well as rotation-vibration interaction corrections. These calculated vibration-rotation correction terms were applied to the experimental rotational constants to obtain mixed theoretical/experimental equilibrium rotational constants (A e , B e , and C e ). These equilibrium rotational constants were then used to obtain an equilibrium (R e ) structure using a least-squares fitting routine. The R e structural parameters are consistent with a previously published R s structure, largely falling within the uncertainty limits of that R s structure. The present R e geometric parameters of HN 3 are determined with exceptionally high accuracy, as a consequence of the large number of isotopologues measured experimentally and the sophisticated (coupled-cluster theoretical treatment (CCSD(T))/ANO2) of the vibration-rotation interactions. The R e structure exhibits remarkable agreement with the CCSD(T)/cc-pCV5Z predicted structure, validating both the accuracy of the ab initio method and the claimed uncertainties of the theoretical/experimental structure determination

  14. Determination of the Structure and Catalytic Mechanism of Sorghum bicolor Caffeic Acid O-Methyltransferase and the Structural Impact of Three brown midrib12 Mutations.

    Science.gov (United States)

    Green, Abigail R; Lewis, Kevin M; Barr, John T; Jones, Jeffrey P; Lu, Fachuang; Ralph, John; Vermerris, Wilfred; Sattler, Scott E; Kang, ChulHee

    2014-08-01

    Using S-adenosyl-methionine as the methyl donor, caffeic acid O-methyltransferase from sorghum (Sorghum bicolor; SbCOMT) methylates the 5-hydroxyl group of its preferred substrate, 5-hydroxyconiferaldehyde. In order to determine the mechanism of SbCOMT and understand the observed reduction in the lignin syringyl-to-guaiacyl ratio of three brown midrib12 mutants that carry COMT gene missense mutations, we determined the apo-form and S-adenosyl-methionine binary complex SbCOMT crystal structures and established the ternary complex structure with 5-hydroxyconiferaldehyde by molecular modeling. These structures revealed many features shared with monocot ryegrass (Lolium perenne) and dicot alfalfa (Medicago sativa) COMTs. SbCOMT steady-state kinetic and calorimetric data suggest a random bi-bi mechanism. Based on our structural, kinetic, and thermodynamic results, we propose that the observed reactivity hierarchy among 4,5-dihydroxy-3-methoxycinnamyl (and 3,4-dihydroxycinnamyl) aldehyde, alcohol, and acid substrates arises from the ability of the aldehyde to stabilize the anionic intermediate that results from deprotonation of the 5-hydroxyl group by histidine-267. Additionally, despite the presence of other phenylpropanoid substrates in vivo, sinapaldehyde is the preferential product, as demonstrated by its low K m for 5-hydroxyconiferaldehyde. Unlike its acid and alcohol substrates, the aldehydes exhibit product inhibition, and we propose that this is due to nonproductive binding of the S-cis-form of the aldehydes inhibiting productive binding of the S-trans-form. The S-cis-aldehydes most likely act only as inhibitors, because the high rotational energy barrier around the 2-propenyl bond prevents S-trans-conversion, unlike alcohol substrates, whose low 2-propenyl bond rotational energy barrier enables rapid S-cis/S-trans-interconversion. © 2014 American Society of Plant Biologists. All Rights Reserved.

  15. Structural and Morphological Features of Acid-Bearing Polymers for PEM Fuel Cells

    DEFF Research Database (Denmark)

    Yang, Yunsong; Siu, Ana; Peckham, Timothy J.

    2008-01-01

    Chemical structure, polymer microstructure, sequence distribution, and morphology of acid-bearing polymers are important factors in the design of polymer electrolyte membranes (PEMs) for fuel cells. The roles of ion aggregation and phase separation in vinylic- and aromatic-based polymers in proton...... conductivity and water transport are described. The formation, dimensions, and connectivity of ionic pathways are consistently found to play an important role in determining the physicochemical properties of PEMs. For polymers that possess low water content, phase separation and ionic channel formation...

  16. Determination and structural correlation of the pKa values of p-substituted trans-2,3-epoxy-4-oxo-4-phenylbutanoic acids

    Directory of Open Access Journals (Sweden)

    I. JURANIC

    2000-11-01

    Full Text Available The pKa values for a series of eight p-substituted trans-2,3-epoxy-4-phenyl butanoic acids (p-substituted trans-b-aroylepoxyacrylic acids have been determined potentiometrically in aqueous media at 25°C at an ionic strength of 0.1 mol/dm3 (NaCl. The transmission of polar effects from the substituents on the phenyl nucleus to the carboxylic group through the side chain involving a carbonyl group and an epoxide ring was investigated. The pKa values were correlated with structure using the Hammett, Taft and Yukawa-Tsuno approaches. The Hammett r constant (0.34 was compared with analogue values for structurally similar acids.

  17. Synthesis, structural, solubility and anticancer activity studies of salts using nucleobases and sulfonic acids coformer

    Science.gov (United States)

    Singh, Neetu; Singh, Udai P.; Nikhil, Kumar; Roy, Partha; Singh, Hariji

    2017-10-01

    The reactions of natural and unnatural nucleobases (cytosine (Cyt), adenine (Ade), 5-aminouracil (AU) and caffeine (Caff)) with sulfonic acids coformer (1,5-naphthalenedisulfonic acid, NDSA; 5-sulfosalicylic acid, SSA) resulted in the formation of salts viz. [NDSA.Cyt] (1), [NDSA.Ade] (2), [NDSA.AU] (3), [NDSA.Caff] (4), [SSA.Cyt] (5), [SSA.Ade] (6), [SSA.AU] (7), and [SSA.Caff] (8). The structural analysis revealed that salts 1, 4, 6 and 7 have intermolecular interactions between adjacent nucleobases which form two different homodimer shown in R22 (8) motif and assembled via complementary Nsbnd H⋯O and Nsbnd H⋯N interactions. However, in all other salts an intermediate supramolecular synthon pattern was observed between nucleobases and sulfonic acids. The lattice energy was also calculated by DFT to investigate whether salts were thermodynamically more stable than its coformer. The same was further confirmed by differential scanning calorimetry-thermogravimetric (DSC-TG) analysis. The anticancer activity study of individual nucleobases and their NDSA salts were also performed on human breast (MCF-7) and lung (A 549) cancer cell. The salts formation of nucleobases with sulfonic acids improved their solubility, thereby demonstrating up to 8-fold increase in solubility of nucleobases.

  18. VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C.; Nesbitt, Anna E.; Hallock, Michael J. [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Rupasinghe, Sanjeewa G. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Tang Ming [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Harris, Jason; Baudry, Jerome [University of Tennessee, Department of Biochemistry, Cellular and Molecular Biology (United States); Schuler, Mary A. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Rienstra, Chad M., E-mail: rienstra@illinois.edu [University of Illinois at Urbana-Champaign, Department of Chemistry (United States)

    2012-01-15

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., {sup 13}C-{sup 13}C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  19. VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C [University of Illinois, Urbana-Champaign; Nesbitt, Anna E [University of Illinois, Urbana-Champaign; Hallock, Michael J [University of Illinois, Urbana-Champaign; Rupasinghe, Sanjeewa [University of Illinois, Urbana-Champaign; Tang, Ming [University of Illinois, Urbana-Champaign; Harris, Jason B [ORNL; Baudry, Jerome Y [ORNL; Schuler, Mary A [University of Illinois, Urbana-Champaign; Rienstra, Chad M [University of Illinois, Urbana-Champaign

    2011-01-01

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  20. Isolation and structural characterization of echinocystic acid triterpenoid saponins from the Australian medicinal and food plant Acacia ligulata

    DEFF Research Database (Denmark)

    Knudsen, Diana Jæger; Ndi, Chi P.; Crocoll, Christoph

    2017-01-01

    The Australian plant Acacia ligulata has a number of traditional food and medicinal uses by Australian Aboriginal people, although no bioactive compounds have previously been isolated from this species. Bioassay-guided fractionation of an ethanolic extract of the mature pods of A. ligulata led...... to the isolation of the two new echinocystic acid triterpenoid saponins, ligulatasides A (1) and B (2), which differ in the fine structure of their glycan substituents. Their structures were elucidated on the basis of 1D and 2D NMR, GC-MS, LC-MS/MS, and saccharide linkage analysis. These are the first isolated...... compounds from A. ligulata and the first fully elucidated structures of triterpenoid saponins from Acacia sensu stricto having echinocystic acid reported as the aglycone. Compounds 1 and 2 were evaluated for cytotoxic activity against a human melanoma cancer cell line (SK-MEL28) and a diploid fibroblast...

  1. Phenolic acids inhibit the formation of advanced glycation end products in food simulation systems depending on their reducing powers and structures.

    Science.gov (United States)

    Chen, Hengye; Virk, Muhammad Safiullah; Chen, Fusheng

    2016-06-01

    The concentration of advanced glycation end products (AGEs) in foods, which are formed by Maillard reaction, has demonstrated as risk factors associated with many chronic diseases. The AGEs inhibitory activities of five common phenolic acids (protocatechuic acid, dihydroferulic acid, p-coumaric acid, p-hydroxybenzoic acid and salicylic acid) with different chemical properties had been investigated in two food simulation systems (glucose-bovine serum albumin (BSA) and oleic acid-BSA). The results substantiated that the AGEs inhibitory abilities of phenolic acids in the oleic acid BSA system were much better than the glucose-BSA system for their strong reducing powers and structures. Among them, dihydrogenferulic acid showed strong inhibition of AGEs formation in oleic acid-BSA system at 0.01 mg/mL compared to nonsignificant AGEs inhibitory effect in oleic acid-BSA system at 10-fold higher concentration (0.1 mg/mL). This study suggests that edible plants rich in phenolic acids may be used as AGEs inhibitor during high-fat cooking.

  2. Structure of the human beta-ketoacyl [ACP] synthase from the mitochondrial type II fatty acid synthase

    DEFF Research Database (Denmark)

    Christensen, Caspar Elo; Kragelund, Birthe B; von Wettstein-Knowles, Penny

    2007-01-01

    Two distinct ways of organizing fatty acid biosynthesis exist: the multifunctional type I fatty acid synthase (FAS) of mammals, fungi, and lower eukaryotes with activities residing on one or two polypeptides; and the dissociated type II FAS of prokaryotes, plastids, and mitochondria with individual...... activities encoded by discrete genes. The beta-ketoacyl [ACP] synthase (KAS) moiety of the mitochondrial FAS (mtKAS) is targeted by the antibiotic cerulenin and possibly by the other antibiotics inhibiting prokaryotic KASes: thiolactomycin, platensimycin, and the alpha-methylene butyrolactone, C75. The high...... degree of structural similarity between mitochondrial and prokaryotic KASes complicates development of novel antibiotics targeting prokaryotic KAS without affecting KAS domains of cytoplasmic FAS. KASes catalyze the C(2) fatty acid elongation reaction using either a Cys-His-His or Cys-His-Asn catalytic...

  3. Modification of oligo-Ricinoleic Acid and Its Derivatives with 10-Undecenoic Acid via Lipase-Catalyzed Esterification

    Directory of Open Access Journals (Sweden)

    M. Claudia Montiel

    2012-04-01

    Full Text Available Lipases were employed under solvent-free conditions to conjugate oligo-ricinoleic acid derivatives with 10-undecenoic acid, to incorporate a reactive terminal double bond into the resultant product. First, undecenoic acid was covalently attached to oligo-ricinoleic acid using immobilized Candida antarctica lipase (CAL at a 30% yield. Thirty percent conversion also occurred for CAL-catalyzed esterification between undecenoic acid and biocatalytically-prepared polyglycerol polyricinoleate (PGPR, with attachment of undecenoic acid occurring primarily at free hydroxyls of the polyglycerol moiety. The synthesis of oligo-ricinoleyl-, undecenoyl- structured triacylglycerols comprised two steps. The first step, the 1,3-selective lipase-catalyzed interesterification of castor oil with undecenoic acid, occurred successfully. The second step, the CAL-catalyzed reaction between ricinoleyl-, undecenoyl structured TAG and ricinoleic acid, yielded approximately 10% of the desired structured triacylglycerols (TAG; however, a significant portion of the ricinoleic acid underwent self-polymerization as a side-reaction. The employment of gel permeation chromatography, normal phase HPLC, NMR, and acid value measurements was effective for characterizing the reaction pathways and products that formed.

  4. Spatial structure peculiarities of influenza A virus matrix M1 protein in an acidic solution that simulates the internal lysosomal medium.

    Science.gov (United States)

    Shishkov, Alexander; Bogacheva, Elena; Fedorova, Natalia; Ksenofontov, Alexander; Badun, Gennadii; Radyukhin, Victor; Lukashina, Elena; Serebryakova, Marina; Dolgov, Alexey; Chulichkov, Alexey; Dobrov, Evgeny; Baratova, Lyudmila

    2011-12-01

    The structure of the C-terminal domain of the influenza virus A matrix M1 protein, for which X-ray diffraction data were still missing, was studied in acidic solution. Matrix M1 protein was bombarded with thermally-activated tritium atoms, and the resulting intramolecular distribution of the tritium label was analyzed to assess the steric accessibility of the amino acid residues in this protein. This technique revealed that interdomain loops and the C-terminal domain of the protein are the most accessible to labeling with tritium atoms. A model of the spatial arrangement of the C-terminal domain of matrix M1 protein was generated using rosetta software adjusted to the data obtained by tritium planigraphy experiments. This model suggests that the C-terminal domain is an almost flat layer with a three-α-helical structure. To explain the high level of tritium label incorporation into the C-terminal domain of the M1 protein in an acidic solution, we also used independent experimental approaches (CD spectroscopy, limited proteolysis and MALDI-TOF MS analysis of the proteolysis products, dynamic light scattering and analytical ultracentrifugation), as well as multiple computational algorithms, to analyse the intrinsic protein disorder. Taken together, the results obtained in the present study indicate that the C-terminal domain is weakly structured. We hypothesize that the specific 3D structural peculiarities of the M1 protein revealed in acidic pH solution allow the protein greater structural flexibility and enable it to interact effectively with the components of the host cell. © 2011 The Authors Journal compilation © 2011 FEBS.

  5. Synthesis, Crystal Structure and Biological Activities of Novel Anthranilic(Isophthalic) Acid Esters

    Institute of Scientific and Technical Information of China (English)

    YAN Tao; YU Guan-ping; LIU Peng-fei; XIONG Li-xia; YU Shu-jing; LI Zheng-ming

    2012-01-01

    In search of environmentally benign insecticides with high activity,low toxicity and low resistance,a series of novel anthranilic(isophthalic) acid esters was designed and synthesized based on the structure of ryanodine modulating agent.All the compounds were characterized by 1H NMR spectra,elemental analysis or high resolution mass spectrometry(HRMS).The preliminary results of biological activity assessment indicate that some of the title compounds exhibit certain but unremarkable insecticidal activity against Mythimna separata Walker at 200 mg/L and fungicidal activities against five funguses at 50 mg/L.

  6. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

    International Nuclear Information System (INIS)

    Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei

    2013-01-01

    We introduce a Python-based program that utilizes the large database of 13 C and 15 N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13 C– 13 C, 15 N– 13 C, or 3D 15 N– 13 C– 13 C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13 C– 13 C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

  7. Crystal structures of two erbium(III complexes with 4-aminobenzoic acid and 4-chloro-3-nitrobenzoic acid

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2015-12-01

    Full Text Available The crystal structures of two erbium(III complexes with 4-aminobenzoic acid (4-ABAH, namely bis(μ2-4-aminobenzoato-κ2O:O′bis[bis(4-aminobenzoato-κ2O,O′diaquaerbium(III] dihydrate, [Er2(C7H6NO26(H2O4]·2H2O, (I, and 4-chloro-3-nitrobenzoic acid (CLNBAH, namely poly[hexakis(μ2-4-chloro-3-nitrobenzoato-κ2O:O′bis(dimethyl sulfoxide-κOdierbium(III], [Er2(C7H3ClNO46(C2H6OS2]n, (II, have been determined. In the structure of solvatomorphic compound (I, the symmetry-related irregular ErO8 coordination polyhedra in the discrete centrosymmetric dinuclear complex comprise two monodentate water molecules and six carboxylate O-atom donors, four from two bidentate carboxylate O,O′-chelate groups and two from the bis-monodentate O:O′-bridging group of the third 4-ABA anion. The Er—O bond-length range is 2.232 (3–2.478 (3 Å and the Er...Er separation in the dinuclear complex unit is 4.7527 (4 Å. One of the coordinating water molecules is involved in an intra-unit O—H...O hydrogen-bonding association with an inversion-related carboxylate O-atom acceptor. In contrast, the anhydrous compound (II is polymeric, based on centrosymmetric dinuclear repeat units comprising ErO7 coordination polyhedra which involve four O-atom donors from two bidentate O:O′-bridging carboxylate groups, one O-atom donor from the monodentate dimethyl sulfoxide ligand and two O-atom donors from the third bridging CLNBA anion. The latter provides the inter-unit link in the one-dimensional coordination polymer extending along [100]. The Er—O bond-length range in (II is 2.239 (6–2.348 (6 Å and the Er...Er separation within the dinuclear unit is 4.4620 (6 Å. In the crystal of (I, extensive inter-dimer O—H...O and N—H...O hydrogen-bonding interactions involving both the coordinating water molecules and the solvent water molecules, as well as the amine groups of the 4-ABA anions, give an overall three-dimensional network structure. Within

  8. Organic compounds containing methoxy and cyanoacrylic acid: Synthesis, characterization, crystal structures, and theoretical studies

    Energy Technology Data Exchange (ETDEWEB)

    Khalaji, A. D., E-mail: alidkhalaji@yahoo.com [Golestan University, Department of Chemistry, Faculty of Science (Iran, Islamic Republic of); Maddahi, E. [Iran University of Science & Technology, Ms.C Educated, Department of Chemistry (Iran, Islamic Republic of); Dusek, M.; Fejfarova, K. [Institute of Physics of the ASCR, v.v.i. (Czech Republic); Chow, T. J. [Academia Sinica, Institute of Chemistry (China)

    2015-12-15

    Metal-free organic compounds 24-SC ((E)-2-cyano-3-(2,4-dimethoxyphenyl)acrylic acid) and 34-SC ((E)-2-cyano-3-(3,4-dimethoxyphenyl)acrylic acid), containing methoxy groups as a donor and the acrylic acid as an acceptor were synthesized and characterized by CHN, FT-IR, UV-Vis, {sup 1}H-NMR and single crystal X-ray diffraction and used as photosensitizers for the application of dye-sensitized solar cells (DSSC). The sensitizing characteristics of them were evaluated. Both compounds contain the natural molecule, its anionic form and the piperidinium cation and they differ by number of these molecules in the asymmetric unit. To get further insight into the effect of molecular structure on the performance of DSSC, their geometry and energies of HOMO and LUMO were optimized by density functional theory calculation at the B3LYP/6-31G(d) level with Gaussian 03. Overall conversion efficiencies of 0.78 under full sunlight irradiation are obtained for DSSCs based on the new metal-free organic dyes 24-SC and 34-SC.

  9. Structure-based mechanism of lipoteichoic acid synthesis by Staphylococcus aureus LtaS

    Science.gov (United States)

    Lu, Duo; Wörmann, Mirka E.; Zhang, Xiaodong; Schneewind, Olaf; Gründling, Angelika; Freemont, Paul S.

    2009-01-01

    Staphylococcus aureus synthesizes polyglycerol-phosphate lipoteichoic acid (LTA) from phosphatidylglycerol. LtaS, a predicted membrane protein with 5 N-terminal transmembrane helices followed by a large extracellular part (eLtaS), is required for staphylococcal growth and LTA synthesis. Here, we report the first crystal structure of the eLtaS domain at 1.2-Å resolution and show that it assumes a sulfatase-like fold with an α/β core and a C-terminal part composed of 4 anti-parallel β-strands and a long α-helix. Overlaying eLtaS with sulfatase structures identified active site residues, which were confirmed by alanine substitution mutagenesis and in vivo enzyme function assays. The cocrystal structure with glycerol-phosphate and the coordination of a Mn2+ cation allowed us to propose a reaction mechanism, whereby the active site threonine of LtaS functions as nucleophile for phosphatidylglycerol hydrolysis and formation of a covalent threonine–glycerolphosphate intermediate. These results will aid in the development of LtaS-specific inhibitors for S. aureus and many other Gram-positive pathogens. PMID:19168632

  10. Crystal structures of Leishmania mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Hai, Yang; Christianson, David W.

    2016-03-16

    Leishmaniaarginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiatesde novopolyamine biosynthesis by catalyzing the hydrolysis of L-arginine to generate L-ornithine and urea. The product L-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray crystal structures ofL. mexicanaarginase complexed with α,α-disubstituted boronic amino-acid inhibitors based on the molecular scaffold of 2-(S)-amino-6-boronohexanoic acid are now reported. Structural comparisons with human and parasitic arginase complexes reveal interesting differences in the binding modes of the additional α-substituents,i.e.the D side chains, of these inhibitors. Subtle differences in the three-dimensional contours of the outer active-site rims among arginases from different species lead to different conformations of the D side chains and thus different inhibitor-affinity trends. The structures suggest that it is possible to maintain affinity while fine-tuning intermolecular interactions of the D side chain of α,α-disubstituted boronic amino-acid inhibitors in the search for isozyme-specific and species-specific arginase inhibitors.

  11. Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid β-glycosyltransferase Involved in Methicillin Resistance.

    Directory of Open Access Journals (Sweden)

    Solmaz Sobhanifar

    2016-12-01

    Full Text Available In recent years, there has been a growing interest in teichoic acids as targets for antibiotic drug design against major clinical pathogens such as Staphylococcus aureus, reflecting the disquieting increase in antibiotic resistance and the historical success of bacterial cell wall components as drug targets. It is now becoming clear that β-O-GlcNAcylation of S. aureus wall teichoic acids plays a major role in both pathogenicity and antibiotic resistance. Here we present the first structure of S. aureus TarS, the enzyme responsible for polyribitol phosphate β-O-GlcNAcylation. Using a divide and conquer strategy, we obtained crystal structures of various TarS constructs, mapping high resolution overlapping N-terminal and C-terminal structures onto a lower resolution full-length structure that resulted in a high resolution view of the entire enzyme. Using the N-terminal structure that encapsulates the catalytic domain, we furthermore captured several snapshots of TarS, including the native structure, the UDP-GlcNAc donor complex, and the UDP product complex. These structures along with structure-guided mutants allowed us to elucidate various catalytic features and identify key active site residues and catalytic loop rearrangements that provide a valuable platform for anti-MRSA drug design. We furthermore observed for the first time the presence of a trimerization domain composed of stacked carbohydrate binding modules, commonly observed in starch active enzymes, but adapted here for a poly sugar-phosphate glycosyltransferase.

  12. Neptunium(V) complexation by natural pyoverdins and related model compounds

    Energy Technology Data Exchange (ETDEWEB)

    Moll, H.; Glorius, M.; Bernhard, G. [Forschungszentrum Dresden-Rossendorf e.V., Inst. of Radiochemistry (Germany); Johnsson, A. [Goeteborg Univ., Microbiology, Dept. of Cell and Molecular Biology (Sweden); Univ. of Copenhagen, Dept. of Chemistry (Denmark); Schaefer, M.; Budzikiewicz, H. [Univ. zu Koeln, Inst. fuer Organische Chemie (Germany); Pedersen, K. [Goeteborg Univ., Microbiology, Dept. of Cell and Molecular Biology (Sweden)

    2010-07-01

    Ubiquitous fluorescent Pseudomonas species secrete bacterial pyoverdin-type siderophores. These bioligands have great potential to bind and transport actinides in the environment due to their hydroxamate and catechol functionalities. We investigated the unknown interaction of the neptunyl cation (NpO{sub 2}{sup +}) with pyoverdins (PYO) released by Pseudomonas fluorescens (CCUG 32456) cells and with simple hydroxamate (salicylhydroxamic acid: SHA and benzohydroxamic acid: BHA) and catechol (2,3-dihydroxynaphthalene: NAP) ligands using near-infrared (NIR) absorption spectroscopy over a wide pH range. NpO{sub 2}{sup +}-bioligand species of the M{sub x}L{sub y}H{sub z} type were identified from the spectrophotometric titrations in all four systems. The 1:1:2, 1:1:1, and 1:1:0 complexes were determined with the pyoverdins. In addition to 1:1 species, SHA, BHA, and NAP also form 1:2:0 species with NpO{sub 2}{sup +}. The stability constants of these neptunyl(V)-bioligand complexes and their individual spectroscopic properties are reported. Our findings indicate that NpO{sub 2}{sup +} has a stronger affinity to the catechol functionality of the pyoverdin molecule. The identified NpO{sub 2}{sup +}-PYO species belong to the strongest NpO{sub 2}{sup +} complexes with organic material reported so far. (orig.)

  13. Use of Calcium and Alendronic Acid Preparations in Correction of Structural and Functional Disorders of Bone Tissue in Thyrotoxicosis

    Directory of Open Access Journals (Sweden)

    O.B. Oliynyk

    2012-02-01

    Full Text Available Impact of calcium and alendronic acid preparations on disorders of structural and functional state of bone tissue in experimental animals at exogenic thyrotoxicosis was studied. It was defined that introduction of calcium preparations reduces bone mineral density loss in female rats with drug thyrotoxicosis, and combined use of calcium and alendronic acid prevents bone tissue loss regardless of thyrotoxicosis duration and presence of ovariectomy.

  14. Structural characterization of Fe−Pd nanowires grown by electrodeposition using an acid electrolyte

    Energy Technology Data Exchange (ETDEWEB)

    Domenichini, P. [Instituto Balseiro, Universidad Nacional de Cuyo, Av. Bustillo 9500, 8400 San Carlos de Bariloche (Argentina); Condó, A.M. [Instituto Balseiro, Universidad Nacional de Cuyo, Av. Bustillo 9500, 8400 San Carlos de Bariloche (Argentina); Centro Atómico Bariloche, Comisión Nacional de Energía Atómica, Av. Bustillo 9500, 8400 San Carlos de Bariloche (Argentina); Haberkorn, N., E-mail: nhaberk@cab.cnea.gov.ar [Instituto Balseiro, Universidad Nacional de Cuyo, Av. Bustillo 9500, 8400 San Carlos de Bariloche (Argentina); Centro Atómico Bariloche, Comisión Nacional de Energía Atómica, Av. Bustillo 9500, 8400 San Carlos de Bariloche (Argentina)

    2016-07-01

    Fe{sub 70}Pd{sub 30} nanostructures have potential application in actuators due to their conventional and magnetic shape memory. Here, we report the microstructure of electrodeposition grown Fe−Pd nanowires in which the process was confined to polycarbonate membranes with a nominal pore diameter of 200 nm. We used an acid electrolyte (pH ≈ 5) in which the solution was stabilized with sulfosalicylic acid. The average chemical concentration of the nanowires can be systematically shifted from rich palladium to rich iron by changing the growth potential. The study of the microstructure by transmission electron microscopy indicates high chemical inhomogeneities due to phase coexistence between rich palladium regions (with FCC structure) and rich iron regions. The latter present a combination of BCC and amorphous phases. The average chemical composition of the nanowires can be better adjusted by using a low frequency square wave voltage excitation (alternating rich Pd and rich Fe regions). However, independently of the growth process, the nanowires morphology collapses after thermal annealing. This could be ascribed to fragile grain boundaries due to the presence of amorphous hydroxides and chemical impurities produced during the electrochemical process. - Highlights: • Synthesis of Fe−Pd nanowires by electrodeposition is reported. • Structural characterization of the nanowires by transmission electron microscopy. • The synthesis of nanowires with austenitic phase is limited by fragile grain boundaries.

  15. Synthesis,crystal structure and properties of inorganic-organic hybrid polymers based on 8-hydroxylquinoline-5-sulfonic acid

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Two new inorganic-organic hybrid polymers, Mn(QS)(H2O) (1) and Co(QS)(H2O)2 (2) (H2QS=8-hydroxyl-quinoline-5-sulfonic acid), based on 8-hydroxylquinoline-5-sulfonate ligand, have been synthesized under solvothermal conditions and their structures were solved by single-crystal X-ray diffraction analysis. Compound 1 is a three-dimensional open framework with rutile topology structure, and compound 2 is a three-dimensional supramolecular structure. These compounds were characterized by powder XRD, infrared spectroscopy, thermogravimetric analysis, fluorescence properties and magnetism properties.

  16. Incorporation of 2(S)-methylbutanoic acid-1-14C into the structure of mevinolin

    International Nuclear Information System (INIS)

    Willard, A.K.; Smith, R.L.

    1982-01-01

    A route to mevinolin approximately equal to (1) bearing (S)-2-methylbutanoic acid -1- 14 C as the ester side chain has been developed. The structure of mevinolin approximately equal to (1) was degraded and selectively protected to provide the alcohol approximately equal to 3 in three steps. Incorporation of 14 C was accomplished by acylation of alcohol approximately equal to 3 with (R,S)-2-methylbutyryl chloride-1- 14 C. Cleavage of the silyl ether protecting group in the resulting mixture of esters approximately equal to 4 provided the two diastereoisomers approximately equal to 5 and approximately equal to 6 which were separated by reverse-phase liquid chromatography. Mevinolin - 14 C approximately equal to (5) was also converted to the ammonium salt approximately equal to 7 of the corresponding dihydroxy acid. (author)

  17. Prediction of protein structural classes by Chou's pseudo amino acid composition: approached using continuous wavelet transform and principal component analysis.

    Science.gov (United States)

    Li, Zhan-Chao; Zhou, Xi-Bin; Dai, Zong; Zou, Xiao-Yong

    2009-07-01

    A prior knowledge of protein structural classes can provide useful information about its overall structure, so it is very important for quick and accurate determination of protein structural class with computation method in protein science. One of the key for computation method is accurate protein sample representation. Here, based on the concept of Chou's pseudo-amino acid composition (AAC, Chou, Proteins: structure, function, and genetics, 43:246-255, 2001), a novel method of feature extraction that combined continuous wavelet transform (CWT) with principal component analysis (PCA) was introduced for the prediction of protein structural classes. Firstly, the digital signal was obtained by mapping each amino acid according to various physicochemical properties. Secondly, CWT was utilized to extract new feature vector based on wavelet power spectrum (WPS), which contains more abundant information of sequence order in frequency domain and time domain, and PCA was then used to reorganize the feature vector to decrease information redundancy and computational complexity. Finally, a pseudo-amino acid composition feature vector was further formed to represent primary sequence by coupling AAC vector with a set of new feature vector of WPS in an orthogonal space by PCA. As a showcase, the rigorous jackknife cross-validation test was performed on the working datasets. The results indicated that prediction quality has been improved, and the current approach of protein representation may serve as a useful complementary vehicle in classifying other attributes of proteins, such as enzyme family class, subcellular localization, membrane protein types and protein secondary structure, etc.

  18. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

    Energy Technology Data Exchange (ETDEWEB)

    Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

    2013-06-15

    We introduce a Python-based program that utilizes the large database of {sup 13}C and {sup 15}N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D {sup 13}C-{sup 13}C, {sup 15}N-{sup 13}C, or 3D {sup 15}N-{sup 13}C-{sup 13}C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D {sup 13}C-{sup 13}C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the C{alpha} and C{beta} chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-C{alpha}-C{beta} or N-C{alpha}-C{beta}), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

  19. Foliar Sprays of Citric Acid and Malic Acid Modify Growth, Flowering, and Root to Shoot Ratio of Gazania (Gazania rigens L.: A Comparative Analysis by ANOVA and Structural Equations Modeling

    Directory of Open Access Journals (Sweden)

    Majid Talebi

    2014-01-01

    Full Text Available Foliar application of two levels of citric acid and malic acid (100 or 300 mg L−1 was investigated on flower stem height, plant height, flower performance and yield indices (fresh yield, dry yield and root to shoot ratio of Gazania. Distilled water was applied as control treatment. Multivariate analysis revealed that while the experimental treatments had no significant effect on fresh weight and the flower count, the plant dry weight was significantly increased by 300 mg L−1 malic acid. Citric acid at 100 and 300 mg L−1 and 300 mg L−1 malic acid increased the root fresh weight significantly. Both the plant height and peduncle length were significantly increased in all applied levels of citric acid and malic acid. The display time of flowers on the plant increased in all treatments compared to control treatment. The root to shoot ratio was increased significantly in 300 mg L−1 citric acid compared to all other treatments. These findings confirm earlier reports that citric acid and malic acid as environmentally sound chemicals are effective on various aspects of growth and development of crops. Structural equations modeling is used in parallel to ANOVA to conclude the factor effects and the possible path of effects.

  20. Dermatan Sulfate Epimerase 1-Deficient Mice Have Reduced Content and Changed Distribution of Iduronic Acids in Dermatan Sulfate and an Altered Collagen Structure in Skin

    DEFF Research Database (Denmark)

    Maccarana, M.; Kalamajski, S.; Kongsgaard, M.

    2009-01-01

    Dermatan sulfate epimerase 1 (DS-epi1) and DS-epi2 convert glucuronic acid to iduronic acid in chondroitin/dermatan sulfate biosynthesis. Here we report on the generation of DS-epi1-null mice and the resulting alterations in the chondroitin/dermatan polysaccharide chains. The numbers of long blocks...... of adjacent iduronic acids are greatly decreased in skin decorin and biglycan chondroitin/dermatan sulfate, along with a parallel decrease in iduronic-2-O-sulfated-galactosamine-4-O-sulfated structures. Both iduronic acid blocks and iduronic acids surrounded by glucuronic acids are also decreased in versican......-derived chains. DS-epi1-deficient mice are smaller than their wild-type littermates but otherwise have no gross macroscopic alterations. The lack of DS-epi1 affects the chondroitin/dermatan sulfate in many proteoglycans, and the consequences for skin collagen structure were initially analyzed. We found...

  1. Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction.

    Science.gov (United States)

    López, Yosvany; Sharma, Alok; Dehzangi, Abdollah; Lal, Sunil Pranit; Taherzadeh, Ghazaleh; Sattar, Abdul; Tsunoda, Tatsuhiko

    2018-01-19

    Post-translational modification is considered an important biological mechanism with critical impact on the diversification of the proteome. Although a long list of such modifications has been studied, succinylation of lysine residues has recently attracted the interest of the scientific community. The experimental detection of succinylation sites is an expensive process, which consumes a lot of time and resources. Therefore, computational predictors of this covalent modification have emerged as a last resort to tackling lysine succinylation. In this paper, we propose a novel computational predictor called 'Success', which efficiently uses the structural and evolutionary information of amino acids for predicting succinylation sites. To do this, each lysine was described as a vector that combined the above information of surrounding amino acids. We then designed a support vector machine with a radial basis function kernel for discriminating between succinylated and non-succinylated residues. We finally compared the Success predictor with three state-of-the-art predictors in the literature. As a result, our proposed predictor showed a significant improvement over the compared predictors in statistical metrics, such as sensitivity (0.866), accuracy (0.838) and Matthews correlation coefficient (0.677) on a benchmark dataset. The proposed predictor effectively uses the structural and evolutionary information of the amino acids surrounding a lysine. The bigram feature extraction approach, while retaining the same number of features, facilitates a better description of lysines. A support vector machine with a radial basis function kernel was used to discriminate between modified and unmodified lysines. The aforementioned aspects make the Success predictor outperform three state-of-the-art predictors in succinylation detection.

  2. Molecular simulation of the water-triolein-oleic acid mixture: Local structure and thermodynamic properties

    Science.gov (United States)

    Couallier, E.; Riaublanc, A.; David Briand, E.; Rousseau, B.

    2018-05-01

    An artificial oil-in-water emulsion analogous to those found in bioresources or food matrices is simulated and studied experimentally. It is composed of one of the major natural free fatty acids (the oleic acid, OA) and the corresponding triacylglyceride (trioleic glyceride, or triolein, GTO). Because of the large time and length scales involved, the molecular simulations are done with the Martini force field, a coarse-grained model. This allowed us to study the water-OA-GTO system at different compositions with more than 20 000 molecules and up to 2 μs. Interfacial tension was measured using the pendant drop method and compared with molecular simulation results. We observe very good agreement at high OA concentrations and deviations up to 15% at low OA concentrations. The water solubility in the lipid phase is in fair agreement with experiments, between 0.03 and 0.32 mol/l, rising with the OA content. The area occupied by OA and GTO at the interface between water and the pure product fitted with experimental data (AOA = 36.6 Å2 and AGTO = 152.1 Å2). The consistency between simulation and experimental results allowed a structural analysis of the interface. A bilayer structure of the lipids at the water/oil interface is proposed, containing preferentially oleic acid but also triolein. Through all these results, the usefulness of coarse-grained simulation for the description of water-oil interfacial organization is demonstrated. This method will be used later to bring local information on the organization of target compounds, necessary in biomass fractionation processes or food additive formulations, for example.

  3. Double-Stranded Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    2001-01-01

    A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker.......A novel class of compounds, known as peptide nucleic acids, form double-stranded structures with one another and with ssDNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker....

  4. Study on the Activation of Scheelite and Wolframite by Lead Nitrate

    Directory of Open Access Journals (Sweden)

    Gang Zhao

    2015-04-01

    Full Text Available The activation of scheelite and wolframite by lead nitrate with benzohydroxamic acid (BHA as collector was investigated by means of micro flotation test, zeta potential measurement, X-ray photoelectron spectroscopy (XPS analyses and density functional theory (DFT calculation. The flotation results confirmed that the addition of lead nitrate can markedly enhance the recovery of scheelite and wolframite. In the zeta potential curves obvious positive shifts were observed with the presence of lead nitrate. Lead was detected on mineral surface in microscopic analysis and the survey XP spectra. Both the electrokinetic study and XPS analyses indicated that lead ion can be adsorbed onto mineral surface. In DFT calculation, the coordination model of BHA with metal hydroxyl ions (Ca(OH+, Mn(OH+, Fe(OH+ and Pb(OH+ was simulated and their binding energy were also calculated. The calculated results revealed that the binding ability of BHA and Pb(OH+ is the strongest, indicating that BHA can preferentially coordinate with Pb ion compared with Ca, Mn and Fe ions.

  5. Structural features of dilute acid, steam exploded, and alkali pretreated mustard stalk and their impact on enzymatic hydrolysis.

    Science.gov (United States)

    Kapoor, Manali; Raj, Tirath; Vijayaraj, M; Chopra, Anju; Gupta, Ravi P; Tuli, Deepak K; Kumar, Ravindra

    2015-06-25

    To overcome the recalcitrant nature of biomass several pretreatment methodologies have been explored to make it amenable to enzymatic hydrolysis. These methodologies alter cell wall structure primarily by removing/altering hemicelluloses and lignin. In this work, alkali, dilute acid, steam explosion pretreatment are systematically studied for mustard stalk. To assess the structural variability after pretreatment, chemical analysis, surface area, crystallinity index, accessibility of cellulose, FT-IR and thermal analysis are conducted. Although the extent of enzymatic hydrolysis varies upon the methodologies used, nevertheless, cellulose conversion increases from adsorption capacity. However, no such relationship is observed for xylose yield. Mass balance of the process is also studied. Dilute acid pretreatment is the best methodology in terms of maximum sugar yield at lower enzyme loading. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Structures of hydroxy fatty acids as the constituents of triacylglycerols in Philippine wild edible mushroom, Ganoderma lucidum

    Science.gov (United States)

    Edible Philippine mushrooms including Ganoderma lucidum have many health benefits. We have recently reported the identities and the contents of 77 molecular species of acylglycerols containing hydroxy fatty acids (HFA) in this mushroom. The structures of these HFA were proposed using the electrospra...

  7. Abscisic acid perception and signaling: structural mechanisms and applications

    Science.gov (United States)

    Ng, Ley Moy; Melcher, Karsten; Teh, Bin Tean; Xu, H Eric

    2014-01-01

    Adverse environmental conditions are a threat to agricultural yield and therefore exert a global effect on livelihood, health and the economy. Abscisic acid (ABA) is a vital plant hormone that regulates abiotic stress tolerance, thereby allowing plants to cope with environmental stresses. Previously, attempts to develop a complete understanding of the mechanisms underlying ABA signaling have been hindered by difficulties in the identification of bona fide ABA receptors. The discovery of the PYR/PYL/RCAR family of ABA receptors therefore represented a major milestone in the effort to overcome these roadblocks; since then, many structural and functional studies have provided detailed insights into processes ranging from ABA perception to the activation of ABA-responsive gene transcription. This understanding of the mechanisms of ABA perception and signaling has served as the basis for recent, preliminary developments in the genetic engineering of stress-resistant crops as well as in the design of new synthetic ABA agonists, which hold great promise for the agricultural enhancement of stress tolerance. PMID:24786231

  8. DFT approach to (benzylthio)acetic acid: Conformational search, molecular (monomer and dimer) structure, vibrational spectroscopy and some electronic properties

    Science.gov (United States)

    Sienkiewicz-Gromiuk, Justyna

    2018-01-01

    The DFT studies were carried out with the B3LYP method utilizing the 6-31G and 6-311++G(d,p) basis sets depending on whether the aim of calculations was to gain the geometry at equilibrium, or to calculate the optimized molecular structure of (benzylthio)acetic acid (Hbta) in the forms of monomer and dimer. The minimum conformational energy search was followed by the potential energy surface (PES) scan of all rotary bonds existing in the acid molecule. The optimized geometrical monomeric and dimeric structures of the title compound were compared with the experimental structural data in the solid state. The detailed vibrational interpretation of experimental infrared and Raman bands was performed on the basis of theoretically simulated ESFF-scaled wavenumbers calculated for the monomer and dimer structures of Hbta. The electronic characteristics of Hbta is also presented in terms of Mulliken atomic charges, frontier molecular orbitals and global reactivity descriptors. Additionally, the MEP and ESP surfaces were computed to predict coordination sites for potential metal complex formation.

  9. Structure-Activity Relationship Study of Ionotropic Glutamate Receptor Antagonist (2S,3R)-3-(3-Carboxyphenyl)pyrrolidine-2-carboxylic Acid

    DEFF Research Database (Denmark)

    Krogsgaard-Larsen, Niels; Storgaard, Morten; Møller, Charlotte

    2015-01-01

    Herein we describe the first structure-activity relationship study of the broad-range iGluR antagonist (2S,3R)-3-(3-carboxyphenyl)pyrrolidine-2-carboxylic acid (1) by exploring the pharmacological effect of substituents in the 4, 4', or 5' positions and the bioisosteric substitution of the distal...... carboxylic acid for a phosphonic acid moiety. Of particular interest is a hydroxyl group in the 4' position 2a which induced a preference in binding affinity for homomeric GluK3 over GluK1 (Ki = 0.87 and 4.8 μM, respectively). Two X-ray structures of ligand binding domains were obtained: 2e in GluA2-LBD...... and 2f in GluK1-LBD, both at 1.9 Å resolution. Compound 2e induces a D1-D2 domain opening in GluA2-LBD of 17.3-18.8° and 2f a domain opening in GluK1-LBD of 17.0-17.5° relative to the structures with glutamate. The pyrrolidine-2-carboxylate moiety of 2e and 2f shows a similar binding mode as kainate...

  10. Solid-state actinide acid phosphites from phosphorous acid melts

    International Nuclear Information System (INIS)

    Oh, George N.; Burns, Peter C.

    2014-01-01

    The reaction of UO 3 and H 3 PO 3 at 100 °C and subsequent reaction with dimethylformamide (DMF) produces crystals of the compound (NH 2 (CH 3 ) 2 )[UO 2 (HPO 2 OH)(HPO 3 )]. This compound crystallizes in space group P2 1 /n and consists of layers of uranyl pentagonal bipyramids that share equatorial vertices with phosphite units, separated by dimethylammonium. In contrast, the reaction of phosphorous acid and actinide oxides at 210 °C produces a viscous syrup. Subsequent dilution in solvents and use of standard solution-state methods results in the crystallization of two polymorphs of the actinide acid phosphites An(HPO 2 OH) 4 (An=U, Th) and of the mixed acid phosphite–phosphite U(HPO 3 )(HPO 2 OH) 2 (H 2 O)·2(H 2 O). α- and β-An(HPO 2 OH) 4 crystallize in space groups C2/c and P2 1 /n, respectively, and comprise a three-dimensional network of An 4+ cations in square antiprismatic coordination corner-sharing with protonated phosphite units, whereas U(HPO 3 )(HPO 2 OH) 2 (H 2 O) 2 ·(H 2 O) crystallizes in a layered structure in space group Pbca that is composed of An 4+ cations in square antiprismatic coordination corner-sharing with protonated phosphites and water ligands. We discuss our findings in using solid inorganic reagents to produce a solution-workable precursor from which solid-state compounds can be crystallized. - Graphical abstract: Reaction of UO 3 and H 3 PO 3 at 100 °C and subsequent reaction with DMF produces crystals of (NH 2 (CH 3 ) 2 )[UO 2 (HPO 2 OH)(HPO 3 )] with a layered structure. Reaction of phosphorous acid and actinide oxides at 210 °C produces a viscous syrup and further solution-state reactions result in the crystallization of the actinide acid phosphites An(HPO 2 OH) 4 (An=U, Th), with a three-dimensional network structure, and the mixed acid phosphite–phosphite U(HPO 3 )(HPO 2 OH) 2 (H 2 O) 2 ·(H 2 O) with a layered structure. - Highlights: • U(VI), U(IV) and Th(IV) phosphites were synthesized by solution

  11. Dielectric properties of supramolecular ionic structures obtained from multifunctional carboxylic acids and amines

    DEFF Research Database (Denmark)

    Gonzalez, Lidia; Yu, Liyun; Hvilsted, Søren

    2014-01-01

    The dielectric properties of several supramolecular ionic polymers and networks, linked by the ammonium salts of hexamethylene diamine (HMDA), tris(2-aminoethyl)amine (TAEA), poly(propylene imine) (PPI) dendrimers and two short bis carboxymethyl ether-terminated poly(ethylene glycol)s (Di......COOH-PEG), are reported in this paper. All supramolecular ionic polymers and networks exhibit very high relative dielectric permittivities ( 3 0 )( 10 2 – 10 6 ) at low frequencies, and signi fi cantly lower values (from 1 up to 26) at high frequencies. Additionally, the dielectric properties of supramolecular ionic......), are investigated. Here the relative dielectric permittivities of the supramolecular ionic structures formed with the multifunctional carboxylic acids were lower than those from the supramolecular ionic structures formed with the two carboxymethyl ether-terminated poly(ethylene glycol)s....

  12. Structural modification of trans-cinnamic acid using Colletotrichum acutatum

    OpenAIRE

    Velasco B., Rodrigo; Gil G., Jesús H.; García P., Carlos M.; Durango R., Diego L.

    2012-01-01

    The biotransformation of trans-cinnamic acid by whole cells of the Colombian native phytopathogenic fungus Colletotrichum acutatum was studied. Initially, fungitoxicity of this compound against C. acutatum was evaluated; trans-cinnamic acid exhibited a moderate to weak toxicity against the microorganism and apparently a detoxification mechanism was present. Then, in order to study such mechanism and explore the capacity of this fungus to biotransform trans-cinnamic acid into value-added produ...

  13. Combined effects of simulated acid rain and lanthanum chloride on chloroplast structure and functional elements in rice.

    Science.gov (United States)

    Hu, Huiqing; Wang, Lihong; Zhou, Qing; Huang, Xiaohua

    2016-05-01

    Acid rain and rare earth element (REE) pollution exist simultaneously in many agricultural regions. However, how REE pollution and acid rain affect plant growth in combination remains largely unknown. In this study, the combined effects of simulated acid rain and lanthanum chloride (LaCl3) on chloroplast morphology, chloroplast ultrastructure, functional element contents, chlorophyll content, and the net photosynthetic rate (P n) in rice (Oryza sativa) were investigated by simulating acid rain and rare earth pollution. Under the combined treatment of simulated acid rain at pH 4.5 and 0.08 mM LaCl3, the chloroplast membrane was smooth, proteins on this membrane were uniform, chloroplast structure was integrated, and the thylakoids were orderly arranged, and simulated acid rain and LaCl3 exhibited a mild antagonistic effect; the Mg, Ca, Mn contents, the chlorophyll content, and the P n increased under this combined treatment, with a synergistic effect of simulated acid rain and LaCl3. Under other combined treatments of simulated acid rain and LaCl3, the chloroplast membrane surface was uneven, a clear "hole" was observed on the surface of chloroplasts, and the thylakoids were dissolved and loose; and the P n and contents of functional elements (P, Mg, K, Ca, Mn, Fe, Ni, Cu, Zn and Mo) and chlorophyll decreased. Under these combined treatments, simulated acid rain and LaCl3 exhibited a synergistic effect. Based on the above results, a model of the combined effects of simulated acid rain and LaCl3 on plant photosynthesis was established in order to reveal the combined effects on plant photosynthesis, especially on the photosynthetic organelle-chloroplast. Our results would provide some references for further understanding the mechanism of the combined effects of simulated acid rain and LaCl3 on plant photosynthesis.

  14. The effect of amino acid backbone length on molecular packing: crystalline tartrates of glycine, β-alanine, γ-aminobutyric acid (GABA) and DL-α-aminobutyric acid (AABA).

    Science.gov (United States)

    Losev, Evgeniy; Boldyreva, Elena

    2018-02-01

    We report a novel 1:1 cocrystal of β-alanine with DL-tartaric acid, C 3 H 7 NO 2 ·C 4 H 6 O 6 , (II), and three new molecular salts of DL-tartaric acid with β-alanine {3-azaniumylpropanoic acid-3-azaniumylpropanoate DL-tartaric acid-DL-tartrate, [H(C 3 H 7 NO 2 ) 2 ] + ·[H(C 4 H 5 O 6 ) 2 ] - , (III)}, γ-aminobutyric acid [3-carboxypropanaminium DL-tartrate, C 4 H 10 NO 2 + ·C 4 H 5 O 6 - , (IV)] and DL-α-aminobutyric acid {DL-2-azaniumylbutanoic acid-DL-2-azaniumylbutanoate DL-tartaric acid-DL-tartrate, [H(C 4 H 9 NO 2 ) 2 ] + ·[H(C 4 H 5 O 6 ) 2 ] - , (V)}. The crystal structures of binary crystals of DL-tartaric acid with glycine, (I), β-alanine, (II) and (III), GABA, (IV), and DL-AABA, (V), have similar molecular packing and crystallographic motifs. The shortest amino acid (i.e. glycine) forms a cocrystal, (I), with DL-tartaric acid, whereas the larger amino acids form molecular salts, viz. (IV) and (V). β-Alanine is the only amino acid capable of forming both a cocrystal [i.e. (II)] and a molecular salt [i.e. (III)] with DL-tartaric acid. The cocrystals of glycine and β-alanine with DL-tartaric acid, i.e. (I) and (II), respectively, contain chains of amino acid zwitterions, similar to the structure of pure glycine. In the structures of the molecular salts of amino acids, the amino acid cations form isolated dimers [of β-alanine in (III), GABA in (IV) and DL-AABA in (V)], which are linked by strong O-H...O hydrogen bonds. Moreover, the three crystal structures comprise different types of dimeric cations, i.e. (A...A) + in (III) and (V), and A + ...A + in (IV). Molecular salts (IV) and (V) are the first examples of molecular salts of GABA and DL-AABA that contain dimers of amino acid cations. The geometry of each investigated amino acid (except DL-AABA) correlates with the melting point of its mixed crystal.

  15. Disruption of sugarcane bagasse lignocellulosic structure by means of dilute sulfuric acid pretreatment with microwave-assisted heating

    International Nuclear Information System (INIS)

    Chen, Wei-Hsin; Tu, Yi-Jian; Sheen, Herng-Kuang

    2011-01-01

    Highlights: → Pretreatment of dilute sulfuric acid on bagasse using microwave heating. → An increase in reaction temperature destroyed bagasse significantly. → Pretreated bagasse particles were characterized by fragmentation and swelling. → When the temperature was 190 o C, the fragmentation of particles became pronounced. → The influence of heating time on bagasse structure was not significant. - Abstract: Disruption of lignocellulosic structure of biomass plays a key role in producing bioethanol from lignocelluloses. This study investigated the impact of dilute sulfuric acid pretreatment on bagasse structure using microwave heating. Three reaction temperatures of 130, 160 and 190 o C with two heating times of 5 and 10 min were considered and a number of instruments were employed to analyze the properties of the bagasse particles. On account of microwave irradiation into the solution with dielectric heating, the experiments indicated that an increase in reaction temperature destroyed the lignocellulosic structure of bagasse in a significant way. The pretreated bagasse particles were simultaneously characterized by fragmentation and swelling. When the reaction temperature was as high as 190 o C, the fragmentation of particles became fairly pronounced so that the specific surface area of the pretreated material grew substantially. Meanwhile, almost all hemicellulose was removed from bagasse and the crystalline structure of cellulose disappeared. In contrast, the feature of lignin was remained clearly. However, a comparison between the heating times of 5 and 10 min revealed that the influence of the heating time on the lignocellulosic structure was not significant, indicating that the pretreatment with 5 min was sufficiently long.

  16. Bioreversible Derivatives of Phenol. 2. Reactivity of Carbonate Esters with Fatty Acid-like Structures Towards Hydrolysis in Aqueous Solutions

    Directory of Open Access Journals (Sweden)

    Claus Larsen

    2007-10-01

    Full Text Available A series of model phenol carbonate ester prodrugs encompassing derivatives with fatty acid-like structures were synthesized and their stability as a function of pH (range 0.4 – 12.5 at 37°C in aqueous buffer solutions investigated. The hydrolysis rates in aqueous solutions differed widely, depending on the selected pro-moieties (alkyl and aryl substituents. The observed reactivity differences could be rationalized by the inductive and steric properties of the substituent groups when taking into account that the mechanism of hydrolysis may change when the type of pro-moiety is altered, e.g. n-alkyl vs. t-butyl. Hydrolysis of the phenolic carbonate ester 2-(phenoxycarbonyloxy-acetic acid was increased due to intramolecular catalysis, as compared to the derivatives synthesized from ω-hydroxy carboxylic acids with longer alkyl chains. The carbonate esters appear to be less reactive towards specific acid and base catalyzed hydrolysis than phenyl acetate. The results underline that it is unrealistic to expect that phenolic carbonate ester prodrugs can be utilized in ready to use aqueous formulations. The stability of the carbonate ester derivatives with fatty acid-like structures, expected to interact with the plasma protein human serum albumin, proved sufficient for further in vitro and in vivo evaluation of the potential of utilizing HSA binding in combination with the prodrug approach for optimization of drug pharmacokinetics.

  17. Structural Modeling of Djenkolic Acid with Sulfur Replaced by Selenium and Tellurium

    Directory of Open Access Journals (Sweden)

    Petr Melnikov

    2014-04-01

    Full Text Available The comparative structural modeling of djenkolic acid and its derivatives containing selenium and tellurium in chalcogen sites (Ch = Se, Te has provided detailed information about the bond lengths and bond angles, filling the gap in what we know about the structural characteristics of these aminoacids. The investigation using the molecular mechanics technique with good approximation confirmed the available information on X-ray refinements for the related compounds methionine and selenomethionine, as well as for an estimate made earlier for telluromethionine. It was shown that the Ch-C(3 and Ch-C(4 bond lengths grow in parallel with the increasing anionic radii. Although the distances C-C, C-O, and C-N are very similar, the geometry of conformers is quite different owing to the possibility of rotation about four carbon atoms, hence the remarkable variability observed in dihedral angles. It was shown that the compounds contain a rigid block with two Ch atoms connected through a methylene group. The standard program Gaussian 03 with graphical interface Gaussview 4.1.2 has proved to be satisfactory tool for the structural description of less-common bioactive compositions when direct X-ray results are absent.

  18. Structure and acidity of individual Fluid Catalytic Cracking catalyst particles studied by synchrotron-based infrared micro-spectroscopy

    NARCIS (Netherlands)

    Buurmans, I.L.C.; Soulimani, F.; Ruiz Martinez, J.; van der Bij, H.E.; Weckhuysen, B.M.

    2013-01-01

    A synchrotron-based infrared micro-spectroscopy study has been conducted to investigate the structure as well as the Brønsted and Lewis acidity of Fluid Catalytic Cracking (FCC) catalyst particles at the individual particle level. Both fresh and laboratory-deactivated catalyst particles have been

  19. Determination of the Structure and Catalytic Mechanism of Sorghum bicolor Caffeic Acid O-Methyltransferase and the Structural Impact of Three brown midrib12 Mutations1[W

    Science.gov (United States)

    Green, Abigail R.; Lewis, Kevin M.; Barr, John T.; Jones, Jeffrey P.; Lu, Fachuang; Ralph, John; Vermerris, Wilfred; Sattler, Scott E.; Kang, ChulHee

    2014-01-01

    Using S-adenosyl-methionine as the methyl donor, caffeic acid O-methyltransferase from sorghum (Sorghum bicolor; SbCOMT) methylates the 5-hydroxyl group of its preferred substrate, 5-hydroxyconiferaldehyde. In order to determine the mechanism of SbCOMT and understand the observed reduction in the lignin syringyl-to-guaiacyl ratio of three brown midrib12 mutants that carry COMT gene missense mutations, we determined the apo-form and S-adenosyl-methionine binary complex SbCOMT crystal structures and established the ternary complex structure with 5-hydroxyconiferaldehyde by molecular modeling. These structures revealed many features shared with monocot ryegrass (Lolium perenne) and dicot alfalfa (Medicago sativa) COMTs. SbCOMT steady-state kinetic and calorimetric data suggest a random bi-bi mechanism. Based on our structural, kinetic, and thermodynamic results, we propose that the observed reactivity hierarchy among 4,5-dihydroxy-3-methoxycinnamyl (and 3,4-dihydroxycinnamyl) aldehyde, alcohol, and acid substrates arises from the ability of the aldehyde to stabilize the anionic intermediate that results from deprotonation of the 5-hydroxyl group by histidine-267. Additionally, despite the presence of other phenylpropanoid substrates in vivo, sinapaldehyde is the preferential product, as demonstrated by its low Km for 5-hydroxyconiferaldehyde. Unlike its acid and alcohol substrates, the aldehydes exhibit product inhibition, and we propose that this is due to nonproductive binding of the S-cis-form of the aldehydes inhibiting productive binding of the S-trans-form. The S-cis-aldehydes most likely act only as inhibitors, because the high rotational energy barrier around the 2-propenyl bond prevents S-trans-conversion, unlike alcohol substrates, whose low 2-propenyl bond rotational energy barrier enables rapid S-cis/S-trans-interconversion. PMID:24948836

  20. Insights on the structure and stability of Licanantase: a trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans

    Directory of Open Access Journals (Sweden)

    Fernando Abarca

    2014-08-01

    Full Text Available Licanantase (Lic is the major component of the secretome of Acidithiobacillus thiooxidans when grown in elemental sulphur. When used as an additive, Lic improves copper recovery from bioleaching processes. However, this recovery enhancement is not fully understood. In this context, our aim is to predict the 3D structure of Lic, to shed light on its structure-function relationships. Bioinformatics analyses on the amino acid sequence of Lic showed a great similarity with Lpp, an Escherichia coli Lipoprotein that can form stable trimers in solution. Lic and Lpp share the secretion motif, intracellular processing and alpha helix structure, as well as the distribution of hydrophobic residues in heptads forming a hydrophobic core, typical of coiled-coil structures. Cross-linking experiments showed the presence of Lic trimers, supporting our predictions. Taking the in vitro and in silico evidence as a whole, we propose that the most probable structure for Lic is a trimeric coiled-coil. According to this prediction, a suitable model for Lic was produced using the de novo algorithm “Rosetta Fold-and-Dock”. To assess the structural stability of our model, Molecular Dynamics (MD and Replica Exchange MD simulations were performed using the structure of Lpp and a 14-alanine Lpp mutant as controls, at both acidic and neutral pH. Our results suggest that Lic was the most stable structure among the studied proteins in both pH conditions. This increased stability can be explained by a higher number of both intermonomer hydrophobic contacts and hydrogen bonds, key elements for the stability of Lic’s secondary and tertiary structure.

  1. Structural insights into the dual strategy of recognition by peptidoglycan recognition protein, PGRP-S: structure of the ternary complex of PGRP-S with lipopolysaccharide and stearic acid.

    Directory of Open Access Journals (Sweden)

    Pradeep Sharma

    Full Text Available Peptidoglycan recognition proteins (PGRPs are part of the innate immune system. The 19 kDa Short PGRP (PGRP-S is one of the four mammalian PGRPs. The concentration of PGRP-S in camel (CPGRP-S has been shown to increase considerably during mastitis. The structure of CPGRP-S consists of four protein molecules designated as A, B, C and D forming stable intermolecular contacts, A-B and C-D. The A-B and C-D interfaces are located on the opposite sides of the same monomer leading to the the formation of a linear chain with alternating A-B and C-D contacts. Two ligand binding sites, one at C-D contact and another at A-B contact have been observed. CPGRP-S binds to the components of bacterial cell wall molecules such as lipopolysaccharide (LPS, lipoteichoic acid (LTA, and peptidoglycan (PGN from both gram-positive and gram-negative bacteria. It also binds to fatty acids including mycolic acid of the Mycobacterium tuberculosis (Mtb. Previous structural studies of binary complexes of CPGRP-S with LPS and stearic acid (SA have shown that LPS binds to CPGRP-S at C-D contact (Site-1 while SA binds to it at the A-B contact (Site-2. The binding studies using surface plasmon resonance showed that LPS and SA bound to CPGRP-S in the presence of each other. The structure determination of the ternary complex showed that LPS and SA bound to CPGRP-S at Site-1 and Site-2 respectively. LPS formed 13 hydrogen bonds and 159 van der Waals contacts (distances ≤4.2 Å while SA formed 56 van der Waals contacts. The ELISA test showed that increased levels of productions of pro-inflammatory cytokines TNF-α and IFN-γ due to LPS and SA decreased considerably upon the addition of CPGRP-S.

  2. Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China.

    Science.gov (United States)

    Jiang, Zhou; Li, Ping; Jiang, Dawei; Dai, Xinyue; Zhang, Rui; Wang, Yanhong; Wang, Yanxin

    2016-01-01

    Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73-0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41-95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.

  3. Preparation of three terbium complexes with p-aminobenzoic acid and investigation of crystal structure influence on luminescence property

    International Nuclear Information System (INIS)

    Ye Chaohong; Sun Haoling; Wang Xinyi; Li Junran; Nie Daobo; Fu Wenfu; Gao Song

    2004-01-01

    Three new rare earth p-aminobenzoic acid complexes, [Tb 2 L 6 (H 2 O) 2 ] n (1), [Tb 2 L 6 (H 2 O) 4 ].2H 2 O (2) and [Tb(phen) 2 L 2 (H 2 O) 2 ](phen)L·4H 2 O (3) (HL: p-aminobenzoic acid; phen: 1, 10-phenanthroline), with different structural forms are reported in this paper. Complex 1 is a polymolecule with a two-dimensional plane structure. Compound 2 is a binuclear molecule, and 3 appears to be a mononuclear complex. The fluorescence intensity, the fluorescence life-time and emission quantum yield of 2, which has two coordination water molecules, is better than those of 1, which has only one coordination water molecule. This is an unusual phenomenon for general fluorescent rare earth complexes. The fluorescence performance of 3 is the most unsatisfactory among the three complexes. Their crystal structures show that the coordination mode of the ligand is an important factor influencing the luminescence properties of a fluorescent rare earth complex

  4. The Role of Structural Enthalpy in Spherical Nucleic Acid Hybridization.

    Science.gov (United States)

    Fong, Lam-Kiu; Wang, Ziwei; Schatz, George C; Luijten, Erik; Mirkin, Chad A

    2018-05-23

    DNA hybridization onto DNA-functionalized nanoparticle surfaces (e.g., in the form of a spherical nucleic acid (SNA)) is known to be enhanced relative to hybridization free in solution. Surprisingly, via isothermal titration calorimetry, we reveal that this enhancement is enthalpically, as opposed to entropically, dominated by ∼20 kcal/mol. Coarse-grained molecular dynamics simulations suggest that the observed enthalpic enhancement results from structurally confining the DNA on the nanoparticle surface and preventing it from adopting enthalpically unfavorable conformations like those observed in the solution case. The idea that structural confinement leads to the formation of energetically more stable duplexes is evaluated by decreasing the degree of confinement a duplex experiences on the nanoparticle surface. Both experiment and simulation confirm that when the surface-bound duplex is less confined, i.e., at lower DNA surface density or at greater distance from the nanoparticle surface, its enthalpy of formation approaches the less favorable enthalpy of duplex formation for the linear strand in solution. This work provides insight into one of the most important and enabling properties of SNAs and will inform the design of materials that rely on the thermodynamics of hybridization onto DNA-functionalized surfaces, including diagnostic probes and therapeutic agents.

  5. Introduction to fatty acids and lipids.

    Science.gov (United States)

    Burdge, Graham C; Calder, Philip C

    2015-01-01

    The purpose of this article is to describe the structure, function and metabolism of fatty acids and lipids that are of particular importance in the context of parenteral nutrition. Lipids are a heterogeneous group of molecules that share the common property of hydrophobicity. Lipids range in structure from simple short hydrocarbon chains to more complex molecules, including triacylglycerols, phospholipids and sterols and their esters. Lipids within each class may differ structurally. Fatty acids are common components of complex lipids, and these differ according to chain length and the presence, number and position of double bonds in the hydrocarbon chain. Structural variation among complex lipids and among fatty acids gives rise to functional differences that result in different impacts upon metabolism and upon cell and tissue responses. Fatty acids and complex lipids exhibit a variety of structural variations that influence their metabolism and their functional effects. © 2015 S. Karger AG, Basel.

  6. Hydrothermal synthesis and crystal structure of a new lanthanum(III coordination polymer with fumaric acid

    Directory of Open Access Journals (Sweden)

    Hayet Anana

    2015-05-01

    Full Text Available The title compound, poly[diaquatris(μ4-but-2-enedioato(μ2-but-2-enedioic aciddilanthanum(III], [La2(C4H2O43(C4H4O4(H2O2]n, was synthesized by the reaction of lanthanum chloride pentahydrate with fumaric acid under hydrothermal conditions. The asymmetric unit comprises an LaIII cation, one and a half fumarate dianions (L2−, one a half-molecule of fumaric acid (H2L and one coordinated water molecule. Each LaIII cation has the same nine-coordinate environment and is surrounded by eight O atoms from seven distinct fumarate moieties, including one protonated fumarate unit and one water molecule in a distorted tricapped trigonal–prismatic environment. The LaO8(H2O polyhedra centres are edge-shared through three carboxylate bridges of the fumarate ligand, forming chains in three dimensions to construct the MOF. The crystal structure is stabilized by O—H...O hydrogen-bond interactions between the coordinated water molecule and the carboxylate O atoms, and also between oxygen atoms of fumaric acid

  7. A new classification of HLA-DRB1 alleles based on acid-base properties of the amino acids located at positions 13, 70 and 71: impact on ACPA status or structural progression, and meta-analysis on 1235 patients with rheumatoid from two cohorts (ESPOIR and EAC cohort).

    Science.gov (United States)

    Ruyssen-Witrand, Adeline; van Steenbergen, Hanna W; van Heemst, Jurgen; Gourraud, Pierre-Antoine; Nigon, Delphine; Lukas, Cédric; Miceli-Richard, Corinne; Jamard, Bénédicte; Cambon-Thomsen, Anne; Cantagrel, Alain; Dieudé, Philippe; van der Helm-van Mil, Annette H M; Constantin, Arnaud

    2015-01-01

    To group HLA-DRB1 alleles based on acid-base properties of amino acids at positions 13, 70 and 71 and analyse their association with the presence of anticitrullinated peptide antibodies (ACPA) and structural progression in 2 cohorts of early rheumatoid arthritis (RA). Patients with RA (N=612) from ESPOIR cohort and from EAC cohort (n=624) were genotyped for HLA-DRB1 alleles. The alleles containing the RAA sequence at positions 72-74 were classified into 3 groups according to the amino acid at positions 13, 70 and 71: BB encoding basic amino acids at positions 13, 70 and 71; A encoding acidic amino acids at positions 70 and 71; and BN encoding either neutral amino acids at position 13 and basic amino acids at positions 70 and 71, or basic amino acid at position 13 and neutral amino acids at positions 70 and 71. The associations between the different alleles and (1) the ACPA presence, and (2) the structural progression were assessed by χ(2) test; a meta-analysis was performed on the 2 cohorts using the Mantel-Haenszel method. After meta-analysis, BB alleles were significantly associated with ACPA presence (OR (95% CI) 4.08 (3.14 to 5.31)) and structural progression (OR (95% CI) 2.33 (1.76 to 3.09)). The alleles protected significantly against ACPA presence (OR (95% CI) 0.37 (0.28 to 0.50)) and structural progression (OR (95% CI) 0.34 (0.23 to 0.50)). This acid-base classification allowed to separate another group BN with an intermediate risk of ACPA production (OR (95% CI) 1.14 (0.91 to 1.44)) and structural progression (OR (95% CI) 1.01 (0.77 to 1.33)). This new classification permitted to make a hierarchy of HLA-DRB1 alleles in terms of association with ACPA presence or structural progression in early RA.

  8. Structure of a microbial community in soil after prolonged addition of low levels of simulated acid rain

    Science.gov (United States)

    Pennanen; Fritze; Vanhala; Kiikkila; Neuvonen; Baath

    1998-06-01

    Humus samples were collected 12 growing seasons after the start of a simulated acid rain experiment situated in the subarctic environment. The acid rain was simulated with H2SO4, a combination of H2SO4 and HNO3, and HNO3 at two levels of moderate acidic loads close to the natural anthropogenic pollution levels of southern Scandinavia. The higher levels of acid applications resulted in acidification, as defined by humus chemistry. The concentrations of base cations decreased, while the concentrations of exchangeable H+, Al, and Fe increased. Humus pH decreased from 3.83 to 3.65. Basal respiration decreased with decreasing humus pH, and total microbial biomass, measured by substrate-induced respiration and total amount of phospholipid fatty acids (PLFA), decreased slightly. An altered PLFA pattern indicated a change in the microbial community structure at the higher levels of acid applications. In general, branched fatty acids, typical of gram-positive bacteria, increased in the acid plots. PLFA analysis performed on the bacterial community growing on agar plates also showed that the relative amount of PLFA specific for gram-positive bacteria increased due to the acidification. The changed bacterial community was adapted to the more acidic environment in the acid-treated plots, even though bacterial growth rates, estimated by thymidine and leucine incorporation, decreased with pH. Fungal activity (measured as acetate incorporation into ergosterol) was not affected. This result indicates that bacteria were more affected than fungi by the acidification. The capacity of the bacterial community to utilize 95 different carbon sources was variable and only showed weak correlations to pH. Differences in the toxicities of H2SO4 and HNO3 for the microbial community were not found.

  9. CryoEM structure of the human SLC4A4 sodium-coupled acid-base transporter NBCe1.

    Science.gov (United States)

    Huynh, Kevin W; Jiang, Jiansen; Abuladze, Natalia; Tsirulnikov, Kirill; Kao, Liyo; Shao, Xuesi; Newman, Debra; Azimov, Rustam; Pushkin, Alexander; Zhou, Z Hong; Kurtz, Ira

    2018-03-02

    Na + -coupled acid-base transporters play essential roles in human biology. Their dysfunction has been linked to cancer, heart, and brain disease. High-resolution structures of mammalian Na + -coupled acid-base transporters are not available. The sodium-bicarbonate cotransporter NBCe1 functions in multiple organs and its mutations cause blindness, abnormal growth and blood chemistry, migraines, and impaired cognitive function. Here, we have determined the structure of the membrane domain dimer of human NBCe1 at 3.9 Å resolution by cryo electron microscopy. Our atomic model and functional mutagenesis revealed the ion accessibility pathway and the ion coordination site, the latter containing residues involved in human disease-causing mutations. We identified a small number of residues within the ion coordination site whose modification transformed NBCe1 into an anion exchanger. Our data suggest that symporters and exchangers utilize comparable transport machinery and that subtle differences in their substrate-binding regions have very significant effects on their transport mode.

  10. Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

    Science.gov (United States)

    Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

    2016-06-01

    Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

  11. Molecular Complex of Lumiflavin and 2-Aminobenzoic Acid : Crystal Structure, Crystal Spectra, and Solution Properties

    OpenAIRE

    Shieh, Huey-Sheng; Ghisla, Sandro; Hanson, Louise Karle; Ludwig, Martha L.; Nordman, Christer E.

    1981-01-01

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N402●C7H7N02●H2O)crystallizes from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 Å, c = 7.045 Å, α = 95.44°, β = 95.86°, and γ = 105.66°. The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating l...

  12. Crystal structures of eight 3D molecular adducts derived from bis-imidazole, bis(benzimidazole), and organic acids

    Science.gov (United States)

    Ding, Aihua; Jin, Shouwen; Jin, Shide; Hu, KaiKai; Lin, Zhihao; Liu, Hui; Wang, Daqi

    2018-01-01

    Cocrystallization of the bis(imidazole)/bis(benzimidazole) with a series of organic acids gave a total of eight molecular adducts with the compositions: (3,6-bis(imidazole-1-yl)pyridazine): (trichloroacetic acid)2(1) [(H2L1)2+ · (tca-)2, L1 = 3,6-bis(imidazole-1-yl)pyridazine, tca- = trichloroacetate], (bis(N-imidazolyl)methane): (suberic acid) (2) [(L2) · (H2suba), L2 = bis(N-imidazolyl)methane, H2suba = suberic acid], bis(N-imidazolyl)methane: (3-nitrophthalic acid): 3H2O (3) [(H2L2)2+ · (3-Hnpa-)2 · 3H2O, 3-Hnpa- = 3-nitro hydrogenphthalate], (bis(N-imidazolyl)butane)0.5: (4-nitrophthalic acid): H2O (4) [(H2L3)0.5+ · (4-Hnpa-)- · H2O, L3 = bis(N-imidazolyl)butane, 4-Hnpa- = 4-nitro hydrogenphthalate], (1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole): (3,5-dinitrosalicylic acid) (5) [(HL4) · (3,5-dns-), L4 = 1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole, 3,5-dns- = 3,5-dinitrosalicylate], (1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole): (3-nitrophthalic acid) (6) [(H2L4) · (3-npa2-), L4 = 1-(3-(1H-benzimidazol-1-yl)propyl)-1H-benzimidazole, 3-npa2-=3-nitrogenphthalate], (bis(N-imidazolyl)butane): (pamoic acid) (7) [(H2L3) · (pam), pam = pamoate], and (3,6-bis(imidazole-1-yl)pyridazine): (1,5-naphthalenedisulfonic acid) [(H2L1)2+ · (npda)2- = 1,5-naphthalenedisulfonate] (8). The eight adducts have been characterized by X-ray diffraction technique, infrared spectrum, and elemental analysis, and the melting points of all adducts were also reported. And their structural and supramolecular aspects are fully analyzed. The result reveals that among the eight investigated crystals both the end ring N in the bis(imidazole) moieties are protonated when the organic acids are deprotonated except 2, and 5, and the crystal packing is interpreted in terms of the strong ionic Nsbnd H⋯O H-bond between the imidazolium and the deprotonated acidic groups. Except the Nsbnd H⋯O H-bond, the Osbnd H⋯O H-bonds were also found at the salts 3, 4

  13. Enhanced Bio-hydrogen Production from Protein Wastewater by Altering Protein Structure and Amino Acids Acidification Type

    Science.gov (United States)

    Xiao, Naidong; Chen, Yinguang; Chen, Aihui; Feng, Leiyu

    2014-01-01

    Enhanced bio-hydrogen production from protein wastewater by altering protein structure and amino acids acidification type via pH control was investigated. The hydrogen production reached 205.2 mL/g-protein when protein wastewater was pretreated at pH 12 and then fermented at pH 10. The mechanism studies showed that pH 12 pretreatment significantly enhanced protein bio-hydrolysis during the subsequent fermentation stage as it caused the unfolding of protein, damaged the protein hydrogen bonding networks, and destroyed the disulfide bridges, which increased the susceptibility of protein to protease. Moreover, pH 10 fermentation produced more acetic but less propionic acid during the anaerobic fermentation of amino acids, which was consistent with the theory of fermentation type affecting hydrogen production. Further analyses of the critical enzymes, genes, and microorganisms indicated that the activity and abundance of hydrogen producing bacteria in the pH 10 fermentation reactor were greater than those in the control. PMID:24495932

  14. Enhanced bio-hydrogen production from protein wastewater by altering protein structure and amino acids acidification type.

    Science.gov (United States)

    Xiao, Naidong; Chen, Yinguang; Chen, Aihui; Feng, Leiyu

    2014-02-05

    Enhanced bio-hydrogen production from protein wastewater by altering protein structure and amino acids acidification type via pH control was investigated. The hydrogen production reached 205.2 mL/g-protein when protein wastewater was pretreated at pH 12 and then fermented at pH 10. The mechanism studies showed that pH 12 pretreatment significantly enhanced protein bio-hydrolysis during the subsequent fermentation stage as it caused the unfolding of protein, damaged the protein hydrogen bonding networks, and destroyed the disulfide bridges, which increased the susceptibility of protein to protease. Moreover, pH 10 fermentation produced more acetic but less propionic acid during the anaerobic fermentation of amino acids, which was consistent with the theory of fermentation type affecting hydrogen production. Further analyses of the critical enzymes, genes, and microorganisms indicated that the activity and abundance of hydrogen producing bacteria in the pH 10 fermentation reactor were greater than those in the control.

  15. Influence of the structure of bile acids on their partition coefficient in dibutyl ether and chloroform

    Directory of Open Access Journals (Sweden)

    Sebenji Ana S.

    2015-01-01

    Full Text Available Bile acids are well known natural surfactants able to modify the per­meability of biological membranes. The logarithm of partition coefficient between, tradi­tionally used, n-octanol and water is a measure of lipophilicity as a predictor of solute membrane partitioning. The aim of this work was to determine partition coefficients of bile acids in a mixture of water and chloroform and dibutyl ether at different pH values and with addition of different concentrations of sodium ions, and to examine the influence of the structure of bile acid nucleus on measured partition coefficients. Partition coefficients of three bile acid salts were determined using shake-flask method and the concentration of bile acids was determined after twelve hours of shaking at the room temperature in aqueous and organic layer using reversed phase HPLC with DAD detector on 210 nm. For all three analysed bile acid salts values of logP are lower in dibutyl ether than in chloroform. At certain pH values, curves representing the dependence of partition coeffi­cient on pH value intersect, and these are the pH values for which partition coefficients are the same for both solvents. Increasing the solution ionic strength, this intersection is shifted toward lower pH values. It is found that, for both organic solvents, after the addition of hy­droxyl group in the steroid nucleus (i.e. if the bile acid is less hydrophobic the value of logP falls, especially if more hydroxyl groups are present. With chloroform as a solvent, system quickly comes to excess with electrolyte ions than with dibutyl ether. [Projekat Ministarstva nauke Republike Srbije, br. 172021

  16. The antimicrobial efficacy and structure activity relationship of novel carbohydrate fatty acid derivatives against Listeria spp. and food spoilage microorganisms.

    Science.gov (United States)

    Nobmann, Patricia; Smith, Aoife; Dunne, Julie; Henehan, Gary; Bourke, Paula

    2009-01-15

    Novel mono-substituted carbohydrate fatty acid (CFA) esters and ethers were investigated for their antibacterial activity against a range of pathogenic and spoilage bacteria focussing on Listeria monocytogenes. Carbohydrate derivatives with structural differences enable comparative studies on the structure/activity relationship for antimicrobial efficacy and mechanism of action. The antimicrobial efficacy of the synthesized compounds was compared with commercially available compounds such as monolaurin and monocaprylin, as well as the pure free fatty acids, lauric acid and caprylic acid, which have proven antimicrobial activity. Compound efficacy was compared using an absorbance based broth microdilution assay to determine the minimum inhibitory concentration (MIC), increase in lag phase and decrease in maximum growth rate. Among the carbohydrate derivatives synthesized, lauric ether of methyl alpha-d-glucopyranoside and lauric ester of methyl alpha-d-mannopyranoside showed the highest growth-inhibitory effect with MIC values of 0.04 mM, comparable to monolaurin. CFA derivatives were generally more active against Gram positive bacteria than Gram negative bacteria. The analysis of both ester and ether fatty acid derivatives of the same carbohydrate, in tandem with alpha and beta configuration of the carbohydrate moiety suggest that the carbohydrate moiety is involved in the antimicrobial activity of the fatty acid derivatives and that the nature of the bond also has a significant effect on efficacy, which requires further investigation. This class of CFA derivatives has great potential for developing antibacterial agents relevant to the food industry, particularly for control of Listeria or other Gram-positive pathogens.

  17. 3.2.1. Synthesis, crystal and molecular structure of catena-(bis(µ1-oxalic acid-µ3-hydrogen oxalate-di-aqua-sodium(I.

    Directory of Open Access Journals (Sweden)

    Olga Kovalchukova*, Sergey Aldoshin, Andrey Utenyshev, Konstantin Bogenko, Valeriy Tkachev

    2015-07-01

    Full Text Available The crystal and molecular structure of catena-(bis(µ- oxalic acid-µ-hydrogen oxalate-di-aqua-sodium(I was detected by X-Ray analysis. The compound crystallizes in the triclinic space group P-1, with a(Å 6.2378(12; b(Å 7,1115(14; c(Å 10.489(2; α(° 94.65(3; β(° 100.12(3; γ(° 97.78(3. The sodium cation in the title compound is eight coordinated and forms a square antiprism. It is surrounded by two molecules of oxalic acid, one hydrogen oxalate anion and one water molecule. Both oxalic acid and hydrogen oxalate anion act as polydentate bridging ligands. Centrosymmetric sodium cations are bounded by hydrogen oxalate anions through a system of H bonds involving the molecules of oxalic acid. In the lattice, the 3D structure stabilized by H bonds is formed.

  18. Syntheses, structures, and photoluminescence of lanthanide coordination polymers based on 4-oxo-1,4-dihydro-2,6-pyridinedicarboxylic acid

    Energy Technology Data Exchange (ETDEWEB)

    Qian, Jing; Li, Lei; Peng, Jing-Wei; Qiao, Wei-Wei; Sun, Mei-Mei [College of Chemistry, Tianjin Normal University, Tianjin (China); Gu, Wen [College of Chemistry, Nankai University, Tianjin (China)

    2018-03-15

    Investigating the coordination chemistry of H{sub 2}CDA (4-oxo-1,4-dihydro-2,6-pyridinedicarboxylic acid) with rare earth salts Ln(NO{sub 3}){sub 3} under hydrothermal conditions, structure transformation phenomenon was observed. The ligand, H{sub 2}CDA charged to its position isomer, enol type structure, H{sub 3}CAM (4-hydroxypyridine-2,6-dicarboxylic acid). Six new lanthanide(III) coordination polymers with the formulas [Ln(CAM)(H{sub 2}O){sub 3}]{sub n} [Ln = La (1), Pr, (2)] and {[Ln(CAM)(H_2O)_3].H_2O}{sub n} [Ln = Nd, (3), Sm, (4), Eu, (5), Y, (6)] were synthesized and characterized. The X-ray structure analyses show two kinds of coordination structures. The complexes 1 and 2 and 3-6 are isostructural. Complexes 1 and 2 crystallize in the monoclinic C{sub 2}/c space group, whereas 3-6 crystallize in the monoclinic system with space group P2{sub 1}/n. In the two kinds of structures, H{sub 3}CAM displays two different coordination modes. The Sm{sup III} and Eu{sup III} complexes exhibit the corresponding characteristic luminescence in the visible region at an excitation of 376 nm. (copyright 2018 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. Carbobenzoxy amino acids: Structural requirements for cholecystokinin receptor antagonist activity

    International Nuclear Information System (INIS)

    Maton, P.N.; Sutliff, V.E.; Jensen, R.T.; Gardner, J.D.

    1985-01-01

    The authors used dispersed acini prepared from guinea pig pancreas to examine 28 carbobenzoxy (CBZ) amino acids for their abilities to function as cholecystokinin receptor antagonists. All amino acid derivatives tested, except for CBZ-alanine, CBZ-glycine, and N alpha-CBZ- lysine, were able to inhibit the stimulation of amylase secretion caused by the C-terminal octapeptide of cholecystokinin. In general, there was a good correlation between the ability of a carbobenzoxy amino acid to inhibit stimulated amylase secretion and the ability of the amino acid derivative to inhibit binding of 125 I-cholecystokinin. The inhibition of cholecystokinin-stimulated amylase secretion was competitive, fully reversible, and specific for those secretagogues that interact with the cholecystokinin receptor. The potencies with which the various carbobenzoxy amino acids inhibited the action of cholecystokinin varied 100-fold and CBZ-cystine was the most potent cholecystokinin receptor antagonist. This variation in potency was primarily but not exclusively a function of the hydrophobicity of the amino acid side chain

  20. Structure and properties of Al-MIL-53-ADP, a breathing MOF based on the aliphatic linker molecule adipic acid.

    Science.gov (United States)

    Reinsch, Helge; Pillai, Renjith S; Siegel, Renée; Senker, Jürgen; Lieb, Alexandra; Maurin, Guillaume; Stock, Norbert

    2016-03-14

    The new aluminium based metal-organic framework [Al(OH)(O2C-C4H8-CO2)]·H2O denoted as Al-MIL-53-ADP-lp (lp stands for large pore) was synthesised under solvothermal conditions. This solid is an analogue of the archetypical aluminium terephthalate Al-MIL-53 based on the aliphatic single-chain linker molecule adipic acid (H2ADP, hexanedioic acid). In contrast to its aromatic counterparts, Al-MIL-53-ADP exhibits a structural breathing behaviour solely upon dehydration/rehydration. The crystal structure of the anhydrous compound denoted as Al-MIL-53-ADP-np (np stands for narrow pore) was determined by a combination of forcefield-based computations and Rietveld refinement of the powder X-ray diffraction data while the structure of the hydrated form Al-MIL-53-ADP-lp was derived computationally by a combination of force field based methods and Density Functional Theory calculations. Both structures were further supported by (1)H, (13)C and (27)Al high-resolution NMR MAS 1D data coupled again with simulations. Al-MIL-53-ADP was further characterised by means of vibrational spectroscopy, elemental analysis, thermogravimetry and water vapour sorption.

  1. Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

    Directory of Open Access Journals (Sweden)

    Leitner Dietmar

    2005-04-01

    Full Text Available Abstract Background A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus trans peptide bond conformation of Xaa-Pro within proteins. For the analysis of the data sets different statistical methods such as the calculation of the Chou-Fasman parameters and occurrence matrices were used. Furthermore we analyzed the relationship between the relative solvent accessibility and the relative occurrence of prolines in the cis and in the trans conformation. Results One of the main results of the statistical investigations is the ranking of the secondary structure and sequence information with respect to the prediction of the Xaa-Pro peptide bond conformation. We observed a significant impact of secondary structure information on the occurrence of the Xaa-Pro peptide bond conformation, while the sequence information of amino acids neighboring proline is of little predictive value for the conformation of this bond. Conclusion In this work, we present an extensive analysis of the occurrence of the cis and trans proline conformation in proteins. Based on the data set, we derived patterns and rules for a possible prediction of the proline conformation. Upon adoption of the Chou-Fasman parameters, we are able to derive statistically relevant correlations between the secondary structure of amino acid fragments and the Xaa-Pro peptide bond conformation.

  2. Structure and photoluminescence property of complexes of aromatic carboxylic acid-functionalized polysulfone with Eu(Ⅲ) and Tb(Ⅲ)

    International Nuclear Information System (INIS)

    Gao, Baojiao; Qiao, Zongwen; Chen, Tao

    2014-01-01

    With chloromethylated polysulfone as starting substance, naphthoic acid (NA) and benzoic acid (BA) were bonded onto the side chains of polysulfone (PSF) via polymer reactions, obtaining two kinds of aromatic carboxyl acid-functionalized polysulfone, PSFNA and PSFBA. Subsequently, the luminescent binary and ternary polymer-rare earth complexes of Eu(Ⅲ) and Tb(Ⅲ) were prepared through coordination reactions, respectively, with PSFNA and PSFBA as macromolecule ligands and with 1,10-phenanthroline (Phen) and 4,4′-bipyridine (Bipy) as small-molecule co-ligands. This work focuses on investigating the relationship between structure and photoluminescence property of these complexes. The experimental results indicate that the macromolecule ligands PSFNA and PSFBA can strongly sensitize the fluorescence emissions of Eu 3+ ion or Tb 3+ ion, and the sensitization effect is strongly dependent on the structure of the ligands and the property of the central ions. The fluorescence emission of the binary complex PSF–(NA) 3 –Eu(Ⅲ) is stronger than that PSF–(BA) 3 –Eu(Ⅲ), suggesting the bonded ligand NA has stronger sensitization action for Eu 3+ ion than ligand BA; The binary complex PSF–(BA) 3 –Tb(Ⅲ) emit very strong characteristic fluorescence of Tb 3+ ion, displaying that ligand BA can strongly sensitize Tb 3+ ion, whereas PSF–(NA) 3 –Tb(Ⅲ) does not emit the characteristic fluorescence of Tb 3+ ion, showing that the bonded ligand NA does not sensitize Tb 3+ ion. The fluorescence intensity of the ternary complexes is stronger than that of the binary complexes in the same series. The solid films of these complexes also emit the strong characteristic fluorescence of Eu 3+ ion or Tb 3+ ion. - Highlights: • We prepared two kinds of aromatic carboxyl acid-functionalized polysulfone, PSFNA and PSFBA via polymer reaction. • Various binary and ternary luminescent polymer-rare earth complexes of Eu(Ⅲ) and Tb (Ⅲ) were obtained. • The relationship

  3. Molecular Features of Humic Acids and Fulvic Acids from Contrasting Environments

    NARCIS (Netherlands)

    Schellekens, Judith; Buurman, Peter; Kalbitz, Karsten; Zomeren, van Andre; Vidal-Torrado, Pablo; Cerli, Chiara; Comans, Rob N.J.

    2017-01-01

    Insight in the molecular structure of humic acid (HA) and fulvic acid (FA) can contribute to identify relationships between their molecular properties, and further our quantitative abilities to model important organic matter functions such as metal complexation and association with mineral

  4. Synthesis, crystal structure and optical property of three coordination polymer constructed from m-phenylenediacrylate acid

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, YiFan; Wang, TingTing; Zeng, HePing, E-mail: hpzeng@scut.edu.cn

    2015-01-15

    Three new complexes of the wholly deprotonated flexible ligand m-phenylenediacrylate acid (H{sub 2}mpda), namely, [Zn (mpda) (H{sub 2}O)] [1], [Pr{sub 2}(mpda){sub 2}(H{sub 2}O){sub 2}(CHOO){sub 2}] [2], and [Mn{sub 2}(mpda){sub 2} (H{sub 2}O){sub 4}] [3], were synthesized by the solvothermal reaction. The complexes were characterized by IR spectroscopy, thermogravimetric analysis, and X-ray single-crystal diffraction. A mixed sample [Nd(mpda)(H{sub 2}O)(CHOO)·Pr(mpda)(H{sub 2}O)(CHOO)] [2{sup ]} was also synthesized and studied. Compounds [1] and [2] exhibit a selective sensing function with respect to acetone, and they are a potential luminescent sensory material for the selective detection of Zn{sup 2+} and Ni{sup 2+} ions, respectively. Furthermore, the fluorescent changes of compound [1] upon the addition of cations (Fe{sup 3+} and Zn{sup 2+}, Bi{sup 2+} and Zn{sup 2+}) are utilized to construct two logic gates at the molecular level. - Graphical abstract: Three new complexes of flexible ligand m-phenylenedicarboxylic acid were synthesized by solvothermal reaction. Three metal−organic frameworks exhibiting 1D, 2D, 3D structures, respectively. - Highlights: • Three new complexes of m-phenylenedicarboxylic acid were synthesized. • Three metal−organic frameworks exhibiting 1D, 2D, 3D structures, respectively. • [1] and [2] exhibits a very high quenching effect with acetone. • [1] and [2] are a potential luminescent sensory material for Zn{sup 2+}, Ni{sup 2+} ions. • Two logic gates have been constructed using compound [1].

  5. Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China.

    Directory of Open Access Journals (Sweden)

    Zhou Jiang

    Full Text Available Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73-0.86. Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation, Sulfolobus (sulfur and iron oxidation, Metallosphaera and Acidicaldus (iron oxidation. Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41-95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.

  6. Synthesis, spectroscopy and antimicrobial activity of vanadium(III) and vanadium(IV) complexes involving Schiff bases derived from tranexamic acid and X-ray structure of Zwitter ion of tranexamic acid

    International Nuclear Information System (INIS)

    Shahzadi, S.; Ali, S.; Badshah, A.; Parvez, M.; Ahmed, E.; Malik, A.

    2007-01-01

    The synthesis of six new vanadium complexes of Schiff base derived from Tranexamic acid is reported. All the complexes were characterized by elemental analysis, infrared, electronic spectra, and mass spectrometry. FTIR data reveals that the Schiff base acts as a bidentate and the complexes exhibit the hexa-coordinated geometry in solid state. These complexes were screened for their biological activity against various bacterial and fungal strains. All the ligands show higher activity after complexation. The crystal structure of the Zwitter ion of the Tranexamic acid has been determined by X-ray single crystal diffraction [ru

  7. Structure-selective hot-spot Raman enhancement for direct identification and detection of trace penicilloic acid allergen in penicillin.

    Science.gov (United States)

    Zhang, Liying; Jin, Yang; Mao, Hui; Zheng, Lei; Zhao, Jiawei; Peng, Yan; Du, Shuhu; Zhang, Zhongping

    2014-08-15

    Trace penicilloic acid allergen frequently leads to various fatal immune responses to many patients, but it is still a challenge to directly discriminate and detect its residue in penicillin by a chemosensing way. Here, we report that silver-coated gold nanoparticles (Au@Ag NPs) exhibit a structure-selective hot-spot Raman enhancement capability for direct identification and detection of trace penicilloic acid in penicillin. It has been demonstrated that penicilloic acid can very easily link Au@Ag NPs together by its two carboxyl groups, locating itself spontaneously at the interparticle of Au@Ag NPs to form strong Raman hot-spot. At the critical concentration inducing the nanoparticle aggregation, Raman-enhanced effect of penicilloic acid is ~60,000 folds higher than that of penicillin. In particular, the selective Raman enhancement to the two carboxyl groups makes the peak of carboxyl group at C6 of penicilloic acid appear as a new Raman signal due to the opening of β-lactam ring of penicillin. The surface-enhanced Raman scattering (SERS) nanoparticle sensor reaches a sensitive limit lower than the prescribed 1.0‰ penicilloic acid residue in penicillin. The novel strategy to examine allergen is more rapid, convenient and inexpensive than the conventional separation-based assay methods. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Multicomponent hydrogen-bonding organic solids constructed from 6-hydroxy-2-naphthoic acid and N-heterocycles: Synthesis, structural characterization and synthon discussion

    Science.gov (United States)

    Zong, Yingxia; Shao, Hui; Pang, Yanyan; Wang, Debao; Liu, Kang; Wang, Lei

    2016-07-01

    Seven novel multicomponent crystals involving various substituted organic amine molecules and 6-hydroxy-2-naphthoic acid were prepared and characterized by using single crystal X-ray diffraction, infrared and thermogravimetric analyses (TGA). Crystal structures with 1,4-bis(imidazol) butane (L1) 1, 1,4-bis(imidazol-1-ylmethyl)benzene (L2) 2, 1-phenyl piperazine 3, 2-amino-4-hydroxy-6-methyl pyrimidine 4, 4,4'-bipyridine 5, 5,5'-dimethyl-2,2'-dipyridine 6, 2-amino-4,6-dimethyl pyrimidine 7 were determined. Among the seven molecular complexes, total proton transfer from 6-hydroxy-2-naphthoic acid to coformer has occurred in crystals 1-4, while the remaining were cocrystals. X-ray single-crystal structures of these complexes reveal that strong hydrogen bonding O-H···O/N-H···O/O-H···N and weak C-H···O/C-H···π/π···π intermolecular interactions direct the packing modes of molecular crystals together. The analysis of supramolecular synthons in the present structures shows that some classical supramolecular synthons like pyridine-carboxylic acid heterosynthon R22 (7) and aminopyridine-carboxylic acid heterosynthon R22 (8), are again observed in constructing the hydrogen-bonding networks in this paper. Besides, we noticed that water molecules act as a significant hydrogen-bonding connector in constructing supramolecular architectures of 3, 4, 6, and 7.

  9. Structural elucidation of the hormonal inhibition mechanism of the bile acid cholate on human carbonic anhydrase II

    Energy Technology Data Exchange (ETDEWEB)

    Boone, Christopher D. [University of Florida, PO Box 100267, Gainesville, FL 32610 (United States); Tu, Chingkuang [University of Florida, PO Box 100245, Gainesville, FL 32610 (United States); McKenna, Robert, E-mail: rmckenna@ufl.edu [University of Florida, PO Box 100267, Gainesville, FL 32610 (United States)

    2014-06-01

    The structure of human carbonic anhydrase II in complex with cholate has been determined to 1.54 Å resolution. Elucidation of the novel inhibition mechanism of cholate will aid in the development of a nonsulfur-containing, isoform-specific therapeutic agent. The carbonic anhydrases (CAs) are a family of mostly zinc metalloenzymes that catalyze the reversible hydration/dehydration of CO{sub 2} into bicarbonate and a proton. Human isoform CA II (HCA II) is abundant in the surface epithelial cells of the gastric mucosa, where it serves an important role in cytoprotection through bicarbonate secretion. Physiological inhibition of HCA II via the bile acids contributes to mucosal injury in ulcerogenic conditions. This study details the weak biophysical interactions associated with the binding of a primary bile acid, cholate, to HCA II. The X-ray crystallographic structure determined to 1.54 Å resolution revealed that cholate does not make any direct hydrogen-bond interactions with HCA II, but instead reconfigures the well ordered water network within the active site to promote indirect binding to the enzyme. Structural knowledge of the binding interactions of this nonsulfur-containing inhibitor with HCA II could provide the template design for high-affinity, isoform-specific therapeutic agents for a variety of diseases/pathological states, including cancer, glaucoma, epilepsy and osteoporosis.

  10. Structural stability of Amandin, a major allergen from almond (Prunus dulcis), and its acidic and basic polypeptides.

    Science.gov (United States)

    Albillos, Silvia M; Menhart, Nicholas; Fu, Tong-Jen

    2009-06-10

    Information relating to the resistance of food allergens to thermal and/or chemical denaturation is critical if a reduction in protein allergenicity is to be achieved through food-processing means. This study examined the changes in the secondary structure of an almond allergen, amandin, and its acidic and basic polypeptides as a result of thermal and chemical denaturation. Amandin ( approximately 370 kDa) was purified by cryoprecipitation followed by gel filtration chromatography and subjected to thermal (13-96 degrees C) and chemical (urea and dithiothreitol) treatments. Changes in the secondary structure of the protein were followed using circular dichroism spectroscopy. The secondary structure of the hexameric amandin did not undergo remarkable changes at temperatures up to 90 degrees C, although protein aggregation was observed. In the presence of a reducing agent, irreversible denaturation occurred with the following experimental values: T(m) = 72.53 degrees C (transition temperature), DeltaH = 87.40 kcal/mol (unfolding enthalpy), and C(p) = 2.48 kcal/(mol degrees C) (heat capacity). The concentration of urea needed to achieve 50% denaturation was 2.59 M, and the Gibbs free energy of chemical denaturation was calculated to be DeltaG = 3.82 kcal/mol. The basic and acidic polypeptides of amandin had lower thermal stabilities than the multimeric protein.

  11. Culturing bone marrow cells with dexamethasone and ascorbic acid improves osteogenic cell sheet structure.

    Science.gov (United States)

    Akahane, M; Shimizu, T; Kira, T; Onishi, T; Uchihara, Y; Imamura, T; Tanaka, Y

    2016-11-01

    To assess the structure and extracellular matrix molecule expression of osteogenic cell sheets created via culture in medium with both dexamethasone (Dex) and ascorbic acid phosphate (AscP) compared either Dex or AscP alone. Osteogenic cell sheets were prepared by culturing rat bone marrow stromal cells in a minimal essential medium (MEM), MEM with AscP, MEM with Dex, and MEM with Dex and AscP (Dex/AscP). The cell number and messenger (m)RNA expression were assessed in vitro, and the appearance of the cell sheets was observed after mechanical retrieval using a scraper. β-tricalcium phosphate (β-TCP) was then wrapped with the cell sheets from the four different groups and subcutaneously implanted into rats. After mechanical retrieval, the osteogenic cell sheets from the MEM, MEM with AscP, and MEM with Dex groups appeared to be fragmented or incomplete structures. The cell sheets cultured with Dex/AscP remained intact after mechanical retrieval, without any identifiable tears. Culture with Dex/AscP increased the mRNA and protein expression of extracellular matrix proteins and cell number compared with those of the other three groups. More bridging bone formation was observed after transplantation of the β-TCP scaffold wrapped with cell sheets cultured with Dex/AscP, than in the other groups. These results suggest that culture with Dex/AscP improves the mechanical integrity of the osteogenic cell sheets, allowing retrieval of the confluent cells in a single cell sheet structure. This method may be beneficial when applied in cases of difficult tissue reconstruction, such as nonunion, bone defects, and osteonecrosis.Cite this article: M. Akahane, T. Shimizu, T. Kira, T. Onishi, Y. Uchihara, T. Imamura, Y. Tanaka. Culturing bone marrow cells with dexamethasone and ascorbic acid improves osteogenic cell sheet structure. Bone Joint Res 2016;5:569-576. DOI: 10.1302/2046-3758.511.BJR-2016-0013.R1. © 2016 Akahane et al.

  12. Effects of Chain Length and Degree of Unsaturation of Fatty Acids on Structure and in Vitro Digestibility of Starch-Protein-Fatty Acid Complexes.

    Science.gov (United States)

    Zheng, Mengge; Chao, Chen; Yu, Jinglin; Copeland, Les; Wang, Shuo; Wang, Shujun

    2018-02-28

    The effects of chain length and degree of unsaturation of fatty acids (FAs) on structure and in vitro digestibility of starch-protein-FA complexes were investigated in model systems. Studies with the rapid visco analyzer (RVA) showed that the formation of ternary complex resulted in higher viscosities than those of binary complex during the cooling and holding stages. The results of differential scanning calorimetry (DSC), Raman, and X-ray diffraction (XRD) showed that the structural differences for ternary complexes were much less than those for binary complexes. Starch-protein-FA complexes presented lower in vitro enzymatic digestibility compared with starch-FAs complexes. We conclude that shorter chain and lower unsaturation FAs favor the formation of ternary complexes but decrease the thermal stability of these complexes. FAs had a smaller effect on the ordered structures of ternary complexes than on those of binary complexes and little effect on enzymatic digestibility of both binary and ternary complexes.

  13. Influence of indium-tin oxide surface structure on the ordering and coverage of carboxylic acid and thiol monolayers

    International Nuclear Information System (INIS)

    Cerruti, Marta; Rhodes, Crissy; Losego, Mark; Efremenko, Alina; Maria, Jon-Paul; Fischer, Daniel; Franzen, Stefan; Genzer, Jan

    2007-01-01

    This paper analyses the variability of self-assembled monolayers (SAMs) formation on ITO depending on the substrate surface features. In particular, we report on the formation of carboxylic acid- and thiol-based SAMs on two lots of commercially prepared indium-tin oxide (ITO) thin films. Contact angle measurements, electrochemical experiments, and near-edge x-ray absorption fine structure (NEXAFS) spectroscopy showed that the quality of monolayers formed differed substantially between the two ITO batches. Only one of the two ITO substrates was capable of forming well-organized thiol- and carboxylic acid-based SAMs. In order to rationalize these observations, atomic force microscopy and x-ray diffraction analyses were carried out, and SAMs were prepared on ITO substrates fabricated by sputtering in our laboratories. An attempt was made to influence the film microstructure and surface morphology by varying substrate temperatures during ITO deposition. Good-quality thiol and carboxylic acid SAMs were obtained on one of the ITO substrates prepared in-house. While our characterization could not single out conclusively one specific parameter in ITO surface structure that could be responsible for good SAMs formation, we could point out homogeneous surface morphology as a relevant factor for the quality of the SAMs. Evidence was also found for ITO crystallographic orientation to be a parameter influencing SAMs organization

  14. The importance of 1,2-dithiolane structure in α-lipoic acid for the downregulation of cell surface β1-integrin expression of human bladder cancer cells.

    Science.gov (United States)

    Yamasaki, Masao; Soda, Shozen; Sakakibara, Yoichi; Suiko, Masahito; Nishiyama, Kazuo

    2014-01-01

    Here, we show that cell surface β1-integrin expression, cell adhesion to fibronectin, migration, and invasion were all significantly inhibited by α-lipoic acid. These effects were not observed when cells were treated with dihydrolipoic acid or caprylic acid. These data reveal that the 1,2-dithiolane structure plays an important role in the action of α-lipoic acid.

  15. Structural and mechanistic studies on β-hydroxydecanoly thioester dehydrase and its inhibition by the suicide substrate, 3-decynoic acid, n-acetylcysteamine thioester

    International Nuclear Information System (INIS)

    Li, W.B.

    1987-01-01

    β-Hydroxydecanoyl thioester dehydrase catalyzes the interconversion of thioesters of (R)-3-hydroxydecanoic acid, (E)-2-decenoic acid, and (Z)-3-decenoic acid. Dehydrase is irreversibly inactivated by the N-acetylcysteamine thioester of 3-decynoic acid (3-decynoyl-NAC). This is the classic example of suicide enzyme inactivation. The structure of the dehydrase-inactivator adduct is still unclear. The purpose of this thesis is to determine the structure of the inactivator moiety and the stoichiometry of the inactivation of this dimeric enzyme, as well as to conduct structural studies on dehydrase itself. 3-[2- 13 C]Decynoyl-NAC was synthesized and incubated with homogeneous dehydrase. The spectra showed that dehydrase adds to the inactivator so as to quickly produce an (E)-3-(N/sup im/-histidinyl)-3-decenoyl thioester adduct at the active site. This species is slowly converted to the 2-decenoyl thioester congener. Titration of dehydrase with 3-[2 13 C]decynoyl-NAC under these conditions clearly indicated that 2 moles of inactivator are bound to each mole of dehydrase dimer. These experiments provide a self-consistent picture of dehydrase inactivation by 3-decynoyl-NAC and normal dehydrase-catalyzed reactions. Dehydrase was cleaved by chemical fragmentation, and the resulting mixture of peptides were separated by reversed-phase HPLC. Partial N-terminal sequences of purified peptides were obtained by automated Edman technology

  16. Silica promoted self-assembled mesoporous aluminas. Impact of the silica precursor on the structural, textural and acidic properties

    NARCIS (Netherlands)

    Perez, Lidia Lopez; Zarubina, Valeriya; Mayoral, Alvaro; Melian-Cabrera, Ignacio

    2015-01-01

    This paper investigates the effect of silica addition on the structural, textural and acidic properties of an evaporation induced self-assembled (EISA) mesoporous alumina. Two silica addition protocols were applied while maintaining the EISA synthesis route. The first route is based on the addition

  17. Detection of nucleic acid sequences by invader-directed cleavage

    Science.gov (United States)

    Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

  18. The first proton sponge-based amino acids: synthesis, acid-base properties and some reactivity.

    Science.gov (United States)

    Ozeryanskii, Valery A; Gorbacheva, Anastasia Yu; Pozharskii, Alexander F; Vlasenko, Marina P; Tereznikov, Alexander Yu; Chernov'yants, Margarita S

    2015-08-21

    The first hybrid base constructed from 1,8-bis(dimethylamino)naphthalene (proton sponge or DMAN) and glycine, N-methyl-N-(8-dimethylamino-1-naphthyl)aminoacetic acid, was synthesised in high yield and its hydrobromide was structurally characterised and used to determine the acid-base properties via potentiometric titration. It was found that the basic strength of the DMAN-glycine base (pKa = 11.57, H2O) is on the level of amidine amino acids like arginine and creatine and its structure, zwitterionic vs. neutral, based on the spectroscopic (IR, NMR, mass) and theoretical (DFT) approaches has a strong preference to the zwitterionic form. Unlike glycine, the DMAN-glycine zwitterion is N-chiral and is hydrolytically cleaved with the loss of glycolic acid on heating in DMSO. This reaction together with the mild decarboxylative conversion of proton sponge-based amino acids into 2,3-dihydroperimidinium salts under air-oxygen was monitored with the help of the DMAN-alanine amino acid. The newly devised amino acids are unique as they combine fluorescence, strongly basic and redox-active properties.

  19. Effects of SPORL and dilute acid pretreatment on substrate morphology, cell physical and chemical wall structures, and subsequent enzymatic hydrolysis of lodgepole pine.

    Science.gov (United States)

    Li, Xinping; Luo, Xiaolin; Li, Kecheng; Zhu, J Y; Fougere, J Dennis; Clarke, Kimberley

    2012-11-01

    The effects of pretreatment by dilute acid and sulfite pretreatment to overcome recalcitrance of lignocellulose (SPORL) on substrate morphology, cell wall physical and chemical structures, along with the subsequent enzymatic hydrolysis of lodgepole pine substrate were investigated. FE-SEM and TEM images of substrate structural morphological changes showed that SPORL pretreatment resulted in fiber separation, where SPORL high pH (4.2) pretreatment exhibited better fiber separation than SPORL low pH (1.9) pretreatment. Dilute acid pretreatment produced very poor fiber separation, consisting mostly of fiber bundles. The removal of almost all hemicelluloses in the dilute acid pretreated substrate did not overcome recalcitrance to achieve a high cellulose conversion when lignin removal was limited. SPORL high pH pretreatment removed more lignin but less hemicellulose, while SPORL low pH pretreatment removed about the same amount of lignin and hemicelluloses in lodgepole pine substrates when compared with dilute acid pretreatment. Substrates pretreated with either SPORL process had a much higher cellulose conversion than those produced with dilute acid pretreatment. Lignin removal in addition to removal of hemicellulose in SPORL pretreatment plays an important role in improving the cellulose hydrolysis of the substrate.

  20. New manganese (II) structures derived from 2,6-dichlorobenzoic acid: Syntheses, crystal structures and magnetism

    International Nuclear Information System (INIS)

    Esteves, D.; Tedesco, J.C.D.; Pedro, S.S.; Cruz, C.; Reis, M.S.; Brandão, P.

    2014-01-01

    One novel coordination polymer [Mn 2 (μ-2,6-DCBA) 3 (μ 2 -CH 3 CO 2 ) 2 (2H 2 O)]·2H 2 O (2,6-DCBA = 2,6-dichlorobenzoato) (compound 1) has been synthesized by self-assembly of bridging ligand 2,6-dichlorobenzoic acid and manganese acetate tetrahydrate. Single crystal X-ray diffraction analysis reveals that this compound crystallizes in space group P2 1 /c with a = 10.1547(7), b = 24.5829(2), c = 12.6606(2) Å, β = 93.707(3), V = 3153.9(3) Å 3 and Z = 4. The Mn(II) ions are connected by 2,6-DCBA and acetate group in μ-bridging mode to form 1D chains. Two water molecules are in the inter-layer space forming strong hydrogen bonds originating 2D layer structure. The preparation of this compound is very sensitive to the synthesis conditions, mainly to the solution pH and solvent yielding other two compounds 2 and 3. In compound 1 Mn(II) atoms in octahedral coordination are arranged in a zig–zag chain, with a trimeric structure repeated periodically along the chain, giving two exchange parameters: J 1 related to a syn–syn bond; and J 2 related to a bond of type anti–anti. A theoretical model was developed and then fitted to the magnetic susceptibility data, revealing an antiferromagnetic arrangement along the chain

  1. L-lysine-L-tartaric acid: New molecular complex with nonlinear optical properties. Structure, vibrational spectra and phase transitions

    International Nuclear Information System (INIS)

    Debrus, S.; Marchewka, M.K.; Baran, J.; Drozd, M.; Czopnik, R.; Pietraszko, A.; Ratajczak, H.

    2005-01-01

    The first X-ray diffraction and vibrational spectroscopic analysis of a novel complex between L-lysine and L-tartaric acid is reported. The structure was solved in two temperatures (320 and 260 K) showing incommensurate phase between them. Room-temperature powder infrared and Raman measurements for the L-lysine-L-tartaric acid molecular complex (1:1) were carried out. DSC measurements on powder samples indicate two phase transitions points at about 295, 300 and 293, 300 K, for heating and cooling, respectively, with noticeable temperature interval between them. Second harmonic generation efficiency d eff =0.35 d eff (KDP)

  2. Synthesis, structure, antitumor activity of novel pharmaceutical co-crystals based on bispyridyl-substituted α, β-unsaturated ketones with gallic acid

    Science.gov (United States)

    Liu, Lian-Dong; Liu, Shu-Lian; Liu, Zhi-Xian; Hou, Gui-Ge

    2016-05-01

    Three novel pharmaceutical co-crystals, (A)·(gallic acid) (1), (B)·(gallic acid) (2), and (C)·(gallic acid) (3) were generated based on 2,6-bis((pyridin-4-yl)methylene)cyclohexanone (A), N-methyl-3,5-bis((pyridin-3-yl)methylene)-4-piperidone (B), N-methyl-3,5-bis((pyridin-4-yl)methylene)-4-piperidone (C) with gallic acid, respectively. They are characterized by elemental analysis, FTIR spectroscopy, 1H NMR and single-crystal X-ray diffraction. Structural analysis reveals that two pharmaceutical ingredients link each other into H-bonding-driven 3D network in 1, 2, or 2D plane in 3. In addition, their antitumor activities against human neoplastic cell lines A549, SGC-7901, MCF-7, OVCA-433, HePG2 and cytotoxicity for HUVEC cell lines by CCK-8 method were evaluated primarily. Compared with gallic acid and free A, B and C, their antitumor activities have improved distinctly, while cytotoxicities have reduced markedly, especially for co-crystal 1. This is mainly because of the synergistic effect between pharmaceutical ingredients A, B, and C and gallic acid.

  3. RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.

    Science.gov (United States)

    Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

    2017-02-01

    Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

  4. N-Acetyl-9-O-L-lactylneuraminic acid, a new acylneuraminic acid from bovine submandibular gland

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Schauer, R.; Haverkamp, J.; Wember, M.; Kamerling, J.P.

    1976-01-01

    The acylneuraminic acid fraction, obtained on mild acid hydrolysis of glycoproteins from bovine submandibular glands, contains approximately 2 % N-acetyl-9-O-l-lactylneuraminic acid. The compound has been isolated and purified by ion-exchange and cellulose column chromatography. The structure has

  5. NMR determination of solvent dependent behavior and XRD structural properties of 4-carboxy phenylboronic acid: A DFT supported study

    Science.gov (United States)

    Dikmen, Gökhan; Alver, Özgür; Parlak, Cemal

    2018-04-01

    Solvent dependent structural properties of 4-carboxy phenylboronic acid (4-cpba) were investigated by X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) spectroscopic methods. The molecular structure and geometric parameters were determined by some computational methods such as B3LYP/6-31 + G(3df,p), HF/aug-cc-pvtz and MP2/6-31G(d). Detailed elucidation of the structural and spectroscopic properties of 4-cpba was carried out with 1H, HETCOR and DOSY NMR experiments. Solvent effects on the structural properties were monitored on the changes of 1H NMR spectra by using various solvents and it was observed that 4-cpba shows serious structural preferences depending on the solvent used.

  6. Copper(II) complexes with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid: Syntheses, crystal structures and antifungal activities

    International Nuclear Information System (INIS)

    Xiong, Pingping; Li, Jie; Bu, Huaiyu; Wei, Qing; Zhang, Ruolin; Chen, Sanping

    2014-01-01

    Reaction of Cu(II) with an asymmetric semi-rigid organic ligand 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid (HL), yielded five compounds, [Cu 0.5 L] n (1), [Cu(HL) 2 Cl 2 ] n (2), [Cu(HL) 2 Cl 2 (H 2 O)] (3), [Cu(L) 2 (H 2 O)] n (4) and [Cu(L)(phen)(HCO 2 )] n (5), which have been fully characterized by infrared spectroscopy, elemental analysis, and single-crystal X-ray diffraction. As for compounds 1, 2 and 5, Cu(II) is bridged through HL, Cl - , and formic acid, respectively, featuring 1D chain-structure. In compound 3, Cu(II) with hexahedral coordination sphere is assembled through hydrogen-bonding into 3D supramolecular framework. In compound 4, 1D chain units –Cu–O–Cu–O– are ligand-bridged into a 3D network. All compounds were tested on fungi (Fusarium graminearum, Altemaria solani, Macrophoma kawatsukai, Alternaria alternata and Colletotrichum gloeosporioides). Compound 1 exhibits a better antifungal effect compared to other compounds. An effect of structure on the antifungal activity has also been correlated. - Graphical abstract: Copper(II) compounds with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid, were prepared, structurally characterized and investigated for antifungal activity. - Highlights: • The title compounds formed by thermodynamics and thermokinetics. • The five compounds show higher inhibition percentage than reactants. • The structure effect on the antifungal activity

  7. Impact of α-amylase combined with hydrochloric acid hydrolysis on structure and digestion of waxy rice starch.

    Science.gov (United States)

    Li, Hongyan; Zhu, Yanqiao; Jiao, Aiquan; Zhao, Jianwei; Chen, Xiaoming; Wei, Benxi; Hu, Xiuting; Wu, Chunsen; Jin, Zhengyu; Tian, Yaoqi

    2013-04-01

    The structure and in vitro digestibility of native waxy rice starch by the combined hydrolysis of α-amylase and hydrochloric acid were investigated in this study. The combined hydrolysis technique generated higher hydrolysis rate and extent than the enzymatic hydrolysis. The granular appearance and chromatograph profile demonstrated that α-amylase and hydrochloric acid exhibited different patterns of hydrolysis. The rise in the ratio of absorbance 1047/1022cm(-1), the melting temperature range (Tc-To), and the melting enthalpy (ΔH) were observed during the combined hydrolysis. These results suggest that α-amylase simultaneously cleaves the amorphous and crystalline regions, whereas the amorphous regions of starch granules are preferentially hydrolyzed during the acid hydrolysis. Furthermore, the combined hydrolysis increased rapidly digestible starch (RDS) while decreased slowly digestible starch (SDS) and resistant starch (RS), indicating that the hydrolysis mode affected the digestion property of native waxy rice starch. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Human acid sphingomyelinase structures provide insight to molecular basis of Niemann–Pick disease

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Yan-Feng; Metcalf, Matthew C.; Garman, Scott C.; Edmunds, Tim; Qiu, Huawei; Wei, Ronnie R. (Sanofi Aventis); (UMASS, Amherst)

    2016-10-26

    Acid sphingomyelinase (ASM) hydrolyzes sphingomyelin to ceramide and phosphocholine, essential components of myelin in neurons. Genetic alterations in ASM lead to ASM deficiency (ASMD) and have been linked to Niemann–Pick disease types A and B. Olipudase alfa, a recombinant form of human ASM, is being developed as enzyme replacement therapy to treat the non-neurological manifestations of ASMD. Here we present the human ASM holoenzyme and product bound structures encompassing all of the functional domains. The catalytic domain has a metallophosphatase fold, and two zinc ions and one reaction product phosphocholine are identified in a histidine-rich active site. The structures reveal the underlying catalytic mechanism, in which two zinc ions activate a water molecule for nucleophilic attack of the phosphodiester bond. Docking of sphingomyelin provides a model that allows insight into the selectivity of the enzyme and how the ASM domains collaborate to complete hydrolysis. Mapping of known mutations provides a basic understanding on correlations between enzyme dysfunction and phenotypes observed in ASMD patients.

  9. Synthesis, structure and topological analysis of glycine templated highly stable cadmium sulfate framework: A New Lewis Acid catalyst

    Science.gov (United States)

    Paul, Avijit Kumar

    2018-04-01

    One new open-framework two-dimensional layer, [Cd(NH3CH2COO)(SO4)], I, has been synthesized using amino acid as templating agent. Single crystal structural analysis shows that the compound crystallizes in monoclinic cell with non-centrosymmetric space group P21, a = 4.9513(1) Å, b = 7.9763(2) Å, c = 8.0967(2) Å, β = 105.917(1)° and V = 307.504(12) Å3. The compound has connectivity between the Cd-centers and the sulfate units forming a two-dimensional layer structure. Sulfate unit is coordinated to metal center with η3, μ4 mode possessing a coordination free oxygen atom. The zwitterionic form of glycine molecule is present in the structure bridging with two metal centers through μ2-mode by carboxylate oxygens. The topological analysis reveals that the two-dimensional network is formed with a novel 4- and 6-connected binodal net of (32,42,52)(34,44,54,63) topology. Although one end of the glycine molecule is free from coordination, the structure is highly stable up to 350 °C. Strong N-H⋯ O hydrogen bonding interactions play an important role in the stabilization and formation of three-dimensional supramolecular structure. The cyanosilylation of imines using the present compounds as heterogeneous catalyst indicates good catalytic behavior. The present study illustrates the usefulness of the amino acid for the structure building in less studied sulfate based framework materials as well as designing of new heterogeneous catalysts for the broad application. The compound has also been characterized through elemental analysis, PXRD, IR, SEM and TG-DT studies.

  10. INTERESTERIFIKASI ENZIMATIS MINYAK IKAN DENGAN ASAM LAURAT UNTUK SINTESIS LIPID TERSTRUKTUR [Enzymatic Interesterification of Fish Oil with Lauric Acid for the Synthesis of Structured Lipid

    OpenAIRE

    Edy Subroto1); Chusnul Hidayat2); Supriyadi2)

    2008-01-01

    Structured lipid (SL) containing of medium chain fatty acid (MCFA) at outer position and polyunsaturated fatty acid (PUFA) at sn-2 position has superior dietary and absorption characteristics. The most methods for the enzymatic synthesis of SL were through two steps process, so that it was inefficient. Caprilic acid was usually used as a source of MCFA. In this research, SL was synthesized by enzymatic interesterification between fish oil and lauric acid. The specific lipase from Mucor miehei...

  11. Improving protein fold recognition and structural class prediction accuracies using physicochemical properties of amino acids.

    Science.gov (United States)

    Raicar, Gaurav; Saini, Harsh; Dehzangi, Abdollah; Lal, Sunil; Sharma, Alok

    2016-08-07

    Predicting the three-dimensional (3-D) structure of a protein is an important task in the field of bioinformatics and biological sciences. However, directly predicting the 3-D structure from the primary structure is hard to achieve. Therefore, predicting the fold or structural class of a protein sequence is generally used as an intermediate step in determining the protein's 3-D structure. For protein fold recognition (PFR) and structural class prediction (SCP), two steps are required - feature extraction step and classification step. Feature extraction techniques generally utilize syntactical-based information, evolutionary-based information and physicochemical-based information to extract features. In this study, we explore the importance of utilizing the physicochemical properties of amino acids for improving PFR and SCP accuracies. For this, we propose a Forward Consecutive Search (FCS) scheme which aims to strategically select physicochemical attributes that will supplement the existing feature extraction techniques for PFR and SCP. An exhaustive search is conducted on all the existing 544 physicochemical attributes using the proposed FCS scheme and a subset of physicochemical attributes is identified. Features extracted from these selected attributes are then combined with existing syntactical-based and evolutionary-based features, to show an improvement in the recognition and prediction performance on benchmark datasets. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Effect of octanols structure on their extraction ability as regards to rhenium(VII) in sulfuric acid solutions

    International Nuclear Information System (INIS)

    Kasikov, A.G.; Petrova, A.M.

    2007-01-01

    It is established that extraction ability of octanols as regards to rhenium(VII) and sulfuric acid depends on the structure of alcohol, but if in passage from octanol-1 to octanol-3 as regard to rhenium(VII) it rises, then for H 2 SO 4 it falls. Dependence of the distribution function of rhenium from the concentration of the acid has maximums at 4-7 mol l 1- that the most distinctly it becomes apparent for secondary alcohols. Decreasing the extraction ability of octyl alcohols with the growth of H 2 SO 4 concentration more than 7 mol l 1- is connected with the change of extractant composition and forms of rhenium(VII) being in the solution [ru

  13. Synthesis of 2-monoacylglycerols and structured triacylglycerols rich in polyunsaturated fatty acids by enzyme catalyzed reactions.

    Science.gov (United States)

    Rodríguez, Alicia; Esteban, Luis; Martín, Lorena; Jiménez, María José; Hita, Estrella; Castillo, Beatriz; González, Pedro A; Robles, Alfonso

    2012-08-10

    This paper studies the synthesis of structured triacylglycerols (STAGs) by a four-step process: (i) obtaining 2-monoacylglycerols (2-MAGs) by alcoholysis of cod liver oil with several alcohols, catalyzed by lipases Novozym 435, from Candida antartica and DF, from Rhizopus oryzae, (ii) purification of 2-MAGs, (iii) formation of STAGs by esterification of 2-MAGs with caprylic acid catalyzed by lipase DF, from R. oryzae, and (iv) purification of these STAGs. For the alcoholysis of cod liver oil, absolute ethanol, ethanol 96% (v/v) and 1-butanol were compared; the conditions with ethanol 96% were then optimized and 2-MAG yields of around 54-57% were attained using Novozym 435. In these 2-MAGs, DHA accounted for 24-31% of total fatty acids. In the operational conditions this lipase maintained a stable level of activity over at least 11 uses. These results were compared with those obtained with lipase DF, which deactivated after only three uses. The alcoholysis of cod liver oil and ethanol 96% catalyzed by Novozym 435 was scaled up by multiplying the reactant amounts 100-fold and maintaining the intensity of treatment constant (IOT=3g lipase h/g oil). In these conditions, the 2-MAG yield attained was about 67%; these 2-MAGs contained 36.6% DHA. The synthesized 2-MAGs were separated and purified from the alcoholysis reaction products by solvent extraction using solvents of low toxicity (ethanol and hexane); 2-MAG recovery yield and purity of the target product were approximately 96.4% and 83.9%, respectively. These 2-MAGs were transformed to STAGs using the optimal conditions obtained in a previous work. After synthesis and purification, 93% pure STAGs were obtained, containing 38% DHA at sn-2 position and 60% caprylic acid (CA) at sn-1,3 positions (of total fatty acids at these positions), i.e. the major TAG is the STAG with the structure CA-DHA-CA. Copyright © 2012 Elsevier Inc. All rights reserved.

  14. Docosahexaenoic acid triglyceride-based microemulsions with an added dendrimer - Structural considerations.

    Science.gov (United States)

    Lidich, Nina; Francesca Ottaviani, M; Hoffman, Roy E; Aserin, Abraham; Garti, Nissim

    2016-12-01

    Omega fatty acids, mainly the triglyceride of docosahexaenoic acid (TG-DHA), are considered important nutraceuticals. These compounds are water-insoluble and their transport across membranes depends on their carriers. Dendrimers are known as drug carriers across cell membranes and also as permeation enhancers. The solubilization of TG-DHA and dendrimer into a microemulsion (ME) system serving as a carrier could be used for a targeted delivery in the future. The interactions between TG-DHA and second generation poly(propyleneimine) dendrimers (PPI-G2) and their effect on structural transitions of ME were explored along the water dilution line using electron paramagnetic resonance and pulsed-gradient spin-echo NMR along with other analytical techniques. The microviscosity, order parameter, and micropolarity of all studied systems decrease upon water dilution. Incorporation of TG-DHA reduces the microviscosity, order, and micropolarity, whereas PPI-G2 leads to an increase in these parameters. The effect of PPI-G2 is more pronounced at relative high contents (1 and 5wt%) where PPI-G2 interacts with the hydrophilic headgroups of the surfactants. In the macroscale, the effects of TG-DHA and PPI-G2 differ mostly in the bicontinuous region, where macroviscosity increases upon TG-DHA incorporation and decreases upon solubilization of 5wt% PPI-G2. From DSC measurements it was concluded that in the presence of TG-DHA the PPI-G2 is intercalated easily at the interface. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Caldensinic acid, a benzoic acid derivative and others compounds from Piper carniconnectivum

    Energy Technology Data Exchange (ETDEWEB)

    Alves, Harley da Silva; Souza, Maria de Fatima Vanderlei de; Chaves, Maria Celia de Oliveira, E-mail: cchaves@ltf.ufpb.b [Universidade Federal da Paraiba (UFPB), Joao Pessoa, PB (Brazil). Lab. de Tecnologia Farmaceutica

    2010-07-01

    A benzoic acid derivative - caldensinic acid, E-phythyl hexadecanoate, {beta}-sitosterol and stigmasterol mixture and phaeophytin a were isolated from the aerial parts of Piper carniconnectivum. The structures of these compounds were established unambiguously by IR, MS, 1D and 2D NMR analysis. (author)

  16. Crystal structures of three co-crystals of 1,2-bis-(pyridin-4-yl)ethane with 4-alk-oxy-benzoic acids: 4-eth-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1), 4-n-propoxybenzoic acid-1,2-bis(pyridin-4-yl)ethane (2/1) and 4-n-but-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1).

    Science.gov (United States)

    Tabuchi, Yohei; Gotoh, Kazuma; Ishida, Hiroyuki

    2015-11-01

    The crystal structures of three hydrogen-bonded co-crystals of 4-alk-oxy-benzoic acid-1,2-bis-(pyridin-4-yl)ethane (2/1), namely, 2C9H10O3·C12H12N2, (I), 2C10H12O3·C12H12N2, (II), and 2C11H14O3·C12H12N2, (III), have been determined at 93, 290 and 93 K, respectively. In (I), the asymmetric unit consists of one 4-eth-oxy-benzoic acid mol-ecule and one half-mol-ecule of 1,2-bis-(pyridin-4-yl)ethane, which lies on an inversion centre. In (II) and (III), the asymmetric units each comprise two crystallographically independent 4-alk-oxy-benzoic acid mol-ecules and one 1,2-bis-(pyridin-4-yl)ethane mol-ecule. In each crystal, the two components are linked by O-H⋯N hydrogen bonds, forming a linear hydrogen-bonded 2:1unit of the acid and the base. Similar to the structure of 2:1 unit of (I), the units of (II) and (III) adopt nearly pseudo-inversion symmetry. The 2:1 units of (I), (II) and (III) are linked via C-H⋯O hydrogen bonds, forming tape structures.

  17. Acidic Ionic Liquids.

    Science.gov (United States)

    Amarasekara, Ananda S

    2016-05-25

    Ionic liquid with acidic properties is an important branch in the wide ionic liquid field and the aim of this article is to cover all aspects of these acidic ionic liquids, especially focusing on the developments in the last four years. The structural diversity and synthesis of acidic ionic liquids are discussed in the introduction sections of this review. In addition, an unambiguous classification system for various types of acidic ionic liquids is presented in the introduction. The physical properties including acidity, thermo-physical properties, ionic conductivity, spectroscopy, and computational studies on acidic ionic liquids are covered in the next sections. The final section provides a comprehensive review on applications of acidic ionic liquids in a wide array of fields including catalysis, CO2 fixation, ionogel, electrolyte, fuel-cell, membrane, biomass processing, biodiesel synthesis, desulfurization of gasoline/diesel, metal processing, and metal electrodeposition.

  18. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    chain, that is, after 34 A. The distance of a phosphorus atom from the fibre axis is 10. A. As the phosphates are on the outside, cations have easy access to them. The structure is an open one, and its water content is rather high. At lower water contents we would expect the bases to tilt so that the structure could become more.

  19. Structured triglycerides containing caprylic (8:0) and oleic (18:1) fatty acids reduce blood cholesterol concentrations and aortic cholesterol accumulation in hamsters.

    Science.gov (United States)

    Wilson, Thomas A; Kritchevsky, David; Kotyla, Timothy; Nicolosi, Robert J

    2006-03-01

    The effects of structured triglycerides containing one long chain fatty acid (oleic acid, C18:1) and one short chain saturated fatty acid (caprylic acid, 8:0) on lipidemia, liver and aortic cholesterol, and fecal neutral sterol excretion were investigated in male Golden Syrian hamsters fed a hypercholesterolemic regimen consisting of 89.9% commercial ration to which was added 10% coconut oil and 0.1% cholesterol (w/w). After 2 weeks on the HCD diet, the hamsters were bled, following an overnight fast (16 h) and placed into one of three dietary treatments of eight animals each based on similar plasma cholesterol levels. The hamsters either continued on the HCD diet or were placed on diets in which the coconut oil was replaced by one of two structured triglycerides, namely, 1(3),2-dicaproyl-3(1)-oleoylglycerol (OCC) or 1,3-dicaproyl-2-oleoylglycerol (COC) at 10% by weight. Plasma total cholesterol (TC) in hamsters fed the OCC and COC compared to the HCD were reduced 40% and 49%, respectively (Pstructured triglyceride oils had lower blood cholesterol levels and lower aortic accumulation of cholesterol compared to the control fed hamsters.

  20. Effects of nucleic acid local structure and magnesium ions on minus-strand transfer mediated by the nucleic acid chaperone activity of HIV-1 nucleocapsid protein

    OpenAIRE

    Wu, Tiyun; Heilman-Miller, Susan L.; Levin, Judith G.

    2007-01-01

    HIV-1 nucleocapsid protein (NC) is a nucleic acid chaperone, which is required for highly specific and efficient reverse transcription. Here, we demonstrate that local structure of acceptor RNA at a potential nucleation site, rather than overall thermodynamic stability, is a critical determinant for the minus-strand transfer step (annealing of acceptor RNA to (−) strong-stop DNA followed by reverse transcriptase (RT)-catalyzed DNA extension). In our system, destabilization of a stem-loop stru...

  1. SucStruct: Prediction of succinylated lysine residues by using structural properties of amino acids.

    Science.gov (United States)

    López, Yosvany; Dehzangi, Abdollah; Lal, Sunil Pranit; Taherzadeh, Ghazaleh; Michaelson, Jacob; Sattar, Abdul; Tsunoda, Tatsuhiko; Sharma, Alok

    2017-06-15

    Post-Translational Modification (PTM) is a biological reaction which contributes to diversify the proteome. Despite many modifications with important roles in cellular activity, lysine succinylation has recently emerged as an important PTM mark. It alters the chemical structure of lysines, leading to remarkable changes in the structure and function of proteins. In contrast to the huge amount of proteins being sequenced in the post-genome era, the experimental detection of succinylated residues remains expensive, inefficient and time-consuming. Therefore, the development of computational tools for accurately predicting succinylated lysines is an urgent necessity. To date, several approaches have been proposed but their sensitivity has been reportedly poor. In this paper, we propose an approach that utilizes structural features of amino acids to improve lysine succinylation prediction. Succinylated and non-succinylated lysines were first retrieved from 670 proteins and characteristics such as accessible surface area, backbone torsion angles and local structure conformations were incorporated. We used the k-nearest neighbors cleaning treatment for dealing with class imbalance and designed a pruned decision tree for classification. Our predictor, referred to as SucStruct (Succinylation using Structural features), proved to significantly improve performance when compared to previous predictors, with sensitivity, accuracy and Mathew's correlation coefficient equal to 0.7334-0.7946, 0.7444-0.7608 and 0.4884-0.5240, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers

    Science.gov (United States)

    Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

    2013-12-01

    Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

  3. Structural Characterization of the Degradation Products of a Minor Natural Sweet Diterpene Glycoside Rebaudioside M under Acidic Conditions

    Directory of Open Access Journals (Sweden)

    Indra Prakash

    2014-01-01

    Full Text Available Degradation of rebaudioside M, a minor sweet component of Stevia rebaudiana Bertoni, under conditions that simulated extreme pH and temperature conditions has been studied. Thus, rebaudioside M was treated with 0.1 M phosphoric acid solution (pH 2.0 and 80 °C temperature for 24 h. Experimental results indicated that rebaudioside M under low pH and higher temperature yielded three minor degradation compounds, whose structural characterization was performed on the basis of 1D (1H-, 13C- & 2D (COSY, HSQC, HMBC NMR, HRMS, MS/MS spectral data as well as enzymatic and acid hydrolysis studies.

  4. Effect of malic acid doping on the structural and superconducting properties of MgB2

    International Nuclear Information System (INIS)

    Ojha, N.; Sudesh; Stuti Rani; Varma, G.D.

    2010-01-01

    The samples have been prepared via standard solid state reaction route with nominal compositions MgB 2 + x wt% malic acid (x = 0, 5 and 10) by sintering at two different temperatures: 800 and 850 deg C in argon atmosphere. Improvement in upper critical fields (H c2 ) and irreversibility field (H irr ) of doped samples as compared to undoped samples have been observed. At 10 K, critical current densities (J c ) of the 5 and 10 wt% malic acid doped MgB 2 samples sintered at 850 deg C have higher values as compared to undoped sample sintered at the same temperature in the fields greater than 3 T. However, J c values of 5 wt% malic acid doped sample are higher than 10 wt% doped sample in the entire applied field region (0 - 7 T). In case of the samples sintered at 800 deg C improvement in J c values of 5 wt% doped sample have been found in entire field region as compared to undoped sample. On the other hand we see deterioration in J c values of 10 wt% doped samples sintered at 800 deg C as compared to undoped samples sintered at same temperature. The correlations between structural and superconducting properties will be described and discussed in this paper. (author)

  5. Trophic structure of cold-water coral communities revealed from the analysis of tissue isotopes and fatty acid composition

    NARCIS (Netherlands)

    Van Oevelen, D.; Duineveld, G.; Lavaleye, M.S.S.; Kutti, T.; Soetaert, K.

    2018-01-01

    The trophic structure of cold-water coral reef communities at two contrasting locations, the 800-m deep Belgica Mounds (Irish margin) and the 300-m deep Træna reefs (Norwegian Shelf), was investigated using stable isotope (δ13C and δ15N) and fatty-acid composition analysis. A broad range of

  6. Structure of trihydrated rare-earth acid diphosphates LnHP2O7·3H2O (Ln=La, Er)

    International Nuclear Information System (INIS)

    Ben Moussa, S.; Ventemillas, S.; Cabeza, A.; Gutierrez-Puebla, E.; Sanz, J.

    2004-01-01

    In trihydrated lanthanum acid-diphosphates LnHP 2 O 7 ·3H 2 O, prepared from acid LnCl 3 and Na 4 P 2 O 7 solutions (pH=1), two crystal forms were obtained. Layered structures of two representative members of this family have been determined by single-crystal X-ray diffraction (XRD) technique. In the case of orthorhombic LaHP 2 O 7 ·3H 2 O (type I), lanthanum cations are ninefold coordinated and diphosphate groups adopt a staggered (alternated) configuration. In the case of triclinic ErHP 2 O 7 ·3H 2 O (type II), erbium cations are eightfold coordinated and diphosphate groups adopt an eclipsed configuration. In agreement with Infrared (IR) spectroscopic data, a bended configuration for diphosphate groups has been deduced. In both structures, one-dimensional chains of edge-sharing rare-earth polyhedra are linked together by diphosphate groups to form the phosphate layers. In both diphosphates, PO 4 and HPO 4 environments have been identified by 31 P MAS-NMR technique. In the two compounds, OH groups of HPO 4 tetrahedra point out of diphosphate planes interacting with adjacent layers. In La-diphosphate, the interaction between HPO 4 groups and water molecules of adjacent layers is favored; however, in Er-diphosphate, the interaction between phosphate acid groups of contiguous layers is produced. Based on structural information deduced, differences detected in IR and NMR spectra of two disphosphates are discussed

  7. Revealing the Molecular Structural Transformation of Hardwood and Softwood in Dilute Acid Flowthrough Pretreatment

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Libing; Pu, Yunqiao; Cort, John R.; Ragauskas, Arthur J.; Yang, Bin

    2016-12-05

    To better understand the intrinsic recalcitrance of lignocellulosic biomass, the main hurdle to its efficient deconstruction, the effects of dilute acid flowthrough pretreatment on the dissolution chemistry of hemicellulose, cellulose, and lignin for both hardwood (e.g. poplar wood) and softwood (e.g. lodgepole pine wood) were investigated at temperatures of 200 °C to 270 °C and a flow rate of 25 mL/minute with 0.05% (w/w) H2SO4. Results suggested that the softwood cellulose was more readily to be degraded into monomeric sugars than that of hardwood under same pretreatment conditions. However, while the hardwood lignin was completely removed into hydrolysate, ~30% of the softwood lignin remained as solid residues under identical conditions, which was plausibly caused by vigorous C5-active recondensation reactions (C-C5). Unique molecular structural features that pronounced the specific recalcitrance of hardwood and softwood to dilute acid pretreatment were identified for the first time in this study, providing important insights to establish the effective biomass pretreatment.

  8. Podospermic acid, 1,3,5-tri-O-(7,8-dihydrocaffeoyl) quinic acid from Podospermum laciniatum (Asteraceae)

    DEFF Research Database (Denmark)

    Zidorn, Christian; Petersen, Bent O.; Udovicic ́, Vedrana

    2005-01-01

    A phytochemical investigation of Podospermum laciniatum (L.) DC. (Asteraceae) yielded the new quinic acid derivative podospermic acid (1,3,5-tridihydrocaffeoylquinic acid), which was named after the genus it was isolated from. The structure was established by HR mass spectrometry and extensive 1D...

  9. Isolation and structural characterization of sugarcane bagasse lignin after dilute phosphoric acid plus steam explosion pretreatment and its effect on cellulose hydrolysis

    Science.gov (United States)

    Jijiao Zeng; Zhaohui Tong; Letian Wang; J.Y. Zhu; Lonnie Ingram

    2014-01-01

    The structure of lignin after dilute phosphoric acid plus steam explosion pretreatment process of sugarcane bagasse in a pilot scale and the effect of the lignin extracted by ethanol on subsequent cellulose hydrolysis were investigated. The lignin structural changes caused by pretreatment were identified using advanced nondestructive techniques such as gel permeation...

  10. Copper(II) complexes with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid: Syntheses, crystal structures and antifungal activities

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Pingping [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi' an 710069 (China); Li, Jie [Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, Xi' an 710069 (China); Bu, Huaiyu, E-mail: 7213792@qq.com [Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, Xi' an 710069 (China); Wei, Qing [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi' an 710069 (China); Zhang, Ruolin [Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, Xi' an 710069 (China); Chen, Sanping, E-mail: sanpingchen@126.com [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi' an 710069 (China)

    2014-07-01

    Reaction of Cu(II) with an asymmetric semi-rigid organic ligand 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid (HL), yielded five compounds, [Cu{sub 0.5}L]{sub n} (1), [Cu(HL){sub 2}Cl{sub 2}]{sub n} (2), [Cu(HL){sub 2}Cl{sub 2}(H{sub 2}O)] (3), [Cu(L){sub 2}(H{sub 2}O)]{sub n} (4) and [Cu(L)(phen)(HCO{sub 2})]{sub n} (5), which have been fully characterized by infrared spectroscopy, elemental analysis, and single-crystal X-ray diffraction. As for compounds 1, 2 and 5, Cu(II) is bridged through HL, Cl{sup -}, and formic acid, respectively, featuring 1D chain-structure. In compound 3, Cu(II) with hexahedral coordination sphere is assembled through hydrogen-bonding into 3D supramolecular framework. In compound 4, 1D chain units –Cu–O–Cu–O– are ligand-bridged into a 3D network. All compounds were tested on fungi (Fusarium graminearum, Altemaria solani, Macrophoma kawatsukai, Alternaria alternata and Colletotrichum gloeosporioides). Compound 1 exhibits a better antifungal effect compared to other compounds. An effect of structure on the antifungal activity has also been correlated. - Graphical abstract: Copper(II) compounds with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid, were prepared, structurally characterized and investigated for antifungal activity. - Highlights: • The title compounds formed by thermodynamics and thermokinetics. • The five compounds show higher inhibition percentage than reactants. • The structure effect on the antifungal activity.

  11. How Does Amino Acid Ligand Modulate Au Core Structure and Characteristics in Peptide Coated Au Nanocluster?

    Science.gov (United States)

    Li, Nan; Li, Xu; Zhao, Hongkang; Zhao, Lina

    2018-03-01

    The atomic structures and the corresponding physicochemical properties of peptide coated Au nanoclusters determine their distinctive biological targeting applications. To learn the modulation of amino acid ligand on the atomic structure and electronic characteristics of coated Au core is the fundamental knowledge for peptide coated Au nanocluster design and construction. Based on our recent coated Au nanocluster configuration study (Nanoscale, 2016, 8, 11454), we built the typically simplified Au13(Cys-Au-Cys) system to more clearly learn the basic modulation information of amino acid ligand on Au core by the density functional theory (DFT) calculations. There are two isomers as ligand adjacent bonding (Iso1) and diagonal bonding (Iso2) to Au13 cores. The geometry optimizations indicate the adjacent bonding Iso1 is more stable than Iso2. More important, the Au13 core of Iso1 distorts much more significantly than that of Iso2 by Cys-Au-Cys bonding through the root-mean-square deviation (RMSD) analysis, which modulate their electronic characteristics in different ways. In addition, the frontier molecular orbital results of Au13(Cys-Au-Cys) isomers confirm that the Au cores mainly determine the blue shifts of Au13(Cys-Au-Cys) systems versus the original Au13 core in their UV-visible absorption spectrum studies. The configuration of Au13 core performs deformation under Cys-Au-Cys ligand modulation to reach new stability with distinct atomic structure and electronic properties, which could be the theory basis for peptide coated AuNCs design and construction.

  12. On the structure of [W6O19]2- anion in the structure of product from W(CO)6 reaction with dimethylformamide and formic acid

    International Nuclear Information System (INIS)

    Kirillova, N.I.; Kolomnikov, I.S.; Zolotarev, Yu.A.; Lysyak, T.V.; Struchkov, Yu.T.

    1977-01-01

    A complete X-ray structural investigation has been performed for the product of interacting W(CO) 6 with formic acid and DMPhA. It has been established that the crystals of the compound are triclinic: a=7.122; b=9.202; c=8.690 A; a=109.0; β=96.9; ν=93.2 deg; Z=1; right group P1. Centrally symmetrical anion [W 6 O 19 ] 2- is present in the structure with six W atoms located octahedrically around the central oxygen atom and united by 12 edge-bridge oxygen atoms; besides each W atom has one end oxoligand which ensures octahedral coordination for metal atoms

  13. Chromophore Structure of Photochromic Fluorescent Protein Dronpa: Acid-Base Equilibrium of Two Cis Configurations.

    Science.gov (United States)

    Higashino, Asuka; Mizuno, Misao; Mizutani, Yasuhisa

    2016-04-07

    Dronpa is a novel photochromic fluorescent protein that exhibits fast response to light. The present article is the first report of the resonance and preresonance Raman spectra of Dronpa. We used the intensity and frequency of Raman bands to determine the structure of the Dronpa chromophore in two thermally stable photochromic states. The acid-base equilibrium in one photochromic state was observed by spectroscopic pH titration. The Raman spectra revealed that the chromophore in this state shows a protonation/deprotonation transition with a pKa of 5.2 ± 0.3 and maintains the cis configuration. The observed resonance Raman bands showed that the other photochromic state of the chromophore is in a trans configuration. The results demonstrate that Raman bands selectively enhanced for the chromophore yield valuable information on the molecular structure of the chromophore in photochromic fluorescent proteins after careful elimination of the fluorescence background.

  14. Oleogels, a promising structured oil for decreasing saturated fatty acid concentrations: Production and food-based applications.

    Science.gov (United States)

    Pehlivanoğlu, Halime; Demirci, Mehmet; Toker, Omer Said; Konar, Nevzat; Karasu, Salih; Sagdic, Osman

    2018-05-24

    Oils and fats are widely used in the food formulations in order to improve nutritional and some quality characteristics of food products. Solid fats produced from oils by hydrogenization, interesterification, and fractionation processes are widely used in different foodstuffs for these aims. In recent years, consumer awareness of relation between diet and health has increased which can cause worry about solid fat including products in terms of their high saturated fatty acid and trans fatty acid contents. Therefore, different attempts have been carried out to find alternative ways to produce solid fat with low saturated fatty acid content. One of the promising ways is using oleogels, structuring oils with oleogelators. In this review, history, raw materials and production methods of the oleogels and their functions in oleogel quality were mentioned. Moreover, studies related with oleogel usage in different products were summarized and positive and negative aspects of oleogel were also mentioned. Considering the results of the related studies, it can be concluded that oleogels can be used in the formulation of bakery products, breakfast spreads, margarines, chocolates and chocolate-derived products and some of the meat products.

  15. Petrophysical and transport parameters evolution during acid percolation through structurally different limestones

    Science.gov (United States)

    Martinez Perez, Laura; Luquot, Linda

    2017-04-01

    Processes affecting geological media often show complex and unpredictable behavior due to the presence of heterogeneities. This remains problematic when facing contaminant transport problems, in the CO2 storage industry or dealing with the mechanisms underneath natural processes where chemical reactions can be observed during the percolation of rock non-equilibrated fluid (e.g. karst formation, seawater intrusion). To understand the mechanisms taking place in a porous medium as a result of this water-rock interaction, we need to know the flow parameters that control them, and how they evolve with time as a result of that concurrence. This is fundamental to ensure realistic predictions of the behavior of natural systems in response of reactive transport processes. We investigate the coupled influence of structural and hydrodynamic heterogeneities in limestone rock samples tracking its variations during chemical reactions. To do so we use laboratory petrophysical techniques such as helium porosimetry, gas permeability, centrifugue, electrical resistivity and sonic waves measurements to obtain the parameters that characterize flow within rock matrix (porosity, permeability, retention curve and pore size distribution, electrical conductivity, formation factor, cementation index and tortuosity) before and after percolation experiments. We built an experimental setup that allows injection of acid brine into core samples under well controlled conditions, monitor changes in hydrodynamic properties and obtain the chemical composition of the injected solution at different stages. 3D rock images were also acquired before and after the experiments using a micro-CT to locate the alteration processes and perform an acurate analysis of the structural changes. Two limestones with distinct textural classification and thus contrasting transport properties have been used in the laboratory experiments: a crinoid limestone and an oolithic limestone. Core samples dimensions were 1 inch

  16. An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides.

    Science.gov (United States)

    Plummer, Chelsea E; Stover, Michele L; Bokatzian, Samantha S; Davis, John T M; Dixon, David A; Cassady, Carolyn J

    2015-07-30

    Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

  17. Waht is 'molybdic acid' or 'polymolybdic acid'?

    International Nuclear Information System (INIS)

    Tytko, K.H.; Baethe, G.; Mehmke, K.

    1987-01-01

    According to a comparative study of the literature, supplemented by well-aimed experimental investigations and equilibrium calculations, the terms 'molybdic acid' or 'polymolybdic acid', used for many substances, species, or solutions in the literature, are applicable to a species, a solution, and two solids: a) The monomeric molybdic acid, most probably having the formula MoO 2 (OH) 2 (H 2 O) 2 (= H 2 MoO 4 , aq), exists in (aqueous) solution only and never exceeds a concentration of ∼ 10 -3 M since at higher concentrations it reacts with other monomeric molybdenum(VI) species to give anionic or cationic polymers. b) A concentrated (> 0.1 M Mo VI ) aqueous molybdate solution of degree of acidification P = 2 (realized, e.g., by a solution of one of the Mo VI oxides; by any molybdate solutions whose cations have been exchanged by H 2 O + on a cation exchanger; by suitable acidification of a molybdate solution) contains 8 H 3 O + and the well-known polyanion Mo 36 O 112 (H 2 O) 16 8- exactly in the stoichiometric proportions. c) A glassy substance, obtained from an alkali metal salt-free solution prepared acording to (b), refers to the compound (H 3 O) 8 [Mo 36 O 112 (H 2 O) 16 ] · xH 2 O, x = 25 - 29. d) A solid having the ideal composition [(H 3 O)Mo 5 O 15 (OH)H 2 O · H 2 O] ∞ consists of a polymolybdate skeleton (the well-known 'decamolybdate' structure), in the tunnels of which H 3 O + and H 2 O are intercalated. The structure is very unstable if only H 3 O + cations are present, but it is enormously stabilized by a partial exchange of H 3 O + by certain alkali or alkaline earth metal cations. For the compounds MoO 3 , MoO 3 ·H 2 O, and MoO 3 · 2 H 2 O the term 'molybdic acid' is unjustified. The commercial product 'molybdic acid, ∼ 85% MoO 3 ' is the well-known polymolybdate (NH 4 ) 2 O · 4 MoO 3 with a layer structure of the polyanion. 84 refs. (author)

  18. Anaerobic accumulation of short-chain fatty acids from algae enhanced by damaging cell structure and promoting hydrolase activity.

    Science.gov (United States)

    Feng, Leiyu; Chen, Yunzhi; Chen, Xutao; Duan, Xu; Xie, Jing; Chen, Yinguang

    2018-02-01

    Short-chain fatty acid (SCFAs) produced from harvested algae by anaerobic fermentation with uncontrolled pH was limited due to the solid cell structure of algae. This study, therefore, was undertaken to enhance the generation of SCFAs from algae by controlling the fermentation pH. pH influenced not only the total SCFAs production, but the percentage of individual SCFA. The maximal yield of SCFAs occurred at pH 10.0 and fermentation time of 6 d (3161 mg COD/L), which mainly contained acetic and iso-valeric acids and was nearly eight times that at uncontrolled pH (392 mg COD/L). Mechanism exploration revealed at alkaline pH, especially at pH 10.0, not only the cell structure of algae was damaged effectively, but also activities and relative quantification of hydrolases as well as the abundance of microorganisms responsible for organics hydrolysis and SCFAs production were improved. Also, the released microcystins from algae were removed efficiently during alkaline anaerobic fermentation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration

    KAUST Repository

    Trujillo, Uldaeliz

    2013-02-28

    The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP

  20. Solution structure of the tandem acyl carrier protein domains from a polyunsaturated fatty acid synthase reveals beads-on-a-string configuration.

    Directory of Open Access Journals (Sweden)

    Uldaeliz Trujillo

    Full Text Available The polyunsaturated fatty acid (PUFA synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect and in structural stabilization of the multidomain protein (synergistic effect. While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of

  1. Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration

    KAUST Repository

    Trujillo, Uldaeliz; Vá zquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J.; Vassallo, David A.; Vega, Irving E.; Arold, Stefan T.; Baerga-Ortiz, Abel

    2013-01-01

    The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP

  2. Acid rain. Les pluies acides

    Energy Technology Data Exchange (ETDEWEB)

    Curren, T

    1979-11-28

    This report was produced for the use of Members of Parliament and House of Commons committees. The document describes the formation of acid rain, emissions of acidifying pollutants in North America, the growth of the problem and its environmental effects on aquatic and terrestrial ecosystems, human health and man-made structures. Areas of Canada which are most susceptible are identified. Actions taken by Parliament are given, including the formation of a sub-committee on acid rain and the passing of Bill C-51 in 1980 to amend the Clean Air Act, bringing it closer to a similar law in the U.S. A chronology of government responses to acid rain at the international, national and provincial level, is given. The most recent government actions included the passing of the US Clean Air Act by the Senate, the amending of the act into law, and commencement of negotiations to develop a Canada-US Air Quality Accord. 10 refs.

  3. Structural and thermodynamic aspects of aqueous solution of trivalent lanthanides complexation by hydrophobic compounds of tartaric acid, by gluconic acid and related molecules. Outlook for liquid-liquid extraction of these cations

    International Nuclear Information System (INIS)

    Giroux, Sebastien

    1999-01-01

    This work deals with the complexation of lanthanide(III) ions by different molecules and with the synthesis of hydrophobic molecules able to extract them of an aqueous solution. Its aim is to describe the systems obtained by the determination of the formation constants of the species and by the description of their structure. The aim of this work is also to obtain a selective complexation of lanthanides(III) towards actinides(III), because this aim presents a great interest in the reprocessing of radioactive wastes. The complexation studies have been followed by potentiometry, NMR, UV-visible spectroscopy and circular dichroism. The first mixtures studied are the couples: lanthanide(III)-gluconic acid (LH). The complexes system they formed has been described and the structures have been specified; a strong complexation has been revealed. The MLH -2 specie induces a selectivity between the lanthanides(III) equivalent to those obtained with EDTA and its uncharged character allows to consider the use of gluconic acid as extractant. The use of ligands as glucosaminic acid or glucamine slows the beginning of the complexation until pH= 6-7. The neutral specie MLH -2 is formed too. In order to use the complexing properties of gluconic acid and its selective character towards lanthanides(III), the synthesis of molecules derived containing a long alkyl chain with a hydrophobic character has been carried out for using them as extracting agents. An original method of the preparation of tartramides is presented. This preparation consists of an amidation of one of the carboxylic functions of the tartaric acid by a fatty amine. These molecules, surface-active, complex the lanthanides(III) and extract them in an organic phase using the tri-n-butyl phosphate as co-extractant. (O.M.)

  4. Revealing the compact structure of lactic acid bacterial hetero-exopolysaccharides by SAXS and DLS

    DEFF Research Database (Denmark)

    Khan, Sanaullah; Birch, Johnny; Harris, Pernille

    2017-01-01

    solution structures of three lactic acid bacterial hetero-exopolysaccharides (HePS-1, HePS-2 and HePS-3). Values of radius of gyration RG, cross-sectional radius of gyration RXS, approximate length L and hydrodynamic diameter were not directly proportional to the molar mass and indicated the HePSs adopted...... Galf residues significantly influence the conformation. Ab initio scattering modeling of HePS-2 and HePS-3 gave excellent curve fittings with χ2 of 0.43 and 0.34 for best-fit models, respectively, compatible with coil-like conformation. The findings disclose solution behaviour of HePS relevant...

  5. Synthesis, structure, and glutathione peroxidase-like activity of amino acid containing ebselen analogues and diaryl diselenides.

    Science.gov (United States)

    Selvakumar, Karuthapandi; Shah, Poonam; Singh, Harkesh B; Butcher, Ray J

    2011-11-04

    The synthesis of some ebselen analogues and diaryl diselenides, which have amino acid functions as an intramolecularly coordinating group (Se···O) has been achieved by the DCC coupling procedure. The reaction of 2,2'-diselanediylbis(5-tert-butylisophthalic acid) or the activated ester tetrakis(2,5-dioxopyrrolidin-1-yl) 2,2'-diselanediylbis(5-tert-butylisophthalate) with different C-protected amino acids (Gly, L-Phe, L-Ala, and L-Trp) afforded the corresponding ebselen analogues. The used precursor diselenides have been found to undergo facile intramolecular cyclization during the amide bond formation reaction. In contrast, the DCC coupling of 2,2'-diselanediyldibenzoic acid with C-protected amino acids (Gly, L/D-Ala and L-Phe) affords the corresponding amide derivatives and not the ebselen analogues. Some of the representative compounds have been structurally characterized by single-crystal X-ray crystallography. The glutathione peroxidase (GPx)-like activities of the ebselen analogues and the diaryl diselenides have been evaluated by using the coupled reductase assay method. Intramolecularly stabilized ebselen analogues show slightly higher maximal velocity (V(max)) than ebselen. However, they do not show any GPx-like activity at low GSH concentrations at which ebselen and related diselenides are active. This could be attributed to the peroxide-mediated intramolecular cyclization of the corresponding selenenyl sulfide and diaryl diselenide intermediates generated during the catalytic cycle. Interestingly, the diaryl diselenides with alanine (L,L or D,D) amide moieties showed excellent catalytic efficiency (k(cat)/K(M)) with low K(M) values in comparison to the other compounds. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. SYNTHESIS OF FLAVANONE-6-CARBOXYLIC ACID DERIVATIVES FROM SALICYLIC ACID DERIVATIVE

    Directory of Open Access Journals (Sweden)

    Muhammad Idham Darussalam Mardjan

    2012-02-01

    Full Text Available Synthesis of flavanone-6-carboxylic acid derivatives had been conducted via the route of chalcone. The synthesis was carried out from salicylic acid derivative, i.e. 4-hydroxybenzoic acid, via esterification, Fries rearrangement, Claisen-Schmidt condensation and 1,4-nucleophilic addition reactions. Structure elucidation of products was performed using FT-IR, 1H-NMR, GC-MS and UV-Vis spectrometers. Reaction of 4-hydroxybenzoic acid with methanol catalyzed with sulfuric acid produced methyl 4-hydroxybenzoate in 87% yield. The acid-catalyzed-acetylation of the product using acetic anhydride gave methyl 4-acetoxybenzoate in 75% yield. Furthermore, solvent-free Fries rearrangement of methyl 4-acetoxybenzoate in the presence of AlCl3 produced 3-acetyl-4-hydroxybenzoic acid as the acetophenone derivatives in 67% yield. Then, Claisen-Schmidt condensation of the acetophenone and benzaldehyde derivatives of p-anisaldehyde and veratraldehyde in basic condition gave 2'-hydroxychalcone-5'-carboxylic acid derivatives  in 81 and 71 % yield, respectively. Finally, the ring closure reaction of the chalcone yielded the corresponding flavanone-6-carboxylic acids in 67 and 59% yield, respectively.

  7. Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.

    Science.gov (United States)

    Schultz, Eric P; Vasquez, Ernesto E; Scott, William G

    2014-09-01

    The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential

  8. Structural basis for the ligand-binding specificity of fatty acid-binding proteins (pFABP4 and pFABP5) in gentoo penguin.

    Science.gov (United States)

    Lee, Chang Woo; Kim, Jung Eun; Do, Hackwon; Kim, Ryeo-Ok; Lee, Sung Gu; Park, Hyun Ho; Chang, Jeong Ho; Yim, Joung Han; Park, Hyun; Kim, Il-Chan; Lee, Jun Hyuck

    2015-09-11

    Fatty acid-binding proteins (FABPs) are involved in transporting hydrophobic fatty acids between various aqueous compartments of the cell by directly binding ligands inside their β-barrel cavities. Here, we report the crystal structures of ligand-unbound pFABP4, linoleate-bound pFABP4, and palmitate-bound pFABP5, obtained from gentoo penguin (Pygoscelis papua), at a resolution of 2.1 Å, 2.2 Å, and 2.3 Å, respectively. The pFABP4 and pFABP5 proteins have a canonical β-barrel structure with two short α-helices that form a cap region and fatty acid ligand binding sites in the hydrophobic cavity within the β-barrel structure. Linoleate-bound pFABP4 and palmitate-bound pFABP5 possess different ligand-binding modes and a unique ligand-binding pocket due to several sequence dissimilarities (A76/L78, T30/M32, underlining indicates pFABP4 residues) between the two proteins. Structural comparison revealed significantly different conformational changes in the β3-β4 loop region (residues 57-62) as well as the flipped Phe60 residue of pFABP5 than that in pFABP4 (the corresponding residue is Phe58). A ligand-binding study using fluorophore displacement assays shows that pFABP4 has a relatively strong affinity for linoleate as compared to pFABP5. In contrast, pFABP5 exhibits higher affinity for palmitate than that for pFABP4. In conclusion, our high-resolution structures and ligand-binding studies provide useful insights into the ligand-binding preferences of pFABPs based on key protein-ligand interactions. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2)

    Science.gov (United States)

    Anderson, Lissa C.; Håkansson, Maria; Walse, Björn; Nilsson, Carol L.

    2017-09-01

    Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments. The enzyme generates glutamate, which is neurotoxic. To elucidate structural coordinates that may confer altered substrate binding or activity of the variant BCAT2 T186R, a 45 kDa protein, we applied combined ETD and CID top-down mass spectrometry in a LC-FT-ICR MS at 21 T, and X-Ray crystallography in the study of both the variant and non-variant intact proteins. The combined ETD/CID fragmentation pattern allowed for not only extensive sequence coverage but also confident localization of the amino acid variant to its position in the sequence. The crystallographic experiments confirmed the hypothesis generated by in silico structural homology modeling, that the Lys59 side-chain of BCAT2 may repulse the Arg186 in the variant protein (PDB code: 5MPR), leading to destabilization of the protein dimer and altered enzyme kinetics. Taken together, the MS and novel 3D structural data give us reason to further pursue BCAT2 T186R as a precision drug target in GBM. [Figure not available: see fulltext.

  10. Fabrication and characterization of novel multilayered structures by stereocomplexion of poly(D-lactic acid/poly(L-lactic acid and self-assembly of polyelectrolytes

    Directory of Open Access Journals (Sweden)

    Elena Dellacasa

    2016-01-01

    Full Text Available The enantiomers poly(D-lactic acid (PDLA and poly(L-lactic acid (PLLA were alternately adsorbed directly on calcium carbonate (CaCO3 templates and on poly(styrene sulfonate (PSS and poly(allylamine hydrochloride (PAH multilayer precursors in order to fabricate a novel layer-by-layer (LBL assembly. A single layer of poly(L-lysine (PLL was used as a linker between the (PDLA/PLLAn stereocomplex and the cores with and without the polymeric (PSS/PAHn/PLL multilayer precursor (PEM. Nuclear magnetic resonance (NMR and gel permeation chromatography (GPC were used to characterize the chemical composition and molecular weight of poly(lactic acid polymers. Both multilayer structures, with and without polymeric precursor, were firstly fabricated and characterized on planar supports. A quartz crystal microbalance (QCM, attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR and ellipsometry were used to evaluate the thickness and mass of the multilayers. Then, hollow, spherical microcapsules were obtained by the removal of the CaCO3 sacrificial template. The chemical composition of the obtained microcapsules was confirmed by differential scanning calorimetry (DSC and wide X-ray diffraction (WXRD analyses. The microcapsule morphology was evaluated by scanning electron microscopy (SEM and transmission electron microscopy (TEM measurements. The experimental results confirm the successful fabrication of this innovative system, and its full biocompatibility makes it worthy of further characterization as a promising drug carrier for sustained release.

  11. Fabrication and characterization of novel multilayered structures by stereocomplexion of poly(D-lactic acid)/poly(L-lactic acid) and self-assembly of polyelectrolytes

    Science.gov (United States)

    Yang, Gesheng; Pastorino, Laura

    2016-01-01

    Summary The enantiomers poly(D-lactic acid) (PDLA) and poly(L-lactic acid) (PLLA) were alternately adsorbed directly on calcium carbonate (CaCO3) templates and on poly(styrene sulfonate) (PSS) and poly(allylamine hydrochloride) (PAH) multilayer precursors in order to fabricate a novel layer-by-layer (LBL) assembly. A single layer of poly(L-lysine) (PLL) was used as a linker between the (PDLA/PLLA)n stereocomplex and the cores with and without the polymeric (PSS/PAH)n/PLL multilayer precursor (PEM). Nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC) were used to characterize the chemical composition and molecular weight of poly(lactic acid) polymers. Both multilayer structures, with and without polymeric precursor, were firstly fabricated and characterized on planar supports. A quartz crystal microbalance (QCM), attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and ellipsometry were used to evaluate the thickness and mass of the multilayers. Then, hollow, spherical microcapsules were obtained by the removal of the CaCO3 sacrificial template. The chemical composition of the obtained microcapsules was confirmed by differential scanning calorimetry (DSC) and wide X-ray diffraction (WXRD) analyses. The microcapsule morphology was evaluated by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) measurements. The experimental results confirm the successful fabrication of this innovative system, and its full biocompatibility makes it worthy of further characterization as a promising drug carrier for sustained release. PMID:26925356

  12. Interaction of humic acids and humic-acid-like polymers with herpes simplex virus type 1

    Science.gov (United States)

    Klöcking, Renate; Helbig, Björn

    The study was performed in order to compare the antiviral activity against herpes simplex virus type 1 (HSV-1) of synthetic humic-acid-like polymers to that of their low-molecular-weight basic compounds and naturally occurring humic acids (HA) in vitro. HA from peat water showed a moderate antiviral activity at a minimum effective concentration (MEC) of 20 µg/ml. HA-like polymers, i.e. the oxidation products of caffeic acid (KOP), hydrocaffeic acid (HYKOP), chlorogenic acid (CHOP), 3,4-dihydroxyphenylacetic acid (3,4-DHPOP), nordihydroguaretic acid (NOROP), gentisinic acid (GENOP), pyrogallol (PYROP) and gallic acid (GALOP), generally inhibit virus multiplication, although with different potency and selectivity. Of the substances tested, GENOP, KOP, 3,4-DHPOP and HYKOP with MEC values in the range of 2 to 10 µg/ml, proved to be the most potent HSV-1 inhibitors. Despite its lower antiviral potency (MEC 40 µg/ml), CHOP has a remarkable selectivity due to the high concentration of this polymer that is tolerated by the host cells (>640 µg/ml). As a rule, the antiviral activity of the synthetic compounds was restricted to the polymers and was not preformed in the low-molecular-weight basic compounds. This finding speaks in favour of the formation of antivirally active structures during the oxidative polymerization of phenolic compounds and, indirectly, of corresponding structural parts in different HA-type substances.

  13. Structural characterization and comparative analysis of human and piscine cartilage acidic protein (CRTAC1/CRTAC2)

    OpenAIRE

    Guerreiro, Marta Lúcia Amaro

    2014-01-01

    Dissertação de mestrado, Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014 CRTAC (Cartilage Acidic Protein) firstly identified as a chondrocyte marker in humans and implicated in a number of diseases. This ancient protein is present from prokaryotes to vertebrates and the teleost are the only group that contain duplicates (CRTAC1/CRTAC2). The structure of CRTACs is poorly characterized and was the starting point of the present study. To establi...

  14. Effects of SPORL and dilute acid pretreatment on substrate morphology, cell physical and chemical wall structures, and subsequent enzymatic hydrolysis of lodgepole pine

    Science.gov (United States)

    Xinping Li; Xiaolin Luo; Kecheng Li; J.Y. Zhu; J. Dennis Fougere; Kimberley Clarke

    2012-01-01

    The effects of pretreatment by dilute acid and sulfite pretreatment to overcome recalcitrance of lignocellulose (SPORL) on substrate morphology, cell wall physical and chemical structures, along with the subsequent enzymatic hydrolysis of lodgepole pine substrate were investigated. FE-SEM and TEM images of substrate structural morphological changes showed that SPORL...

  15. Mapping the Hydropathy of Amino Acids Based on Their Local Solvation Structure

    KAUST Repository

    Bonella, S.

    2014-06-19

    In spite of its relevant biological role, no general consensus exists on the quantitative characterization of amino acid\\'s hydropathy. In particular, many hydrophobicity scales exist, often producing quite different rankings for the amino acids. To make progress toward a systematic classification, we analyze amino acids\\' hydropathy based on the orientation of water molecules at a given distance from them as computed from molecular dynamics simulations. In contrast with what is usually done, we argue that assigning a single number is not enough to characterize the properties of an amino acid, in particular when both hydrophobic and hydrophilic regions are present in a residue. Instead we show that appropriately defined conditional probability densities can be used to map the hydrophilic and hydrophobic groups on the amino acids with greater detail than possible with other available methods. Three indicators are then defined based on the features of these probabilities to quantify the specific hydrophobicity and hydrophilicity of each amino acid. The characterization that we propose can be used to understand some of the ambiguities in the ranking of amino acids in the current scales. The quantitative indicators can also be used in combination with standard bioinformatics tools to predict the location of transmembrane regions of proteins. The method is sensitive to the specific environment of the amino acids and can be applied to unnatural and modified amino acids, as well as to other small organic molecules. © 2014 American Chemical Society.

  16. Structures of two cell wall-associated polysaccharides of a Streptococcus mitis biovar 1 strain. A unique teichoic acid-like polysaccharide and the group O antigen which is a C-polysaccharide in common with pneumococci

    DEFF Research Database (Denmark)

    Bergström, N; Jansson, P.-E.; Kilian, Mogens

    2000-01-01

    The cell wall of Streptococcus mitis biovar 1 strain SK137 contains the C-polysaccharide known as the common antigen of a closely related species Streptococcus pneumoniae, and a teichoic acid-like polysaccharide with a unique structure. The two polysaccharides are different entities and could...... be partially separated by gel chromatography. The structures of the two polysaccharides were determined by chemical methods and by NMR spectroscopy. The teichoic acid-like polymer has a heptasaccharide phosphate repeating unit with the following structure: The structure neither contains ribitol nor glycerol...... phosphate as classical teichoic acids do, thus we have used the expression teichoic acid-like for this polysaccharide. The following structure of the C-polysaccharide repeating unit was established: where AAT is 2-acetamido-4-amino-2,4, 6-trideoxy-D-galactose. It has a carbohydrate backbone identical...

  17. Structural basis and functions of abscisic acid receptors PYLs

    Science.gov (United States)

    Zhang, Xing L.; Jiang, Lun; Xin, Qi; Liu, Yang; Tan, Jian X.; Chen, Zhong Z.

    2015-01-01

    Abscisic acid (ABA) plays a key role in many developmental processes and responses to adaptive stresses in plants. Recently, a new family of nucleocytoplasmic PYR/PYL/RCAR (PYLs) has been identified as bona fide ABA receptors. PYLs together with protein phosphatases type-2C (PP2Cs), Snf1 (Sucrose-non-fermentation 1)-related kinases subfamily 2 (SnRK2s) and downstream substrates constitute the core ABA signaling network. Generally, PP2Cs inactivate SnRK2s kinases by physical interaction and direct dephosphorylation. Upon ABA binding, PYLs change their conformations and then contact and inhibit PP2Cs, thus activating SnRK2s. Here, we reviewed the recent progress in research regarding the structures of the core signaling pathways of ABA, including the (+)-ABA, (−)-ABA and ABA analogs pyrabactin as well as 6AS perception by PYLs, SnRK2s mimicking PYLs in binding PP2Cs. PYLs inhibited PP2Cs in both the presence and absence of ABA and activated SnRK2s. The present review elucidates multiple ABA signal perception and transduction by PYLs, which might shed light on how to design small chemical compounds for improving plant performance in the future. PMID:25745428

  18. Zinc oxide modified with benzylphosphonic acids as transparent electrodes in regular and inverted organic solar cell structures

    Energy Technology Data Exchange (ETDEWEB)

    Lange, Ilja; Reiter, Sina; Kniepert, Juliane; Piersimoni, Fortunato; Brenner, Thomas; Neher, Dieter, E-mail: neher@uni-potsdam.de [Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam (Germany); Pätzel, Michael; Hildebrandt, Jana; Hecht, Stefan [Department of Chemistry and IRIS Adlershof, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin (Germany)

    2015-03-16

    An approach is presented to modify the work function of solution-processed sol-gel derived zinc oxide (ZnO) over an exceptionally wide range of more than 2.3 eV. This approach relies on the formation of dense and homogeneous self-assembled monolayers based on phosphonic acids with different dipole moments. This allows us to apply ZnO as charge selective bottom electrodes in either regular or inverted solar cell structures, using poly(3-hexylthiophene):phenyl-C71-butyric acid methyl ester as the active layer. These devices compete with or even surpass the performance of the reference on indium tin oxide/poly(3,4-ethylenedioxythiophene) polystyrene sulfonate. Our findings highlight the potential of properly modified ZnO as electron or hole extracting electrodes in hybrid optoelectronic devices.

  19. Experiment and theory at the convergence limit: accurate equilibrium structure of picolinic acid by gas-phase electron diffraction and coupled-cluster computations.

    Science.gov (United States)

    Vogt, Natalja; Marochkin, Ilya I; Rykov, Anatolii N

    2018-04-18

    The accurate molecular structure of picolinic acid has been determined from experimental data and computed at the coupled cluster level of theory. Only one conformer with the O[double bond, length as m-dash]C-C-N and H-O-C[double bond, length as m-dash]O fragments in antiperiplanar (ap) positions, ap-ap, has been detected under conditions of the gas-phase electron diffraction (GED) experiment (Tnozzle = 375(3) K). The semiexperimental equilibrium structure, rsee, of this conformer has been derived from the GED data taking into account the anharmonic vibrational effects estimated from the ab initio force field. The equilibrium structures of the two lowest-energy conformers, ap-ap and ap-sp (with the synperiplanar H-O-C[double bond, length as m-dash]O fragment), have been fully optimized at the CCSD(T)_ae level of theory in conjunction with the triple-ζ basis set (cc-pwCVTZ). The quality of the optimized structures has been improved due to extrapolation to the quadruple-ζ basis set. The high accuracy of both GED determination and CCSD(T) computations has been disclosed by a correct comparison of structures having the same physical meaning. The ap-ap conformer has been found to be stabilized by the relatively strong NH-O hydrogen bond of 1.973(27) Å (GED) and predicted to be lower in energy by 16 kJ mol-1 with respect to the ap-sp conformer without a hydrogen bond. The influence of this bond on the structure of picolinic acid has been analyzed within the Natural Bond Orbital model. The possibility of the decarboxylation of picolinic acid has been considered in the GED analysis, but no significant amounts of pyridine and carbon dioxide could be detected. To reveal the structural changes reflecting the mesomeric and inductive effects due to the carboxylic substituent, the accurate structure of pyridine has been also computed at the CCSD(T)_ae level with basis sets from triple- to 5-ζ quality. The comprehensive structure computations for pyridine as well as for

  20. Structure of Vibrio cholerae ToxT reveals a mechanism for fatty acid regulation of virulence genes

    Energy Technology Data Exchange (ETDEWEB)

    Lowden, Michael J.; Skorupski, Karen; Pellegrini, Maria; Chiorazzo, Michael G.; Taylor, Ronald K.; Kull, F. Jon (Dartmouth)

    2010-03-04

    Cholera is an acute intestinal infection caused by the bacterium Vibrio cholerae. In order for V. cholerae to cause disease, it must produce two virulence factors, the toxin-coregulated pilus (TCP) and cholera toxin (CT), whose expression is controlled by a transcriptional cascade culminating with the expression of the AraC-family regulator, ToxT. We have solved the 1.9 {angstrom} resolution crystal structure of ToxT, which reveals folds in the N- and C-terminal domains that share a number of features in common with AraC, MarA, and Rob as well as the unexpected presence of a buried 16-carbon fatty acid, cis-palmitoleate. The finding that cis-palmitoleic acid reduces TCP and CT expression in V. cholerae and prevents ToxT from binding to DNA in vitro provides a direct link between the host environment of V. cholerae and regulation of virulence gene expression.

  1. Docosahexaenoic Acid-Derived Fatty Acid Esters of Hydroxy Fatty Acids (FAHFAs) With Anti-inflammatory Properties.

    Science.gov (United States)

    Kuda, Ondrej; Brezinova, Marie; Rombaldova, Martina; Slavikova, Barbora; Posta, Martin; Beier, Petr; Janovska, Petra; Veleba, Jiri; Kopecky, Jan; Kudova, Eva; Pelikanova, Terezie; Kopecky, Jan

    2016-09-01

    White adipose tissue (WAT) is a complex organ with both metabolic and endocrine functions. Dysregulation of all of these functions of WAT, together with low-grade inflammation of the tissue in obese individuals, contributes to the development of insulin resistance and type 2 diabetes. n-3 polyunsaturated fatty acids (PUFAs) of marine origin play an important role in the resolution of inflammation and exert beneficial metabolic effects. Using experiments in mice and overweight/obese patients with type 2 diabetes, we elucidated the structures of novel members of fatty acid esters of hydroxy fatty acids-lipokines derived from docosahexaenoic acid (DHA) and linoleic acid, which were present in serum and WAT after n-3 PUFA supplementation. These compounds contained DHA esterified to 9- and 13-hydroxyoctadecadienoic acid (HLA) or 14-hydroxydocosahexaenoic acid (HDHA), termed 9-DHAHLA, 13-DHAHLA, and 14-DHAHDHA, and were synthesized by adipocytes at concentrations comparable to those of protectins and resolvins derived from DHA in WAT. 13-DHAHLA exerted anti-inflammatory and proresolving properties while reducing macrophage activation by lipopolysaccharides and enhancing the phagocytosis of zymosan particles. Our results document the existence of novel lipid mediators, which are involved in the beneficial anti-inflammatory effects attributed to n-3 PUFAs, in both mice and humans. © 2016 by the American Diabetes Association.

  2. Crystal Structures of Active Fully Assembled Substrate- and Product-Bound Complexes of UDP-N-Acetylmuramic Acid:l-Alanine Ligase (MurC) from Haemophilus influenzae

    OpenAIRE

    Mol, Clifford D.; Brooun, Alexei; Dougan, Douglas R.; Hilgers, Mark T.; Tari, Leslie W.; Wijnands, Robert A.; Knuth, Mark W.; McRee, Duncan E.; Swanson, Ronald V.

    2003-01-01

    UDP-N-acetylmuramic acid:l-alanine ligase (MurC) catalyzes the addition of the first amino acid to the cytoplasmic precursor of the bacterial cell wall peptidoglycan. The crystal structures of Haemophilus influenzae MurC in complex with its substrate UDP-N-acetylmuramic acid (UNAM) and Mg2+ and of a fully assembled MurC complex with its product UDP-N-acetylmuramoyl-l-alanine (UMA), the nonhydrolyzable ATP analogue AMPPNP, and Mn2+ have been determined to 1.85- and 1.7-Å resolution, respective...

  3. Novel bacteriocins from lactic acid bacteria (LAB): various structures and applications.

    Science.gov (United States)

    Perez, Rodney H; Zendo, Takeshi; Sonomoto, Kenji

    2014-08-29

    Bacteriocins are heat-stable ribosomally synthesized antimicrobial peptides produced by various bacteria, including food-grade lactic acid bacteria (LAB). These antimicrobial peptides have huge potential as both food preservatives, and as next-generation antibiotics targeting the multiple-drug resistant pathogens. The increasing number of reports of new bacteriocins with unique properties indicates that there is still a lot to learn about this family of peptide antibiotics. In this review, we highlight our system of fast tracking the discovery of novel bacteriocins, belonging to different classes, and isolated from various sources. This system employs molecular mass analysis of supernatant from the candidate strain, coupled with a statistical analysis of their antimicrobial spectra that can even discriminate novel variants of known bacteriocins. This review also discusses current updates regarding the structural characterization, mode of antimicrobial action, and biosynthetic mechanisms of various novel bacteriocins. Future perspectives and potential applications of these novel bacteriocins are also discussed.

  4. Catalyzed oxidation reactions. IV. Picolinic acid catalysis of chromic acid oxidations

    International Nuclear Information System (INIS)

    Rocek, J.; Peng, T.Y.

    1977-01-01

    Picolinic acid and several closely related acids are effective catalysts in the chromic acid oxidation of primary and secondary alcohols; the oxidation of other substrates is accelerated only moderately. The reaction is first order in chromium-(VI), alcohol, and picolinic acid; it is second order in hydrogen ions at low acidity and approaches acidity independence at high perchloric acid concentrations. A primary deuterium kinetic isotope effect is observed at high but not at low acidities. At low acidity the reaction has a considerably lower activation energy and more negative activation entropy than at higher acidities. The reactive intermediate in the proposed mechanism is a negatively charged termolecular complex formed from chromic acid, picolinic acid, and alcohol. The rate-limiting step of the reaction changes with the acidity of the solution. At higher acidities the intermediate termolecular complex is formed reversibly and the overall reaction rate is determined by the rate of its decomposition into reaction products; at low acidities the formation of the complex is irreversible and hence rate limiting. Picolinic acids with a substituent in the 6 position show a greatly reduced catalytic activity. This observation is interpreted as suggesting a square pyramidal or octahedral structure for the reactive chromium (VI) intermediate. The temperature dependence of the deuterium isotope effect has been determined and the significance of the observed large values for E/sub a//sup D/ - E/sub a//sup H/ and A/sup D//A/sup H/ is discussed

  5. A rapid NMR-based method for discrimination of strain-specific cell wall teichoic acid structures reveals a third backbone type in Lactobacillus plantarum.

    Science.gov (United States)

    Tomita, Satoru; Tanaka, Naoto; Okada, Sanae

    2017-03-01

    The lactic acid bacterium Lactobacillus plantarum is capable of producing strain-specific structures of cell wall teichoic acid (WTA), an anionic polysaccharide found in the Gram-positive bacterial cell wall. In this study, we established a rapid, NMR-based procedure to discriminate WTA structures in this species, and applied it to 94 strains of L. plantarum. Six previously reported glycerol- and ribitol-containing WTA subtypes were successfully identified from 78 strains, suggesting that these were the dominant structures. However, the level of structural variety differed markedly among bacterial sources, possibly reflecting differences in strain-level microbial diversity. WTAs from eight strains were not identified based on NMR spectra and were classified into three groups. Structural analysis of a partial degradation product of an unidentified WTA produced by strain TUA 1496L revealed that the WTA was 1-O-β-d-glucosylglycerol. Two-dimensional NMR analysis of the polymer structure showed phosphodiester bonds between C-3 and C-6 of the glycerol and glucose residues, suggesting a polymer structure of 3,6΄-linked poly(1-O-β-d-glucosyl-sn-glycerol phosphate). This is the third WTA backbone structure in L. plantarum, following 3,6΄-linked poly(1-O-α-d-glucosyl-sn-glycerol phosphate) and 1,5-linked poly(ribitol phosphate). © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Structural and surface morphological studies of long chain fatty acid thin films deposited by Langmuir-Blodgett technique

    Energy Technology Data Exchange (ETDEWEB)

    Das, Nayan Mani, E-mail: nayanmanidas3@gmail.com [Department of Applied Physics, Indian School of Mines, Dhanbad 826004 (India); Roy, Dhrubojyoti [Department of Applied Physics, Indian School of Mines, Dhanbad 826004 (India); Gupta, Mukul [UGC-DAE Consortium for Scientific Research, University Campus, Khandwa Road, Indore 452017 (India); Gupta, P.S. [Department of Applied Physics, Indian School of Mines, Dhanbad 826004 (India)

    2012-12-15

    In the present work we aim to study the structural and surface morphological characteristics of divalent cation (cadmium ion, Cd{sup 2+}) induced thin mono- to multilayer films of fatty acids such as arachidic acid and stearic acid prepared by the Langmuir-Blodgett (LB) technique. These ultra thin films of various numbers of layers were studied by X-ray diffraction (XRD), X-ray reflectivity (XRR) and Atomic Force Microscopy (AFM). In this specific Y-type deposition, it was found that as the individual layer thickness increases, the corresponding layer by layer interfacial electron density of the thin films decreases. Since the fatty acid chain tries to maintain its minimum value of cross-sectional area, tilting occurs with respect to its nearest neighbor. The tilt angle calculated for 9 layers of cadmium arachidate (CdA{sub 2}) and cadmium stearate (CdSt{sub 2}) are 18 Degree-Sign and 19.5 Degree-Sign , respectively. An asymmetric air gap of thickness {approx}3 A was also seen between the tail parts of 2 molecular chains. The RMS roughness and average height factors calculated through AFM studies show non-uniform surface morphology of both CdA{sub 2} and CdSt{sub 2}, although the calculated topographic variations were found to have more irregularity in case of CdSt{sub 2} than in case of CdA{sub 2}.

  7. Generation of deviation parameters for amino acid singlets, doublets ...

    Indian Academy of Sciences (India)

    We present a new method, secondary structure prediction by deviation parameter (SSPDP) for predicting the secondary structure of proteins from amino acid sequence. Deviation parameters (DP) for amino acid singlets, doublets and triplets were computed with respect to secondary structural elements of proteins based on ...

  8. Hydrazinonicotinic acid derivatization for selective ionization and improved glycan structure characterization by MALDI-MS.

    Science.gov (United States)

    Jiao, Jing; Yang, Lijun; Zhang, Ying; Lu, Haojie

    2015-08-21

    The analysis of glycan is important for understanding cell biology and disease processes because the glycans play a key role in many important biological behaviors, such as cell division, cellular localization, tumor immunology and inflammation. Nevertheless, it is still hard work to analyze glycans by MALDI-MS, which generally stems from the inherent low abundance and the low ionization efficiency of glycans. Moreover, the difficulty in generating informative fragmentations further hinders glycans structure characterization. In this work, hydrazinonicotinic acid (HYNIC) was used as a novel derivatized reagent for improved and selective detection of glycans. Through tagging the reducing terminus of glycans with the diazanyl group of HYNIC, significant enhancement of the ionization efficiency of glycans was achieved. After derivatization, the signal to noise ratio (S/N) of the maltoheptaose was improved by more than one order of magnitude in positive mode. HYNIC derivatization also allowed the sensitive detection of sialylated glycan in negative mode, with a 15 fold enhancement of S/N. Interestingly, it is noteworthy that the HYNIC reagent not only effectively labeled the reducing end of glycans in the presence of tryptic peptides, but also suppressed the ionization of peptides, enabling the direct detection of glycans from glycoprotein without separation. Therefore, analysis of glycans became easier due to the omission of a pre-separation step. Importantly, by using different acid reagents as the catalyst, derivatized product signals corresponding to [M + Na](+) or [M + H](+) were obtained respectively, which yield complementary fragmentation patterns for the structure elucidation of glycans. Finally, more than 40 N-glycans were successfully detected in 10 μL human serum using this method.

  9. New Umami Amides: Structure-Taste Relationship Studies of Cinnamic Acid Derived Amides and the Natural Occurrence of an Intense Umami Amide in Zanthoxylum piperitum.

    Science.gov (United States)

    Frerot, Eric; Neirynck, Nathalie; Cayeux, Isabelle; Yuan, Yoyo Hui-Juan; Yuan, Yong-Ming

    2015-08-19

    A series of aromatic amides were synthesized from various acids and amines selected from naturally occurring structural frameworks. These synthetic amides were evaluated for umami taste in comparison with monosodium glutamate. The effect of the substitution pattern of both the acid and the amine parts on umami taste was investigated. The only intensely umami-tasting amides were those made from 3,4-dimethoxycinnamic acid. The amine part was more tolerant to structural changes. Amides bearing an alkyl- or alkoxy-substituted phenylethylamine residue displayed a clean umami taste as 20 ppm solutions in water. Ultraperformance liquid chromatography coupled with a high quadrupole-Orbitrap mass spectrometer (UPLC/MS) was subsequently used to show the natural occurrence of these amides. (E)-3-(3,4-Dimethoxyphenyl)-N-(4-methoxyphenethyl)acrylamide was shown to occur in the roots and stems of Zanthoxylum piperitum, a plant of the family Rutaceae growing in Korea, Japan, and China.

  10. Cleaving Double-Stranded DNA with Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    1997-01-01

    Peptide nucleic acids and analogues of peptide nucleic acids are used to form duplex, triplex, and other structures with nucleic acids and to modify nucleic acids. The peptide nucleic acids and analogues thereof also are used to modulate protein activity through, for example, transcription arrest......, transcription initiation, and site specific cleavage of nucleic acids....

  11. Influence of herbicide structure, clay acidity, and humic acid coating on acetanilide herbicide adsorption on homoionic clays.

    Science.gov (United States)

    Liu, Weiping; Gan, Jianying; Yates, Scott R

    2002-07-03

    Adsorption of chloroacetanilide herbicides on homoionic montmorillonite was studied by coupling batch equilibration and FT-IR analysis. Adsorption decreased in the order metolachlor > acetochlor > alachlor > propachlor on Ca(2+)- or Mg(2+)-saturated clays and in the order metolachlor > alachlor > acetachlor > propachlor on Al(3+)- or Fe(3+)-saturated clays. FT-IR spectra showed that the carbonyl group of the herbicide molecule was involved in bonding. For the same herbicide, adsorption of alachlor, acetachlor, and metolachlor on clay followed the order Ca(2+) approximately Mg(2+) < Al(3+) < or = Fe(3+), which coincided with the increasing acidity of homoionic clays. Adsorption of propachlor, however, showed an opposite dependence, suggesting a different governing interaction. In clay and humic acid mixtures, herbicide adsorption was less than that expected from independent additive adsorption by the individual constituents, and the deviation was dependent on the clay-to-humic acid ratio, with the greatest deviation consistently occurring at a 60:40 clay-to-humic acid ratio.

  12. Effect of Gallic acid on mechanical and water barrier properties of zein-oleic acid composite films.

    Science.gov (United States)

    Masamba, Kingsley; Li, Yue; Hategekimana, Joseph; Liu, Fei; Ma, Jianguo; Zhong, Fang

    2016-05-01

    In this study, the effect of gallic acid on mechanical and water barrier properties of zein-oleic acid 0-4 % composite films was investigated. Molecular weight distribution analysis was carried out to confirm gallic acid induced cross linking through change in molecular weight in fraction containing zein proteins. Results revealed that gallic acid treatment increased tensile strength from 17.9 MPa to 26.0 MPa, decreased water vapour permeability from 0.60 (g mm m(-2) h(-1) kPa(-1)) to 0.41 (g mm m(-2) h(-1) kPa(-1)), increased solubility from 6.3 % to 10.2 % and marginally increased elongation at break from 3.7 % to 4.2 % in zein films only. However, gallic acid treatment in zein-oleic composite films did not significantly influence mechanical and water barrier properties and in most instances irrespective of oleic acid concentration, the properties were negatively affected. Results from scanning electron microscopy showed that both gallic acid treated and untreated zein films and composite films containing 3 % oleic acid had a compact and homogeneous structure while those containing 4 % oleic acid had inhomogeneous structure. The findings have demonstrated that gallic acid treatment can significantly improve mechanical and water barrier properties especially in zein films only as opposed to when used in composite films using zein and oleic acid.

  13. Structure of Co(2), Ni(2) and VO(2) complexes with 4-phenylthiosemicarbaziddiacetic acid

    International Nuclear Information System (INIS)

    Kravtsov, V.Kh.; Kipkovskij, Ya.; Bologa, O.A.; Lozan, V.I.; Simonov, Yu.A.; Gehrbehlehu, N.V.; Malinovskij, T.I.; AN Moldavskoj SSR, Kishinev

    1995-01-01

    Structure of complex compounds VO(2)(3) with 4-phyenylthiosemicarbaziddiacetic acid is determined through X-ray diffraction method. Monocrystal compounds are monoclinic, sp.gr. P2 1 /n (a=6.703(2), b=12.470(7), c=1695(6) A, γ=95.10(4) deg). The organic molecule in the complexes is expressed in form of twofold deprotonated tetradentate, ligand joining to metal according to the tripod type with application of donor atoms S, N, O, O and forming three metallocycles. The coordination surrounding of the central atom is supplemented by one oxygen vanadyl atom and one water molecule. 17 refs.; 4 figs.; 5 tabs

  14. A Strategy Combining Higher Energy C-Trap Dissociation with Neutral Loss- and Product Ion-Based MSn Acquisition for Global Profiling and Structure Annotation of Fatty Acids Conjugates.

    Science.gov (United States)

    Bi, Qi-Rui; Hou, Jin-Jun; Yang, Min; Shen, Yao; Qi, Peng; Feng, Rui-Hong; Dai, Zhuo; Yan, Bing-Peng; Wang, Jian-Wei; Shi, Xiao-Jian; Wu, Wan-Ying; Guo, De-An

    2017-03-01

    Fatty acids conjugates (FACs) are ubiquitous but found in trace amounts in the natural world. They are composed of multiple unknown substructures and side chains. Thus, FACs are difficult to be analyzed by traditional mass spectrometric methods. In this study, an integrated strategy was developed to global profiling and targeted structure annotation of FACs in complex matrix by LTQ Orbitrap. Dicarboxylic acid conjugated bufotoxins (DACBs) in Venenum bufonis (VB) were used as model compounds. The new strategy (abbreviated as HPNA) combined higher-energy C-trap dissociation (HCD) with product ion- (PI), neutral loss- (NL) based MS n (n ≥ 3) acquisition in both positive-ion mode and negative-ion mode. Several advantages are presented. First, various side chains were found under HCD in negative-ion mode, which included both known and unknown side chains. Second, DACBs with multiple side chains were simultaneously detected in one run. Compared with traditional quadrupole-based mass method, it greatly increased analysis throughput. Third, the fragment ions of side chain and steroids substructure could be obtained by PI- and NL-based MS n acquisition, respectively, which greatly increased the accuracy of the structure annotation of DACBs. In all, 78 DACBs have been discovered, of which 68 were new compounds; 25 types of substructure formulas and seven dicarboxylic acid side chains were found, especially five new side chains, including two saturated dicarboxylic acids [(azelaic acid (C 9 ) and sebacic acid (C 10 )] and three unsaturated dicarboxylic acids (u-C 8 , u-C 9 , and u-C 10 ). All these results greatly enriched the structures of DACBs in VB. Graphical Abstract ᅟ.

  15. Monolayer arrangement of fatty hydroxystearic acids on graphite: Influence of hydroxyl groups

    Energy Technology Data Exchange (ETDEWEB)

    Medina, S. [Laboratorio de Rayos-X, Centro de Investigación Tecnología e Innovación, de la Universidad de Sevilla (CITIUS), Universidad de Sevilla, Avenida Reina Mercedes, 4B. 41012, Sevilla (Spain); Benítez, J.J.; Castro, M.A. [Instituto de Ciencia de Materiales de Sevilla, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, Avenida Américo Vespucio, 49. 41092, Sevilla (Spain); Cerrillos, C. [Servicio de Microscopía, Centro de Investigación Tecnología e Innovación, de la Universidad de Sevilla (CITIUS), Universidad de Sevilla, Avenida Reina Mercedes, 4B. 41012, Sevilla (Spain); Millán, C. [Instituto de Ciencia de Materiales de Sevilla, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, Avenida Américo Vespucio, 49. 41092, Sevilla (Spain); Alba, M.D., E-mail: alba@icmse.csic.es [Instituto de Ciencia de Materiales de Sevilla, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla, Avenida Américo Vespucio, 49. 41092, Sevilla (Spain)

    2013-07-31

    Previous studies have indicated that long-chain linear carboxylic acids form commensurate packed crystalline monolayers on graphite even at temperatures above their melting point. This study examines the effect on the monolayer formation and structure of adding one or more secondary hydroxyl, functional groups to the stearic acid skeleton (namely, 12-hydroxystearic and 9,10-dihydroxystearic acid). Moreover, a comparative study of the monolayer formation on recompressed and monocrystalline graphite has been performed through X-ray diffraction (XRD) and Scanning Tunneling Microscopy (STM), respectively. The Differential Scanning Calorimetry (DSC) and XRD data were used to confirm the formation of solid monolayers and XRD data have provided a detailed structural analysis of the monolayers in good correspondence with obtained STM images. DSC and XRD have demonstrated that, in stearic acid and 12-hydroxystearic acid adsorbed onto graphite, the monolayer melted at a higher temperature than the bulk form of the carboxylic acid. However, no difference was observed between the melting point of the monolayer and the bulk form for 9,10-dihydroxystearic acid adsorbed onto graphite. STM results indicated that all acids on the surface have a rectangular p2 monolayer structure, whose lattice parameters were uniaxially commensurate on the a-axis. This structure does not correlate with the initial structure of the pure compounds after dissolving, but it is conditioned to favor a) hydrogen bond formation between the carboxylic groups and b) formation of hydrogen bonds between secondary hydroxyl groups, if spatially permissible. Therefore, the presence of hydroxyl functional groups affects the secondary structure and behavior of stearic acid in the monolayer. - Highlights: • Hydroxyl functional groups affect structure and behavior of acids in the monolayer. • Acids on the surface have a rectangular p2 monolayer structure. • Lattice parameters of acids are uniaxially

  16. Structural and Biochemical Changes in Salicylic-Acid-Treated Date Palm Roots Challenged with Fusarium oxysporum f. sp. albedinis

    Directory of Open Access Journals (Sweden)

    Abdelhi Dihazi

    2011-01-01

    Full Text Available Histochemical and ultrastructural analyses were carried out to assess structural and biochemical changes in date palm roots pretreated with salicylic acid (SA then inoculated with Fusarium oxysporum f. sp. albedinis (Foa. Flavonoids, induced proteins, and peroxidase activity were revealed in root tissues of SA-treated plants after challenge by Foa. These reactions were closely associated with plant resistance to Foa. Host reactions induced after inoculation of SA-treated plants with Foa included the plugging of intercellular spaces, the deposition of electron-dense materials at the sites of pathogen penetration, and several damages to fungal cells. On the other hand, untreated inoculated plants showed marked cell wall degradation and total cytoplasm disorganization, indicating the protective effects provided by salicylic acid in treated plants.

  17. Amino Acid Interaction (INTAA) web server.

    Science.gov (United States)

    Galgonek, Jakub; Vymetal, Jirí; Jakubec, David; Vondrášek, Jirí

    2017-07-03

    Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein-DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein-DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid-deoxyribonucleotide pairs found at the protein-DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Insights into the Structure, Function, and Ligand Discovery of the Large Neutral Amino Acid Transporter 1, LAT1

    Directory of Open Access Journals (Sweden)

    Natesh Singh

    2018-04-01

    Full Text Available The large neutral amino acid transporter 1 (LAT1, or SLC7A5 is a sodium- and pH-independent transporter, which supplies essential amino acids (e.g., leucine, phenylalanine to cells. It plays an important role at the Blood–Brain Barrier (BBB where it facilitates the transport of thyroid hormones, pharmaceuticals (e.g., l-DOPA, gabapentin, and metabolites into the brain. Moreover, its expression is highly upregulated in various types of human cancer that are characterized by an intense demand for amino acids for growth and proliferation. Therefore, LAT1 is believed to be an important drug target for cancer treatment. With the crystallization of the arginine/agmatine antiporter (AdiC from Escherichia Coli, numerous homology models of LAT1 have been built to elucidate the substrate binding site, ligand–transporter interaction, and structure–function relationship. The use of these models in combination with molecular docking and experimental testing has identified novel chemotypes of ligands of LAT1. Here, we highlight the structure, function, transport mechanism, and homology modeling of LAT1. Additionally, results from structure–function studies performed on LAT1 are addressed, which have enhanced our knowledge of the mechanism of substrate binding and translocation. This is followed by a discussion on ligand- and structure-based approaches, with an emphasis on elucidating the molecular basis of LAT1 inhibition. Finally, we provide an exhaustive summary of different LAT1 inhibitors that have been identified so far, including the recently discovered irreversible covalent inhibitors.

  19. Relationships between soil properties and community structure of soil macroinvertebrates in oak-history forests along an acidic deposition gradient

    Energy Technology Data Exchange (ETDEWEB)

    Kuperman, R.G. [Argonne National Lab., IL (United States). Environmental Assessment Div.

    1996-02-01

    Soil macroinvertebrate communities were studied in ecologically analogous oak-hickory forests across a three-state atmospheric pollution gradient in Illinois, Indiana, and Ohio. The goal was to investigate changes in the community structure of soil fauna in study sites receiving different amounts of acidic deposition for several decades and the possible relationships between these changes and physico-chemical properties of soil. The study revealed significant differences in the numbers of soil animals among the three study sites. The sharply differentiated pattern of soil macroinvertebrate fauna seems closely linked to soil chemistry. Significant correlations of the abundance of soil macroinvertebrates with soil parameters suggest that their populations could have been affected by acidic deposition in the region. Abundance of total soil macroinvertebrates decreased with the increased cumulative loading of acidic deposition. Among the groups most sensitive to deposition were: earthworms gastropods, dipteran larvae, termites, and predatory beetles. The results of the study support the hypothesis that chronic long-term acidic deposition could aversely affect the soil decomposer community which could cause lower organic matter turnover rates leading to an increase in soil organic matter content in high deposition sites.

  20. Mechanosynthesis, structural, thermal and magnetic characteristics of oleic acid coated Fe{sub 3}O{sub 4} nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Marinca, T.F., E-mail: traian.marinca@stm.utcluj.ro [Materials Science and Engineering Department, Technical University of Cluj-Napoca, 103-105, Muncii Avenue, 400641 Cluj-Napoca (Romania); Chicinaş, H.F.; Neamţu, B.V. [Materials Science and Engineering Department, Technical University of Cluj-Napoca, 103-105, Muncii Avenue, 400641 Cluj-Napoca (Romania); Isnard, O. [Université Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Institut NEEL, 25 rue des Martyrs, BP166, F-38042 Grenoble (France); Pascuta, P. [Physics and Chemistry Department, Technical University of Cluj-Napoca, 103-105, Muncii Avenue, 400641 Cluj-Napoca (Romania); Lupu, N.; Stoian, G. [National Institute of Research & Development for Technical Physics, 47 Mangeron Boulevard, Iasi 700050 (Romania); Chicinaş, I. [Materials Science and Engineering Department, Technical University of Cluj-Napoca, 103-105, Muncii Avenue, 400641 Cluj-Napoca (Romania)

    2016-03-01

    Oleic acid coated iron ferrite-magnetite nanoparticles (Fe{sub 3}O{sub 4}) have been synthesized via a new combined route, ceramic method and subsequent wet mechanical milling, starting from a stoichiometric mixture of the easily accessible Fe and Fe{sub 2}O{sub 3} precursors. In the first step, the magnetite has been obtained in well crystallised state by heat treatment of precursor's mixture. In the second step, the as obtained magnetite powder has been wet milled in a high energy planetary ball mill using oleic acid as process control agent. Using the same conditions dry milled magnetite samples have been obtained for comparison. The as obtained powders have been characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), magnetic measurements M = f(H), scanning electron microscopy (SEM) and differential scanning calorimetry (DSC). According to XRD analysis two different processing mechanisms are observed for dry and wet milling modes. The magnetite mean crystallite size is 19 nm according to XRD after 240 min of wet mechanical milling. The High Resolution SEM confirmed that the powder consists in nanoparticles that have particles with the size up to 30 nm. The bond of the oleic acid to the magnetite nanoparticles has been observed by FTIR and DSC investigations. The presence of free and bonded oleic acid is revealed and the free oleic acid can be removed controlled by heat treatment. The magnetisation of the milled samples is lower as compared to the magnetisation of the un-milled sample due to several causes such as disordered structure, finite size effect and powder contamination. A powder contamination with iron occurs during milling and this leads to the formation of a wüstite-FeO phase for the dry milled samples. In the case of the wet milled samples, due to an oleic acid layer the FeO phase formation is prevented. - Highlights: • Oleic acid coated magnetite has been synthetized by a new combined route. • XRD

  1. Molecular and crystal structures of the products of crystallization of (N'-furfurylidene)isonicotinoylhydrazide from aqueous solutions of hydrochloric and acetic acids

    International Nuclear Information System (INIS)

    Chuev, I.I.; Nikonova, L.A.; Atovmyan, E.G.; Utenyshev, A.N.; Aldoshin, S.M.

    2001-01-01

    Crystals of (N ' -furfurylidene)isonicotinoylhydrazide (I), which have been isolated from a water-methanol solution of hydrochloric acid (Ia) and an aqueous solution (∼50%) of acetic acid (Ib), are studied by X-ray diffraction. In Ia, the nitrogen atom of the pyridine ring is protonated. In the crystal, the intermolecular C=O···HN(Py) hydrogen bonds link the I · H + cations into chains which are bound through centrosymmetric NH···W···Cl - ···W ' ···H ' N ' bridges. In molecule Ib, no protonation occurs; however, its pyridine N atom is blocked by the hydroxyl H atom of a solvate molecule of acetic acid. Crystals Ib have a layered structure. The crystallization water molecule is involved in the formation of three intermolecular hydrogen bonds, namely, those with the H atom of the amide group and the carbonyl O atoms of molecule I and an acetic acid molecule of the neighboring layer

  2. Characterization of molecular associations involving L-ornithine and α-ketoglutaric acid: crystal structure of L-ornithinium α-ketoglutarate.

    Science.gov (United States)

    Allouchi, H; Céolin, R; Berthon, L; Tombret, F; Rietveld, I B

    2014-07-01

    The crystal structure of L-ornithinium α-ketoglutarate (C5H13N2O2, C5H5O5) has been solved by direct methods using single crystal X-ray diffraction data. It crystallizes in the monoclinic system, space group P21, unit cell parameters a=15.4326(3), b=5.2015(1), c=16.2067(3) Å and β=91.986(1)°, containing two independent pairs of molecular ions in the asymmetric unit. An extensive hydrogen-bond network and electrostatic charges due to proton transfer provide an important part of the cohesive energy of the crystal. The conformational versatility of L-ornithine and α-ketoglutaric acid is illustrated by the present results and crystal structures available from the Cambridge Structural Database. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  3. The fifth solvatomorph of gallic acid with a supramolecular channel structure: Structural complexity and phase transitions

    Science.gov (United States)

    Thomas, Sajesh P.; Kaur, Ramanpreet; Kaur, Jassjot; Sankolli, Ravish; Nayak, Susanta K.; Guru Row, Tayur N.

    2013-01-01

    A new solvatomorph of gallic acid was generated using chiral additive technique and characterized by single crystal and powder X-ray diffraction, C-13 NMR, IR spectroscopic techniques and thermal analysis. The supramolecular channels formed by hexameric motifs of gallic acid and solvent molecules contain highly disordered solvent molecules with fractional occupancies.

  4. Roles of unsaturated fatty acids (especially omega-3 fatty acids) in the brain at various ages and during ageing.

    Science.gov (United States)

    Bourre, J M

    2004-01-01

    Among various organs, in the brain, the fatty acids most extensively studied are omega-3 fatty acids. Alpha-linolenic acid (18:3omega3) deficiency alters the structure and function of membranes and induces minor cerebral dysfunctions, as demonstrated in animal models and subsequently in human infants. Even though the brain is materially an organ like any other, that is to say elaborated from substances present in the diet (sometimes exclusively), for long it was not accepted that food can have an influence on brain structure, and thus on its function. Lipids, and especially omega-3 fatty acids, provided the first coherent experimental demonstration of the effect of diet (nutrients) on the structure and function of the brain. In fact the brain, after adipose tissue, is the organ richest in lipids, whose only role is to participate in membrane structure. First it was shown that the differentiation and functioning of cultured brain cells requires not only alpha-linolenic acid (the major component of the omega-3, omega3 family), but also the very long omega-3 and omega-6 carbon chains (1). It was then demonstrated that alpha-linolenic acid deficiency alters the course of brain development, perturbs the composition and physicochemical properties of brain cell membranes, neurones, oligodendrocytes, and astrocytes (2). This leads to physicochemical modifications, induces biochemical and physiological perturbations, and results in neurosensory and behavioural upset (3). Consequently, the nature of polyunsaturated fatty acids (in particular omega-3) present in formula milks for infants (premature and term) conditions the visual and cerebral abilities, including intellectual. Moreover, dietary omega-3 fatty acids are certainly involved in the prevention of some aspects of cardiovascular disease (including at the level of cerebral vascularization), and in some neuropsychiatric disorders, particularly depression, as well as in dementia, notably Alzheimer's disease. Recent

  5. Effect of citric acid on noncovalent interactions in biopolymer jellies

    Directory of Open Access Journals (Sweden)

    Kuanyzhbek Musabekov

    2015-09-01

    Full Text Available The effect of citric acid on the formation of gels based on gelatine, melon pulp and sugar has been studied. It is found that the structuring of gelatin the presence of melon pulp is due to hydrogen bonds between the amino acids of gelatin and pectin melon by hydrogen bonds. It is shown that the structuring of gelatin and gelatin – melon pulp depends on the concentration of sugar. The addition of acid in the pectin-gelatin composition reduces the pH, the solubility of pectin and accelerates the formation of jelly. This is due to the fact that in the presence of citric acid reduced the degree of dissociation of galacturonic acid. The intensity of the effect of citric acid on the structure in the presence of melon pulp could be explained by the formation of hydrogen bonds between pectin and citric acid.

  6. Investigation of emulsified, acid and acid-alkali catalyzed mesoporous bioactive glass microspheres for bone regeneration and drug delivery

    Energy Technology Data Exchange (ETDEWEB)

    Miao, Guohou [School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641 China (China); National Engineering Research Center for Tissue Restoration and Reconstruction, Guangzhou 510006 China (China); Guangdong Province Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou 510006 China (China); Chen, Xiaofeng, E-mail: chenxf@scut.edu.cn [School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641 China (China); National Engineering Research Center for Tissue Restoration and Reconstruction, Guangzhou 510006 China (China); Guangdong Province Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou 510006 China (China); Dong, Hua [National Engineering Research Center for Tissue Restoration and Reconstruction, Guangzhou 510006 China (China); Guangdong Province Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou 510006 China (China); School of Biological Science and Engineering, South China University of Technology, Guangzhou 510006 (China); Fang, Liming; Mao, Cong; Li, Yuli; Li, Zhengmao; Hu, Qing [School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641 China (China); National Engineering Research Center for Tissue Restoration and Reconstruction, Guangzhou 510006 China (China); Guangdong Province Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou 510006 China (China)

    2013-10-15

    Acid-catalyzed mesoporous bioactive glass microspheres (MBGMs-A) and acid-alkali co-catalyzed mesoporous bioactive glass microspheres (MBGMs-B) were successfully synthesized via combination of sol-gel and water-in-oil (W/O) micro-emulsion methods. The structural, morphological and textural properties of mesoporous bioactive glass microspheres (MBGMs) were characterized by various techniques. Results show that both MBGMs-A and MBGMs-B exhibit regularly spherical shape but with different internal porous structures, i.e., a dense microstructure for MBGMs-A and internally porous structure for MBGMs-B. {sup 29}Si NMR data reveal that MGBMs have low polymerization degree of silica network. The in vitro bioactivity tests indicate that the apatite formation rate of MBGMs-B was faster than that of MBGMs-A after soaking in simulated body fluid (SBF) solution. Furthermore, the two kinds of MBGMs have similar storage capacity of alendronate (AL), and the release behaviors of AL could be controlled due to their unique porous structure. In conclusion, the microspheres are shown to be promising candidates as bone-related drug carriers and filling materials of composite scaffold for bone repair. - Graphical abstract: The morphologies and microstructures of acid-catalyzed mesoporous bioactive glass microspheres (MBGMs-A) and acid-alkali co-catalyzed mesoporous bioactive glass microspheres (MBGMs-B) were observed by scanning electron microscope and transmission electron microscope. MBGMs-A exhibits a dense structure and a porous can be observed in MBGMs-B. The microspheres have a quick inducing-apatite formation ability and show a sustained release of alendronate (AL). Highlights: • A rapid method was reported to prepare mesoporous bioactive glass microspheres. • The addition of ammonia significantly shortens the preparation time. • Acid and acid-alkali co-catalyzed microspheres were studied for the first time. • The materials exhibited excellent in vitro bioactivity and

  7. Comparative analysis of QSAR models for predicting pK(a) of organic oxygen acids and nitrogen bases from molecular structure.

    Science.gov (United States)

    Yu, Haiying; Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit

    2010-11-22

    For 1143 organic compounds comprising 580 oxygen acids and 563 nitrogen bases that cover more than 17 orders of experimental pK(a) (from -5.00 to 12.23), the pK(a) prediction performances of ACD, SPARC, and two calibrations of a semiempirical quantum chemical (QC) AM1 approach have been analyzed. The overall root-mean-square errors (rms) for the acids are 0.41, 0.58 (0.42 without ortho-substituted phenols with intramolecular H-bonding), and 0.55 and for the bases are 0.65, 0.70, 1.17, and 1.27 for ACD, SPARC, and both QC methods, respectively. Method-specific performances are discussed in detail for six acid subsets (phenols and aromatic and aliphatic carboxylic acids with different substitution patterns) and nine base subsets (anilines, primary, secondary and tertiary amines, meta/para-substituted and ortho-substituted pyridines, pyrimidines, imidazoles, and quinolines). The results demonstrate an overall better performance for acids than for bases but also a substantial variation across subsets. For the overall best-performing ACD, rms ranges from 0.12 to 1.11 and 0.40 to 1.21 pK(a) units for the acid and base subsets, respectively. With regard to the squared correlation coefficient r², the results are 0.86 to 0.96 (acids) and 0.79 to 0.95 (bases) for ACD, 0.77 to 0.95 (acids) and 0.85 to 0.97 (bases) for SPARC, and 0.64 to 0.87 (acids) and 0.43 to 0.83 (bases) for the QC methods, respectively. Attention is paid to structural and method-specific causes for observed pitfalls. The significant subset dependence of the prediction performances suggests a consensus modeling approach.

  8. An Organic Puzzle Using Meldrum's Acid

    Science.gov (United States)

    Crouch, R. David; Holden, Michael S.

    2002-04-01

    Meldrum's acid or 2,2-dimethyl-1,3-dioxane-4,6-dione undergoes a Knoevenagel condensation with formaldehyde to form an active Michael acceptor for a second molecule of Meldrum's acid. The structure of the resulting product is determined by correlation of the products of possible reactions of Meldrum's acid and formaldehyde with the NMR spectrum of the product.

  9. QUAFRINOIC ACIDS: TWO NEW TRITERPENIODS FROM ...

    African Journals Online (AJOL)

    From the stem bark of Quassia africana, two new triterpenoids with the ursolic acid skeleton, characterized as 3-oxo-urs-12-en-27a, 28di-oic acid and its dihydro derivative, 3β-urs-12-en-27α, 28di-oic acid have been isolated. The structures were determined using spectroscopic techniques. KEY WORDS: Quassia africana; ...

  10. Structural, morphological and catalytic characterization of neutral Ag salt of 12-tungstophosphoric acid: Influence of preparation conditions

    Energy Technology Data Exchange (ETDEWEB)

    Holclajtner-Antunović, Ivanka; Bajuk-Bogdanović, Danica [Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade (Serbia); Popa, Alexandru [Institute of Chemistry Timişoara, Bl. Mihail Viteazul 24, 300223 Timişoara (Romania); Nedić Vasiljević, Bojana [Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade (Serbia); Krstić, Jugoslav [Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11001 Belgrade (Serbia); Mentus, Slavko [Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade (Serbia); Uskoković-Marković, Snežana, E-mail: snezaum@pharmacy.bg.ac.rs [Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade (Serbia)

    2015-02-15

    Graphical abstract: - Highlights: • Preparation conditions influence to self-assembly of nanocrystallites of Ag{sub 3}PW{sub 12}O{sub 40}. • Ag{sub 3}PW{sub 12}O{sub 40} obtained by filtration is microporous, Ag{sub 3}PW{sub 12}O{sub 40} obtained by evaporation is non-porous. • Thermal properties of Ag{sub 3}PW{sub 12}O{sub 40}, H{sub 3}PW{sub 12}O{sub 40} and its soluble salts are similar. - Abstract: The objective of this study is the structural and morphological characterization of the Ag{sub 3}PW{sub 12}O{sub 40} salts (AgWPA) of 12-tungstophosphoric acid (WPA) obtained under different preparation conditions and testing of their acid catalytic activity in dehydration of ethanol. The structure, morphology and physicochemical characteristics were determined by Fourier transform infrared (FT-IR) and Raman spectroscopy, X-ray diffraction (XRD), nitrogen physisorption at −196 °C, scanning electron microscopy (SEM) and differential thermal (DTA) and thermogravimetric analysis (TGA). It is shown that the preparation process has a significant influence on the morphological properties of the obtained materials which may be explained by the supposed mechanism of the formation of nanocrystallite′s aggregates with more or less epitaxial connection. Neutral AgWPA obtained by filtration from supernatant forms porous aggregates of a symmetric dodecahedral shape, having average sizes about 2 μm. This sample shows higher specific area in comparison with the salt obtained by evaporation due to the higher micropore volume, while mesopore volumes are the same for both salts. Thus conversion of ethanol and selectivities of the main products, ethylene and diethyl ether, are almost the same and constant for both prepared salts, while their values are changed over the reaction time for the parent WPA acid.

  11. Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2011-01-01

    Full Text Available Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

  12. Non-Acidic Free Fatty Acid Receptor 4 Agonists with Antidiabetic Activity

    DEFF Research Database (Denmark)

    Goncalves de Azavedo, Carlos M. B. P.; Watterson, Kenneth R; Wargent, Ed T

    2016-01-01

    The free fatty acid receptor 4 (FFA4 or GPR120) has appeared as an interesting potential target for the treatment of metabolic disorders. At present, most FFA4 ligands are carboxylic acids that are assumed to mimic the endogenous long-chain fatty acid agonists. Here, we report preliminary structure......-activity relationship studies of a previously disclosed non-acidic sulfonamide FFA4 agonist. Mutagenesis studies indicate that the compounds are orthosteric agonists despite the absence of a carboxylate function. The preferred compounds showed full agonist activity on FFA4 and complete selectivity over FFA1, although...... a significant fraction of these non-carboxylic acids also showed partial antagonistic activity on FFA1. Studies in normal and diet-induced obese (DIO) mice with the preferred compound 34 showed improved glucose tolerance after oral dosing in an oral glucose tolerance test. Chronic dosing of 34 in DIO mice...

  13. Structural and spectroscopic features of proton hydrates in the crystalline state. Solid-state DFT study on HCl and triflic acid hydrates

    Science.gov (United States)

    Vener, M. V.; Chernyshov, I. Yu.; Rykounov, A. A.; Filarowski, A.

    2018-01-01

    Crystalline HCl and CF3SO3H hydrates serve as excellent model systems for protonated water and perfluorosulphonic acid membranes, respectively. They contain characteristic H3O+, H5О+2, H7О+3 and H3O+(H2O)3 (the Eigen cation) structures. The properties of these cations in the crystalline hydrates of strong monobasic acids are studied by solid-state density function theory (DFT). Simultaneous consideration of the HCl and CF3SO3H hydrates reveals the impact of the size of a counter ion and the crystalline environment on the structure and infrared active bands of the simplest proton hydrates. The H7O+3 structure is very sensitive to the size of the counter ion and symmetry of the local environment. This makes it virtually impossible to identify the specific features of H7O+3 in molecular crystals. The H3O+ ion can be treated as the Eigen-like cation in the crystalline state. Structural, infrared and electron-density features of H5О+2 and the Eigen cation are virtually insensitive to the size of the counter ion and the symmetry of the local crystalline environment. These cations can be considered as the simplest stable proton hydrates in the condensed phase. Finally, the influence of the Grimme correction on the structure and harmonic frequencies of the molecular crystals with short (strong) intermolecular O-H···O bonds is discussed.

  14. Protein structure recognition: From eigenvector analysis to structural threading method

    Science.gov (United States)

    Cao, Haibo

    In this work, we try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. We found a strong correlation between amino acid sequence and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, we give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part include discussions of interactions among amino acids residues, lattice HP model, and the designablity principle. In the second part, we try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in our eigenvector study of protein contact matrix. We believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, we discuss a threading method based on the correlation between amino acid sequence and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, we list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

  15. Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Haibo [Iowa State Univ., Ames, IA (United States)

    2003-01-01

    In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

  16. Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

    International Nuclear Information System (INIS)

    Haibo Cao

    2003-01-01

    In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches

  17. The Hydrogen Bonded Structures of Two 5-Bromobarbituric Acids and Analysis of Unequal C5–X and C5–X′ Bond Lengths (X = X′ = F, Cl, Br or Me in 5,5-Disubstituted Barbituric Acids

    Directory of Open Access Journals (Sweden)

    Thomas Gelbrich

    2016-04-01

    Full Text Available The crystal structure of the methanol hemisolvate of 5,5-dibromobarbituric acid (1MH displays an H-bonded layer structure which is based on N–H∙∙∙O=C, N–H∙∙∙O(MeOH and (MeOHO–H∙∙∙O interactions. The barbiturate molecules form an H-bonded substructure which has the fes topology. 5,5′-Methanediylbis(5-bromobarbituric acid 2, obtained from a solution of 5,5-dibromobarbituric acid in nitromethane, displays a N–H···O=C bonded framework of the sxd type. The conformation of the pyridmidine ring and the lengths of the ring substituent bonds C5–X and C5–X′ in crystal forms of 5,5-dibromobarbituric acid and three closely related analogues (X = X′ = Br, Cl, F, Me have been investigated. In each case, a conformation close to a C5-endo envelope is correlated with a significant lengthening of the axial C5–X′ in comparison to the equatorial C5–X bond. Isolated molecule geometry optimizations at different levels of theory confirm that the C5-endo envelope is the global conformational energy minimum of 5,5-dihalogenbarbituric acids. The relative lengthening of the axial bond is therefore interpreted as an inherent feature of the preferred envelope conformation of the pyrimidine ring, which minimizes repulsive interactions between the axial substituent and pyrimidine ring atoms.

  18. Method for distinctive estimation of stored acidity forms in acid mine wastes.

    Science.gov (United States)

    Li, Jun; Kawashima, Nobuyuki; Fan, Rong; Schumann, Russell C; Gerson, Andrea R; Smart, Roger St C

    2014-10-07

    Jarosites and schwertmannite can be formed in the unsaturated oxidation zone of sulfide-containing mine waste rock and tailings together with ferrihydrite and goethite. They are also widely found in process wastes from electrometallurgical smelting and metal bioleaching and within drained coastal lowland soils (acid-sulfate soils). These secondary minerals can temporarily store acidity and metals or remove and immobilize contaminants through adsorption, coprecipitation, or structural incorporation, but release both acidity and toxic metals at pH above about 4. Therefore, they have significant relevance to environmental mineralogy through their role in controlling pollutant concentrations and dynamics in contaminated aqueous environments. Most importantly, they have widely different acid release rates at different pHs and strongly affect drainage water acidity dynamics. A procedure for estimation of the amounts of these different forms of nonsulfide stored acidity in mining wastes is required in order to predict acid release rates at any pH. A four-step extraction procedure to quantify jarosite and schwertmannite separately with various soluble sulfate salts has been developed and validated. Corrections to acid potentials and estimation of acid release rates can be reliably based on this method.

  19. Bioisosteric modifications of 2-arylureidobenzoic acids

    DEFF Research Database (Denmark)

    Valgeirsson, Jon; Nielsen, Elsebet O; Peters, Dan

    2004-01-01

    2-Arylureidobenzoic acids (AUBAs) have recently been presented as the first series of selective noncompetitive GluR5 antagonists. In this paper we have modified the acidic moiety of the AUBAs by introducing different acidic and neutral groups, and similarly, we have replaced the urea linker...... of the AUBAs with other structurally related linkers. Replacing the acid with neutral substituents led to inactive compounds in all instances, showing that an acidic moiety is necessary for activity. Replacing the carboxylic moiety in 2a with a sulfonic acid (5c) or a tetrazole ring (5d) improved the potency...

  20. Ravynic acid, an antibiotic polyeneyne tetramic acid from Penicillium sp. elucidated through synthesis.

    Science.gov (United States)

    Myrtle, J D; Beekman, A M; Barrow, R A

    2016-09-21

    A new antibiotic natural product, ravynic acid, has been isolated from a Penicillium sp. of fungus, collected from Ravensbourne National Park. The 3-acylpolyenyne tetramic acid structure was definitively elucidated via synthesis. Highlights of the synthetic method include the heat induced formation of the 3-acylphosphorane tetramic acid and a selective Wittig cross-coupling to efficiently prepare the natural compounds carbon skeleton. The natural compound was shown to inhibit the growth of Staphylococcus aureus down to concentrations of 2.5 µg mL(-1).

  1. Viscosity and sedimentation behaviors of the magnetorheological suspensions with oleic acid/dimer acid as surfactants

    Science.gov (United States)

    Yang, Jianjian; Yan, Hua; Hu, Zhide; Ding, Ding

    2016-11-01

    This work deals with the role of polar interactions on the viscosity and sedimentation behaviors of magnetorheological suspensions with micro-sized magnetic particles dispersed in oil carriers. The oleic acid and dimer acid were employed to make an adjustment of the hydrophobicity of iron particles, in the interest of performing a comparative evaluation of the contributions of the surface polarity. The viscosity tests show that the adsorbed surfactant layer may impose a hindrance to the movement of iron particles in the oil medium. The polar attractions between dimer acid covered particles gave rise to a considerable increase in viscosity, indicating flocculation structure developed in the suspensions. The observed plateau-like region in the vicinity of 0.1 s-1 for MRF containing dimer acid is possibly due to the flocculation provoked by the carboxylic polar attraction, in which the structure is stable against fragmentation. Moreover, a quick recovery of the viscosity and a higher viscosity-temperature index also suggest the existence of particle-particle polar interaction in the suspensions containing dimer acid. The sedimentation measurements reveal that the steric repulsion of oleic acid plays a limited role in the stability of suspensions only if a large quantity of surfactant was used. The sedimentation results observed in the dimer acid covered particles confirm that loose and open flocculation was formed and enhanced sedimentation stability.

  2. Crystal structures of 2-(N,N-dimethylaminoalkyl)ferroceneboronic acids and their diol derivatives. The quest for a B-N intramolecular bond in the solid state

    DEFF Research Database (Denmark)

    Norrild, Jens Chr.; Søtofte, Inger

    2001-01-01

    The crystal structures of (S,S)-2-(N,N-dimethyl-1-aminoethyl)ferroceneboronic acid (2), (S,S)-1-(N,N-dimethyl-1-aminoethyl)-2-(4,4,5,5-tetraphenyl-1,3,2-dioxaborolan-2-yl)ferrocene (3), rac-2-(N,N-dimethylaminomethyl)-ferroceneboronic acid (rac-4), (S)-[(1S,2S,3R,5S)-pinane-1,2-diyl] 2-(N...

  3. Transport of C-13-labelled linoleic and C-13-labelled caprylic acid in rat plasma after administration of specific structured triacylglycerols

    DEFF Research Database (Denmark)

    Vistisen, Bodil; Høy, Carl-Erik

    2004-01-01

    the transport of dietary C-13-labelled fatty acids in rat plasma to compare the chylomicron fatty acid metabolism after administration of specific structured, long chain and medium chain triacylglycerols. Rats were fed ML*M, M*LM*, L*L*L* or M*M*M* (L=linoleic acid, 18:2n-6, M=caprylic acid, 8:0, * = C-13......-labelled fatty acid) by gavage. A maximum transport of 0.5% of the administered C-13-labelled 18:2n-6 was observed in 1mL rat plasma both after administration of L*L*L* and ML*M, while approximately 0.04% of the administered C-13-labelled 8:0 was detected in 1mL plasma following administration of M......*M*M* or M*LM*. After L*L*L* administration C-13-labelled 20:4n-6 was observed in plasma, probably formed by elongation and desaturation of 18:2n-6 in the enterocyte or liver cells. Furthermore, C-13-labelled 16:0, 48:0, 18: 1n-9 and 20:4n-6 were observed in plasma of rats fed M*M*M* and M*LM* due...

  4. Syntheses and structures of three heterometallic coordination polymers derived from 4-pyridin-3-yl-benzoic acid

    International Nuclear Information System (INIS)

    Fang, Wei-Hui; Yang, Guo-Yu

    2014-01-01

    Three lanthanide–transition-metal coordination polymers, namely, [Er 2 L 6 (H 2 O)][Cu 2 I 2 ] (1), [ErL 3 ][CuI] (2), and [Dy 2 L 6 (BPDC) 0.5 (H 2 O) 4 ][Cu 3 I 2 ] (3) (HL=4-pyridin-3-yl-benzoic acid, H 2 BPDC=4,4′-biphenyldicarboxylic acid) have been made by reacting Ln 2 O 3 and CuI with HL at different temperatures under hydrothermal conditions. All the complexes are characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, powder X-ray diffraction, and single-crystal X-ray diffraction, respectively. 1–3 all construct from dimeric (Ln 2 ) and (Cu 2 ) units and exhibit two types of the structural features: 1 is a two-dimensional layer, 2–3 are three-dimensional frameworks. Interestingly, the in situ formation of the BPDC ligand is found in the structure of 3. The distinct architectures of these complexes indicated that the reaction temperature plays an important role in the formation of higher dimensional coordination polymers. - Graphical abstract: By hydrothermal reaction of lanthanide oxide, copper halide, and 4-pyridin-3-yl-benzoic ligand at different temperatures, a series of 1-D to 3-D 3d–4f coordination polymers, namely [ErL 3 (H 2 O) 2 ][CuI], [Er 2 L 6 (H 2 O)][Cu 2 I 2 ], [ErL 3 ][CuI], and [Dy 2 L 6 (BPDC) 0.5 (H 2 O) 4 ][Cu 3 I 2 ], have been made, respectively. - Highlights: • Three novel heterometallic coordination polymers derived from 4-pyridin-3-yl-benzoic acid have been hydrothermally synthesized. • Mixed dinuclear motifs of (Ln 2 ) and (Cu 2 ) serve as secondary building units to generate 2-D layer and 3-D frameworks. • It is proved that higher temperature is apt to permit construction of high dimensional architectures

  5. Structurally modified fatty acids - clinical potential as tracers of metabolism

    International Nuclear Information System (INIS)

    Dudczak, R.; Schmoliner, R.; Angelberger, P.; Knapp, F.F.; Goodman, M.M.

    1985-01-01

    Recently 15-p-iodophenyl-betamethyl-pentadecanoic acid (BMPPA) was proposed for myocardial scintigraphy, as possible probe of metabolic processes other than β-oxidation. In 19 patients myocardial scintigraphy was done after i.v. BMPPA (2 to 4 mCi). Data were collected (LAO 45 0 /14; anterior/5) for 100 minutes in the fasted patients. From heart (H) and liver (L) organ to background (BG) ratios were calculated, and the elimination (E) behavior was analyzed from BG (V. cava region) corrected time activity curves. In 10 patients plasma and urine were examined. By CHCl 3 /MeOH extraction of plasma samples (90 min. pi) both in water and in organic medium soluble catabolites were found. TLC fractionation showed that those were co-migrating, compared to standards, with benzoic acid, BMPPA and triglycerides. In urine (0 to 2h pi: 4.1% dose) hippuric acid was found. It is concluded that BMPPA is a useful agent for myocardial scintigraphy. Its longer retention in the heart compared to unbranched radioiodinated fatty acids may facilitate SPECT studies. Rate of elimination and plasma analysis indicate the metabolic breakdown of BMPPA. Yet, the complexity of the supposed mechanism may impede curve interpretation in terms of specific metabolic pathways. 19 refs., 5 tabs

  6. A novel isoindoline, porritoxin sulfonic acid, from Alternaria porri and the structure-phytotoxicity correlation of its related compounds.

    Science.gov (United States)

    Horiuchi, Masayuki; Ohnishi, Keiichiro; Iwase, Noriyasu; Nakajima, Yoshikazu; Tounai, Kenji; Yamashita, Masakazu; Yamada, Yasumasa

    2003-07-01

    Novel zinniol-related compound 3, named porritoxin sulfonic acid, with an isoindoline skeleton was isolated from the culture liquid of Alternaria porri. The structure was determined to be 2-(2"-sulfoethyl)-4-methoxy-5-methyl-6-(3'-methyl-2'-butenyloxy)-2,3-dihydro-1H-isoindol-1-one. The phytotoxic activities of three isoindolines (1-3) were evaluated in a seedling-growth assay against stone leek and lettuce.

  7. Applications of Tandem Mass Spectrometry in the Structure Determination of Permethylated Sialic Acid-containing Oligosaccharides

    International Nuclear Information System (INIS)

    Yoo, Eun Sun; Yoon, In Mo

    2005-01-01

    Sets of sialic acid-containing trisaccharides having different internal and terminal linkages have been synthesized to develop a sensitive method for analysis of the reducing terminal linkage positions. The trisaccharides, sialyl(α 2-3)Gal(β 1-3)GalNAc and sialyl(α 2-3)Gal(β 1-X)GlcNAc where X=3, 4 and 6, were synthesized and examined using electrospray ionization (ESI)-collision induced dissociation (CID) tandem mass spectrometry (MS/MS). The compounds chosen for this study are related to terminal groups likely to be found on polylactosamine-like glycoproteins and glycolipids which occur on the surface of mammalian cells. The purpose of this study is to develop tandem mass spectrometral methods to determine detailed carbohydrate structures on permethylated or partially methylated oligosaccharides for future applications on biologically active glycoconjugates and to exploit a faster method of synthesizing a series of structural isomeric oligosaccharides to be used for further mass spectrometry and instrumental analysis

  8. Chromium(III) Complex Obtained from Dipicolinic Acid: Synthesis, Characterization, X-Ray Crystal Structure and Electrochemical Studies

    Energy Technology Data Exchange (ETDEWEB)

    Ghasemi, Khaled; Rezvani, Ali Reza; Ghasemi, Fatemeh [Univ. of Sistan and Baluchestan, Zahedan (Iran, Islamic Republic of); Razak, Ibrahim Abdul; Rosli, Mohd Mustaqim [Universiti Sains Malaysia, Penang (Malaysia)

    2013-10-15

    The synthesis, X-ray crystallography, spectroscopic (IR, UV-vis), and electrochemical properties of the title compound, [H{sub 3}O][Cr(dipic){sub 2}] [H{sub 3}O{sup +}.Cl{sup -}] (1), (H{sub 2}dipic = 2,6-pyridinedicarboxylic acid), are reported. This complex crystallizes in the monoclinic space group Cc with a = 14.9006(10) A, b = 12.2114(8) A, c = 8.6337(6) A, α = 90.00 .deg., β = 92.7460(10) .deg., γ = 90.00 .deg., and V = 1569.16(18) A3 with Z = 4. The hydrogen bonding and noncovalent interactions play roles in the stabilization of the structure. In order to gain a better understanding of the most important geometrical parameters in the structure of the complex, atoms in molecules (AIM) method at B3LYP/6-31G level of theory has been employed.

  9. Simultaneous detection of ascorbic acid, uric acid and homovanillic acid at copper modified electrode

    International Nuclear Information System (INIS)

    Selvaraju, T.; Ramaraj, R.

    2007-01-01

    The copper was deposited on glassy carbon (GC) and indium tin oxide (ITO) electrodes by electrochemical method. The copper structures on electrode were characterized by atomic force microscope, X-ray diffractometeric pattern and differential pulse voltammetric studies. Optimal conditions for uniform growth of copper structures on the electrode were established. Voltammetric sensor was fabricated using the copper deposited GC electrode for the simultaneous detection and determination of uric acid (UA) and homovanillic acid (HVA) in the presence of excess concentrations of ascorbic acid (AA). The voltammetric signals due to AA and UA oxidation were well separated with a potential difference of 400 mV and AA did not interfere with the measurement of UA and HVA at the GC/Cu electrode. Linear calibration curves were obtained in the concentration range 1-40 μM for AA and 20-50 μM for UA at physiological pH and a detection limit of 10 nM of UA in the presence of 10-fold excess concentrations of AA was achieved. The simultaneous detection of submicromolar concentrations of AA, UA and HVA was achieved at the GC/Cu electrode. The practical utility of the present GC/Cu modified electrode was demonstrated by measuring the AA content in Vitamin C tablet, UA content in human urine and blood serum samples with satisfactory results

  10. Scale-free behaviour of amino acid pair interactions in folded proteins

    DEFF Research Database (Denmark)

    Petersen, Steffen B.; Neves-Petersen, Maria Teresa; Mortensen, Rasmus J.

    2012-01-01

    The protein structure is a cumulative result of interactions between amino acid residues interacting with each other through space and/or chemical bonds. Despite the large number of high resolution protein structures, the ‘‘protein structure code’’ has not been fully identified. Our manuscript...... presents a novel approach to protein structure analysis in order to identify rules for spatial packing of amino acid pairs in proteins. We have investigated 8706 high resolution non-redundant protein chains and quantified amino acid pair interactions in terms of solvent accessibility, spatial and sequence...... which amino acid paired residues contributed to the cells with a population above 50, pairs of Ala, Ile, Leu and Val dominate the results. This result is statistically highly significant. We postulate that such pairs form ‘‘structural stability points’’ in the protein structure. Our data shows...

  11. Rhenium(V) oxo complexes relevant to technetium renal imaging agents derived from mercaptoacetylglycylglycylaminobenzoic acid isomers. Structural and molecular mechanics studies

    International Nuclear Information System (INIS)

    Hansen, L.; Taylor, A. Jr; Marzilli, L.G.; Cini, R.

    1992-01-01

    The synthesis and characterization of three rhenium(V) oxo complexes derived from isomers of mercaptoacetylglycylglycylaminobenzoic acid (MAG 2 -ABAH 5 ) are reported. The isomers were synthesized from o-, m- and p-aminobenzoic acid and differed in the position of the terminal carboxyl group. The anions of 8-10, [ReO(MAG 2 -*ABAH)] - (* = para (8), meta (9), ortho (10)), contained the tetraanionic form of the ligands with the carboxyl group protonated. Compounds 8,9, and 10 were synthesized by exchange reactions of ReOCl 3 (Me 2 SO)(Ph 3 P) under moderate conditions and were isolated as [Ph 4 P] + , [Bu 4 N] + , and [Ph 4 P] + salts, respectively. The structures of 8 and 10 were determined by X-ray diffraction methods; except for the location of the carboxyl group, the structures are similar. The coordination geometry is pseudo square pyramidal, with nitrogen and sulfur donor atoms forming a square base and the oxo ligand at the apex. The orientation of the carboxyl group in 10 is anti to the Re double-bond O group. Since the carboxyl groups are protonated in 8 and 10 and in other relevant structures from this class of radiopharmaceuticals including [Ph 4 As][TcO(MAG 3 H)] (MAG 3 H = tetraanionic form of mercaptoacetyltriglycine), the authors developed molecular mechanics parameters that allowed them to calculate the structures of 8, 10, and [TcO(MAG 3 H)] - . They then extended the calculations to all three isomeric complexes in their deprotonated forms and to [TcO(MAG 3 )] 2- in order to approximate their solution phase structures. They conclude that the [TcO(MAG 3 )] 2- species is conformationally flexible, and they have made an initial assessment of structures vs renal clearance

  12. Does lactobionic acid affect the colloidal structure and skin moisturizing potential of the alkyl polyglucoside-based emulsion systems?

    Science.gov (United States)

    Tasic-Kostov, M Z; Reichl, S; Lukic, M Z; Jaksic, I N; Savic, S D

    2011-11-01

    Moisturizing creams are the most prescribed products in dermatology, essential in maintaining healthy skin as well as in the topical treatment of some diseases. The irritation potential of commonly used emulsifiers and moisturizing ingredients, but also their mutual interactions, could affect the functionality and safety of those dermopharmaceutics. The aim of this study was to promote moisturizing alkyl polyglucoside (APG)-based emulsion as vehicle for lactobionic acid (LA), advantageous representative of the alphahydroxyacids (AHAs)-multifunctional moisturizers, assessing the safety for use (in vitro acute skin irritation test using cytotoxicity assay compared with in vivo data obtained using skin bioengineering methods) and in vivo moisturizing capacity (bioengineering of the skin). In order to investigate possible interactions between APG mild natural emulsifier-based emulsion and LA, a deeper insight into the colloidal structure of the placebo and the emulsion with LA was given using polarization and transmission electron microscopy, rheology, thermal and texture analysis. This study showed that APG-based emulsions could be promoted as safe cosmetic/dermopharmaceutical vehicles and carriers for extremely acidic and hygroscopic AHA class of actives (specifically LA); prospective safety for human use of both APG and LA with the correlation between in vivo and in vitro findings was shown. However, it was revealed that LA strongly influenced the colloidal structure of the emulsion based on APGs and promoted the formation of lamellar structures which reflects onto the mode of water distribution within the cream. The advantageous skin hydrating potential of LA-containing emulsion vs. placebo was unlikely to be achieved, pointing that emulsions stabilized by lamellar liquid crystalline structures probably are not satisfying carriers for highly hygroscopic actives in order to reach the full moisturizing potential. Safe and effective use on dry skin is presumed.

  13. Properties of nanocellulose isolated from corncob residue using sulfuric acid, formic acid, oxidative and mechanical methods.

    Science.gov (United States)

    Liu, Chao; Li, Bin; Du, Haishun; Lv, Dong; Zhang, Yuedong; Yu, Guang; Mu, Xindong; Peng, Hui

    2016-10-20

    In this work, nanocellulose was extracted from bleached corncob residue (CCR), an underutilized lignocellulose waste from furfural industry, using four different methods (i.e. sulfuric acid hydrolysis, formic acid (FA) hydrolysis, 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO)-mediated oxidation, and pulp refining, respectively). The self-assembled structure, morphology, dimension, crystallinity, chemical structure and thermal stability of prepared nanocellulose were investigated. FA hydrolysis produced longer cellulose nanocrystals (CNCs) than the one obtained by sulfuric acid hydrolysis, and resulted in high crystallinity and thermal stability due to its preferential degradation of amorphous cellulose and lignin. The cellulose nanofibrils (CNFs) with fine and individualized structure could be isolated by TEMPO-mediated oxidation. In comparison with other nanocellulose products, the intensive pulp refining led to the CNFs with the longest length and the thickest diameter. This comparative study can help to provide an insight into the utilization of CCR as a potential source for nanocellulose production. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Recommendations for the presentation of NMR structures of proteins and nucleic acids - IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy

    International Nuclear Information System (INIS)

    Markley, John L.; Bax, Ad; Arata, Yoji; Hilbers, C. W.; Kaptein, Robert; Sykes, Brian D.; Wright, Peter E.; Wuethrich, Kurt

    1998-01-01

    The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms

  15. Identification of a Herbal Powder by Deoxyribonucleic Acid Barcoding and Structural Analyses.

    Science.gov (United States)

    Sheth, Bhavisha P; Thaker, Vrinda S

    2015-10-01

    Authentic identification of plants is essential for exploiting their medicinal properties as well as to stop the adulteration and malpractices with the trade of the same. To identify a herbal powder obtained from a herbalist in the local vicinity of Rajkot, Gujarat, using deoxyribonucleic acid (DNA) barcoding and molecular tools. The DNA was extracted from a herbal powder and selected Cassia species, followed by the polymerase chain reaction (PCR) and sequencing of the rbcL barcode locus. Thereafter the sequences were subjected to National Center for Biotechnology Information (NCBI) basic local alignment search tool (BLAST) analysis, followed by the protein three-dimension structure determination of the rbcL protein from the herbal powder and Cassia species namely Cassia fistula, Cassia tora and Cassia javanica (sequences obtained in the present study), Cassia Roxburghii, and Cassia abbreviata (sequences retrieved from Genbank). Further, the multiple and pairwise structural alignment were carried out in order to identify the herbal powder. The nucleotide sequences obtained from the selected species of Cassia were submitted to Genbank (Accession No. JX141397, JX141405, JX141420). The NCBI BLAST analysis of the rbcL protein from the herbal powder showed an equal sequence similarity (with reference to different parameters like E value, maximum identity, total score, query coverage) to C. javanica and C. roxburghii. In order to solve the ambiguities of the BLAST result, a protein structural approach was implemented. The protein homology models obtained in the present study were submitted to the protein model database (PM0079748-PM0079753). The pairwise structural alignment of the herbal powder (as template) and C. javanica and C. roxburghii (as targets individually) revealed a close similarity of the herbal powder with C. javanica. A strategy as used here, incorporating the integrated use of DNA barcoding and protein structural analyses could be adopted, as a novel

  16. Synthesis, characterization and crystal structure of (2RS,4R)-2-(2-hydroxy-3-methoxyphenyl)thiazolidine-4-carboxylic acid

    Science.gov (United States)

    Muche, Simon; Müller, Matthias; Hołyńska, Małgorzata

    2018-03-01

    The condensation reaction of ortho-vanillin and L-cysteine leads to formation of a racemic mixture of (2RS,4R)-2-(2-hydroxy-3-methoxyphenyl)thiazolidine-4-carboxylic acid and not, as reported in the available literature, to a Schiff base. The racemic mixture was fully characterized by 1D and 2D NMR techniques, ESI-MS and X-ray diffraction. Addition of ZnCl2 led to formation of crystals in form of colorless needles, suitable for X-ray diffraction studies. The measured crystals were identified as the diastereomer (2R,4R)-2-(2-hydroxy-3-methoxyphenyl)thiazolidine-4-carboxylic acid 1. The bulk material is racemic. Thiazolidine exists as zwitterion in solid state, as indicated by the crystal structure.

  17. In vitro inhibition of canine distemper virus by flavonoids and phenolic acids: implications of structural differences for antiviral design.

    Science.gov (United States)

    Carvalho, O V; Botelho, C V; Ferreira, C G T; Ferreira, H C C; Santos, M R; Diaz, M A N; Oliveira, T T; Soares-Martins, J A P; Almeida, M R; Silva, A

    2013-10-01

    Infection caused by canine distemper virus (CDV) is a highly contagious disease with high incidence and lethality in the canine population. Antiviral activity of flavonoids quercetin, morin, rutin and hesperidin, and phenolic cinnamic, trans-cinnamic and ferulic acids were evaluated in vitro against the CDV using the time of addition assay to determine which step of the viral replicative cycle was affected. All flavonoids displayed great viral inhibition when they were added at the times 0 (adsorption) and 1h (penetration) of the viral replicative cycle. Both quercetin and hesperidin presented antiviral activity at the time 2h (intracellular). In the other hand, cinnamic acid showed antiviral activity at the times 0 and 2h while trans-cinnamic acid showed antiviral effect at the times -1h (pre-treatment) and 0 h. Ferulic acid inhibited CDV replicative cycle at the times 0 and 1h. Our study revealed promising candidates to be considered in the treatment of CDV. Structural differences among compounds and correlation to their antiviral activity were also explored. Our analysis suggest that these compounds could be useful in order to design new antiviral drugs against CDV as well as other viruses of great meaning in veterinary medicine. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Structural Analysis and Immuno-Stimulating Activity of an Acidic Polysaccharide from the Stems of Dendrobium nobile Lindl.

    Science.gov (United States)

    Wang, Jun-Hui; Zuo, Shu-Rong; Luo, Jian-Ping

    2017-04-10

    Dendrobium nobile Lindl., an epiphytic herb distributed in the Southeast Asia, is used as a tonic and antipyretic herbal medicine in China. In this study, a water-soluble acidic heteropolysaccharide, DNP-W4, containing mannose, glucose, galactose, xylose, rhamnose, and galacturonic acid, in the molar ratios of 1.0:4.9:2.5:0.5:1.0:0.9, was obtained from the stems of Dendrobium nobile Lindl. Using methylation analysis, partial acid hydrolysis, pectolyase treatment, NMR, and ESI-MS, the structure of DNP-W4 was elucidated. The obtained data indicated that DNP-W4 was a complex heteropolysaccharide and possessed a backbone composed of (1→4)-linked β-d-Glcp, (1→6)-linked β-d-Glcp, and (1→6)-linked β-d-Galp, with substitutes at O-4/6 of Glcp residues and O-3 of Galp. The branches of DNP-W4 were composed of terminal Manp, (1→6)-linked β-d-Manp, (1→3)-linked β-d-Glcp, β-d-Glcp, β-d-Galp, (1→4)-linked α-d-GalAp, (1→2)-linked α-L-Rhap, and Xylp. DNP-W4 had little immunological activities, but its derivatives had immuno-stimulating activities to some extent.

  19. Influence of dietary triacylglycerol structure and level of n-3 fatty acids administered during development on brain phospholipids and memory and learning ability of rats

    DEFF Research Database (Denmark)

    Hartvigsen, M.S.; Mu, Huiling; Hougaard, K.S.

    2004-01-01

    of the nervous system. Methods: Pregnant rats were fed experimental diets from the 8th day of pregnancy throughout lactation. After weaning and until 13 weeks of age, the pups were fed the same diet as their dams. The experimental diets contained either a structured oil, a linseed oil, or a fish oil...... and 22:6n-3 adding up to a total of 2 mol% n-3 fatty acids. The effects of the experimental diets were compared to the effect of a chow diet. Results: The amount of 22:6n-3 in brain phosphatidyl ethanolamine (PE) and phosphatidyl serine (PS) of dams and offspring (3 and 13 weeks of age) was not affected......The objective of this study was to examine the effects of triacylglycerol (TAG) structure and level of n-3 fatty acids on fatty acid profile of brain phospholipids (PL) of dams and offspring, and the memory and learning ability of the offspring, when administered during initial development...

  20. Estimation of Physical Properties of Amino Acids by Group-Contribution Method

    DEFF Research Database (Denmark)

    Jhamb, Spardha Virendra; Liang, Xiaodong; Gani, Rafiqul

    2018-01-01

    In this paper, we present group-contribution (GC) based property models for estimation of physical properties of amino acids using their molecular structural information. The physical properties modelled in this work are normal melting point (Tm), aqueous solubility (Ws), and octanol....../water partition coefficient (Kow) of amino acids. The developed GC-models are based on the published GC-method by Marrero and Gani (J. Marrero, R. Gani, Fluid Phase Equilib. 2001, 183-184, 183-208) with inclusion of new structural parameters (groups and molecular weight of compounds). The main objective...... of introducing these new structural parameters in the GC-model is to provide additional structural information for amino acids having large and complex structures and thereby improve predictions of physical properties of amino acids. The group-contribution values were calculated by regression analysis using...