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Sample records for benzohydroxamic acid structure

  1. 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.

  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. Adsorption of Some Benzohydroxamic Acid Derivatives on Cooper Oxide: Assignment and Interpretation of SERS Spectra.

    Czech Academy of Sciences Publication Activity Database

    Blajiev, O.; Terryn, H.; Hubin, A.; Soukupová, Ludmila; Geerlings, P.

    2006-01-01

    Roč. 37, 7 (2006) , s. 777-788 ISSN 0377-0486 Institutional research plan: CEZ:AV0Z40720504 Keywords : benzohydroxamic acid * spectral assignment * adsorption geometry Subject RIV: CC - Organic Chemistry Impact factor: 2.133, year: 2006

  4. 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.

  5. Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron

    Energy Technology Data Exchange (ETDEWEB)

    Lietzan, Adam D.; Nagar, Mitesh; Pellmann, Elise A.; Bourque, Jennifer R.; Bearne, Stephen L.; Maurice, Martin St. (Dalhousie U.); (Marquette)

    2012-05-09

    Mandelate racemase (MR, EC 5.1.2.2) from Pseudomonas putida catalyzes the Mg{sup 2+}-dependent interconversion of the enantiomers of mandelate, stabilizing the altered substrate in the transition state by 26 kcal/mol relative to the substrate in the ground state. To understand the origins of this binding discrimination, we determined the X-ray crystal structures of wild-type MR complexed with two analogues of the putative aci-carboxylate intermediate, benzohydroxamate and Cupferron, to 2.2-{angstrom} resolution. Benzohydroxamate is shown to be a reasonable mimic of the transition state and/or intermediate because its binding affinity for 21 MR variants correlates well with changes in the free energy of transition state stabilization afforded by these variants. Both benzohydroxamate and Cupferron chelate the active site divalent metal ion and are bound in a conformation with the phenyl ring coplanar with the hydroxamate and diazeniumdiolate moieties, respectively. Structural overlays of MR complexed with benzohydroxamate, Cupferron, and the ground state analogue (S)-atrolactate reveal that the para carbon of the substrate phenyl ring moves by 0.8-1.2 {angstrom} between the ground state and intermediate state, consistent with the proposal that the phenyl ring moves during MR catalysis while the polar groups remain relatively fixed. Although the overall protein structure of MR with bound intermediate analogues is very similar to that of MR with bound (S)-atrolactate, the intermediate-Mg{sup 2+} distance becomes shorter, suggesting a tighter complex with the catalytic Mg{sup 2+}. In addition, Tyr 54 moves closer to the phenyl ring of the bound intermediate analogues, contributing to an overall constriction of the active site cavity. However, site-directed mutagenesis experiments revealed that the role of Tyr 54 in MR catalysis is relatively minor, suggesting that alterations in enzyme structure that contribute to discrimination between the altered substrate in the

  6. 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

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

    Science.gov (United States)

    Luo, Xianping; Zhu, Sipin; Wang, Junyu; Wang, Chunying; Wu, Min

    2017-11-28

    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 SO₄ 2- , inhibited the degradation of BHA by Yb/TiO₂, and their inhibition effects followed the order of HCO₃ - > NO₃ - > SO₄ 2- > Cl - . Cations of Na⁺, K⁺, Ca 2+ , and Mg 2+ 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 Yb 3+ and Yb 2+ could promote the separation of electron-hole pairs.

  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. 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.

  10. 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

  11. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    A structure for nucleic acid has already been proposed by Pauling and Corey [1]. They kindly made'their manuscript available to us in advance of publication. Their model consists of three inter-twined chains, with the phosphates near the fibre axis, and the bases on the outside. In our opinion, this structure is unsatisfactory ...

  12. 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.

  13. 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

  14. 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.

  15. Vibrational structure of the polyunsaturated fatty acids eicosapentaenoic acid and arachidonic acid studied by infrared spectroscopy

    Science.gov (United States)

    Kiefer, Johannes; Noack, Kristina; Bartelmess, Juergen; Walter, Christian; Dörnenburg, Heike; Leipertz, Alfred

    2010-02-01

    The spectroscopic discrimination of the two structurally similar polyunsaturated C 20 fatty acids (PUFAs) 5,8,11,14,17-eicosapentaenoic acid and 5,8,11,14-eicosatetraenoic acid (arachidonic acid) is shown. For this purpose their vibrational structures are studied by means of attenuated total reflection (ATR) Fourier-transform infrared (FT-IR) spectroscopy. The fingerprint regions of the recorded spectra are found to be almost identical, while the C-H stretching mode regions around 3000 cm -1 show such significant differences as results of electronic and molecular structure alterations based on the different degree of saturation that both fatty acids can be clearly distinguished from each other.

  16. 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.

  17. 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

  18. Structural Phase Transition in Adipic Acid

    Science.gov (United States)

    Srinivasa Gopalan, R.; Kumaradhas, P.; Kulkarni, G. U.

    1999-11-01

    The structure of adipic acid undergoing phase transition at ∼136 K has been investigated using single-crystal x-ray diffraction. On lowering the temperature, the a parameter of the room temperature monoclinic cell decreases by ∼0.25 Å. Accompanying the transition, the b parameter nearly triples while a reverts back to the room temperature value. Two-thirds of the molecules in the structure loses center of symmetry. Packing diagrams of the high- and low-temperature phases on superposition reveal that there exist alternating domains perpendicular to the b direction, which contain molecules with and without symmetry. Unsymmetric molecules show displacements along the ac diagonal. Intermolecular hydrogen contacts involving carboxylic oxygens and the methylene hydrogens seem to increase interchain interactions in the low-temperature phase.

  19. Modulating the electronic structure of amino acids: interaction of model lewis acids with anthranilic acid

    Directory of Open Access Journals (Sweden)

    Tareq Irshaidat

    2014-01-01

    Full Text Available On the basis of theoretical B3LYP calculations, Yáñez and co-workers (J. Chem. Theory Comput. 2012, 8, 2293 illustrated that beryllium ions are capable of significantly modulating (changing the electronic structures of imidazole. In this computational organic chemistry study, the interaction of this β-amino acid and five model Lewis acids (BeF1+, Be2+, AlF2(1+, AlF2+, and Al3+ were investigated. Several aspects were addressed: natural bond orbitals, including second order perturbation analysis of intra-molecular charge delocalization and the natural population analysis atomic charges; molecular geometries; selected infrared stretching frequencies (C-N, C-O, and N-H, and selected ¹H-NMR chemical shifts. The data illustrate that this interaction can weaken the H-O bond and goes beyond strengthening the intra-molecular hydrogen bond (N...H-O to cause a spontaneous transfer of the proton to the nitrogen atom in five cases generating zwitterion structures. Many new features are observed. Most importantly, the zwitterion structures include a stabilizing hydrogen bond (N-H...O that varies in relative strength according to the Lewis acid. These findings explain the experimental observations of α-amino acids (for example: J. Am. Chem. Soc. 2001, 123, 3577 and are the first reported fundamental electronic structure characterization of β-amino acids in zwitterion form.

  20. Nucleic Acid Backbone Structure Variations: Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    Nielsen, Peter E.

    2010-01-01

    Synthetic analogues and mimics of the natural genetic material deoxyribonucleic acid (DNA) are potential gene therapeutic (antisense or antigene) drugs. One of these mimics, peptide nucleic acids (PNAs), are chemically closer to peptides and proteins than to DNA, but nonetheless have retained many...

  1. 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...

  2. Interactive Hangman Teaches Amino Acid Structures and Abbreviations

    Science.gov (United States)

    Pennington, Britney O.; Sears, Duane; Clegg, Dennis O.

    2014-01-01

    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…

  3. 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 ...

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

    African Journals Online (AJOL)

    NICO

    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 picolinic acid ligand that bonds bidentately to the cadmium ion via both carboxylate oxygens. Two nitrates coordinate to the metal centre ...

  5. 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).

  6. 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.

  7. 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.

  8. 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

  9. Analyzing and Building Nucleic Acid Structures with 3DNA

    OpenAIRE

    Colasanti, Andrew V.; Lu, Xiang-Jun; Olson, Wilma K.

    2013-01-01

    The 3DNA software package is a popular and versatile bioinformatics tool with capabilities to analyze, construct, and visualize three-dimensional nucleic acid structures. This article presents detailed protocols for a subset of new and popular features available in 3DNA, applicable to both individual structures and ensembles of related structures. Protocol 1 lists the set of instructions needed to download and install the software. This is followed, in Protocol 2, by the analysis of a nucleic...

  10. Effect of structure on extraction ability of phosphoric acid amides

    International Nuclear Information System (INIS)

    Laskorin, B.N.; Buchikhin, E.P.; Yakshin, V.V.

    1976-01-01

    Effective constants of uranium (6) extraction with amides and esteroamides based on the acids of phosphorus of various structures have been determined. The component analysis of the complexes obtained points to the formation of a compound with the metal/ligand ratio = 2. The introduction of alkyl amine substituents in the molecule of the neutral esters of organophosphoric acids is shown to lead to a substantial increase in their extraction capacity [ru

  11. 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.

  12. Pyrene appended bile acid conjugates: Synthesis and a structure ...

    Indian Academy of Sciences (India)

    us to connect the existing gelator motifs into hybrid structures and study their gelation properties in solu- tion. We envisioned that by adding a pyrene moiety ...... seen with the simplest pyrene molecule 1-pyrene car- boxylic acid (19) or its mixture with 1-aminopyrene. (20) (prepared by heating the 1:1 mixture of the amine.

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

    International Nuclear Information System (INIS)

    Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S.

    2013-01-01

    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.

  14. Properties and structure of raised bog peat humic acids

    Science.gov (United States)

    Klavins, Maris; Purmalis, Oskars

    2013-10-01

    Humic substances form most of the organic components of soil, peat and natural waters, and their structure and properties differ very much depending on their source. The aims of this study are to characterize humic acids (HAs) from raised bog peat, to evaluate the homogeneity of peat HAs within peat profiles, and to study peat humification impact on properties of HAs. A major impact on the structure of peat HAs have lignin-free raised bog biota (dominantly represented by bryophytes of different origin). On diagenesis scale, peat HAs have an intermediate position between the living organic matter and coal organic matter, and their structure is formed in a process in which more labile structures (carbohydrates, amino acids, etc.) are destroyed, while thermodynamically more stable aromatic and polyaromatic structures emerge as a result of abiotic synthesis. However, in comparison with soil, aquatic and other HAs, aromaticity of peat HAs is much lower. Comparatively, the raised bog peat HAs are at the beginning of the transformation process of living organic matter. Concentrations of carboxyl and phenolic hydroxyl groups change depending on the peat age and decomposition degree from where HAs have been isolated, and carboxylic acidity of peat HAs increases with peat depth and humification degree.

  15. 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

    networks, formed by mixing multifunctional carboxylic acids such as citric acid (CA), tricarballylic acid (TCAA), trimesic acid (TMA), ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DETPA) with two di ff erent Je ff amine polyetheramines (designated as D400 and D2000......), 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....

  16. The crystal structure of urea oxalic acid (2:1)

    NARCIS (Netherlands)

    Harkema, Sybolt; Bats, J.W.; Weyenberg, A.M.; Feil, D.

    1972-01-01

    The crystal structure of urea oxalic acid, 2[CO(NH2)2].(COOH)2 has been determined using three-dimensional X-ray data, collected on an automatic diffractometer. The space group is P21/c. The lattice constants are: a = 5.058 (3), b = 12.400 (3), c = 6.964 (2) A, fl= 98"13 (7) °. The number of

  17. Structure and function analysis of protein-nucleic acid complexes

    Science.gov (United States)

    Kuznetsova, S. A.; Oretskaya, T. S.

    2016-05-01

    The review summarizes published data on the results and achievements in the field of structure and function analysis of protein-nucleic acid complexes by means of main physical and biochemical methods, including X-ray diffraction, nuclear magnetic resonance spectroscopy, electron and atomic force microscopy, small-angle X-ray and neutron scattering, footprinting and cross-linking. Special attention is given to combined approaches. The advantages and limitations of each method are considered, and the prospects of their application for wide-scale structural studies in vivo are discussed. The bibliography includes 145 references.

  18. Detect and exploit hidden structure in fatty acid signature data

    Science.gov (United States)

    Budge, Suzanne; Bromaghin, Jeffrey; Thiemann, Gregory

    2017-01-01

    Estimates of predator diet composition are essential to our understanding of their ecology. Although several methods of estimating diet are practiced, methods based on biomarkers have become increasingly common. Quantitative fatty acid signature analysis (QFASA) is a popular method that continues to be refined and extended. Quantitative fatty acid signature analysis is based on differences in the signatures of prey types, often species, which are recognized and designated by investigators. Similarly, predator signatures may be structured by known factors such as sex or age class, and the season or region of sample collection. The recognized structure in signature data inherently influences QFASA results in important and typically beneficial ways. However, predator and prey signatures may contain additional, hidden structure that investigators either choose not to incorporate into an analysis or of which they are unaware, being caused by unknown ecological mechanisms. Hidden structure also influences QFASA results, most often negatively. We developed a new method to explore signature data for hidden structure, called divisive magnetic clustering (DIMAC). Our DIMAC approach is based on the same distance measure used in diet estimation, closely linking methods of data exploration and parameter estimation, and it does not require data transformation or distributional assumptions, as do many multivariate ordination methods in common use. We investigated the potential benefits of the DIMAC method to detect and subsequently exploit hidden structure in signature data using two prey signature libraries with quite different characteristics. We found that the existence of hidden structure in prey signatures can increase the confusion between prey types and thereby reduce the accuracy and precision of QFASA diet estimates. Conversely, the detection and exploitation of hidden structure represent a potential opportunity to improve predator diet estimates and may lead to new

  19. 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.

  20. 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...

  1. 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.

  2. Structural and functional diversity of acidic scorpion potassium channel toxins.

    Directory of Open Access Journals (Sweden)

    Zong-Yun Chen

    Full Text Available BACKGROUND: Although the basic scorpion K(+ channel toxins (KTxs are well-known pharmacological tools and potential drug candidates, characterization the acidic KTxs still has the great significance for their potential selectivity towards different K(+ channel subtypes. Unfortunately, research on the acidic KTxs has been ignored for several years and progressed slowly. PRINCIPAL FINDINGS: Here, we describe the identification of nine new acidic KTxs by cDNA cloning and bioinformatic analyses. Seven of these toxins belong to three new α-KTx subfamilies (α-KTx28, α-KTx29, and α-KTx30, and two are new members of the known κ-KTx2 subfamily. ImKTx104 containing three disulfide bridges, the first member of the α-KTx28 subfamily, has a low sequence homology with other known KTxs, and its NMR structure suggests ImKTx104 adopts a modified cystine-stabilized α-helix-loop-β-sheet (CS-α/β fold motif that has no apparent α-helixs and β-sheets, but still stabilized by three disulfide bridges. These newly described acidic KTxs exhibit differential pharmacological effects on potassium channels. Acidic scorpion toxin ImKTx104 was the first peptide inhibitor found to affect KCNQ1 channel, which is insensitive to the basic KTxs and is strongly associated with human cardiac abnormalities. ImKTx104 selectively inhibited KCNQ1 channel with a K(d of 11.69 µM, but was less effective against the basic KTxs-sensitive potassium channels. In addition to the ImKTx104 toxin, HeTx204 peptide, containing a cystine-stabilized α-helix-loop-helix (CS-α/α fold scaffold motif, blocked both Kv1.3 and KCNQ1 channels. StKTx23 toxin, with a cystine-stabilized α-helix-loop-β-sheet (CS-α/β fold motif, could inhibit Kv1.3 channel, but not the KCNQ1 channel. CONCLUSIONS/SIGNIFICANCE: These findings characterize the structural and functional diversity of acidic KTxs, and could accelerate the development and clinical use of acidic KTxs as pharmacological tools and

  3. 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.

  4. 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. PMID:23150809

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

    Science.gov (United States)

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

    2015-10-01

    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.

  6. 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

  7. Enamel structural changes induced by hydrochloric and phosphoric acid treatment.

    Science.gov (United States)

    Bertacci, Angelica; Lucchese, Alessandra; Taddei, Paola; Gherlone, Enrico F; Chersoni, Stefano

    2014-12-30

    The aim of this study was to evaluate enamel acid-induced structural changes after 2 different treatments, by means of Raman and infrared (IR) spectroscopy analyses, and to correlate these findings with permeability measured as fluid discharge from outer enamel. Two different treatments were investigated: 10 enamel slices were etched with 15% hydrochloric acid (HCl) for 120 seconds and 10 slices with 37% phosphoric acid gel (H3PO4) for 30 seconds, rinsed for 30 seconds and then air-dried for 20 seconds. Powders of enamel treated as previously described were produced. Replicas of enamel subjected to the same treatments were obtained to evaluate the presence of fluid droplets on enamel surface. Raman and IR spectroscopy showed that the treatment with both hydrochloric and phosphoric acids induced a decrease in the carbonate content of the enamel apatite. At the same time, both acids induced the formation of HPO42- ions. After H3PO4 treatment, the bands due to the organic component of enamel decreased in intensity, while they increased after HCl treatment. Replicas of H3PO4 treated enamel showed a strongly reduced permeability. Replicas of HCl 15% treated samples showed a maintained permeability. A decrease of the enamel organic component, as resulted after H3PO4 treatment, involves a decrease in enamel permeability, while the increase of the organic matter (achieved by HCl treatment) still maintains enamel permeability.The results suggested a correlation between organic matter and enamel permeability. Permeability was affected by etching technique and could be involved in marginal seal, gap and discoloration at the enamel interface, still causes of restoration failure.

  8. 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.

  9. Structural-phase transformations in bentonite after acid treatment

    Directory of Open Access Journals (Sweden)

    Vlasova M.

    2003-01-01

    Full Text Available The methods of X-ray diffraction, Fourier transform infra-red spectroscopy (FTIR, X-ray microanalysis, electron microscopy, BET and cation exchange capacity (CEC were used for investigation of the structural-phase transformations in bentonite under the influence of hydrochloric acid and temperature treatment (100-800ºC. It is established that in HCl medium during temperature treatment, dehydration and dehydroxilation of montmorillonite occur. The presence of gypsum and barium chloride results in an intercalation of interlayer space of montmorillonite by Ca and Ba ions Temperature treatment of intercalated montmorillonite leads to the formation of pores.

  10. Analysis of branched nucleic acid structure using comparative gel electrophoresis.

    Science.gov (United States)

    Lilley, David M J

    2008-02-01

    Electrophoresis in polyacrylamide gels provides a simple yet powerful means of analyzing the relative disposition of helical arms in branched nucleic acids. The electrophoretic mobility of DNA or RNA with a central discontinuity is determined by the angle subtended between the arms radiating from the branchpoint. In a multi-helical branchpoint, comparative gel electrophoresis can provide a relative measure of all the inter-helical angles and thus the shape and symmetry of the molecule. Using the long-short arm approach, the electrophoretic mobility of all the species with two helical arms that are longer than all others is compared. This can be done as a function of conditions, allowing the analysis of ion-dependent folding of branched DNA and RNA species. Notable successes for the technique include the four-way (Holliday) junction in DNA and helical junctions in functionally significant RNA species such as ribozymes. Many of these structures have subsequently been proved correct by crystallography or other methods, up to 10 years later in the case of the Holliday junction. Just as important, the technique has not failed to date. Comparative gel electrophoresis can provide a window on both fast and slow conformational equilibria such as conformer exchange in four-way DNA junctions. But perhaps the biggest test of the approach has been to deduce the structures of complexes of four-way DNA junctions with proteins. Two recent crystallographic structures show that the global structures were correctly deduced by electrophoresis, proving the worth of the method even in these rather complex systems. Comparative gel electrophoresis is a robust method for the analysis of branched nucleic acids and their complexes.

  11. Rotational Spectrum and Carbon Atom Structure of Dihydroartemisinic Acid

    Science.gov (United States)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Dihydroartemisinic acid (DHAA, C15H24O2, five chiral centers) is a precursor in proposed low-cost synthetic routes to the antimalarial drug artemisinin. In one reaction process being considered in pharmaceutical production, DHAA is formed from an enantiopure sample of artemisinic acid through hydrogenation of the alkene. This reaction needs to properly set the stereochemistry of the asymmetric carbon for the synthesis to produce artemisinin. A recrystallization process can purify the diastereomer mixture of the hydrogenation reaction if the unwanted epimer is produced in less than 10% abundance. There is a need in the process analytical chemistry to rapidly (less than 1 min) measure the diastereomer excess and current solutions, such a HPLC, lack the needed measurement speed. The rotational spectrum of DHAA has been measured at 300:1 signal-to-noise ratio in a chirped-pulsed Fourier transform microwave spectrometer operating from 2-8 GHz using simple heating of the compound. The 13C isotope analysis provides a carbon atom structure that confirms the diastereomer. This structure is in excellent agreement with quantum chemistry calculations at the B2PLYPD3/ 6-311++G** level of theory. The DHAA spectrum is expected to be fully resolved from the unwanted diastereomer raising the potential for fast diastereomer excess measurement by rotational spectroscopy in the pharmaceutical production process.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Polyacrylic acids-bovine serum albumin complexation: Structure and dynamics.

    Science.gov (United States)

    Othman, Mohamed; Aschi, Adel; Gharbi, Abdelhafidh

    2016-01-01

    The study of the mixture of BSA with polyacrylic acids at different masses versus pH allowed highlighting the existence of two regimes of weak and strong complexation. These complexes were studied in diluted regime concentration, by turbidimetry, dynamic light scattering (DLS), zeta-potential measurements and nuclear magnetic resonance (NMR). We have followed the pH effect on the structure and properties of the complex. This allowed refining the interpretation of the phase diagram and understanding the observed phenomena. The NMR measurements allowed probing the dynamics of the constituents versus the pH. The computational method was used to precisely determine the electrostatic potential of BSA and how the polyelectrolyte binds to it at different pH. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. 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

  18. 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

  19. 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...

  20. 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)

  1. On the structures of the diterpenes licamichauxiioic acids A and B.

    Science.gov (United States)

    Fraga, Braulio M; Cabrera, Inmaculada; Amaro-Luis, Juan M

    2008-11-01

    The structures of the diterpenes licamichauxiioic acids A and B, isolated from Licania michauxii, which had been reported as 15-oxo-ent-kaur-9(11),16-dien-19-oic acid (1) and 15-oxo-ent-kaur-13,16-dien-19-oic acid (3), respectively, are not correct. Starting from grandiflorenic acid (6) we had prepared a compound with the proposed structure for licamichauxiioic acid A, and its spectroscopic data are different from those given for this acid. In the case of licamichauxiioic acid B, its NMR data are not in accordance with the proposed structure 3, which also violates Bredt's rule. In addition, we described a useful method for the separation of grandiflorenic and grandiflorolic acids.

  2. Structural diversity and biological significance of lipoteichoic acid in Gram-positive bacteria: focusing on beneficial probiotic lactic acid bacteria.

    Science.gov (United States)

    Shiraishi, Tsukasa; Yokota, Shinichi; Fukiya, Satoru; Yokota, Atsushi

    2016-01-01

    Bacterial cell surface molecules are at the forefront of host-bacterium interactions. Teichoic acids are observed only in Gram-positive bacteria, and they are one of the main cell surface components. Teichoic acids play important physiological roles and contribute to the bacterial interaction with their host. In particular, lipoteichoic acid (LTA) anchored to the cell membrane has attracted attention as a host immunomodulator. Chemical and biological characteristics of LTA from various bacteria have been described. However, most of the information concerns pathogenic bacteria, and information on beneficial bacteria, including probiotic lactic acid bacteria, is insufficient. LTA is structurally diverse. Strain-level structural diversity of LTA is suggested to underpin its immunomodulatory activities. Thus, the structural information on LTA in probiotics, in particular strain-associated diversity, is important for understanding its beneficial roles associated with the modulation of immune response. Continued accumulation of structural information is necessary to elucidate the detailed physiological roles and significance of LTA. In this review article, we summarize the current state of knowledge on LTA structure, in particular the structure of LTA from lactic acid bacteria. We also describe the significance of structural diversity and biological roles of LTA.

  3. 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.

  4. 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.

  5. Microwave spectra and structure of the cyclopropanecarboxylic acid-formic acid dimer

    Energy Technology Data Exchange (ETDEWEB)

    Pejlovas, Aaron M.; Kukolich, Stephen G. [Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 (United States); Lin, Wei [Department of Chemistry, University of Texas Rio Grande Valley, Brownsville, Texas 78520 (United States)

    2015-09-28

    The rotational spectrum of the cyclopropanecarboxylic acid–formic acid doubly hydrogen bonded dimer has been measured in the 4-11 GHz region using a Flygare-Balle type pulsed-beam Fourier transform microwave spectrometer. Rotational transitions were measured for the parent, four unique singly substituted {sup 13}C isotopologues, and a singly deuterated isotopologue. Splittings due to a possible concerted double proton tunneling motion were not observed. Rotational constants (A, B, and C) and centrifugal distortion constants (D{sub J} and D{sub JK}) were determined from the measured transitions for the dimer. The values of the rotational (in MHz) and centrifugal distortion constants (in kHz) for the parent isotopologue are A = 4045.4193(16), B = 740.583 80(14), C = 658.567 60(23), D{sub J} = 0.0499(16), and D{sub JK} = 0.108(14). A partial gas phase structure of the dimer was derived from the rotational constants of the measured isotopologues, previous structural work on each monomer units and results of the calculations.

  6. Production and applications of rosmarinic acid and structurally related compounds.

    Science.gov (United States)

    Kim, Gun-Dong; Park, Yong Seek; Jin, Young-Ho; Park, Cheung-Seog

    2015-03-01

    Rosmarinic acid (α-o-caffeoyl-3,4-dihydroxyphenyllactic acid; RA) is a naturally occurring hydroxylated compound commonly found in species of the subfamily Nepetoideae of the Lamiaceae and Boraginaceae, such as Rosmarinus officinalis, Salvia officinalis, and Perilla frutescens. RA is biosynthesized from the amino acids L-phenylalanine and L-tyrosine by eight enzymes that include phenylalanine ammonia lyase and cinnamic acid 4-hydroxylase. RA can also be chemically produced by the esterification of caffeic acid and 3,4-dihydroxyphenyllactic acid. RA and its numerous derivatives containing one or two RA with other aromatic moieties are well known and include lithospermic acid, yunnaneic acid, salvianolic acid, and melitric acid. Recently, RA and its derivatives have attracted interest for their biological activities, which include anti-inflammatory, anti-oxidant, anti-angiogenic, anti-tumor, and anti-microbial functions. Clinically, RA attenuates T cell receptor-mediated signaling, attenuates allergic diseases like allergic rhinitis and asthma, and 2,4-dinitrofluorobenzene-induced atopic dermatitis-like symptoms, protects from neurotoxicity, and slows the development of Alzheimer's disease. These attributes have increased the demand for the biotechnological production and application of RA and its derivatives. The present review discusses the function and application of RA and its derivatives including the molecular mechanisms underlying clinical efficacy.

  7. 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

  8. Synthesis, coordination and structure of pentacoordinated oxovanadium(IV) complexes of hippuric and nicotinic acids

    International Nuclear Information System (INIS)

    Kumar, G.; Singh, Ranjana; Singh, N.P.

    1981-01-01

    Pentacoordinated oxovanadium(IV) complexes formed with hippuric acid (VOL 2 ) and nicotinic acid ((VO) 2 L 2 (OH) 2 ) 5 H 2 O have been synthesized and their structures investigated by magnetochemical and spectra (i.r., U.V. and reflectance) measurements. The I.R. studies indicate that in the bis-hippurato complex the carboxylate group itself acts as a bidentate chelating group, whereas, with nicotinic acid, coordination occurs through both the pyridine N and COO - group. Electronic spectra show them to have pentacoordinated structures. Magnetic studies suggest that the complex formed with nicotinic acid possibly has a binuclear structure with subnormal magnetic moment. (author)

  9. Parahydrogen-induced polarization of carboxylic acids: a pilot study of valproic acid and related structures.

    Science.gov (United States)

    Lego, Denise; Plaumann, Markus; Trantzschel, Thomas; Bargon, Joachim; Scheich, Henning; Buntkowsky, Gerd; Gutmann, Torsten; Sauer, Grit; Bernarding, Johannes; Bommerich, Ute

    2014-07-01

    Parahydrogen-induced polarization (PHIP) is a promising new tool for medical applications of MR, including MRI. The PHIP technique can be used to transfer high non-Boltzmann polarization, derived from parahydrogen, to isotopes with a low natural abundance or low gyromagnetic ratio (e.g. (13)C), thus improving the signal-to-noise ratio by several orders of magnitude. A few molecules acting as metabolic sensors have already been hyperpolarized with PHIP, but the direct hyperpolarization of drugs used to treat neurological disorders has not been accomplished until now. Here, we report on the first successful hyperpolarization of valproate (valproic acid, VPA), an important and commonly used antiepileptic drug. Hyperpolarization was confirmed by detecting the corresponding signal patterns in the (1)H NMR spectrum. To identify the optimal experimental conditions for the conversion of an appropriate VPA precursor, structurally related molecules with different side chains were analyzed in different solvents using various catalytic systems. The presented results include hyperpolarized (13)C NMR spectra and proton images of related systems, confirming their applicability for MR studies. PHIP-based polarization enhancement may provide a new MR technique to monitor the spatial distribution of valproate in brain tissue and to analyze metabolic pathways after valproate administration. Copyright © 2014 John Wiley & Sons, Ltd.

  10. Nucleoside phosphonic acids in thymidine phosphorylase inhibition: Structure - activity relationship

    Czech Academy of Sciences Publication Activity Database

    Panova, Natalya; Kóšiová, Ivana; Petrová, Magdalena; Vaněk, Václav; Liboska, Radek; Kovačková, Soňa; Kočalka, Petr; Králíková, Šárka; Točík, Zdeněk; Páv, Ondřej; Pačes, Ondřej; Rejman, Dominik; Rosenberg, Ivan

    -, č. 52 (2008), s. 665-666 ISSN 0261-3166. [Joint Symposium of the International Roundtable on Nucleosides, Nucleotides and Nucleic Acids /18./ and the International Symposium on Nucleic Acid Chemistry /35./. Kyoto, 08.09.2008-12.09.2008] R&D Projects: GA MŠk(CZ) LC06061; GA MŠk(CZ) LC06077; GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : thymidine phosphorylase * inhibitors * phosphonic acids Subject RIV: CC - Organic Chemistry

  11. 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

    2017-10-01

    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 CCl4 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 6500-4000 cm- 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.

  12. Structure of unsaturated fatty acids in 2D system.

    Science.gov (United States)

    Fidalgo Rodríguez, J L; Dynarowicz-Latka, P; Miñones Conde, J

    2017-10-01

    The behaviour of Langmuir monolayers corresponding to unsaturated fatty acids belonging to the omega-9 (oleic acid), omega-3 (α-linolenic and stearidonic acids) and omega-6 (linoleic, γ-linolenic and eicosadienoic acids) series was studied in order to get insight into the influence of various factors (such as subphase temperature, length, degree of unsaturation and position of the double bonds in the aliphatic chains) on the molecular conformation of these fatty acids spread at the A/W interface. The obtained results derived from the surface pressure - area isotherms, compressibility modulus and monolayer thickness prove that the lift-off and the limiting areas of investigated films increase both with the number of double bonds and length of the hydrocarbon chain. Also, the monolayers are more compressible (more fluid) upon increasing their tails unsaturation degree. However, eicosadienoic (EA) film is more rigid due to its longer acyl chain. Polyunsaturated fatty acids (PUFAs) monolayers, except for EA, exhibit anomalous temperature dependence (area contraction with increasing temperature), which was attributed to the increased solubility of PUFAs molecules with temperature. The recorded thickness values of the monolayers were compared with those estimated from theoretical molecular conformations in order to establish the orientation and configuration of molecules in different surface states of their monolayer. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Crystal structure of febuxostat–acetic acid (1/1

    Directory of Open Access Journals (Sweden)

    Min Wu

    2015-05-01

    Full Text Available The asymmetric unit of the title compound [systematic name: 2-(3-cyano-4-isobutyloxyphenyl-4-methylthiazole-5-carboxylic acid–acetic acid (1/1], C16H16N2O3S·CH3COOH, contains a febuxostat molecule and an acetic acid molecule. In the febuxostat molecule, the thiazole ring is nearly coplanar with the benzene ring [dihedral angle = 3.24 (2°]. In the crystal, the febuxostat and acetic acid molecules are linked by O—H...O, O—H...N hydrogen bonds and weak C—H...O hydrogen bonds, forming supramolecular chains propagating along the b-axis direction. π–π stacking is observed between nearly parallel thiazole and benzene rings of adjacent molecules; the centroid-to-centroid distances are 3.8064 (17 and 3.9296 (17 Å.

  14. 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

  15. Crystal structure of (E-pent-2-enoic acid

    Directory of Open Access Journals (Sweden)

    Tim Peppel

    2015-05-01

    Full Text Available The molecule of the title compound, C5H8O2, a low-melting α,β-unsaturated carboxylic acid, is essentially planar [maximum displacement = 0.0239 (13 Å]. In the crystal, molecules are linked into centrosymmetric dimers via pairs of O—H...O hydrogen bonds.

  16. Effects of phenolic acid structures on meadow hay digestibility

    NARCIS (Netherlands)

    Rodrigues, M.A.M.; Guedes, C.M.; Cone, J.W.; Gelder, van A.H.; Ferreira, L.M.M.; Sequeira, C.A.

    2007-01-01

    The objectives were to evaluate effects of phenolic acid content and composition on the digestibility of six meadow hays from Northern Portugal. Digestibility was assessed by gas production, in vitro and in situ degradation methods. Four cows fed diets at energy maintenance were used for in situ

  17. 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.

  18. Relevance, structure and analysis of ferulic acid in maize cell walls.

    Science.gov (United States)

    Bento-Silva, Andreia; Vaz Patto, Maria Carlota; do Rosário Bronze, Maria

    2018-04-25

    Phenolic compounds in foods have been widely studied due to their health benefits. In cereals, phenolic compounds are extensively linked to cell wall polysaccharides, mainly arabinoxylans, which cross-link with each other and with other cell wall components. In maize, ferulic acid is the phenolic acid present in the highest concentration, forming ferulic acid dehydrodimers, trimers and tetramers. The cross-linking of polysaccharides is important for the cell wall structure and growth, and may protect against pathogen invasion. In addition to the importance for maize physiology, ferulic acid has been recognized as an important chemical structure with a wide range of health benefits when consumed in a diet rich in fibre. This review paper presents the different ways ferulic acid can be present in maize, the importance of ferulic acid derivatives and the methodologies that can be used for their analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. EVALUATION OF THE SYNTHESIS AND STRUCTURE OF NEW AZETIDIN-2-ONES OF FERULIC ACID.

    Science.gov (United States)

    Stan, Cătălina Daniela; Drăgan, Maria; Pânzariu, Andreea; Profire, Lenuţa

    2016-01-01

    To synthesize some new azetidin-2-ones of ferulic acid and to evaluate them from physicochemical and spectral point of view. The synthesis was carried out in several steps: (i) obtaining the ferulic acid chloride; (ii) obtaining the ferulic acid hydrazide with hydrazine hydrate (98%); (iii) condensation of ferulic acid hydrazide with different benzaldehydes (2-hydroxy-/2-nitro-/4-chloro-/4- fluoro-/4-bromo-benzaldehyde) in order to obtain the corresponding hydrazones; (iv) cy- clization of ferulic acid hydrazones with chloroacethyl chloride in freshly distilled toluene medium and in the presence of triethylamine, resulting in the corresponding azetidin-2-ones. Six new azetidin-2-ones of ferulic acid were synthesized. They were characterized in terms of their physicochemical properties and their structure was confirmed by IR and 1H-NMR spectroscopy. Six new azetidin-2-ones of ferulic acid were synthesized, physicochemically characterized and validated spectrally. A

  20. 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...

  1. Peroxynitrous acid induces structural and functional modifications to basement membranes and its key component, laminin

    DEFF Research Database (Denmark)

    Degendorfer, Georg; Chuang, Christine Y.; Hammer, Astrid

    2015-01-01

    Basement membranes (BM) are specialized extracellular matrices underlying endothelial cells in the artery wall. Laminin, the most abundant BM glycoprotein, is a structural and biologically active component. Peroxynitrous acid (ONOOH), a potent oxidizing and nitrating agent, is formed in vivo...

  2. 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.

  3. 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

  4. Nucleic Acid i-Motif Structures in Analytical Chemistry.

    Science.gov (United States)

    Alba, Joan Josep; Sadurní, Anna; Gargallo, Raimundo

    2016-09-02

    Under the appropriate experimental conditions of pH and temperature, cytosine-rich segments in DNA or RNA sequences may produce a characteristic folded structure known as an i-motif. Besides its potential role in vivo, which is still under investigation, this structure has attracted increasing interest in other fields due to its sharp, fast and reversible pH-driven conformational changes. This "on/off" switch at molecular level is being used in nanotechnology and analytical chemistry to develop nanomachines and sensors, respectively. This paper presents a review of the latest applications of this structure in the field of chemical analysis.

  5. 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.

  6. 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.

  7. Silica Content and Structure from Corncob Ash with Various Acid Treatment (HCl, HBr, and Citric Acid

    Directory of Open Access Journals (Sweden)

    Gladys Ayu Paramita Kusumah Wardhani

    2017-11-01

    Full Text Available In this study, a simple method to obtain silica from corncob ash has been investigated using a nonthermal and thermal method. The Nonthermal method was done by various acid treatment with HCl, HBr and citric acid at room temperature. Thermal method was performed for HCl-leached, HBr-leached, and citric acid-leached corncob in the furnace at 750 ºC for 5 hours. Corncob ash was characterized by Energy Dispersive X-ray fluorescence spectroscopy (EDXRF, Fourier transforms infrared spectroscopy (FTIR, X-Ray diffraction (XRD, and Scanning electron microscope-electron dispersive X-ray (SEM-EDX. In this study silica content increase after acid treatment (leaching and combustion at high temperatures. The result established that silica is most obtained with HCl treatment that is equal to 79,95% with lower metallic oxide impurity content. The FTIR spectra with different intensity shows silanol group at 1636 – 1641 cm-1, whereas siloxane group at 1037 – 1106 cm-1, 616–797 cm-1, and 459–469 cm-1. X-Ray diffractogram shows silica transition pf amorphous (2θ = 21 - 25º to quartz crystalline (2θ = 26.66º phase. The surface morphology of silica that characterized with SEM-EDX shows amorphous and crystalline silica corresponds to XRD result. The high intensity spectra of Si and O in EDX shows the presence of silica in corncob ash.

  8. 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......, and there are no clear correlations to the molecular mechanisms behind the RA's toxicity. In this study we unravel the molecular interactions of the three closely related RAs dehydroabietic acid, neoabietic acid, and the synthetic analogue dichlorodehydroabietic acid with dipalmitoylphosphatidylcholine (DPPC) model...... are correlated with the physical chemical properties of the RA and their toxicity....

  9. 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.

  10. 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.

  11. Testing for spatial clustering of amino acid replacements within protein tertiary structure

    DEFF Research Database (Denmark)

    Yu, Jiaye; Thorne, Jeffrey L

    2006-01-01

    Widely used models of protein evolution ignore protein structure. Therefore, these models do not predict spatial clustering of amino acid replacements with respect to tertiary structure. One formal and biologically implausible possibility is that there is no tendency for amino acid replacements...... to be spatially clustered during evolution. An alternative to this is that amino acid replacements are spatially clustered and this spatial clustering can be fully explained by a tendency for similar rates of amino acid replacement at sites that are nearby in protein tertiary structure. A third possibility...... is that the amount of clustering exceeds that which can be explained solely on the basis of independently evolving protein sites with spatially clustered replacement rates. We introduce two simple and not very parametric hypothesis tests that help distinguish these three possibilities. We then apply these tests...

  12. 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)

  13. Crystal structure of dimethylammonium hydrogen oxalate hemi(oxalic acid

    Directory of Open Access Journals (Sweden)

    Waly Diallo

    2015-05-01

    Full Text Available Single crystals of the title salt, Me2NH2+·HC2O4−·0.5H2C2O4, were isolated as a side product from the reaction involving Me2NH, H2C2O4 and Sn(n-Bu3Cl in a 1:2 ratio in methanol or by the reaction of the (Me2NH22C2O4 salt and Sn(CH33Cl in a 2:1 ratio in ethanol. The asymmetric unit comprises a dimethylammonium cation (Me2NH2+, an hydrogenoxalate anion (HC2O4−, and half a molecule of oxalic acid (H2C2O4 situated about an inversion center. From a supramolecular point of view, the three components interact together via hydrogen bonding. The Me2NH2+ cations and the HC2O4− anions are in close proximity through bifurcated N—H...(O,O hydrogen bonds, while the HC2O4− anions are organized into infinite chains via O—H...O hydrogen bonds, propagating along the a-axis direction. In addition, the oxalic acid (H2C2O4 molecules play the role of connectors between these chains. Both the carbonyl and hydroxyl groups of each diacid are involved in four intermolecular interactions with two Me2NH2+ and two HC2O4− ions of four distinct polymeric chains, via two N—H...O and two O—H...O hydrogen bonds, respectively. The resulting molecular assembly can be viewed as a two-dimensional bilayer-like arrangement lying parallel to (010, and reinforced by a C—H...O hydrogen bond.

  14. Structure of three acidic O-linked carbohydrate chains of porcine zona pellucida glycoproteins

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Hokke, C.H.; Damm, J.B.L.; Kamerling, J.P.

    1993-01-01

    Structural analysis by ID and 2D 1H NMR spectroscopy of three acidic O-linked oligosaccharide alditols, released from porcine zona pellucida glycoproteins by alkaline borohydride treatment, afforded the following structures: Gal beta l-4(6SO4-)GlcNAc beta l-3Gal beta l-4GlcNAc beta 1-3Gal beta

  15. Structural studies of S-7, another exocellular polysaccharide containing 2-deoxy-arabino-hexuronic acid.

    Science.gov (United States)

    Gulin, S; Kussak, A; Jansson, P E; Widmalm, G

    2001-04-12

    The exocellular polysaccharide S-7, a heteropolysaccharide from Azotobacter indicus var. myxogenes has been studied using methylation analysis, Smith degradation, partial acid hydrolysis, NMR spectroscopy and mass spectrometry as the principal methods. It is concluded that the repeating unit has the following structure: [structure: see text] The absolute configuration of the deoxyhexuronic acid was deduced from 1H NMR chemical shifts and is most likely D. Approximately two O-acetyl groups per repeating unit are present, one of which is presumably on the Rha residue. The structure bears great resemblance to another polysaccharide, recently studied, produced by Sphingomonas paucimobilis I-886.

  16. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

    International Nuclear Information System (INIS)

    Labudde, D.; Leitner, D.; Krueger, M.; Oschkinat, H.

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the α-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely α-helix, β-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time

  17. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts.

    Science.gov (United States)

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bera, Asim K; Aukema, Kelly G.; Elias, Mikael; Wackett, Lawrence P. (UMM)

    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.

  19. 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.

  20. Structural Determination and Occurrence in Ahiflower Oil of Stearidonic Acid Trans Fatty Acids.

    Science.gov (United States)

    Delmonte, Pierluigi; Milani, Andrea; Bhangley, Shivani

    2018-02-01

    Several marine oils and seed oils on the market contain relevant quantities of stearidonic acid (18:4n-3, SDA). The formation of 18:4n-3 trans fatty acids (tFA) during the refining of these oils necessitates the development of a method for their quantification. In this study, 18:4n-3 was isolated from Ahiflower and isomerized to obtain its 16 geometric isomers. The geometric isomers of 18:4n-3 were isolated by silver ion HPLC (Ag + -HPLC) and characterized by partial reduction with hydrazine followed by gas chromatography analysis. The elution order of all 16 isomers was established using a 100 m × 0.25 mm 100% poly(biscyanopropyl siloxane) capillary column and at the elution temperature of 180 °C. The 4 mono-trans-18:4n-3 isomers produced during the refining of oils rich in 18:4n-3 were chromatographically resolved from each other, but c6,t9,c12,c15-18:4 coeluted with the tetra-cis isomer. These 2 fatty acids (FA) were resolved by reducing the separation temperature to 150 °C, but this change caused tetra-cis-18:4n-3 to coelute with t6,c9,c12,c15-18:4. Combining the results from 2 isothermal separations (180 and 150 °C) was necessary to quantify the 4 mono-trans 18:4n-3 FA in Ahiflower oil. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

  1. Structure and tautomerism of tenuazonic acid – A synergetic computational and spectroscopic approach

    Energy Technology Data Exchange (ETDEWEB)

    Mikula, Hannes, E-mail: hannes.mikula@tuwien.ac.at [Vienna University of Technology, Institute of Applied Synthetic Chemistry, Getreidemarkt 9/163-OC, 1060 Vienna (Austria); University of Natural Resources and Life Sciences, Institute of Applied Genetics and Cell Biology, Muthgasse 18, 1190 Wien (Austria); Horkel, Ernst; Hans, Philipp; Hametner, Christian; Fröhlich, Johannes [Vienna University of Technology, Institute of Applied Synthetic Chemistry, Getreidemarkt 9/163-OC, 1060 Vienna (Austria)

    2013-04-15

    Highlights: ► Many published structures for tenuazonic acid (TeA) are incorrect. ► DFT calculations were used for quantum chemical treatment of tenuazonic acid. ► This article reports the confirmation of the main tautomeric structures of TeA. ► A synergetic computational and spectroscopic approach was applied. -- Abstract: All reasonable tautomers and rotamers of tenuazonic acid, which is considered to be of the highest toxicity amongst the Alternaria mycotoxins, were investigated by DFT calculations at different levels of theory in gas phase and in solution to obtain optimized geometries for further examinations. Calculated NMR spectra of tautomeric structures are being presented and compared to experimental data to finally achieve a synergetic computational and spectroscopic approach for structure elucidation of 3-acetyltetramic acids, affording the predominant tautomer of tenuazonic acid in aqueous solution. Furthermore we were able to simulate the less hindered rotation of the exocyclic acetyl group, which occurs after dissociation of tenuazonic acid in protic solvents.

  2. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Matte, Allan; Grosse, Stephan; Bergeron, Hélène; Abokitse, Kofi; Lau, Peter C.K. (Biotech Res.)

    2012-04-30

    The decarboxylation of phenolic acids, including ferulic and p-coumaric acids, to their corresponding vinyl derivatives is of importance in the flavoring 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 -barrel structure and two -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 -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.

  4. 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...

  5. Comparison Study on Polysaccharide Fractions from Laminaria japonica: Structural Characterization and Bile Acid Binding Capacity.

    Science.gov (United States)

    Gao, Jie; Lin, Lianzhu; Sun, Baoguo; Zhao, Mouming

    2017-11-08

    Our previous study has suggested that the crude polysaccharide obtained from Laminaria japonica by acid assisted extraction (LP-A) have significant bile acid-binding capacity, which probably ascribed to its specific structure characterization. The relationship between structure characterization and bile acid-binding capacity of the purified LP-A fractions are still unknown. This paper conducted a comparison study on the structure characterization and bile acid-binding capacity of three LP-A fractions (LP-A4, LP-A6, and LP-A8). The results indicated that LP-A4, LP-A6, and LP-A8, characterized as mannoglucan, fucomannoglucan, and fucogalactan, had significantly different structure characterization. Furthermore, the bile acid-binding capacity of LP-A8 was obviously higher than the other fractions, which may be attributed to its highly branched structure, abundant sulfate, fucose, and galactose in chemical composition and denser interconnected macromolecule network in molecular morphology. This study provides scientific evidence for the potential utilization of LP-A8 as an attractive functional food supplement candidate for the hyperlipidemia population.

  6. Relationship between serum uric acid and metabolic syndrome: an analysis by structural equation modeling.

    Science.gov (United States)

    Lu, Wenli; Song, Kun; Wang, Yuan; Zhang, Qing; Li, Wen; Jiao, Huanli; Wang, Guolin; Huang, Guowei

    2012-01-01

    To investigate the nature of the relationships between uric acid and metabolic syndrome (MetS) components. Body mass index, waist circumference, serum uric acid, fasting glucose, lipid profiles, and blood pressure were measured in 13,811 subjects aged between 18 and 85 years of age. Two structural equation models (SEMs) were used to test a hypothesis regarding the linking roles of uric acid in the occurrence of MetS components in male and female separately. The findings of the SEM demonstrated that increased uric acid level was associated with fasting glucose (beta = 0.221, P uric acid level was associated with decreased fasting glucose (beta = -0.071, P uric acid and lipid profiles than those between uric acid and other MetS components. By using SEM, we were able to confirm the intimate relationships between uric acid and MetS components, particularly in women. The associations between uric acid and MetS components were gender specific, and the nature of such association requires further exploration. Copyright © 2012 National Lipid Association. Published by Elsevier Inc. All rights reserved.

  7. 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

    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...... and differences in production/purification, which caused lower tocopherol content and higher initial levels of primary and secondary oxidation products in SL compared with RL and SO. Grindox 117 and gallic acid did not exert a distinct antioxidative effect in the SL oil samples during storage......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...

  8. 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...... or cow's milk fat contain most of their 16:0 in the outer positions of the triacylglycerol molecules. Furthermore, human milk contains long-chain polyunsaturated fatty acids, which are not present in either cow's milk or vegetable oils. Methods: By standard lipid analysis procedures, we examined...... the triacylglycerol structures and fatty acid profiles of fats from 28 infant formulas or formulas for special indications available in the Danish market from 1999 to 2003. Results: The total fatty acid compositions of the formulas showed a 16:0 content almost similar to human milk, whereas the content in the sn2...

  9. Crystal structure of 5-hydroxy-5-propylbarbituric acid

    Directory of Open Access Journals (Sweden)

    Thomas Gelbrich

    2015-11-01

    Full Text Available Molecules of the title compound, C7H10N2O4, systematic name 5-hydroxy-5-propylpyrimidine-2,4,6(1H,3H,5H-trione, form a hydrogen-bonded framework which is based on three independent hydrogen bonds, N—H...O(carbonyl, N—H...O(hydroxy and O—H...O(carbonyl. This framework has the topology of the 5-connected nov net. Each molecule is linked to five other molecules via six hydrogen bonds, and the descriptor of the hydrogen-bonded structure is F65[44.66-nov]. The crystal packing is isostructural with that of the previously reported 5-hydroxy-5-ethyl analogue.

  10. Hydrogen-bonding interactions in thiosemicarbazones of carboxylic acids: Structure of 2-ketobutyric acid thiosemicarbazone hemihydrate

    International Nuclear Information System (INIS)

    Sonawane, P.; Chikate, R.; Kumbhar, A.; Padhye, S.; Doedens, R.J.

    1991-01-01

    2-Thiosemicarbazonobutanoic acid hemihydrate, C 5 H 9 N 3 O 2 S.0.5H 2 O, M r =184.22, triclinic, Panti 1, a=8.163(2), b=8.868(2), c=12.438(2) A, α=72.99(2), β=79.47(2), γ=84.06(2)deg, V=845.3(3) A 3 , Z=4, D x =1.447 Mg m -3 , λ(Mo Kα)=0.71073 A, μ=0.332 mm -1 , F(000)=392, T=296 K, R=0.038 for 3830 independent reflections with I>3σ(I). Three hydrogen bonds link the two crystallographically independent molecules in a pairwise fashion. The two molecules both have E configurations about each C-N and N-N bond, but differ by nearly 180deg in the orientation of the -COOH group. (orig.)

  11. Dog and human acid beta-D-galactosidases are structurally similar.

    Science.gov (United States)

    Hubert, J J; O'Brien, J S

    1983-01-01

    The purification of dog liver acid beta-galactosidase is described. The dog enzyme migrated as a single major band on polyacrylamide-gel electrophoresis in the presence of sodium dodecyl sulphate, with a molecular weight of 60000. Antiserum raised against purified human liver acid beta-galactosidase cross-reacted with beta-galactosidase from dog liver, but not with those from cat liver or Escherichia coli. Tryptic peptide maps of the dog and human acid beta-galactosidases indicate that 21 of the 24 peptides observed were homologous; a similar result was obtained after chymotryptic peptide mapping. We conclude that dog and human acid beta-galactosidases are structurally similar, and that canine GM1 gangliosidosis (acid beta-galactosidase deficiency) is an excellent model for the same disease in man. Images Fig. 1. Fig. 3. PMID:6412684

  12. Structural basis for substrate recognition in the salicylic acid carboxyl methyltransferase family.

    Science.gov (United States)

    Zubieta, Chloe; Ross, Jeannine R; Koscheski, Paul; Yang, Yue; Pichersky, Eran; Noel, Joseph P

    2003-08-01

    Recently, a novel family of methyltransferases was identified in plants. Some members of this newly discovered and recently characterized methyltransferase family catalyze the formation of small-molecule methyl esters using S-adenosyl-L-Met (SAM) as a methyl donor and carboxylic acid-bearing substrates as methyl acceptors. These enzymes include SAMT (SAM:salicylic acid carboxyl methyltransferase), BAMT (SAM:benzoic acid carboxyl methyltransferase), and JMT (SAM:jasmonic acid carboxyl methyltransferase). Moreover, other members of this family of plant methyltransferases have been found to catalyze the N-methylation of caffeine precursors. The 3.0-A crystal structure of Clarkia breweri SAMT in complex with the substrate salicylic acid and the demethylated product S-adenosyl-L-homocysteine reveals a protein structure that possesses a helical active site capping domain and a unique dimerization interface. In addition, the chemical determinants responsible for the selection of salicylic acid demonstrate the structural basis for facile variations of substrate selectivity among functionally characterized plant carboxyl-directed and nitrogen-directed methyltransferases and a growing set of related proteins that have yet to be examined biochemically. Using the three-dimensional structure of SAMT as a guide, we examined the substrate specificity of SAMT by site-directed mutagenesis and activity assays against 12 carboxyl-containing small molecules. Moreover, the utility of structural information for the functional characterization of this large family of plant methyltransferases was demonstrated by the discovery of an Arabidopsis methyltransferase that is specific for the carboxyl-bearing phytohormone indole-3-acetic acid.

  13. 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.

  14. 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.

  15. Structures of Tris(2-hydroxyethyl)ammonium Salts of Succinic Acid

    Science.gov (United States)

    Loginov, S. V.; Dain, I. A.; Rybakov, V. B.; Ofitserov, E. N.; Gordeev, D. A.; Storozhenko, P. A.

    2018-01-01

    Succinic acid salts-tris(2-hydroxyethyl)ammonium succinate (C6H16NO3) 2 + C4H4O 4 2- (monoclinic crystals, sp. gr. P21/ c, Z = 4) and tris(2-hydroxyethyl)ammonium hydrogen succinate (C6H16NO3)+C4H5O 4 - (monoclinic crystals, sp. gr. P21/ c, Z = 4)—were synthesized and structurally characterized. The specific features of the three-dimensional structures of tris(2-hydroxyethyl)ammonium salts of succinic acid are considered. The role of interionic electrostatic interactions in the structure stabilization and the formation of products of composition 1: 1 and 1: 2 derived from succinic acid is discussed.

  16. Theoretical Structures of Triflic Acid-Water Clusters and the Molecular Mechanism of Proton Dissociation

    Energy Technology Data Exchange (ETDEWEB)

    Paddison, S.J.; Pratt, L.R.; Zawodzinski, T.A.

    1998-11-01

    Structural and energetic information required for recently proposed quasi-chemical theories of solution chemistry have been obtained for clusters of water with triflic acid, CF{sub 3}SO{sub 3}H(H{sub 2}O){sub n} for n=1-6. Quantum mechanical calculations on the clusters indicate that the acid proton does not dissociate with n=1 or 2 hydrating water molecules, but does dissociate for n>=3 water molecule partners. The computed minimum energy structures indicate that both ''Eigen'' (H{sub 9}O{sub 4}{sup +}) (n=3,4,6) and ''Zundel'' (H{sub 5}O{sub 2}{sup +}) (n=5) structures are likely to play a role in the molecular mechanism of acid dissociation in Nafion{reg_sign}.

  17. Crystal structure of the tumor-promoter okadaic acid bound to protein phosphatase-1.

    Science.gov (United States)

    Maynes, J T; Bateman, K S; Cherney, M M; Das, A K; Luu, H A; Holmes, C F; James, M N

    2001-11-23

    Protein phosphatase-1 (PP1) plays a key role in dephosphorylation in numerous biological processes such as glycogen metabolism, cell cycle regulation, smooth muscle contraction, and protein synthesis. Microorganisms produce a variety of inhibitors of PP1, which include the microcystin class of inhibitors and okadaic acid, the latter being the major cause of diarrhetic shellfish poisoning and a powerful tumor promoter. We have determined the crystal structure of the molecular complex of okadaic acid bound to PP1 to a resolution of 1.9 A. This structure reveals that the acid binds in a hydrophobic groove adjacent to the active site of the protein and interacts with basic residues within the active site. Okadaic acid exhibits a cyclic structure, which is maintained via an intramolecular hydrogen bond. This is reminiscent of other macrocyclic protein phosphatase inhibitors. The inhibitor-bound enzyme shows very little conformational change when compared with two other PP1 structures, except in the inhibitor-sensitive beta12-beta13 loop region. The selectivity of okadaic acid for protein phosphatases-1 and -2A but not PP-2B (calcineurin) may be reassessed in light of this study.

  18. 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.

  19. 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

  20. 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...... 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....

  1. The crystal structure of tryptophan hydroxylase with bound amino acid substrate

    DEFF Research Database (Denmark)

    Windahl, Michael Skovbo; Petersen, Charlotte Rode; Christensen, Hans Erik Mølager

    2008-01-01

    of the neurotransmitter and hormone serotonin (5-hydroxytryptamine). We have determined the 1.9 Å resolution crystal structure of the catalytic domain (Δ1−100/Δ415−445) of chicken TPH isoform 1 (TPH1) in complex with the tryptophan substrate and an iron-bound imidazole. This is the first structure of any aromatic amino...... acid hydroxylase with bound natural amino acid substrate. The iron coordination can be described as distorted trigonal bipyramidal coordination with His273, His278, and Glu318 (partially bidentate) and one imidazole as ligands. The tryptophan stacks against Pro269 with a distance of 3.9 Å between...

  2. Structural characteristics of marine sedimentary humic acids by CP/MAS sup(13)C NMR spectroscopy

    Digital Repository Service at National Institute of Oceanography (India)

    Sardessai, S.; Wahidullah, S.

    acides humiques de la mer d’Arabie ; les acides humiques des stdiments estuariens et &tiers de la baie du Bengale sont dominks par les hyd.rates de carbone et les structures aro- matiques, ainsi que, dans une moindre mesure, par les structures... ont CtC Ctudiks dans diffkrents environnements de d6pp8ts par RMN du 13C (&at solide) et les rksultats ont Ctt cornparks avec les analyses chimiques traditionnelles en milieu liquide. Les donnkes obte- nues sont en accord avec la littkrature...

  3. 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....

  4. The role of polysialic acid and other carbohydrate polymers in neural structural plasticity.

    Science.gov (United States)

    Fryer, H J; Hockfield, S

    1996-02-01

    Polysialic acid (PSA) fulfills several criteria for a molecule involved in structural plasticity, including expression in regions capable of plasticity, re-expression in structures undergoing synaptic rearrangement in the adult, downregulation following innervation, and regulation by activity. In addition, removal of PSA reduces the capacity for structural plasticity. PSA may be paradigmatic for other large polymeric carbohydrates, such as glycosaminoglycans and proteoglycans, which also are highly charged and can be extensively hydrated. These carbohydrates may affect structural plasticity by altering cell-cell and/or cell-matrix interactions by increasing intermolecular spacing through hydration.

  5. 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

  6. Optimization of the Synthesis of Structured Phosphatidylcholine with Medium Chain Fatty Acid.

    Science.gov (United States)

    Ochoa-Flores, Angélica A; Hernández-Becerra, Josafat A; Cavazos-Garduño, Adriana; Vernon-Carter, Eduardo J; García, Hugo S

    2017-11-01

    Structured phosphatidylcholine was successfully produced by acidolysis between phosphatidylcholine and free medium chain fatty acid, using phospholipase A 1 immobilized on Duolite A568. Response surface methodology was applied to optimize the reaction system using three process parameters: molar ratio of substrates (phosphatidylcholine to free medium chain fatty acid), enzyme loading, and reaction temperature. All parameters evaluated showed linear and quadratic significant effects on the production of modified phosphatidylcholine; molar ratio of substrates contributed positively, but temperature influenced negatively. Increased enzyme loading also led to increased production of modified phosphatidylcholine but only during the first 9 hours of the acidolysis reaction. Optimal conditions obtained from the model were a ratio of phosphatidylcholine to free medium chain fatty acid of 1:15, an enzyme loading of 12%, and a temperature of 45°C. Under these conditions a production of modified phosphatidylcholine of 52.98 % were obtained after 24 h of reaction. The prediction was confirmed from the verification experiments; the production of modified phosphatidylcholine was 53.02%, the total yield of phosphatidylcholine 64.28% and the molar incorporation of medium chain fatty acid was 42.31%. The acidolysis reaction was scaled-up in a batch reactor with a similar production of modified phosphatidylcholine, total yield of phosphatidylcholine and molar incorporation of medium chain fatty acid. Purification by column chromatography of the structured phosphatidylcholine yielded 62.53% of phosphatidylcholine enriched with 42.52% of medium chain fatty acid.

  7. Low sat-structured fats enriched in α-linolenic acid: physicochemical properties and crystallization characteristics.

    Science.gov (United States)

    Stahl, Marcella Aparecida; Buscato, Monise Helen Masuchi; Grimaldi, Renato; Cardoso, Lisandro Pavie; Ribeiro, Ana Paula Badan

    2017-10-01

    This work sought to obtain and evaluate zero trans-fat reduced in saturated fatty acids, with higher content of unsaturated fatty acids. Palm oil (PO) was used as the reference of zero trans lipid base. Different amounts of linseed oil (LO) were added to PO, obtaining the following blends: 100:0; 80:20; 60:40; 40:60; 20:80 and 0:100 of PO:LO (w/w%), respectively. These blends were added to fully hydrogenated soybean oil (FHSO) as the crystallization modifying agent, and to sorbitan monostearate (SMS) as the structuring element, both at a proportion of 3% to build the structured fractions. The control and the structured blends were evaluated for fatty acid composition, solid fat content, consistency, crystallization kinetics, thermal behavior, microstructure and polymorphism. With the addition of LO to the PO, an increase of up to 80% was observed in the content of alpha-linolenic acid and a reduction of saturated fatty acids to 47% in the blends. FHSO and SMS offered thermal resistance to the blends, with relevant changes in the crystallization kinetics and microstructure, affecting macroscopic characteristics with the increase in consistence. It was possible to obtain a lipid formulation with features of plasticity and enhanced nutritional quality, compatible with several food applications.

  8. Crystal structure of an indole-3-acetic acid amido synthetase from grapevine involved in auxin homeostasis.

    Science.gov (United States)

    Peat, Thomas S; Böttcher, Christine; Newman, Janet; Lucent, Del; Cowieson, Nathan; Davies, Christopher

    2012-11-01

    Auxins are important for plant growth and development, including the control of fruit ripening. Conjugation to amino acids by indole-3-acetic acid (IAA)-amido synthetases is an important part of auxin homeostasis. The structure of the auxin-conjugating Gretchen Hagen3-1 (GH3-1) enzyme from grapevine (Vitis vinifera), in complex with an inhibitor (adenosine-5'-[2-(1H-indol-3-yl)ethyl]phosphate), is presented. Comparison with a previously published benzoate-conjugating enzyme from Arabidopsis thaliana indicates that grapevine GH3-1 has a highly similar domain structure and also undergoes a large conformational change during catalysis. Mutational analyses and structural comparisons with other proteins have identified residues likely to be involved in acyl group, amino acid, and ATP substrate binding. Vv GH3-1 is a monomer in solution and requires magnesium ions solely for the adenlyation reaction. Modeling of IAA and two synthetic auxins, benzothiazole-2-oxyacetic acid (BTOA) and 1-naphthaleneacetic acid (NAA), into the active site indicates that NAA and BTOA are likely to be poor substrates for this enzyme, confirming previous enzyme kinetic studies. This suggests a reason for the increased effectiveness of NAA and BTOA as auxins in planta and provides a tool for designing new and effective auxins.

  9. 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.

  10. 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.

  11. 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).

  12. 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).

  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. Phase-separated structures of mixed Langmuir-Blodgett films of fatty acid and hybrid carboxylic acid.

    Science.gov (United States)

    Kimura, Hideto; Watanabe, Satoshi; Shibata, Hirobumi; Azumi, Reiko; Sakai, Hideki; Abe, Masahiko; Matsumoto, Mutsuyoshi

    2008-12-04

    Phase separation often occurs in mixed Langmuir-Blodgett (LB) films. Usually circular domains at the micrometer length scale form in the LB films. The size and shape of the domains are governed by a compromise between two competing interactions of line tension and dipole-dipole interaction. An attempt was made to control the line tension by varying systematically the hydrophobic moieties of the film-forming molecules. Phase-separated structures of two-component mixed LB films of fatty acid [C(k)H(2k+1)COOH (HkA)] and hybrid carboxylic acid [C(m)F(2m+1)C(n)H(2n)COOH (FmHnA)] were investigated. IR spectra of the mixed LB films of H17A and F8H10A revealed that the alkyl chains were in an all-trans conformation and that the molecular orientation remained unchanged when the two components were mixed. Nanowires formed in the mixed LB films of HkA and F8H10A. The width of the nanowires increased with an increase in k. Domain size and shape in the mixed LB films of H17A and FmHnA depended strongly on the values of m and n. Circular domains at the micrometer length scale formed in the region m + n or = 16 except for F6H10A. These results were explained by using a lattice model that considers the effect of the hydrophobic moieties of fatty acid and hybrid carboxylic acid on the line tension.

  15. 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.

  16. 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.

  17. Crystal structure of the bis(cyclohexylammonium succinate succinic acid salt adduct

    Directory of Open Access Journals (Sweden)

    Modou Sarr

    2015-08-01

    Full Text Available The crystal structure of the title salt adduct, 2C6H14N+·C4H4O42−·C4H6O4, consists of two cyclohexylammonium cations, one succcinate dianion and one neutral succinic acid molecule. Succinate dianions and succinic acid molecules are self-assembled head-to-tail through O—H...O hydrogen bonds and adopt a syn–syn configuration, leading to a strand-like arrangement along [101]. The cyclohexylammonium cations have a chair conformation and act as multidentate hydrogen-bond donors linking adjacent strands through intermolecular N—H...O interactions to both the succinate and the succinic acid components. This results in two-dimensional supramolecular layered structures lying parallel to (010.

  18. 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.

  19. Cyanuric acid and melamine on Au(111): Structure and energetics of hydrogen-bonded networks

    NARCIS (Netherlands)

    Xu, H.; Xu, Wei; Dong, Mingdong; Gersen, H.; Rauls, Eva; Vazquez Campos, M.S.; Vazquez-Campos, Socorro; Crego Calama, Mercedes; Reinhoudt, David; Stensgaard, Ivan; Laegsgaard, Erik; Linderoth, Trolle R.; Besenbacher, Flemming

    2007-01-01

    Expect the unexpected: The interaction between cyanuric acid (CA) and melamine (M) molecules is a key structural motif in supramolecular chemistry. The adsorption and coadsorption of M and CA on a Au(111) surface under ultrahigh vacuum (UHV) is investigated using STM with submolecular resolution. In

  20. Solution structure of fatty acid-binding protein from human brain.

    NARCIS (Netherlands)

    Rademacher, M.; Zimmerman, A.W.; Ruterjans, H.; Veerkamp, J.H.; Lucke, C.

    2002-01-01

    Human brain-type fatty acid-binding protein (B-FABP) has been recombinantly expressed in Escherichia coli both unlabelled and 15N-enriched for structure investigation in solution using high-resolution NMR spectroscopy. The sequential assignments of the 1H and 15N resonances were achieved by applying

  1. 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

  2. Isolation and structural determination of DTX-6, a new okadaic acid derivative.

    Science.gov (United States)

    Suárez-Gómez, B; Souto, M L; Norte, M; Fernández, J J

    2001-10-01

    Diarrhetic shellfish poisoning is an illness caused by toxins accumulated in shellfish and produced by dinoflagellates, mainly of the Dinophysis and Prorocentrum genera. This paper reports the isolation and spectroscopic structural elucidation of a new compound, DTX-6 (2), an ester derivative of okadaic acid (OA) (1), isolated from an artificial culture of strain PLV2 of Prorocentrum lima.

  3. 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...

  4. 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...

  5. Expression and structural-functional alterations of α-1-acid glycoprotein at the pathological state

    Directory of Open Access Journals (Sweden)

    Kulinich A. O.

    2010-07-01

    Full Text Available The review analyzes up-to-date knowledge on structure and biological functions of α-acid glycoprotein. The special attention is given to alterations of fucosylation, sialylation and branching of orosomucoid at the acute, chronic inflammation and oncotransformations.

  6. Structural insights into the binding of lauric acid to CYP107L2 from Streptomyces avermitilis.

    Science.gov (United States)

    Han, Songhee; Pham, Tan-Viet; Kim, Joo-Hwan; Lim, Young-Ran; Park, Hyoung-Goo; Jeong, Dabin; Yun, Chul-Ho; Chun, Young-Jin; Kang, Lin-Woo; Kim, Donghak

    2017-01-22

    Streptomyces avermitilis is an actinobacterium known to produce clinically useful macrolides including avermectins. CYP107L2 from S. avermitilis shares a high sequence similarity with the PikC (CYP107L1) from S. venezuelae. To elucidate the structural features of CYP107L2, we conducted biochemical and structural characterization of CYP107L2 from S. avermitilis. The CYP107L2 gene was cloned, and its recombinant protein was expressed and purified. The CYP107L2 showed a low-spin state of heme, and the reduced form yielded the CO difference spectra with a maximal absorption at 449 nm. Binding of pikromycin and lauric acid yielded the typical type I spectra with K d values of 4.8 ± 0.3 and 111 ± 9 μM, respectively. However, no metabolic product was observed in the enzyme reaction. X-ray crystal structures of the ligand-free CYP107L2 and its complex with lauric acid were determined at the resolution of 2.6 and 2.5 Å, respectively. CYP107L2 showed a well-conserved CYP structure with a wide-open substrate-binding cavity. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Glu-40 and Leu-382 residues in the CYP107L2 complex with lauric acid showed significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site. Copyright © 2016 Elsevier Inc. All rights reserved.

  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. 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.

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

    International Nuclear Information System (INIS)

    Pegan, Scott D.; Serrano, Hector; Whitman, Christian P.; Mesecar, Andrew D.

    2008-01-01

    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

  10. 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.

  11. Crystal Structure of Autotaxin, a Lysophospholipase D that Produces Lipid Mediator Lysophosphatidic Acids

    Science.gov (United States)

    Nishimasu, Hiroshi; Takagi, Junichi; Aoki, Junken; Nureki, Osamu

    Autotaxin (ATX), also known as Enpp2, is a secreted lysophospholipase D that hydrolyzes lysophosphatidylcholine to generate lysophosphatidic acid (LPA), a lipid mediator that activates G-protein coupled receptors to evoke various cellular responses. We solved the crystal structures of mouse ATX alone and in complex with LPAs with different acyl-chain lengths and saturations. The structures reveal a multidomain architecture that may maintain the structure of the hydrophobic pocket, in which the respective LPA molecules are accommodated in distinct conformations. Moreover, our data suggest that the produced LPAs are transferred from the catalytic pocket to cognate receptors through a hydrophobic channel.

  12. Dithiol amino acids can structurally shape and enhance the ligand-binding properties of polypeptides.

    Science.gov (United States)

    Chen, Shiyu; Gopalakrishnan, Ranganath; Schaer, Tifany; Marger, Fabrice; Hovius, Ruud; Bertrand, Daniel; Pojer, Florence; Heinis, Christian

    2014-11-01

    The disulfide bonds that form between two cysteine residues are important in defining and rigidifying the structures of proteins and peptides. In polypeptides containing multiple cysteine residues, disulfide isomerization can lead to multiple products with different biological activities. Here, we describe the development of a dithiol amino acid (Dtaa) that can form two disulfide bridges at a single amino acid site. Application of Dtaas to a serine protease inhibitor and a nicotinic acetylcholine receptor inhibitor that contain disulfide constraints enhanced their inhibitory activities 40- and 7.6-fold, respectively. X-ray crystallographic and NMR structure analysis show that the peptide ligands containing Dtaas have retained their native tertiary structures. We furthermore show that replacement of two cysteines by Dtaas can avoid the formation of disulfide bond isomers. With these properties, Dtaas are likely to have broad application in the rational design or directed evolution of peptides and proteins with high activity and stability.

  13. Transformations of griseofulvin in strong acidic conditions--crystal structures of 2'-demethylgriseofulvin and dimerized griseofulvin.

    Science.gov (United States)

    Leśniewska, Barbara; Jebors, Said; Coleman, Anthony W; Suwińska, Kinga

    2012-03-01

    The structure of griseofulvic acid, C16H15ClO6, at 100 K has orthorhombic (P2(1)2(1)2) symmetry. It is of interest with respect to biological activity. The structure displays intermolecular O-H...O, C-H...O hydrogen bonding as well as week C-H...pi and pi...pi interactions. In strong acidic conditions the griseofulvin undergoes dimerization. The structure of dimerized griseofulvin, C34H32C12O12 x C2H6O x H2O, at 100 K has monoclinic (P2(1)) symmetry. The molecule crystallized as a solvate with one ethanol and one water molecule. The dimeric molecules form intermolecular O-H...O hydrogen bonds to solvents molecules only but they interact via week C-H...O, C-H...pi, C-Cl...pi and pi...pi interactions with other dimerized molecules.

  14. Dithiol amino acids can structurally shape and enhance the ligand-binding properties of polypeptides

    Science.gov (United States)

    Chen, Shiyu; Gopalakrishnan, Ranganath; Schaer, Tifany; Marger, Fabrice; Hovius, Ruud; Bertrand, Daniel; Pojer, Florence; Heinis, Christian

    2014-11-01

    The disulfide bonds that form between two cysteine residues are important in defining and rigidifying the structures of proteins and peptides. In polypeptides containing multiple cysteine residues, disulfide isomerization can lead to multiple products with different biological activities. Here, we describe the development of a dithiol amino acid (Dtaa) that can form two disulfide bridges at a single amino acid site. Application of Dtaas to a serine protease inhibitor and a nicotinic acetylcholine receptor inhibitor that contain disulfide constraints enhanced their inhibitory activities 40- and 7.6-fold, respectively. X-ray crystallographic and NMR structure analysis show that the peptide ligands containing Dtaas have retained their native tertiary structures. We furthermore show that replacement of two cysteines by Dtaas can avoid the formation of disulfide bond isomers. With these properties, Dtaas are likely to have broad application in the rational design or directed evolution of peptides and proteins with high activity and stability.

  15. 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

  16. Complex coacervates of hyaluronic acid and lysozyme: effect on protein structure and physical stability.

    Science.gov (United States)

    Water, Jorrit J; Schack, Malthe M; Velazquez-Campoy, Adrian; Maltesen, Morten J; van de Weert, Marco; Jorgensen, Lene

    2014-10-01

    Complex coacervates of hyaluronic acid and lysozyme, a model protein, were formed by ionic interaction using bulk mixing and were characterized in terms of binding stoichiometry and protein structure and stability. The complexes were formed at pH 7.2 at low ionic strength (6mM) and the binding stoichiometry was determined using solution depletion and isothermal titration calorimetry. The binding stoichiometry of lysozyme to hyaluronic acid (870 kDa) determined by solution depletion was found to be 225.9 ± 6.6 mol, or 0.1 bound lysozyme molecules per hyaluronic acid monomer. This corresponded well with that obtained by isothermal titration calorimetry of 0.09 bound lysozyme molecules per hyaluronic acid monomer. The complexation did not alter the secondary structure of lysozyme measured by Fourier-transform infrared spectroscopy overlap analysis and had no significant impact on the Tm of lysozyme determined by differential scanning calorimetry. Furthermore, the protein stability of lysozyme was found to be improved upon complexation during a 12-weeks storage study at room temperature, as shown by a significant increase in recovered protein when complexed (94 ± 2% and 102 ± 5% depending on the polymer-protein weight to weight ratio) compared to 89 ± 2% recovery for uncomplexed protein. This study shows the potential of hyaluronic acid to be used in combination with complex coacervation to increase the physical stability of pharmaceutical protein formulations. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. 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

  18. 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).

  19. PreSSAPro: a software for the prediction of secondary structure by amino acid properties.

    Science.gov (United States)

    Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2007-10-01

    PreSSAPro is a software, available to the scientific community as a free web service designed to provide predictions of secondary structures starting from the amino acid sequence of a given protein. Predictions are based on our recently published work on the amino acid propensities for secondary structures in either large but not homogeneous protein data sets, as well as in smaller but homogeneous data sets corresponding to protein structural classes, i.e. all-alpha, all-beta, or alpha-beta proteins. Predictions result improved by the use of propensities evaluated for the right protein class. PreSSAPro predicts the secondary structure according to the right protein class, if known, or gives a multiple prediction with reference to the different structural classes. The comparison of these predictions represents a novel tool to evaluate what sequence regions can assume different secondary structures depending on the structural class assignment, in the perspective of identifying proteins able to fold in different conformations. The service is available at the URL http://bioinformatica.isa.cnr.it/PRESSAPRO/.

  20. Acetic acid-water complex: The first observation of structures containing the higher-energy acetic acid conformer

    Science.gov (United States)

    Lopes, Susy; Fausto, Rui; Khriachtchev, Leonid

    2016-02-01

    Non-covalent interaction of acetic acid (AA) and water is studied experimentally by IR spectroscopy in a nitrogen matrix and theoretically at the MP2 and coupled-cluster with single and double and perturbative triple excitations [CCSD(T)]/6-311++G(2d,2p) levels of theory. This work is focused on the first preparation and characterization of complexes of higher-energy (cis) conformer of AA with water. The calculations show three 1:1 structures for the trans-AA⋯H2O complexes and three 1:1 structures for the cis-AA⋯H2O complexes. Two trans-AA⋯H2O and two cis-AA⋯H2O complexes are found and structurally assigned in the experiments. The two cis-AA⋯ ṡ H2O complexes are obtained by annealing of a matrix containing water and cis-AA molecules prepared by selective vibrational excitation of the ground-state trans form. The less stable trans-AA⋯H2O complex is obtained by vibrational excitation of the less stable cis-AA⋯H2O complex. In addition, the 1:2 complexes of trans-AA and cis-AA with water molecules are studied computationally and the most stable forms of the 1:2 complexes are experimentally identified.

  1. Structural basis of the inhibition of class C acid phosphatases by adenosine 5;#8242;-phosphorothioate

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Harkewal; Reilly, Thomas J.; Tanner, John J. (UMC)

    2012-01-20

    The inhibition of phosphatases by adenosine 5'-phosphorothioate (AMPS) was first reported in the late 1960s; however, the structural basis for the inhibition has remained unknown. Here, it is shown that AMPS is a submicromolar inhibitor of class C acid phosphatases, a group of bacterial outer membrane enzymes belonging to the haloacid dehalogenase structural superfamily. Furthermore, the 1.35-{angstrom} resolution crystal structure of the inhibited recombinant Haemophilus influenzae class C acid phosphatase was determined; this is the first structure of a phosphatase complexed with AMPS. The conformation of AMPS is identical to that of the substrate 5'-AMP, except that steric factors force a rotation of the thiophosphoryl out of the normal phosphoryl-binding pocket. This conformation is catalytically nonproductive, because the P atom is not positioned optimally for nucleophilic attack by Asp64, and the O atom of the scissile O-P bond is too far from the Asp (Asp66) that protonates the leaving group. The structure of 5'-AMP complexed with the Asp64 {yields} Asn mutant enzyme was also determined at 1.35-{angstrom} resolution. This mutation induces the substrate to adopt the same nonproductive binding mode that is observed in the AMPS complex. In this case, electrostatic considerations, rather than steric factors, underlie the movement of the phosphoryl. The structures not only provide an explanation for the inhibition by AMPS, but also highlight the precise steric and electrostatic requirements of phosphoryl recognition by class C acid phosphatases. Moreover, the structure of the Asp64 {yields} Asn mutant illustrates how a seemingly innocuous mutation can cause an unexpected structural change.

  2. 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

  3. Biochemical and Structural Characterization of a Ureidoglycine Aminotransferase in the Klebsiella pneumoniae Uric Acid Catabolic Pathway

    Energy Technology Data Exchange (ETDEWEB)

    French, Jarrod B.; Ealick, Steven E. (Cornell)

    2010-09-03

    Many plants, fungi, and bacteria catabolize allantoin as a mechanism for nitrogen assimilation. Recent reports have shown that in plants and some bacteria the product of hydrolysis of allantoin by allantoinase is the unstable intermediate ureidoglycine. While this molecule can spontaneously decay, genetic analysis of some bacterial genomes indicates that an aminotransferase may be present in the pathway. Here we present evidence that Klebsiella pneumoniae HpxJ is an aminotransferase that preferentially converts ureidoglycine and an {alpha}-keto acid into oxalurate and the corresponding amino acid. We determined the crystal structure of HpxJ, allowing us to present an explanation for substrate specificity.

  4. 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.

  5. Synthesis and structural characterization of derivatives of 2- and 3-benzo[b]furan carboxylic acids with potential cytotoxic activity.

    Science.gov (United States)

    Kossakowski, Jerzy; Ostrowska, Kinga; Hejchman, Elzbieta; Wolska, Irena

    2005-01-01

    Derivatives of 2- and 3-benzo[b]furancarboxylic acids were prepared and evaluated for their cytotoxic potential in the National Cancer Institute, Bethesda, USA. Six compounds: 7-acetyl-6-hydroxy-3-methyl-2-benzofurancarboxylic acid (2), 6-hydroxy-7-(p-methoxycinnamoyl)-3-methyl-2-benzofurancarboxylic acid (4), 5-bromo-7-hydroxy-6-methoxy-2-benzofurancarboxylic acid methyl ester (6a), 6-acetyl-5-(O-ethyl-2'-diethylamino)-2-methyl-3-benzofurancarboxylic acid methyl ester (1f), 6-(O-ethyl-2'-diethylamino)-7-p-methoxycinnamoyl)-3-methyl-2-benzofurancarboxylic acid methyl ester hydrochloride (4b), 5-bromo-7-(O-ethyl-2'-diethylamino)-6-methoxy-2-benzofurancarboxylic acid methyl ester (6b) showed significant cytotoxic activities against human cancer cell lines. In addition the crystal structures of 7-methoxy-2-benzofurancarboxylic acid methyl ester (7a) has been solved by X-ray structure analysis of single crystals.

  6. Structural Analysis of Metabolites of Asiatic Acid and Its Analogue Madecassic Acid in Zebrafish Using LC/IT-MSn

    Directory of Open Access Journals (Sweden)

    Binbin Xia

    2015-02-01

    Full Text Available Although zebrafish has become a significant animal model for drug discovery and screening, drug metabolism in zebrafish remains largely unknown. Asiatic acid (AA and madecassic acid (MA, two natural pentacyclic triterpenoids mainly obtained from Centella asiatica (L. Urban, have been found to possess many pharmacological effects. This study is to probe the metabolic capability of zebrafish via investigation of the drug metabolism of AA and MA in zebrafish, using a sensitive LC/IT-MSn method. In addition, the main fragmentation pathways of AA and MA were reported for the first time. Nineteen metabolites of AA and MA were firstly identified after zebrafish was exposed to the drug, which all were the phase I metabolites and mainly formed from hydroxylation, dehydrogenation, hydroxylation and dehydrogenation, dihydroxylation and dehydrogenation, and dehydroxylation reaction. The results indicated that zebrafish possessed strong metabolic capacity, and the metabolites of AA and MA were formed via similar metabolic pathways and well matched with the known metabolic rules in vivo and in vitro, which supports the widely use of this system in drug metabolism research. This investigation would also contribute to the novel information on the structural elucidation, in vivo metabolites and metabolic mechanism of pentacyclic triterpenoids.

  7. Spectroscopic investigation on structure and pH dependent Cocrystal formation between gamma-aminobutyric acid and benzoic acid

    Science.gov (United States)

    Du, Yong; Xue, Jiadan; Cai, Qiang; Zhang, Qi

    2018-02-01

    Vibrational spectroscopic methods, including terahertz absorption and Raman scattering spectroscopy, were utilized for the characterization and analysis of gamma-aminobutyric acid (GABA), benzoic acid (BA), and the corresponding GABA-BA cocrystal formation under various pH values of aqueous solution. Vibrational spectroscopic results demonstrated that the solvent GABA-BA cocrystal, similar as grinding counterpart, possessed unique characteristic features compared with that of starting parent compounds. The change of vibrational modes for GABA-BA cocrystal comparing with starting components indicates there is strong inter-molecular interaction between GABA and BA molecules during its cocrystallization process. Formation of GABA-BA cocrystal under slow solvent evaporation is impacted by the pH value of aqueous solution. Vibrational spectra indicate that the GABA-BA cocrystal could be stably formed with the solvent condition of 2.00 ≤ pH ≤ 7.00. In contrast, such cocrystallization did not occur and the cocrystal would dissociate into its parent components when the pH value of solvent is lower than 2.00. This study provides experimental benchmark to discriminate and identify the structure of cocrystal and also pH-dependent cocrystallization effect with vibrational spectroscopic techniques in solid-state pharmaceutical fields.

  8. 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.

  9. The Crystal Structure and Behavior of Fenamic Acid-Acridine Complex Under High Pressure.

    Science.gov (United States)

    Jerzykiewicz, Lucjan; Sroka, Adam; Majerz, Irena

    2016-12-01

    The crystal structure of fenamic acid-acridine complex is determined by X-ray diffraction. The strong OHN hydrogen bond linking the complex components and other interactions responsible for packing of the molecules into a crystal are investigated within the Quantum Theory of Atom in Molecule theory. The crystal structure is compared with the structure optimized at B3LYP/6-311++G** level and with the theoretical structures optimized under systematically changed pressure. Analysis of the lattice constants, hydrogen bond lengths, and angles of the inter- and intramolecular hydrogen bond under compression is performed. The structural transformation observed at 5 GPa is connected with a change in the intermolecular OHN hydrogen bond. The proton shifts to acceptor and a new interaction in the crystal appears. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

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

    Czech Academy of Sciences Publication Activity Database

    Biedermannová, Lada; Schneider, Bohdan

    2015-01-01

    Roč. 71, č. 11 (2015), s. 2178-2202 ISSN 1399-0047 Institutional support: RVO:86652036 Keywords : protein hydration * structural biology * X-ray crystallography Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.674, year: 2014

  11. 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.

  12. The crystal structure of benzoic acid: a redetermination with X-rays at room temperature

    International Nuclear Information System (INIS)

    Feld, R.; Lehmann, M.S.; Muir, K.W.; Speakman, J.C.

    1981-01-01

    The crystal structure of benzoic acid, C 6 H 5 CO 2 H, has been redetermined by X-ray diffraction at room temperature. Extensive neutron-diffraction measurements have also been made; by single-crystal methods at room temperature and 130 K; and, at 130 K and 5 K, by powder-profile analysis on C 6 D 5 CO 2 H. The structure consists of centrosymmetric dimers, in which two molecules are linked by a pair of hydrogen bonds between their carboxyl groups. Better precision attaches to the X-ray results. Full-matrix refinement, on 1011 independent reflexions, converged at R = 3.7%. This refinement was indeed based on a model that was formally ordered, so far as concerns all atoms except the acidic hydrogen. However the structural results implied an averaged molecule, with the C - O distances 1.258, 1.268(2)Angstroem and the C - C - O angles 118.7, 117.8(1) 0 ; and the acidic hydrogen appeared as two half atoms on the hydrogen bond, 0.9 Angstroem from each oxygen atom. These findings are most simply interpreted as due to disorder; the two configurations, A and B (of Fig. 1), occur randomly and in nearly equal proportions. Owing to difficulties inherent in the crystal texture of benzoic acid, the neutron results were less satisfactory. Large single crystals were affected by twinning. Though the powder method avoids this difficulty, the structure, further confused by modulation, is rather too complicated for profile refinement. At 5 K however, the structure may be ordered, consisting wholly of dimers in the A-configuration. (orig.)

  13. The use of the SPASIBA spectroscopic potential for reproducing the structures and vibrational frequencies of a sries of acids: acetic acid, pivalic acid, succinic acid, adipic acid and ?-glutamic acid

    Science.gov (United States)

    Chhiba, M.; Derreumaux, P.; Vergoten, G.

    1994-01-01

    Normal coordinate analyses have been performed on acetic, pivalic, succinic and adipic acid dimers (including their deutero analogues) and the L-glutamic acid dimer. It is shown that the calculated potential energy surfaces and harmonic vibrational frequencies are in very good accordance with the experimental results. For all the observed vibrational modes below 1750 cm -1, the standard deviation between the 381 calculated and observed frequencies is approximately 12 cm -1. Comparison with previous assignments underlines a quasi-agreement for the four former molecules. In contrast, new assignments are given for some vibrational bands of L-glutamic acid.

  14. THE INFLUENCE OF NIOBIUM ON THE ACIDITY AND STRUCTURE OF GAMMA-ALUMINA-SUPPORTED VANADIUM OXIDES

    Directory of Open Access Journals (Sweden)

    Sathler M.N.B.

    1998-01-01

    Full Text Available Gamma-alumina-supported niobium oxide was used as a support for vanadium oxides. The influence of the addition of niobium oxide was studied by looking for changes in the structure and acid-base character of superficial species. Vanadium oxide was deposited using the continuous adsorption method; niobium oxide was impregnated using the incipient wetness method. The catalysts were characterized by XPS, UV-visible and IR spectroscopy. Catalytic tests were performed using propane oxidation reaction at 400oC. For coverage below the monolayer, both vanadium and niobium oxides were observed in slightly condensed superficial species. The presence of vanadium oxide on the support was found to increase the Lewis acidity and create some Bronsted acidity. Higher catalytic activity and selectivity for propene were associated with vanadium oxides. The presence of niobium did not contribute to the modification of the chemical properties of superficial vanadium but did decrease the adsorption of vanadium on the alumina.

  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. 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.

  17. Structure of a NADH-insensitive hexameric citrate synthase that resists acid inactivation.

    Science.gov (United States)

    Francois, Julie A; Starks, Courtney M; Sivanuntakorn, Sasitorn; Jiang, Hong; Ransome, Aaron E; Nam, Jeong-Won; Constantine, Charles Z; Kappock, T Joseph

    2006-11-14

    Acetobacter aceti converts ethanol to acetic acid, and strains highly resistant to both are used to make vinegar. A. aceti survives acetic acid exposure by tolerating cytoplasmic acidification, which implies an unusual adaptation of cytoplasmic components to acidic conditions. A. aceti citrate synthase (AaCS), a hexameric type II citrate synthase, is required for acetic acid resistance and, therefore, would be expected to function at low pH. Recombinant AaCS has intrinsic acid stability that may be a consequence of strong selective pressure to function at low pH, and unexpectedly high thermal stability for a protein that has evolved to function at approximately 30 degrees C. The crystal structure of AaCS, complexed with oxaloacetate (OAA) and the inhibitor carboxymethyldethia-coenzyme A (CMX), was determined to 1.85 A resolution using protein purified by a tandem affinity purification procedure. This is the first crystal structure of a "closed" type II CS, and its active site residues interact with OAA and CMX in the same manner observed in the corresponding type I chicken CS.OAA.CMX complex. While AaCS is not regulated by NADH, it retains many of the residues used by Escherichia coli CS (EcCS) for NADH binding. The surface of AaCS is abundantly decorated with basic side chains and has many fewer uncompensated acidic charges than EcCS; this constellation of charged residues is stable in varied pH environments and may be advantageous in the A. aceti cytoplasm.

  18. Structural study of α-amino-acid crystals by 1H CRAMPS NMR spectroscopy

    Science.gov (United States)

    Kimura, Hideaki; Nakamura, Kaori; Eguchi, Akiko; Sugisawa, Hisashi; Deguchi, Kenzo; Ebisawa, Kazuyoshi; Suzuki, Ei-ichiro; Shoji, Akira

    1998-06-01

    1H CRAMPS (combined rotation and multiple pulse spectroscopy) NMR was applied to structural analysis of polymorphic forms of α-amino acid crystals in order to test the power of 1H CRAMPS NMR compared with the 13C and 15N NMR methods. We have studied two different stages of α-amino acid crystals: α-glycine and γ-glycine, and A-histidine and B-histidine. As a result, it was found that the α-methylene proton (H α) signal of α-glycine splits into two peaks (4.4 and 3.4 ppm), but that of γ-glycine gives a singlet peak (3.3 ppm), which was reasonably explained by the 1H electrostatic potential charge calculation for this glycine system. Furthermore, it was found that the 1H chemical shift difference between the H 2 and H 5 peaks from the imidazole ring of A-histidine (0.4 ppm) could easily be distinguished from that of B-histidine (0.9 ppm). Thus, the 1H chemical shifts of α-amino acids are very sensitive to a slight difference in magnetic surroundings of protons as well as to differences of the hydrogen bond network. Therefore, the 1H CRAMPS NMR spectra are very useful for the structural analysis of α-amino acid crystals.

  19. 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.

  20. Structure of the LPS O-chain from Fusobacterium nucleatum strain 10953, containing sialic acid.

    Science.gov (United States)

    Vinogradov, Evgeny; St Michael, Frank; Homma, Kiyonobu; Sharma, Ashu; Cox, Andrew D

    2017-02-22

    Fusobacterium nucleatum is an anaerobic bacterium found in the human mouth where it causes periodontitis. Recently, it has been gaining attention as a potential causative agent for colorectal cancer and is strongly linked with pregnancy complications including pre-term and still births. Little is known about virulence factors of this organism and thus we have initiated studies to examine the bacterial surface glycochemistry. Consistent with a recent paper suggesting that F. nucleatum strain 10593 can synthesize sialic acid, a staining technique identified sialic acid on the bacterial surface. We isolated lipopolysaccharide from this F. nucleatum strain and performed structural analysis on the O-antigen. Our studies identified a trisaccharide repeating unit of the O-antigen with the following structure: -[→4)-α-Neup5Ac-(2 → 4)-β-d-Galp-(1 → 3)-α-d-FucpNAc4NAc-(1-]- where Ac indicates 4-N-acetylation of ∼30% FucNAc4N residues. The presence of sialic acid as a constituent of the O-antigen is consistent with recent data identifying de novo sialic acid synthesis in this strain. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. 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...

  2. 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

  3. 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...... [18:1 n-9], M = caprylic acid [8:0]) for 2 wk. Then lymph was collected 24 h following administration of a single bolus of C-13-labeled MLM or LLL. The total lymphatic recovery of exogenous 18:1 n-9 24 h after administration of a single bolus of MLM or LLL was similar in rats on the LLL diet (43......% 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...

  4. 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.

  5. 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.

  6. 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.

  7. 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)

  8. 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...

  9. Nucleic and amino acid sequences support structure-based viral classification

    OpenAIRE

    Robert M., Sinclair; Janne J., Ravantti; Dennis H., Bamford

    2017-01-01

    Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome, capsid and between individual capsid proteins (i.e. “capsid architecture”) are intimate and expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made...

  10. Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification

    OpenAIRE

    Sinclair, Robert M.; Ravantti, Janne J.; Bamford, Dennis H.

    2017-01-01

    ABSTRACT Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classifi...

  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. 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.

  13. Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification.

    Science.gov (United States)

    Sinclair, Robert M; Ravantti, Janne J; Bamford, Dennis H

    2017-04-15

    Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly

  14. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

    Energy Technology Data Exchange (ETDEWEB)

    Sievers, Stuart A.; Karanicolas, John; Chang, Howard W.; Zhao, Anni; Jiang, Lin; Zirafi, Onofrio; Stevens, Jason T.; Münch, Jan; Baker, David; Eisenberg, David (UCLA); (UWASH); (UL); (Kansas); (Ulm)

    2011-09-20

    Many globular and natively disordered proteins can convert into amyloid fibrils. These fibrils are associated with numerous pathologies as well as with normal cellular functions, and frequently form during protein denaturation. Inhibitors of pathological amyloid fibril formation could be useful in the development of therapeutics, provided that the inhibitors were specific enough to avoid interfering with normal processes. Here we show that computer-aided, structure-based design can yield highly specific peptide inhibitors of amyloid formation. Using known atomic structures of segments of amyloid fibrils as templates, we have designed and characterized an all-D-amino-acid inhibitor of the fibril formation of the tau protein associated with Alzheimer's disease, and a non-natural L-amino-acid inhibitor of an amyloid fibril that enhances sexual transmission of human immunodeficiency virus. Our results indicate that peptides from structure-based designs can disrupt the fibril formation of full-length proteins, including those, such as tau protein, that lack fully ordered native structures. Because the inhibiting peptides have been designed on structures of dual-{beta}-sheet 'steric zippers', the successful inhibition of amyloid fibril formation strengthens the hypothesis that amyloid spines contain steric zippers.

  15. X-ray crystal structure of N-6 adenine deoxyribose nucleic acid methyltransferase from Streptococcus pneumoniae

    Science.gov (United States)

    Tran, Phidung Hong

    X-ray diffraction by using resonant anomalous scattering has become a popular tool for solving crystal structures in the last ten years with the expanded availability of tunable synchrotron radiation for protein crystallography. Mercury atoms were used for phasing. The crystal structure of N-6 deoxyribose nucleic acid methyltransferase from Streptoccocus pneumoniae (DpnM) was solved by using the Multiple Anomalous Diffraction technique. The crystal structure reveals the formation of mercaptide between the mercury ion and the thiol group on the cysteine amino acid in a hydrophobic environment. The crystal structure contains the bound ligand, S- adenosyl-l-methionine on the surface of the concave opening. The direction of the β-strands on the beta sheets are identical to other solved methyltransferases. The highly conserved motifs, DPPY and the FxGxG, are found to be important in ligand binding and possibly in methyl group transfer. The structure has a concave cleft with an opening on the order of 30 Å that can accommodate a DNA duplex. By molecular modelling coupled to sequence alignment, two other highly conserved residues Arg21 and Gly19 are found to be important in catalysis.

  16. 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.

  17. STUDY OF DOUBLE PROTONS MIGRATION MECHANISM IN SUPRAMOLECULAR STRUCTURES OF ACETIC ACID-WATER AND ACETIC ACID-AMMONIA BY AB INITIO METHOD

    Directory of Open Access Journals (Sweden)

    Karna Wijaya

    2010-06-01

    Full Text Available The theoretical study of double protons migration mechanism on acetic acid-water and acetic acid-ammonia associations has been carried out. The research covered determinations the reactant, transition state and product structures. To gain the goal, the research was conducted in three steps, i.e. (i designing the reactant, transition state and product models, (ii optimizing of structures, and (iii calculating of their uncorrected total energy and frequencies with ab initio methods (basis set 6-31G**. All calculations were performed using Hyperchem ver 5.0 for Windows and Gaussian 94W package program. The computational study result showed that the calculated structures were in good agreement with the hypothetical structures.   Keywords: double protons migration, acetic acid, water, ammonia, molecular mechanics and ab-initio

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

    Energy Technology Data Exchange (ETDEWEB)

    Li, Fangxu; Zhong, Hong, E-mail: zhongh@csu.edu.cn; Zhao, Gang; Wang, Shuai; Liu, Guangyi, E-mail: guangyi.liu@163.com

    2015-10-30

    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.

  19. 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.

  20. 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.

  1. IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences.

    Science.gov (United States)

    McGuffin, Liam J; Atkins, Jennifer D; Salehe, Bajuna R; Shuid, Ahmad N; Roche, Daniel B

    2015-07-01

    IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. 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

  3. 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.

  4. Gold(I) thiolates containing amino acid moieties. Cytotoxicity and structure-activity relationship studies.

    Science.gov (United States)

    Gutiérrez, Alejandro; Gracia-Fleta, Lucia; Marzo, Isabel; Cativiela, Carlos; Laguna, Antonio; Gimeno, M Concepción

    2014-12-07

    Several gold(I) complexes containing a thiolate ligand functionalised with several amino acid or peptide moieties of the type [Au(SPyCOR)(PPh2R')] (where R = OH, amino acid or dipeptide and R' = Ph or Py) were prepared. These thiolate gold complexes bearing biological molecules possess potential use as antitumor agents. Cytotoxicity assays in different tumour cell lines such as A549 (lung carcinoma), Jurkat (T-cell leukaemia) and MiaPaca2 (pancreatic carcinoma) revealed that the complexes exhibit good antiproliferative activity, with IC50 values in the low micromolar range. Several structural modifications such as in the type of phosphine, number of metal atoms and amino acid (type, stereochemistry and functionalisation) were carried out in order to establish the structure-activity relationship in this family of complexes, which has led to the design of new and more potent cytotoxic complexes. Observations of different cellular events after addition of the complexes indicated the possible mechanism of action or the biological targets of this type of new gold(I) drug.

  5. Augmentation of ferulic acid-induced vasorelaxation with aging and its structure importance in thoracic aorta of spontaneously hypertensive rats.

    Science.gov (United States)

    Fukuda, Toshihiko; Kuroda, Takahiro; Kono, Miki; Hyoguchi, Mai; Tanaka, Mitsuru; Matsui, Toshiro

    2015-10-01

    Aging deteriorates vascular functions such as vascular reactivity and stiffness. Thus far, various reports suggest that bioactive compounds can improve vascular functions. However, few age-related studies of natural bioactive compounds are available. The present study attempted to evaluate age-related vasorelaxation of bioactive cinnamic acids, caffeic acid, and ferulic acid using aged rat thoracic aorta. Vasorelaxation was evaluated in thoracic aorta from both 8, 18, and 40 weeks old Wistar-Kyoto rats (WKY) and spontaneously hypertensive rats (SHR) respectively. The result indicated that caffeic acid possessed the vasorelaxation regardless of aging in WKY and SHR. Moreover, the vasorelaxation of ferulic acid enhanced with aging in SHR. The vasorelaxation behavior was acted in an endothelium-independent manner. To access structure importance of enhanced vasorelaxation, analogues of ferulic acid were tested. In 40 weeks old SHR, 3,4-dimethoxycinnamic acid and coniferyl alcohol exhibited equivalent vasorelaxation activity with ferulic acid, providing the structural importance of methoxy-modified 3-position on the phenyl ring and 2-propenoic moiety. These results firstly demonstrated that enhanced vasorelaxation of ferulic acid with aging and 3,4-dimethoxycinnamic acid and coniferyl alcohol, along with ferulic acid, might exhibit the therapeutic potential of vasoactive power with aging.

  6. Synthesis, structure and cytotoxic activity of acetylenic derivatives of betulonic and betulinic acids

    Science.gov (United States)

    Bębenek, Ewa; Chrobak, Elwira; Wietrzyk, Joanna; Kadela, Monika; Chrobak, Artur; Kusz, Joachim; Książek, Maria; Jastrzębska, Maria; Boryczka, Stanisław

    2016-02-01

    A series of acetylenic derivatives of betulonic and betulinic acids has been synthesized and characterized by 1H and 13C NMR, IR and MS spectroscopy. The structure of propargyl betulonate 4 and propargyl betulinate-DMF solvate 8A was solved by X-ray diffraction. Thermal properties were examined using a DSC technique. The resulting alkynyl derivatives, as well as betulin 1 and betulinic acid 3, were evaluated in vitro for their cytotoxic activity against human T47D breast cancer, CCRF/CEM leukemia, SW707 colorectal, murine P388 leukemia and BALB3T3 normal fibroblasts cell lines. Several of the obtained compounds have a favorable cytotoxic profile than betulin 1. Propargyl betulinate 8 was the most active derivative, being up to 3-fold more potent than betulin 1 against the human leukemia (CCRF/CEM) cell line, with an IC50 value of 3.9 μg/mL.

  7. Structure elucidation of new compounds from acidic treatment of the progestins gestodene and drospirenone.

    Science.gov (United States)

    Colombo, Diego; Bombieri, Gabriella; Lenna, Roberto; Marchini, Nicoletta; Modica, Emilia; Scala, Antonio

    2006-08-01

    Gestodene acidic treatment afforded a single rearrangement product, namely 13-beta-ethyl-18,19-dinorpregna-4,14,16-trien-3,20-dione 3, which was originated through HCl-catalyzed Rupe rearrangement. Drospirenone acidic treatment yielded two epimeric lactones by addition of HCl to the 6beta,7beta-cyclopropane ring, namely 7beta-(chloromethyl)-15beta,16beta-methylene-3-oxo-17beta-pregn-4-ene-21,17-carbolactone 4 and 7beta-(chloromethyl)-15beta,16beta-methylene-3-oxo-17alpha-pregn-4-ene-21,17-carbolactone 5. The structure of the compounds was assessed by spectroscopic and crystallographic methods.

  8. 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)

  9. 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.

  10. 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.

  11. 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.

  12. Multi-walled carbon nanotube dispersion by the adsorbed humic acids with different chemical structures.

    Science.gov (United States)

    Zhang, Di; Pan, Bo; Cook, Robert L; Xing, Baoshan

    2015-01-01

    Dissolved humic acid (disHA) is effective for suspending carbon nanotubes (CNTs), but the suspending mechanism is still unclear. This study used bleached and hydrolyzed humic acids as suspending agents to investigate effects of chemical structures on CNTs suspension. The adsorption of aromatic moieties enriched disHA to CNTs was lower than aliphatic components-enriched disHA, but the former was better at suspending CNTs. These findings led to the development of a model, in which disHA with aromatic structures results in stable suspension of CNTs due to stronger steric hindrance. Because of their flexible structures, aliphatic components-enriched disHA molecules easily conformed to CNTs leading to higher adsorption to CNTs but weaker steric hindrance between CNTs. Therefore, the bridging and less suspension of CNTs was observed. This study emphasizes that suspending CNTs by disHA is not only controlled by the adsorbed amount of disHA, but also the chemical nature of disHA.

  13. 1-, 2-, and 4-Ethynylpyrenes in the Structure of Twisted Intercalating Nucleic Acids: Structure, Thermal Stability, and Fluorescence Relationship

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    stabilized. Alterations in the thermal stability were highly influenced by the ethynylpyrene isomers used. This also led to TINAs with different changes in fluorescence spectra depending on the secondary structures formed. Stokes shift of approximately 100 nm was detected for pyren-2-yl......A postsynthetic, on-column Sonogashira reaction was applied on DNA molecules modified by 2- or 4-iodophenylmethylglycerol in the middle of the sequence, to give the corresponding ortho- and para-twisted intercalating nucleic acids (TINA) with 1-, 2-, and 4-ethynylpyrene residues. The convenient......,3-dichloro-5,6-dicyanoACHTUNGTRENUNG-1,4-benzoquinone, and a Vilsmeier-Haack-Arnold transformation followed by a Bodendorf fragmentation. Significant alterations in thermal stability of parallel triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para...

  14. 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.

  15. 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.

  16. 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

    On account of its sensitivity to chirality Raman optical activity (ROA), which may be measured as a small difference in vibrational Raman scattering from chiral molecules in right- and left-circularly polarized incident light, is a powerful probe of structure and behaviour of biomolecules...... 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....

  17. 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

  18. Structural elucidation and physicochemical properties of an organic NLO crystal: 4-Nitrotoluene-2-sulphonic acid dihydrate

    Science.gov (United States)

    Sangeetha, K.; Guru Prasad, L.; Mathammal, R.

    2018-03-01

    4-nitrotoluene-2-sulphonic acid dihydrate single crystals have been developed using slow evaporation technique in methanol. Lattice parameters of the NTSAD crystal have been calculated and it confirms the grown material. The intermolecular interactions are studied from the 3D Hirshfeld surface analysis and 2D fingerprint plots. The NMR spectral analysis has been carried out to confirm the molecular structure of the grown material. Optical properties have been obtained from UV-VIS spectral analysis and photoluminescence studies. Frequency conversion property of the NTSAD crystal was investigated with the aid of Kurtz and Perry method.

  19. 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...... in the design of the next generation of PEMs....

  20. Secondary Structures in a Freeze-Dried Lignite Humic Acid Fraction Caused by Hydrogen-Bonding of Acidic Protons with Aromatic Rings.

    Science.gov (United States)

    Cao, Xiaoyan; Drosos, Marios; Leenheer, Jerry A; Mao, Jingdong

    2016-02-16

    A lignite humic acid (HA) was separated from inorganic and non-HA impurities (i.e., aluminosilicates, metals) and fractionated by a combination of dialysis and XAD-8 resin. Fractionation revealed a more homogeneous structure of lignite HA. New and more specific structural information on the main lignite HA fraction is obtained by solid-state nuclear magnetic resonance (NMR) spectroscopy. Quantitative (13)C multiple cross-polarization (multiCP) NMR indicated oxidized phenyl propane structures derived from lignin. MultiCP experiments, conducted on potassium HA salts titrated to pH 10 and pH 12, revealed shifts consistent with carboxylate and phenolate formation, but structural changes associated with enolate formation from aromatic beta keto acids were not detected. Two-dimensional (1)H-(13)C heteronuclear correlation (2D HETCOR) NMR indicated aryl-aliphatic ketones, aliphatic and aromatic carboxyl groups, phenol, and methoxy phenyl ethers. Acidic protons from carboxyl groups in both the lignite HA fraction and a synthetic HA-like polycondensate were found to be hydrogen-bonded with electron-rich aromatic rings. Our results coupled with published infrared spectra provide evidence for the preferential hydrogen bonding of acidic hydrogens with electron-rich aromatic rings rather than adjacent carbonyl groups. These hydrogen-bonding interactions likely result from stereochemical arrangements in primary structures and folding.

  1. Rigidity of poly-L-glutamic acid scaffolds: Influence of secondary and supramolecular structure

    Energy Technology Data Exchange (ETDEWEB)

    Perticaroli, Stefania [ORNL; Ehlers, Georg [ORNL; Feygenson, Mikhail [ORNL; Sokolov, Alexei P [ORNL

    2015-01-01

    Poly-L-glutamic acid (PGA) is a widely used biomaterial, with applications ranging from drug delivery and biological glues to food products and as a tissue engineering scaffold. A biodegradable material with flexible conjugation functional groups, tunable secondary structure, and mechanical properties, PGA has potential as a tunable matrix material in mechanobiology. Some recent studies in proteins connecting dynamics, nanometer length scale rigidity, and secondary structure suggest a new point of view from which to analyze and develop this promising material. Our paper characterizes the structure, topology, and rigidity properties of PGA prepared with different molecular weights and secondary structures through various techniques including scanning electron microscopy, FTIR, light, and neutron scattering spectroscopy. On the length scale of a few nanometers, rigidity is determined by hydrogen bonding interactions in the presence of neutral species and by electrostatic interactions when the polypeptide is negatively charged. Finally, when probed over hundreds of nanometers, the rigidity of these materials is modified by long range intermolecular interactions that are introduced by the supramolecular structure.

  2. 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.

  3. Crystal structures and hydrogen bonding in the morpholinium salts of four phenoxyacetic acid analogues

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2015-11-01

    Full Text Available The anhydrous salts morpholinium (tetrahydro-2-H-1,4-oxazin-4-ium phenoxyacetate, C4H10NO+·C8H7O3−, (I, morpholinium (4-fluorophenoxyacetate, C4H10NO+·C8H6 FO3−, (II, and isomeric morpholinium (3,5-dichlorophenoxyacetate (3,5-D, (III, and morpholinium (2,4-dichlorophenoxyacetic acid (2,4-D, C4H10NO+·C8H5Cl2O3−, (IV, have been determined and their hydrogen-bonded structures are described. In the crystals of (I, (III and (IV, one of the the aminium H atoms is involved in a three-centre asymmetric cation–anion N—H...O,O′ R12(4 hydrogen-bonding interaction with the two carboxyl O-atom acceptors of the anion. With the structure of (II, the primary N—H...O interaction is linear. In the structures of (I, (II and (III, the second N—H...Ocarboxyl hydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV, the ion pairs are linked though inversion-related N—H...O hydrogen bonds [graph set R42(8], giving a cyclic heterotetrameric structure.

  4. 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.

  5. D-amino acid residue in a defensin-like peptide from platypus venom: effect on structure and chromatographic properties.

    Science.gov (United States)

    Torres, Allan M; Tsampazi, Chryssanthi; Geraghty, Dominic P; Bansal, Paramjit S; Alewood, Paul F; Kuchel, Philip W

    2005-10-15

    The recent discovery that the natriuretic peptide OvCNPb (Ornithorhynchus venom C-type natriuretic peptide B) from platypus (Ornithorynchus anatinus) venom contains a D-amino acid residue suggested that other D-amino-acid-containing peptides might be present in the venom. In the present study, we show that DLP-2 (defensin-like peptide-2), a 42-amino-acid residue polypeptide in the platypus venom, also contains a D-amino acid residue, D-methionine, at position 2, while DLP-4, which has an identical amino acid sequence, has all amino acids in the L-form. These findings were supported further by the detection of isomerase activity in the platypus gland venom extract that converts DLP-4 into DLP-2. In the light of this new information, the tertiary structure of DLP-2 was recalculated using a new structural template with D-Met2. The structure of DLP-4 was also determined in order to evaluate the effect of a D-amino acid at position 2 on the structure and possibly to explain the large retention time difference observed for the two molecules in reverse-phase HPLC. The solution structures of the DLP-2 and DLP-4 are very similar to each other and to the earlier reported structure of DLP-2, which assumed that all amino acids were in the L-form. Our results suggest that the incorporation of the D-amino acid at position 2 has minimal effect on the overall fold in solution.

  6. 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)

  7. 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

  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. 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.

  10. Effect of demineralization on the physiochemical structure and thermal degradation of acid treated indigenous rice husk

    Directory of Open Access Journals (Sweden)

    Aslam Umair

    2016-09-01

    Full Text Available Energy generation from biomass presents some serious problems like slagging, fouling and corrosion of boilers. To address these problems, demineralization of biomass is performed using different leaching agents. This study is focused on determining the influence of leaching agents and leaching time on the physiochemical structure of rice husk during demineralization. Dilute (5% wt solutions of HCl and H2SO4 were used for the demineralization of rice husk separately with leaching time of 15, 60 and 120 minutes. It is shown that H2SO4 exhibited higher removal of alkali and alkaline earth metals (AAEM comparatively as depicted by the 34.2% decrease in ash content along with an increase of 7.10% in the heating value. The acid has been seen to induce more notable changes in physiochemical structure as depicted by the FTIR spectra and SEM micrographs. The thermal degradation behavior of the demineralized rice husk has also been reported.

  11. Quantitative structure activity relationships of some pyridine derivatives as corrosion inhibitors of steel in acidic medium.

    Science.gov (United States)

    El Ashry, El Sayed H; El Nemr, Ahmed; Ragab, Safaa

    2012-03-01

    Quantum chemical calculations using the density functional theory (B3LYP/6-31G DFT) and semi-empirical AM1 methods were performed on ten pyridine derivatives used as corrosion inhibitors for mild steel in acidic medium to determine the relationship between molecular structure and their inhibition efficiencies. Quantum chemical parameters such as total negative charge (TNC) on the molecule, energy of highest occupied molecular orbital (E (HOMO)), energy of lowest unoccupied molecular orbital (E (LUMO)) and dipole moment (μ) as well as linear solvation energy terms, molecular volume (Vi) and dipolar-polarization (π) were correlated to corrosion inhibition efficiency of ten pyridine derivatives. A possible correlation between corrosion inhibition efficiencies and structural properties was searched to reduce the number of compounds to be selected for testing from a library of compounds. It was found that theoretical data support the experimental results. The results were used to predict the corrosion inhibition of 24 related pyridine derivatives.

  12. Improvement in Aqueous Solubility of Retinoic Acid Receptor (RAR) Agonists by Bending the Molecular Structure.

    Science.gov (United States)

    Hiramatsu, Michiaki; Ichikawa, Yuki; Tomoshige, Shusuke; Makishima, Makoto; Muranaka, Atsuya; Uchiyama, Masanobu; Yamaguchi, Takao; Hashimoto, Yuichi; Ishikawa, Minoru

    2016-08-05

    Aqueous solubility is a key requirement for many functional molecules, e. g., drug candidates. Decrease of the partition coefficient (log P) by chemical modification, i.e., introduction of hydrophilic group(s) into molecules, is a classical strategy for improving aqueous solubility. We have been investigating alternative strategies for improving the aqueous solubility of pharmaceutical compounds by disrupting intermolecular interactions. Here, we show that introducing a bend into the molecular structure of retinoic acid receptor (RAR) agonists by changing the substitution pattern from para to meta or ortho dramatically enhances aqueous solubility by up to 890-fold. We found that meta analogs exhibit similar hydrophobicity to the parent para compound, and have lower melting points, supporting the idea that the increase of aqueous solubility was due to decreased intermolecular interactions in the solid state as a result of the structural changes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Study of the structure of free radicals in gamma irradiated amino acid derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Aydin, Murat, E-mail: maydin@adiyaman.edu.t [Adyyaman University, Adyaman (Turkey). Faculty of Education

    2010-12-15

    Electron paramagnetic resonance spectroscopy has been used for the study of the free radicals produced in the powders of L-arginine monohydrochloride, ala-ala and DL-{beta}-leucine gamma-irradiated at room temperature. The structures of the radicals formed in compounds were determined as NH{sub 2}(NH)NHCHCH{sub 2}CH{sub 2}CH(NH{sub 2})CO OH, CH{sub 3}CHCOOH and (CH{sub 3}){sub 2} CCH(NH{sub 2})CH{sub 2}COOH respectively. The paramagnetic species were found to be stable at room temperature more than three months. It was determined that unpaired electron interacted with nearby protons and {sup 14}N nucleus in these radicals. The g values of the radicals and the hyperfine structure constants of the free electron were also measured. These results were compared with the earlier studies in amino acid and derivatives radicals and discussed. (author)

  14. 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

  15. Structure of the magnetite-oleic acid-decalin magnetic fluid from small-angle neutron scattering data

    Science.gov (United States)

    Nagornyi, A. V.; Petrenko, V. I.; Bulavin, L. A.; Avdeev, M. V.; Almásy, L.; Rosta, L.; Aksenov, V. L.

    2014-01-01

    Structural parameters of the magnetite-oleic acid-decalin magnetic fluid at various excesses of oleic acid (up to 25 vol %) have been determined using small-angle neutron scattering. Based on the comparison of the behavior of oleic acid in the magnetic fluid and in the pure solvent (decalin), it has been concluded that the interaction between the molecules of free (unadsorbed) surfactant changes in the presence of magnetic nanoparticles. However, the system remains stable and does not form aggregates of magnetic particles or free oleic acid. These results are compared with the previously presented data for similar benzene-based magnetic fluids.

  16. Synergic application of spectroscopic and theoretical methods to the chlorogenic acid structure elucidation

    Science.gov (United States)

    Marković, Svetlana; Tošović, Jelena; Dimitrić Marković, Jasmina M.

    2016-07-01

    Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary polyphenol known for its pharmacological and nutritional properties, its structural features have not been completely elucidated. This is the first study whose aim is to contribute to clarification of the 5CQA structure by comparing the experimental and simulated IR, Raman, 1H NMR, 13C NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution (DMSO and methanol). The lowest-energy conformers were used to predict the spectra at two levels of theory: B3LYP-D3/and M06-2X/6-311+G(d,p) in combination with the CPCM solvation model. Both methods provide very good agreement between all experimental and simulated spectra, thus indicating correct arrangement of the atoms in the 5CQA molecule. The quinic moiety is characterized with directed hydrogen bonds, where the carboxylic hydrogen is not oriented towards the carbonyl oxygen of the carboxylic group, but towards the oxygen of the proximate hydroxyl group. In the gas-state the lowest-energy conformers are characterized with the O4sbnd H4 ⋯ O9‧ hydrogen bond, whereas in the solvated state the structures with the O4sbnd H4 ⋯ O10‧ hydrogen bond prevail. Knowing the fine structural details, i.e. the proper conformation of 5CQA, provides a solid base for all further investigations related to this compound.

  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. Conformational, electronic, and spectroscopic characterization of isophthalic acid (monomer and dimer structures) experimentally and by DFT.

    Science.gov (United States)

    Bardak, F; Karaca, C; Bilgili, S; Atac, A; Mavis, T; Asiri, A M; Karabacak, M; Kose, E

    2016-08-05

    Isophthalic acid (C6H4(CO2H)2) is a noteworthy organic compound widely used in coating and synthesis of resins and the production of commercially important polymers such as drink plastic bottles. The effects of isophthalic acid (IPA) on human health, toxicology, and biodegradability are the main focus of many researchers. Because structural and spectroscopic investigation of molecules provides a deep understanding of interactional behaviors of compounds, this study stands for exploring those features. Therefore, the spectroscopic, structural, electronic, and thermodynamical properties of IPA were thoroughly studied in this work experimentally using UV-Vis, (1)H and (13)C NMR, FT-IR, FT-Raman and theoretically via DFT and TD-DFT calculations. The UV-Vis absorption spectrum in water was taken in the region 200-400nm. The NMR chemical shifts ((1)H and (13)C) were recorded in DMSO solution. The infrared and Raman spectra of the solid IPA were recorded in the range of 4000-400cm(-1) and 3500-50cm(-1), respectively. DFT and TD-DFT calculations were performed at the level of B3LYP/6-311++G(d,p) in determination of geometrical structure, electronic structure analysis and normal mode. The (13)C and (1)H nuclear magnetic resonance (NMR) spectra were estimated by using the gauge-invariant atomic orbital (GIAO) method. The scaled quantum mechanics (SQM) method was used to determine the total energy distribution (TED) to assign the vibrational modes accurately. Weak interactions such as hydrogen bonding and Van der Walls were analyzed via reduced density gradient (RDG) analysis in monomeric and dimeric forms. Furthermore, the excitation energies, density of state (DOS) diagram, thermodynamical properties, molecular electro-static potential (MEP), and nonlinear optical (NLO) properties were obtained. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. 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...

  20. Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure

    Science.gov (United States)

    Kozlov, I. A.; Politis, P. K.; Van Aerschot, A.; Busson, R.; Herdewijn, P.; Orgel, L. E.; Bada, J. L. (Principal Investigator); Dolan, M. (Principal Investigator)

    1999-01-01

    Hexitol nucleic acid (HNA) is an analogue of DNA containing the standard nucleoside bases, but with a phosphorylated 1,5-anhydrohexitol backbone. HNA oligomers form duplexes having the nucleic acid A structure with complementary DNA or RNA oligomers. The HNA decacytidylate oligomer is an efficient template for the oligomerization of the 5'-phosphoroimidazolides of guanosine or deoxyguanosine. Comparison of the oligomerization efficiencies on HNA, RNA, and DNA decacytidylate templates under various conditions suggests strongly that only nucleic acid double helices with the A structure support efficient template-directed synthesis when 5'-phosphoroimidazolides of nucleosides are used as substrates.

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

    Energy Technology Data Exchange (ETDEWEB)

    Wang Shutao [Center for Molecular Science, Institute of Chemistry, Beijing 100080 (China); Song Yanlin [Center for Molecular Science, Institute of Chemistry, Beijing 100080 (China); Jiang Lei [Center for Molecular Science, Institute of Chemistry, Beijing 100080 (China)

    2007-01-10

    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.

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

    Science.gov (United States)

    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.

  3. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers.

    Science.gov (United States)

    Nap, R J; Tagliazucchi, M; Szleifer, I

    2014-01-14

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads

  4. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers

    Science.gov (United States)

    Nap, R. J.; Tagliazucchi, M.; Szleifer, I.

    2014-01-01

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads

  5. Effect of molecular structure of aniline-formaldehyde copolymers on corrosion inhibition of mild steel in hydrochloric acid solution.

    Science.gov (United States)

    Zhang, Yan; Nie, Mengyan; Wang, Xiutong; Zhu, Yukun; Shi, Fuhua; Yu, Jianqiang; Hou, Baorong

    2015-05-30

    Aniline-formaldehyde copolymers with different molecular structures have been prepared and investigated for the purpose of corrosion control of mild steel in hydrochloric acid. The copolymers were synthesized by a condensation polymerization process with different ratios of aniline to formaldehyde in acidic precursor solutions. The corrosion inhibition efficiency of as-synthesized copolymers for Q235 mild steel was investigated in 1.0 mol L(-1) hydrochloric acid solution by weight loss measurement, potentiodynamic polarization, and electrochemical impedance spectroscopy, respectively. All the results demonstrate that as-prepared aniline-formaldehyde copolymers are efficient mixed-type corrosion inhibitors for mild steels in hydrochloric acid. The corrosion inhibition mechanism is discussed in terms of the role of molecular structure on adsorption of the copolymers onto the steel surface in acid solution. Copyright © 2015. Published by Elsevier B.V.

  6. Study on mutual interactions and electronic structures of hyaluronan with Lysine, 6-Aminocaproic acid and Arginine.

    Science.gov (United States)

    Chytil, Martin; Trojan, Martin; Kovalenko, Alexander

    2016-05-20

    Interactions between polyelectrolytes and oppositely charged surfactants have been in a great interest for several decades, yet the conventional surfactants may cause a problem in medical applications. Interactivity between polysaccharide hyaluronan (HA) and amino acids Lysine, 6-Aminocaproic acid (6-AcA), and Arginine as an alternative system is reported. The interactions were investigated by means of rheology and electric conductance and the electronic structures were explored by the density functional theory (DFT). Lysine exhibits the strongest interaction of all, which was manifested, e.g. by nearly 6-time drop of the initial viscosity comparing with only 1.3-time lower value in the case of 6-AcA. Arginine interaction with HA was surprisingly weaker in terms of viscosity than that of Lysine due to a lower and delocalized charge density on its guanidine group. According to the DFT calculations, the binding of Lysine to HA was found to be more flexible, while Arginine creates more rigid structure with HA. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Fatty acid synthase inhibitors from plants: isolation, structure elucidation, and SAR studies.

    Science.gov (United States)

    Li, Xing-Cong; Joshi, Alpana S; ElSohly, Hala N; Khan, Shabana I; Jacob, Melissa R; Zhang, Zhizheng; Khan, Ikhlas A; Ferreira, Daneel; Walker, Larry A; Broedel, Sheldon E; Raulli, Robert E; Cihlar, Ronald L

    2002-12-01

    Fatty acid synthase (FAS) has been identified as a potential antifungal target. FAS prepared from Saccharomyces cerevisiae was employed for bioactivity-guided fractionation of Chlorophora tinctoria,Paspalum conjugatum, Symphonia globulifera, Buchenavia parviflora, and Miconia pilgeriana. Thirteen compounds (1-13), including three new natural products (1, 4, 12), were isolated and their structures identified by spectroscopic interpretation. They represented five chemotypes, namely, isoflavones, flavones, biflavonoids, hydrolyzable tannin-related derivatives, and triterpenoids. 3'-Formylgenistein (1) and ellagic acid 4-O-alpha-l-rhamnopyranoside (9) were the most potent compounds against FAS, with IC(50) values of 2.3 and 7.5 microg/mL, respectively. Furthermore, 43 (14-56) analogues of the five chemotypes from our natural product repository and commercial sources were tested for their FAS inhibitory activity. Structure-activity relationships for some chemotypes were investigated. All these compounds were further evaluated for antifungal activity against Candida albicans and Cryptococcus neoformans. Although there were several antifungal compounds in the set, correlation between the FAS inhibitory activity and antifungal activity could not be defined.

  8. Structural insights into two inorganic-organic hybrids based on chiral amino acids and polyoxomolybdates

    Science.gov (United States)

    Arefian, Mina; Mirzaei, Masoud; Eshtiagh-Hosseini, Hossein

    2018-03-01

    A new chiral inorganic-organic hybrid with the formula (L-His)2(H7CoMo6O24)·6H2O (1), based on natural amino acid and Anderson type polyoxomolybdate was synthesized through mild condition. The chiral L-histidine molecules induced chirality to the whole structure through various types of strong and unconventional hydrogen bond (HB) interactions (CH⋯O, NH⋯O and CH···π interactions), as well as bifurcated hydrogen bonds (BHBs) between L-histidine amino acid, hexamer water cluster molecules, and H7CoMo6O24·xH2O. Following, important non-covalent CH⋯O interactions is investigated in another chiral inorganic-organic hybrid structure, (L-Pro)3(PMo12O40).4.5H2O (2), in detail. The CH⋯O hydrogen bonds lead to a chiral network similar to the DNA strands affording a promising candidate to bio-inorganic studies.

  9. Structural insight into the active site of mushroom tyrosinase using phenylbenzoic acid derivatives.

    Science.gov (United States)

    Oyama, Takahiro; Yoshimori, Atsushi; Takahashi, Satoshi; Yamamoto, Tetsuya; Sato, Akira; Kamiya, Takanori; Abe, Hideaki; Abe, Takehiko; Tanuma, Sei-Ichi

    2017-07-01

    So far, many inhibitors of tyrosinase have been discovered for cosmetic and clinical agents. However, the molecular mechanisms underlying the inhibition in the active site of tyrosinase have not been well understood. To explore this problem, we examined here the inhibitory effects of 4'-hydroxylation and methoxylation of phenylbenzoic acid (PBA) isomers, which have a unique scaffold to inhibit mushroom tyrosinase. The inhibitory effect of 3-PBA, which has the most potent inhibitory activity among the isomers, was slightly decreased by 4'-hydroxylation and further decreased by 4'-methoxylation against mushroom tyrosinase. Surprisingly, 4'-hydroxylation but not methoxylation of 2-PBA appeared inhibitory activity. On the other hand, both 4'-hydroxylation and methoxylation of 4-PBA increased the inhibitory activity against mushroom tyrosinase. In silico docking analyses using the crystallographic structure of mushroom tyrosinase indicated that the carboxylic acid or 4'-hydroxyl group of PBA derivatives could chelate with cupric ions in the active site of mushroom tyrosinase, and that the interactions of Asn260 and Phe264 in the active site with the adequate-angled biphenyl group are involved in the inhibitory activities of the modified PBAs, by parallel and T-shaped π-π interactions, respectively. Furthermore, Arg268 could fix the angle of the aromatic ring of Phe264, and Val248 is supposed to interact with the inhibitors as a hydrophobic manner. These results may enhance the structural insight into mushroom tyrosinase for the creation of novel tyrosinase inhibitors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. 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.

  11. Interactions, structure and properties in poly(lactic acid/thermoplastic polymer blends

    Directory of Open Access Journals (Sweden)

    B. Imre

    2014-01-01

    Full Text Available Blends were prepared from poly(lactic acid (PLA and three thermoplastics, polystyrene (PS, polycarbonate (PC and poly(methyl methacrylate (PMMA. Rheological and mechanical properties, structure and component interactions were determined by various methods. The results showed that the structure and properties of the blends cover a relatively wide range. All three blends have heterogeneous structure, but the size of the dispersed particles differs by an order of magnitude indicating dissimilar interactions for the corresponding pairs. Properties change accordingly, the blend containing the smallest dispersed particles has the largest tensile strength, while PLA/PS blends with the coarsest structure have the smallest. The latter blends are also very brittle. Component interactions were estimated by four different methods, the determination of the size of the dispersed particles, the calculation of the Flory-Huggins interaction parameter from solvent absorption, from solubility parameters, and by the quantitative evaluation of the composition dependence of tensile strength. All approaches led to the same result indicating strong interaction for the PLA/PMMA pair and weak for PLA and PS. A general correlation was established between interactions and the mechanical properties of the blends.

  12. Synthesis, crystal structure and magnetic properties of a novel copper(II) complex with sulfoisophthalic acid

    Science.gov (United States)

    Kurc, Teresa; Videnova-Adrabinska, Veneta; Turowska-Tyrk, Ilona; Duczmal, Marek; Jerzykiewicz, Maria

    2013-12-01

    A new Cu(II) complex, [Cu2(μ2-OH2)2(HSIP)2(H2O)6] (H3SIP = 5-sulfoisophthalic acid), has been synthesized and characterized by single crystal X-ray diffraction, EPR spectroscopy (X- (9.5 GHz) and Q-band (35 GHz)) and magnetic measurements. The solid state structure of the complex consists of coordination dimers [Cu2(μ2-OH2)2(HSIP)2(H2O)6] which are hydrogen bonded into 3D network. The neighbouring metal ions form a rare example of centrosymetric dinuclear core [Cu2(μ2-OH2)2] with equatorial - axial positions of the bridging ligands. The coordination dimers are organized into inorganic monolayers via water-sulfonate hydrogen bond intractions, and further linked in 3D structure via carboxylic-carboxylic hydrogen bond intractions. The magnetic properties and EPR spectra are discussed in terms of crystal structure features. The X- and Q-band EPR spectra exhibit fine structure signals due to S = 1 and the simulated parameters indicate small zero field splitting parameter Dexp (-0.035 cm-1) dominated by Ddip (-0.031 cm-1). A usually forbidden ΔMs = 2 line of lower intensity is observed in the half field region at about 150 mT. The susceptibility data have been analyzed using a spin-ladder model with both ferromagnetic (rungs) and antiferromagnetic (legs) coupling.

  13. Comparison of the structural and physical properties of human hair eumelanin following enzymatic or acid/base extraction.

    Science.gov (United States)

    Liu, Yan; Kempf, Valerie R; Nofsinger, J Brian; Weinert, Emily E; Rudnicki, Mark; Wakamatsu, Kazumasa; Ito, Shosuke; Simon, John D

    2003-08-01

    Eumelanin was isolated from a sample of black, Indonesian human hair using three different published procedures: two different acid/base extractions and an enzymatic extraction. The morphology and spectroscopic properties of the isolated pigments differ significantly. The acid/base procedures both yield an amorphous material, while enzymatic extraction yields ellipsoidal melanosomes. Amino acid analysis shows that there is protein associated with the isolated pigments, accounting for 52, 40 and 14% of the total mass for the two acid/base extractions and the enzymatic extraction, respectively. The amino acid compositions do not correlate with those of keratin or tyrosinase. Metal elemental analysis shows that the acid/base extraction removes a majority of many metal ions bound to the pigment. Chemical degradation analysis by KMnO4/H+ and H2O2/OH- indicates significant differences between the pigments isolated by acid/base and enzymatic extraction. After correction for the protein mass in the two pigments, the lower yields of both pyrrole-2,3,5-tricarboxylic acid and pyrrole-2,3-dicarboxylic acid, eumelanin degradation products, indicate acid/base extraction modifies the chemical structure of the melanin, consistent with the result of Soluene solubilization assay. While the optical absorption spectra of the bulk pigments are similar, the spectra of the molecular weight less than 1000 mass fractions differ significantly. The data clearly indicate that pigment obtained from human hair by acid/base extraction contains significant protein, exhibits destruction of the melanosome, and possesses altered molecular structure. The acid/base extracted hair melanin is not representative of the natural material and is a poor model system for studying the physical and biological properties of melanins. The enzymatically extracted hair melanin, on the contrary, retains the morphology of intact melanosomes and is an excellent source of human melanin.

  14. 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.

  15. 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.

  16. Triacylglycerol structure and interesterification of palmitic and stearic acid-rich fats: an overview and implications for cardiovascular disease.

    Science.gov (United States)

    Berry, Sarah E E

    2009-06-01

    The position of fatty acids in the TAG molecule (sn-1, sn-2 and sn-3) determines the physical properties of the fat, which affects its absorption, metabolism and distribution into tissues, which may have implications for the risk of CHD. The TAG structure of fats can be manipulated by the process of interesterification, which is of increasing commercial importance, as it can be used to change the physical characteristics of a fat without the generation of trans-fatty acids. Interesterified fats rich in long-chain SFA are commercially important, but few studies have investigated their health effects. Evidence from animal and human infant studies suggests that TAG structure and interesterification affect digestibility, atherogenicity and fasting lipid levels, with fats containing palmitic and stearic acid in the sn-2 position being better digested and considered to be more atherogenic. However, chronic studies in human adults suggest that TAG structure has no effect on digestibility or fasting lipids. The postprandial effects of fats with differing TAG structure are better characterised but the evidence is inconclusive; it is probable that differences in the physical characteristics of fats resulting from interesterification and changes in TAG structure are key determinants of the level of postprandial lipaemia, rather than the position of fatty acids in the TAG. The present review gives an overview of TAG structure and interesterified palmitic and stearic acid-rich fats, their physical properties and their acute and chronic effects in human adults in relation to CHD.

  17. 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.

  18. Similar, but different: structurally related azelaic acid and hexanoic acid trigger differential metabolomic and transcriptomic responses in tobacco cells.

    Science.gov (United States)

    Djami-Tchatchou, Arnaud T; Ncube, Efficient N; Steenkamp, Paul A; Dubery, Ian A

    2017-11-29

    Plants respond to various stress stimuli by activating an enhanced broad-spectrum defensive ability. The development of novel resistance inducers represents an attractive, alternative crop protection strategy. In this regard, hexanoic acid (Hxa, a chemical elicitor) and azelaic acid (Aza, a natural signaling compound) have been proposed as inducers of plant defense, by means of a priming mechanism. Here, we investigated both the mode of action and the complementarity of Aza and Hxa as priming agents in Nicotiana tabacum cells in support of enhanced defense. Metabolomic analyses identified signatory biomarkers involved in the establishment of a pre-conditioned state following Aza and Hxa treatment. Both inducers affected the metabolomes in a similar manner and generated common biomarkers: caffeoylputrescine glycoside, cis-5-caffeoylquinic acid, feruloylglycoside, feruloyl-3-methoxytyramine glycoside and feruloyl-3-methoxytyramine conjugate. Subsequently, quantitative real time-PCR was used to investigate the expression of inducible defense response genes: phenylalanine ammonia lyase, hydroxycinnamoyl CoA quinate transferase and hydroxycinnamoyl transferase to monitor activation of the early phenylpropanoid pathway and chlorogenic acids metabolism, while ethylene response element-binding protein, small sar1 GTPase, heat shock protein 90, RAR1, SGT1, non-expressor of PR genes 1 and thioredoxin were analyzed to report on signal transduction events. Pathogenesis-related protein 1a and defensin were quantified to investigate the activation of defenses regulated by salicylic acid and jasmonic acid respectively. The qPCR results revealed differential expression kinetics and, in general (except for NPR1, Thionin and PR1a), the relative gene expression ratios observed in the Hxa-treated cells were significantly greater than the expression observed in the cells treated with Aza. The results indicate that Aza and Hxa have a similar priming effect through activation of genes

  19. 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)

  20. Photoluminescence Enhancement and Structure Repairing of Monolayer MoSe 2 by Hydrohalic Acid Treatment

    KAUST Repository

    Han, Hau-Vei

    2015-12-30

    Atomically thin two-dimensional transition-metal dichalcogenides (TMDCs) have attracted much attention recently due to their unique electronic and optical properties for future optoelectronic devices. The chemical vapor deposition (CVD) method is able to generate TMDCs layers with a scalable size and a controllable thickness. However, the TMDC monolayers grown by CVD may incorporate structural defects, and it is fundamentally important to understand the relation between photoluminescence and structural defects. In this report, point defects (Se vacancies) and oxidized Se defects in CVD-grown MoSe2 monolayers are identified by transmission electron microscopy and X-ray photoelectron spectroscopy. These defects can significantly trap free charge carriers and localize excitons, leading to the smearing of free band-to-band exciton emission. Here, we report that the simple hydrohalic acid treatment (such as HBr) is able to efficiently suppress the trap-state emission and promote the neutral exciton and trion emission in defective MoSe2 monolayers through the p-doping process, where the overall photoluminescence intensity at room temperature can be enhanced by a factor of 30. We show that HBr treatment is able to activate distinctive trion and free exciton emissions even from highly defective MoSe2 layers. Our results suggest that the HBr treatment not only reduces the n-doping in MoSe2 but also reduces the structural defects. The results provide further insights of the control and tailoring the exciton emission from CVD-grown monolayer TMDCs.

  1. Adsorption performance of salicylic acid on a novel resin with distinctive double pore structure.

    Science.gov (United States)

    Xiao, Guqing; Wen, Ruiming; Liu, Aijiao; He, Guowen; Wu, Dan

    2017-05-05

    Two approaches were used to synthesize two resins with different pore structures. In one way, the CH 2 Cl groups in macroporous chloromethylated polystyrene resin were transformed to methylene bridges, and achieved a hypercrosslinked resin with plentiful micropores (denoted GQ-06). In the other way, 50% of the CH 2 Cl groups in chloromethylated polystyrene resin was used to produce micropores, while the residual 50% of the CH 2 Cl groups was reacted with 2-aminopyridine, and prepared another resin with double pore structure of hypercrosslinked resin and macroporous resin (denoted GQ-11). The adsorption of salicylic acid (SA) on GQ-11 was investigated using GQ-06 as the reference adsorbent. The effect of pH on the adsorption of SA on GQ-06 was consistent with the dissociation curve of SA. The maximum adsorption capacity of SA on GQ-11 was observed at the solution pH of 2.64. The greater adsorption rate of SA on GQ-11 than that of GQ-06 was attributed to its double pore structure. The multifunctional adsorption mechanism of anion exchange and hydrophobic interaction resulted in the larger equilibrium capacity of SA on GQ-11 than that of GQ-06. GQ-06 and GQ-11 could be regenerated by absolute alcohol and 80% of alcohol -0.5mol/L of sodium hydroxide aqueous solution, respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Kinetic mechanism and structural requirements of the amine-catalyzed decarboxylation of oxaloacetic acid.

    Science.gov (United States)

    Thalji, Nabil K; Crowe, William E; Waldrop, Grover L

    2009-01-02

    The kinetic and chemical mechanism of amine-catalyzed decarboxylation of oxaloacetic acid at pH 8.0 has been reevaluated using a new and versatile assay. Amine-catalyzed decarboxylation of oxaloacetic acid proceeds via the formation of an imine intermediate, followed by decarboxylation of the intermediate and hydrolysis to yield pyruvate. The decrease in oxaloacetic acid was coupled to NADH formation by malate dehydrogenase, which allowed the rates of both initial carbinolamine formation (as part of the imination step) and decarboxylation to be determined. By comparing the rates observed for a variety of amines and, in particular, diamines, the structural and electronic requirements for diamine-catalyzed decarboxylation at pH 8.0 were identified. At pH 8.0, monoamines were found to be very poor catalysts, whereas some diamines, most notably ethylenediamine, were excellent catalysts. The results indicate that the second amino group of diamines enhances the rate of imine formation by acting as a proton shuttle during the carbinolamine formation step, which enables diamines to overcome high levels of solvation that would otherwise inhibit carbinolamine, and thus imine, formation. The presence of the second amino group may also enhance the rate of the carbinolamine dehydration step. In contrast to the findings of previous reports, the second amino group participates in the reaction by enhancing the rate of decarboxylation via hydrogen-bonding to the imine nitrogen to either stabilize the negative charge that develops on the imine during decarboxylation or preferentially stabilize the reactive imine over the unreactive enamine tautomer. These results provide insight into the precise catalytic mechanism of several enzymes whose reactions are known to proceed via an imine intermediate.

  3. Structural, physicochemical, antioxidant and antitumor property of an acidic polysaccharide from Polygonum multiflorum.

    Science.gov (United States)

    Zhu, Weili; Xue, Xiaoping; Zhang, Zhanjun

    2017-03-01

    In this study, the structural characterization, physicochemical property, antioxidant and antitumor activity of an acidic polysaccharide (APS) from Polygonum multiflorum were investigated. Monosaccharide composition analysis showed APS was composed of arabinose, rhamnose, galactose and galacturonic acid in the molar ratio of 1.23:1.32:1.48:1.00. The presence of uronic acid was also confirmed by the bands at 1740, 1645 and 1425cm -1 on Fourier transform-infrared spectroscopy. Methylation and nuclear magnetic resonance analyses showed APS was mainly composed by the residues of →5)-α-l-Araf-(1→, →3)-β-d-Galp-(1→, →3,6)-β-d-Galp-(1→, →4)-α-d-GalAp-(1→ and →2)-α-l-Rhap-(1→ in the backbone. The non-reducing terminal α-l-Araf-(1→ was probably attached to the O-6 position of →3,6)-β-d-Galp-(1→ residues. Besides, APS exhibited rod-like and flaky shapes with rough surface. The initial decomposition of APS occurred at 172°C, and the rapidest weight loss rate of APS appeared at 320°C. Antioxidant activity assay showed the DPPH radical scavenging activity of APS was 67.5% at 1mg/mL. At the concentration of 400μg/mL, the antiproliferation activities of APS against HepG-2 and BGC-823 cells were 65.28% and 51.57%, respectively. Our results suggested APS could be a potential antioxidant and antitumor agent. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. 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.

  5. 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.

  6. A comparative chemical-structural study of fossil humic acids and those extracted from urban wastes

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, C.; Hernandez, T.; Costa, F.; Ceccanti, B.; Polo, A. (Centro de Edafologia y Biologia Aplicada del Segura, Murcia (Spain))

    1992-05-01

    Chemical-structural features of commercial humic acids (HAs) from leonardite or lignite were studied and the data obtained were compared with those of humic acids extracted from composted urban wastes. The greatest differences showed by the elemental analysis between the three HAs were in N and H contents, both of which diminished with the oxidation degree of the starting materials. FTIR spectra did not show differences between HAs from evolved materials such as leonardite or lignite. However, differences were found between these HAs and those extracted from composts of urban wastes, which showed a greater aliphatic character and a more pronounced peak in the absorption band attributed to secondary amides and in that of carbohydrates. The {sup 13}C-NMR spectra were similar for both HAs from leonardite regardless of their oxidation degree. The percentage of aromaticity of these HAs was 45%. The spectra of compost HAs showed a low aromaticity degree for these HAs as a consequence of the pronounced peak appearing at 73 ppm corresponding to carbon of carbohydrates and/or polyalcohols and aminoacids. Py-GC revealed a high content of benzene and toluene in all the commercial HAs. The values of these fragments as well as those of the ratios between pyrolitic fragments, used as humification index for soils, were the highest in the HA extracted from the more oxidized leonardite. 17 refs., 1 fig., 5 tabs.

  7. Comparative studies of the structure, morphology and electrical conductivity of polyaniline weakly doped with chlorocarboxylic acids

    International Nuclear Information System (INIS)

    Gmati, Fethi; Fattoum, Arbi; Bohli, Nadra; Dhaoui, Wadia; Mohamed, Abdellatif Belhadj

    2007-01-01

    We report the results of studies on two series of polyaniline (PANI), doped with dichloroacetic (DCA) and trichloroacetic (TCA) acids, respectively, at various doping rates and obtained by the in situ polymerization method. Samples were characterized by x-ray diffraction, scanning electron microscopy and conductivity measurements. The direct current (dc) and alternating current (ac) electrical conductivities of PANI salts have been investigated in the temperature range 100-310 K and frequency range 7-10 6 Hz. The results of this study indicate better chain ordering and higher conductivity for PANI doped with TCA. The dc conductivity of all samples is suitably fitted to Mott's three-dimensional variable-range hopping (VRH) model. Different Mott parameters such as characteristic temperature T 0 , density of states at the Fermi level (N(E F )), average hopping energy (W) and the average hopping distance (R) have been evaluated. The dependence of such values on the dopant acid used is discussed. At high frequencies, the ac conductivity follows the power law σ ac (ω,T) A(T)ω s(T,ω) , which is characteristic for charge transport in disordered materials by hopping or tunnelling processes. The observed increase in the frequency exponent s with temperature suggests that the small-polaron tunnelling model best describes the dominant ac conduction mechanism. A direct correlation between conductivity, structure and morphology was obtained in our systems

  8. 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.

  9. Antiatherogenic effects of structured lipid containing conjugated linoleic acid in C57BL/6J mice.

    Science.gov (United States)

    Lee, Jeung Hee; Cho, Kyung Hyun; Lee, Ki-Teak; Kim, Mee Ree

    2005-09-07

    Conjugated linoleic acids (CLA) were enzymatically acidolyzed with olive oil to produce structured lipids (SL), and their antiatherosclerotic properties were investigated in C57BL/6J mice. Twenty-eight mice were divided into four groups and fed control diet or atherogenic diets supplemented with high cholesterol and high fat (HCHF) containing 5% of lard, olive oil, or SL based on control diet for 4 weeks. The supplementation of SL diet (0.6% CLA) significantly reduced the levels of serum total cholesterol and total triglyceride and increased high-density lipoprotein cholesterol level as compared to lard and olive oil diet groups (p PE) (0.47 mol %) than in phosphatidylcholine (PC) (0.05 mol %) of hepatic phospholipids. Hepatic phospholipids (PC and PE) of mice fed the SL diet contained reduced contents of arachidonic and linoleic acid compared with mice fed the olive oil or lard diet. The present study suggests that SL could be considered as a functional oil for preventing risks of atheroscelerosis.

  10. 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.

  11. 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.

  12. On dependence of stability of lanthanum complexes with aminopolycarboxylic acids on the complex structure

    International Nuclear Information System (INIS)

    Poluehktov, N.S.; Meshkova, S.B.; Danilkovich, M.M.; Topilova, Z.M.

    1985-01-01

    Regularities in changes of stability constants of lanthanum complexes with aminopolycarboxylic acids (APA) versus their structure are studied, The stability of lathanum-APA complexes depends mainly on the number of carboxyl groups in a ligand molecule. At that, the highest stability constant is characteristic of a complex with a ligand, containing 3 nitrogen atoms and 5 carboxyl groups, in the presenoe of which the lanthanum ion coordination sphere gets satupated. The oxyethy group introduction into a ligand molecule also improves the lanthanum complex stability but to a lesser degree than during the introduction of a carboxyl group. The number of nitrogen atoms in a ligand polecule affects insignificantly the complex stability constant value, and the elongation of a chain of CH 2 groups, separating nitrogen atoms, reduces the constant to a -0.6 power

  13. 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...

  14. Influence of chalcopyrite structure on their leaching by sodium nitrate in sulphuric acid

    Directory of Open Access Journals (Sweden)

    Miroslav Sokić

    2014-03-01

    Full Text Available During the chalcopyrite leaching by sodium nitrate and sulfuric acid solution, leaching rate decreases with increasing the time and a part of chalcopyrite mineral grains remains in the leach residue. In chalcopyrite concentrate, 95.5 % of chalcopyrite mineral occurs as in liberated grains, and the rest is in association with gangue minerals, which is very favorably from the aspect of hydrometallurgical treatment. Complex forms, like impregnations and complex intergrowths, do not exist. After experiments carried out, leaching of copper achieved 84 % at temperature 80 o C and time 240 min. In the all leach residues, 97 % chalcopyrite mineral grains occur as liberated with highly corroded surfaces. Therefore, the structural assembly of chalcopyrite grains is favorable and no reason to reduce the leaching rate in the final stage of reaction. Reason for this is elemental sulfur, which was formed during the reaction, precipitated at the particle surfaces, and slowed down the leaching rate in the final stage of leaching process.

  15. Probing Ion Channel Structure and Function Using Light-Sensitive Amino Acids.

    Science.gov (United States)

    Klippenstein, Viktoria; Mony, Laetitia; Paoletti, Pierre

    2018-04-10

    Approaches to remotely control and monitor ion channel operation with light are expanding rapidly in the biophysics and neuroscience fields. A recent development directly introduces light sensitivity into proteins by utilizing photosensitive unnatural amino acids (UAAs) incorporated using the genetic code expansion technique. The introduction of UAAs results in unique molecular level control and, when combined with the maximal spatiotemporal resolution and poor invasiveness of light, enables direct manipulation and interrogation of ion channel functionality. Here, we review the diverse applications of light-sensitive UAAs in two superfamilies of ion channels (voltage- and ligand-gated ion channels; VGICs and LGICs) and summarize existing UAA tools, their mode of action, potential, caveats, and technical considerations to their use in illuminating ion channel structure and function. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. Lead-acid batteries with polymer-structured electrodes for electric-vehicle applications

    Science.gov (United States)

    Soria, M. L.; Fullea, J.; Sáez, F.; Trinidad, F.

    Some years ago a consortium of enterprises and a university from different European countries and industrial sectors was established to work together in the development of lighter lead-acid batteries for electrical and conventional vehicles with new innovative materials and process techniques, with the final goal of increasing the energy density by means of a battery weight reduction. Its main idea was to substitute the heavy lead alloy grids (mechanical support of the active masses and collectors of the current produced during the charge and discharge reactions) by lightweight metallised polymeric network structures (PNS) with reduced mesh dimensions in comparison to conventional grids. The network was then coated with conductive materials and corrosion resistant layers to conduct the current flow. In this paper, the electrode characteristics and the design features of the batteries prepared in the project will be described and their electrical performance presented.

  17. Plantain starch granules morphology, crystallinity, structure transition, and size evolution upon acid hydrolysis.

    Science.gov (United States)

    Hernández-Jaimes, C; Bello-Pérez, L A; Vernon-Carter, E J; Alvarez-Ramirez, J

    2013-06-05

    Plantain native starch was hydrolysed with sulphuric acid for twenty days. Hydrolysis kinetics was described by a logistic function, with a zero-order rate during the first seven days, followed by a slower kinetics dynamics at longer times. X-ray diffraction results revealed a that gradual increase in crystallinity occurred during the first seven days, followed by a decrease to values similar to those found in the native starch. Differential scanning calorimetry analysis suggested a sharp structure transition by the seventh day probably due to a molecular rearrangement of the starch blocklets and inhomogeneous erosion of the amorphous regions and semi crystalline lamellae. Scanning electron micrographs showed that starch granules morphology was continually degraded from an initial oval-like shape to irregular shapes due to aggregation effects. Granule size distribution broadened as hydrolysis time proceeded probably due to fragmentation and agglomeration phenomena of the hydrolysed starch granules. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Amino acid sequences and structures of chicken and turkey beta 2-microglobulin

    DEFF Research Database (Denmark)

    Welinder, K G; Jespersen, H M; Walther-Rasmussen, J

    1991-01-01

    The complete amino acid sequences of chicken and turkey beta 2-microglobulins have been determined by analyses of tryptic, V8-proteolytic and cyanogen bromide fragments, and by N-terminal sequencing. Mass spectrometric analysis of chicken beta 2-microglobulin supports the sequence-derived Mr of 11......,048. The higher apparent Mr obtained for the avian beta 2-microglobulins as compared to human beta 2-microglobulin by SDS-PAGE is not understood. Chicken and turkey beta 2-microglobulin consist of 98 residues and deviate at seven positions: 60, 66, 74-76, 78 and 82. The chicken and turkey sequences are identical...... to human beta 2-microglobulin at 46 and 47 positions, respectively, and to bovine beta 2-microglobulin at 47 positions, i.e. there is about 47% identity between avian and mammalian beta 2-microglobulins. The known X-ray crystallographic structures of bovine beta 2-microglobulin and human HLA-A2 complex...

  19. 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.

  20. 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

  1. 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.

  2. DFT and ab initio study of structure of dyes derived from 2-hydroxy and 2,4-dihydroxy benzoic acids.

    Science.gov (United States)

    Dabbagh, Hossein A; Teimouri, Abbas; Chermahini, Alireza Najafi; Shahraki, Maryam

    2008-02-01

    We present a detailed analysis of the structural, infrared spectra and visible spectra of a series of azo dyes preparation of salicylic acid and 2,4-dihydroxy benzoic acid derivatives as the coupling component. The preparation of these azo dyes with salicylic acid and 2,4-dihydroxy benzoic acid derivatives (salicylic acid, methyl salicylate, ethyl salicylate, butyl salicylate, methyl 2,4-dihydroxy benzoate, ethyl 2,4-dihydroxy benzoate, salicylaldehyde, salicylamide, 2,4-dihydroxy benzamide, salicylaldoxime) have been investigated theoretically by performing HF and DFT levels of theory using the standard 6-31G* basis set. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from solid phase FT-IR spectra are assigned modes based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with the calculations.

  3. Chemistry of formation and properties of sapropelitic coals. III. Extraction of aliphatic carboxylic acids and ketones of normal structure

    Energy Technology Data Exchange (ETDEWEB)

    Bodoev, N.V.; Rokosov, Y.V.; Koptyug, V.A.

    1989-05-01

    Aliphatic carboxylic acids and ketones of normal structure produced in high yields by the reaction of Taimylyr boghead or Matagan gagat with water and sodium hydroxide at elevated pressure and at temperatures from 400 to 450 degrees C have been investigated. The compositions of these compounds have been studied by IRS, NMR and chromato-mass-spectrometry. The possible ways of formation of aliphatic carboxylic acids and ketones during the fossilization process have been discussed. 14 refs., 6 figs.

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

    Directory of Open Access Journals (Sweden)

    Caihong Sun

    2016-06-01

    Full Text Available 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.

  5. 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

  6. Amino acid profiles and quantitative structure-property relationship models as markers for Merlot and Torrontés wines.

    Science.gov (United States)

    Duchowicz, Pablo R; Giraudo, Miguel A; Castro, Eduardo A; Pomilio, Alicia B

    2013-09-01

    Quantitative structure-property relationships (QSPRs) were applied to the aminograms obtained by HPLC in our laboratories for Torrontés and Merlot wines. Dragon theoretical descriptors were derived for a set of optimized amino acid structures with the purpose of establishing QSPR models. The statistical Replacement Method was used for designing the best multi-parametric linear regression models, which included structural features selected from a pool containing 1497 constitutional, topological, geometrical or electronic molecular descriptors. Predicted QSPR results were in good agreement with experimental amino acid profiles. The developed QSPR approach showed to be of practical value for distinguishing each wine varietal, and for calculating experimentally non-available amino acid concentrations of Torrontés and Merlot wines. It was also useful for assessing wine authenticity; the models were especially suitable for Merlot and Torrontés wines. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. 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

  8. 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.

  9. Effect of Nerolidol and/or Levulinic Acid on the Thermotropic Behavior of Lipid Lamellar Structures in the Stratum Corneum.

    Science.gov (United States)

    Utsumi, Shunichi; Nakamura, Tomohiro; Obata, Yasuko; Ohta, Noboru; Takayama, Kozo

    2016-01-01

    Permeation enhancers are required to deliver drugs through the skin efficiently and maintain effective blood concentrations. Studies of the barrier function of the stratum corneum using l-menthol, a monocyclic monoterpene widely used in medicines and foods, have revealed an interaction between characteristic intercellular lipid structures in the stratum corneum and permeation enhancers. The variety of permeation enhancers that can be used to contribute to transdermal delivery systems beyond l-menthol is increasing. In this study, we focused on nerolidol and levulinic acid and investigated their influence on stratum corneum lipid structures. Nerolidol, a sesquiterpene, has been reported to enhance the permeation of various drugs. Levulinic acid is reported to enhance the permeability of buprenorphine and is used as a component of the buprenorphine ® patch. Synchrotron X-ray diffraction and attenuated total reflectance Fourier transform IR spectroscopy measurements revealed that nerolidol disturbs the rigidly arranged lipid structure and increases lipid fluidity. Levulinic acid had a smaller effect on stratum corneum lipid structures, but did increase lipid fluidity when co-administered with nerolidol or heat. We found that nerolidol has an effect on stratum corneum lipids similar to that of l-menthol, and levulinic acid had an effect similar to that of oleic acid.

  10. Computational exploration of the chemical structure space of possible reverse tricarboxylic acid cycle constituents.

    Science.gov (United States)

    Meringer, Markus; Cleaves, H James

    2017-12-13

    The reverse tricarboxylic acid (rTCA) cycle has been explored from various standpoints as an idealized primordial metabolic cycle. Its simplicity and apparent ubiquity in diverse organisms across the tree of life have been used to argue for its antiquity and its optimality. In 2000 it was proposed that chemoinformatics approaches support some of these views. Specifically, defined queries of the Beilstein database showed that the molecules of the rTCA are heavily represented in such compound databases. We explore here the chemical structure "space," e.g. the set of organic compounds which possesses some minimal set of defining characteristics, of the rTCA cycle's intermediates using an exhaustive structure generation method. The rTCA's chemical space as defined by the original criteria and explored by our method is some six to seven times larger than originally considered. Acknowledging that each assumption in what is a defining criterion making the rTCA cycle special limits possible generative outcomes, there are many unrealized compounds which fulfill these criteria. That these compounds are unrealized could be due to evolutionary frozen accidents or optimization, though this optimization may also be for systems-level reasons, e.g., the way the pathway and its elements interface with other aspects of metabolism.

  11. Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Jun; Byrne, Noel; Wang, John; Bricogne, Gerard; Brown, Frank K.; Chobanian, Harry R.; Colletti, Steven L.; Di Salvo, Jerry; Thomas-Fowlkes, Brande; Guo, Yan; Hall, Dawn L.; Hadix, Jennifer; Hastings, Nicholas B.; Hermes, Jeffrey D.; Ho, Thu; Howard, Andrew D.; Josien, Hubert; Kornienko, Maria; Lumb, Kevin J.; Miller, Michael W.; Patel, Sangita B.; Pio, Barbara; Plummer, Christopher W.; Sherborne, Bradley S.; Sheth, Payal; Souza, Sarah; Tummala, Srivanya; Vonrhein, Clemens; Webb, Maria; Allen, Samantha J.; Johnston, Jennifer M.; Weinglass, Adam B.; Sharma, Sujata; Soisson, Stephen M. (Merck); (Globel Phasing)

    2017-06-05

    Clinical studies indicate that partial agonists of the G-protein-coupled, free fatty acid receptor 1 GPR40 enhance glucose-dependent insulin secretion and represent a potential mechanism for the treatment of type 2 diabetes mellitus. Full allosteric agonists (AgoPAMs) of GPR40 bind to a site distinct from partial agonists and can provide additional efficacy. We report the 3.2-Å crystal structure of human GPR40 (hGPR40) in complex with both the partial agonist MK-8666 and an AgoPAM, which exposes a novel lipid-facing AgoPAM-binding pocket outside the transmembrane helical bundle. Comparison with an additional 2.2-Å structure of the hGPR40–MK-8666 binary complex reveals an induced-fit conformational coupling between the partial agonist and AgoPAM binding sites, involving rearrangements of the transmembrane helices 4 and 5 (TM4 and TM5) and transition of the intracellular loop 2 (ICL2) into a short helix. These conformational changes likely prime GPR40 to a more active-like state and explain the binding cooperativity between these ligands.

  12. Inhibition of strigolactone receptors by N-phenylanthranilic acid derivatives: structural and functional insights.

    Science.gov (United States)

    Hamiaux, Cyril; Drummond, Revel S M; Luo, Zhiwei; Lee, Hui Wen; Sharma, Prachi; Janssen, Bart J; Perry, Nigel B; Denny, William A; Snowden, Kimberley C

    2018-03-09

    The strigolactone (SL) family of plant hormones regulates a broad range of physiological processes affecting plant growth and development and also plays essential roles in controlling interactions with parasitic weeds and symbiotic fungi. Recent progress elucidating details of SL biosynthesis, signalling, and transport offer many opportunities for discovering new plant growth regulators via chemical interference. Here, using high throughput screening and downstream biochemical assays, we identified N -phenylanthranilic acid derivatives as potent inhibitors of the SL receptors from petunia (DAD2), rice (OsD14) and Arabidopsis (AtD14). Crystal structures of DAD2 and OsD14 in complex with inhibitors further provided detailed insights into the inhibition mechanism, and in silico modeling of 19 other plant strigolactone receptors suggested that these compounds are active across a large range of plant species. Altogether, these results provide chemical tools for investigating SL signaling and further define a framework for structure-based approaches to design and validate optimized inhibitors of SL receptors for specific plant targets. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  13. New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

    Directory of Open Access Journals (Sweden)

    Assem Barakat

    2015-11-01

    Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

  14. Variation of structures of ingredients of desiccated coconut during hydrolysis by hydrochloric acid at low temperature

    Directory of Open Access Journals (Sweden)

    Jian XIONG

    2017-10-01

    Full Text Available Abstract Owing to the high content of lignocellulose, desiccated coconut become a healthy material for dietary fiber supplementation. In this study, the changes in solubility of the fibers of desiccated coconut were evaluated. The changes of the pHs and weight losses were studied. Furthermore, variations of the ingredient structures of desiccated coconut by hydrolysis by hydrochloric acid were characterized by Fourier transform infrared spectroscopy (FTIR, X-ray diffraction (XRD and scanning electron microscopy (SEM. After hydrolysis 30 s, the pHs of all systems increased, while six hours later, the pH of only system with initial pH = 1.00 decreased. The decline of pH only existed in hydrolysis systems with initial pH = 1.00, there is no relevant with the quantities of desiccated coconut. The lower initial pH of hydrolysis system was, the less the intrinsic viscosity of the desiccated coconut after hydrolysis was, the small the crystallinity was. After hydrolysis, the microstructure of the desiccated coconut become looser, and the secondary structure of the coconut protein became more stable and ordered. The results suggest that the hydrolysis of desiccated coconut mainly occurred in the branched chain and the non-crystalline region of lignocellulose, which transforms some insoluble dietary fiber into soluble dietary fiber. This improves the nutritional value of desiccated coconut.

  15. Lanthanoid tagging via an unnatural amino acid for protein structure characterization.

    Science.gov (United States)

    Jiang, Wen-Xue; Gu, Xin-Hua; Dong, Xu; Tang, Chun

    2017-04-01

    Lanthanoid pseudo-contact shift (PCS) provides long-range structural information between a paramagnetic tag and protein nuclei. However, for proteins with native cysteines, site-specific attachment may only utilize functional groups orthogonal to sulfhydryl chemistry. Here we report two lanthanoid probes, DTTA-C3-yne and DTTA-C4-yne, which can be conjugated to an unnatural amino acid pAzF in the target protein via azide-alkyne cycloaddition. Demonstrated with ubiquitin and cysteine-containing enzyme EIIB, we show that large PCSs of distinct profiles can be generated for each tag/lanthanoid combination. The DTTA-based lanthanoid tags are associated with large magnetic susceptibility tensors owing to the rigidity of the tags. In particular, introduction of the DTTA-C3 tag affords intermolecular PCSs and enables structural characterization of a transient protein complex between ubiquitin and a UBA domain. Together, we have expanded the repertoire of paramagnetic tags and the applicability of paramagnetic NMR.

  16. High orientation of long chain branched poly (lactic acid) with enhanced blood compatibility and bionic structure.

    Science.gov (United States)

    Li, Zhengqiu; Ye, Lin; Zhao, Xiaowen; Coates, Phil; Caton-Rose, Fin; Martyn, Michasel

    2016-05-01

    Highly oriented poly (lactic acid) (PLA) with bionic microgrooves was fabricated through solid hot drawing technology for further improving the mechanical properties and blood biocompatibility of PLA. In order to enhance the melt strength and thus obtain high orientation degree, long chain branched PLA was prepared at first through a two-step ring-opening reaction during processing. Linear viscoelasticity combined with branch-on-branch model was used to predict probable compositions and chain topologies of the products, and it was found that the molecular weight of PLA increased and topological structures with star like chain with three arms and tree-like chain with two generations formed during reactive processing, and consequently draw ratio as high as1200% can be achieved during the subsequent hot stretching. With the increase of draw ratio, the tensile strength and orientation degree of PLA increased dramatically. Long chain branching and orientation could significantly enhance the blood compatibility of PLA by prolonging clotting time and decreasing platelet activation. Microgrooves can be observed on the surface of the oriented PLA which were similar to the intimal layer of blood vessel, and such bionic structure resulted from the formation of the oriented shish kebab-like crystals along the draw direction. © 2016 Wiley Periodicals, Inc.

  17. Effects of acid rain and surfactant pollution on the foliar structure of some tree species

    International Nuclear Information System (INIS)

    Raddi, P.; Moricca, S.; Paoletti, E.

    1994-01-01

    For 10 years we have been studying the effects of acid rain and ABS (a surfactant always found in sea aerosols) on several tree species. Alterations of the leaf structure were considered as damage index. We tried to quantify the damage to the wax structure by scoring in accordance with a damage scale given by SEM observations and by computing a damage index that allowed for a comparison among tree provenances and within individuals of the same provenance or clone. We tested the response of several species: Norway spruce, silver fir, cypress, London plane, chestnut, walnut, Italian alder, tree of heaven, common maple, European white elm, manna ash, holm oak, European beech. The different species exhibited different levels of damage in relation to the type of treatment: when ABS was present, the damage was always more severe. In the broadleaved trees, the most frequent disturbances noted were: erosion of the epicuticular wax, alterations in the stomata, lesions, abscission and/or alternation of hairs. Damage from ABS treatments was compared to damge observed in coastal vegetation after strong sea winds. By comparing natural and induced damage, we were able to demonstrate that ABS is one of the possible causes of coastal vegetation decline and that ABS may also impact significantly on vegetation growing far away from the sea. (orig.)

  18. 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

  19. Acetic acid dimers in a nitrogen matrix: Observation of structures containing the higher-energy conformer

    Science.gov (United States)

    Lopes, Susy; Domanskaya, Alexandra V.; Räsänen, Markku; Khriachtchev, Leonid; Fausto, Rui

    2015-09-01

    Acetic acid (AA) dimers are studied experimentally by infrared spectroscopy in a N2 matrix and theoretically at the MP2/6-311++G(2d,2p) level of approximation. This work is focused on the first preparation and characterization of structures containing the higher-energy (cis) conformer of AA. Nine trans-trans, fourteen trans-cis, and six cis-cis dimers are theoretically predicted. Five trans-trans and a number of trans-cis dimers are identified in the experiments, but no indication of cis-cis dimers is found. Two trans-trans dimers and the trans-cis dimers are reported for the first time. One trans-cis dimer is prepared by selective vibrational excitation of the structurally related trans-trans dimer, which converts one of the trans subunits to the cis form. Several trans-cis dimers are obtained by annealing of a matrix containing both trans and cis monomers of AA. Tunneling-induced conversion of the trans-cis dimers into trans-trans forms (including two new trans-trans forms) is observed at low temperatures.

  20. 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.

  1. Positional distribution of decanoic acid: Effect on chylomicron and VLDL TAG structures and postprandial lipemia

    DEFF Research Database (Denmark)

    Yli-Jokipii, K.M.; Schwab, U.S.; Tarvonen, R.L.

    2004-01-01

    Although medium-chain FA (MCFA) are mainly absorbed via the portal venous system, they are also incorporated into chylomicron TAG; therefore, the positional distribution of MCFA in TAG is likely to affect their metabolic fate. We studied chylomicron and VLDL TAG structures, as well as the magnitu...... or in FFA concentrations. Thus, the positional distribution of MCFA in TAG affects their metabolic fate, but the magnitude of postprandial lipemia does not seem to be dependent on the positional distribution of MCFA in the ingested fat.......Although medium-chain FA (MCFA) are mainly absorbed via the portal venous system, they are also incorporated into chylomicron TAG; therefore, the positional distribution of MCFA in TAG is likely to affect their metabolic fate. We studied chylomicron and VLDL TAG structures, as well as the magnitude...... of postprandial lipemia, after two oral fat loads containing decanoic acid (10:0) predominantly at the sn-1 (3),2 (MML) or at the sn-1,3 positions (MLM) of TAG in a randomized, double-blind,,crossover clinical trial with 10 healthy, normal-weight volunteers. An MS-MS method was used to analyze TAG regioisomers...

  2. SYNTHESIS AND CRYSTAL STRUCTURE OF A Mg(II COMPLEX WITH 2,6-PYRIDINEDICARBOXYLIC ACID

    Directory of Open Access Journals (Sweden)

    XI-SHI TAI

    2015-05-01

    Full Text Available A Mg(II complex, [MgL·(H2O3]·2H2O (H2L = 2,6-pyridinedicarboxylic acid, has been synthesized and characterized by elemental analysis, IR and X-ray single crystal diffraction analysis. The Mg(II complex belongs to monoclinic, space group P21/n with a = 8.9318(18 Å, b = 10.002(2 Å, c = 13.290(3 Å, β = 96.86(3º, V= 1178.8(4 Å3, Z = 4, Dc = 1.575 mg·m-3, μ = 0.192 mm-1, F(000 = 584, and final R1 = 0.0349, ωR2 = 0.1212. Structural analysis shows that the Mg(II center is six-coordination with a NO5 distorted octahedral coordination environment. The Mg(II complex forms 1D chain structure by the interaction of hydrogen bonds and π-π stacking.

  3. Electronic Structures and Optical Properties of Phenyl C71 Butyric Acid Methyl Esters

    Directory of Open Access Journals (Sweden)

    Cai-Rong Zhang

    2013-01-01

    Full Text Available Phenyl C71 butyric acid methyl ester (PC71BM has been adopted as electron acceptor materials in bulk heterojunction solar cells with relatively higher power conversion efficiency. The understanding of the mechanism and performance for the devices based upon PC71BM requires the information of conformations, electronic structures, optical properties, and so forth. Here, the geometries, IR and Raman, electronic structures, polarizabilities, and hyperpolarizabilities of PC71BM isomers are studied by using density functional theory (DFT; the absorption and excitation properties are investigated via time-dependent DFT with B3LYP, PBE0, and CAM-B3LYP functionals. The calculated results show that [6,6]PC71BM is more stable than [5,6]PC71BM due to the lower total energy. The vibrational modes of the isomers at IR and Raman peaks are quite similar. As to absorption properties, CAM-B3LYP functional is the suitable functional for describing the excitations of PC71BM because the calculated results with CAM-B3LYP functional agree well with that of the experiment. The analysis of transition configurations and molecular orbitals demonstrated that the transitions at the absorption maxima in UV/Vis region are localized π-π* transitions in fullerenes cages. Furthermore, the larger isotropic polarizability of PC71BM indicates that the response of PC71BM to applied external electric field is stronger than that of PC61BM, and therefore resulting into better nonlinear optical properties.

  4. Crystalline structure of annealed polylactic acid and its relation to processing

    Directory of Open Access Journals (Sweden)

    2010-10-01

    Full Text Available This paper focuses on the crystalline structure of injection moulding grade poly(lactic acid (PLA and the effect of crystalline structure on the processing. The research is induced by the significant differences in crystallinity of the pure PLA resin, and the injection moulded product, and thus the reprocessing of PLA products. 2 mm thick PLA sheets were injection moulded and re-crystallized in a conventional oven at 60–140°C, for 10–60 minutes to achieve various crystalline contents. The properties of these sheets were investigated by dynamic mechanical analysis (DMA, differential scanning calorimetry (DSC, and wide angle X-ray diffraction (WAXD. In a processing plant the rejected parts are recycled and reused as raw material for further cycles, accordingly the various crystalline content PLA products were reprocessed as a resin, to investigate the processing itself. When PLA products are reprocessed, due to the adherent feature of amorphous PLA processing difficulties may occur. This adherent effect of the amorphous PLA was investigated and characterized.

  5. Development of structure and properties during thermal calendering of polylactic acid (PLA fiber webs

    Directory of Open Access Journals (Sweden)

    2008-01-01

    Full Text Available Due to its thermoplastic and biodegradable nature, poly(lactic acid (PLA holds good promise in its increasing use in the form of fibers for medical, agricultural, apparel, upholstery, hygiene, and other applications. Most of the research being done on PLA fibers is to understand their production by melt spinning, solution spinning, and the structure-property relationships during fiber formation. Nonwovens are one of the important forms of the materials into which PLA polymer can be converted to create many useful products. Thermal bonding is the most widely used bonding technique employed to impart strength, and other useful characteristics to the nonwovens. However, there is limited research done to study the behavior of PLA fibers during thermal bonding of nonwovens. Hence the research was carried out to investigate the thermal bonding of nonwovens made from PLA staple fibers. The PLA fibers were carded and then calendered at different temperatures. The webs were characterized for their structure and properties. The observed results are discussed with respect to the investigated processing conditions.

  6. Effect of Humic Acids and pesticides on Agricultural Soil Structure and Stability and Its Implication on Soil Quality

    Science.gov (United States)

    Gaonkar, O. D.; Nambi, I. M.; G, S. K.

    2016-12-01

    The functional and morphological aspects of soil structure determine the soil quality. The dispersion of colloidal soil particles, especially the clay fraction and rupture of soil aggregates, both of which play an important role in soil structure development, lead to degradation of soil quality. The main objective of this work was to determine the effect of behaviour of soil colloids on the agricultural soil structure and quality. The effect of commercial humic acid, organophosphate pesticides and soil natural organic matter on the electrical and structural properties of the soil colloids was also studied. Agricultural soil, belonging to the sandy loam texture class from northern part of India was considered in this study. In order to understand the changes in the soil quality in the presence and absence of humic acids, the soil fabric and structure was analyzed by X-ray diffraction (XRD), Fourier Transform Infrared (FTIR) Spectroscopy and Scanning Electron Microscopy (SEM). Electrical properties of natural soil colloids in aqueous suspensions were assessed by zeta potential measurements at varying pH values with and without the presence of humic acids and pesticides. The influence of natural organic matter was analyzed by oxidizing the natural soil organic matter with hydrogen peroxide. The zeta potential of the soil colloids was found to be negative in the pH range studied. The results indicated that hydrogen peroxide treatment lead to deflocculation of colloidal soil particles. In addition, the humic acids undergoes effective adsorption onto the soil surface imparting more negative zeta potential to the colloidal soil particles. The soil hydrophilicity decreased in the presence of humic acids which was confirmed by surface free energy determination. Thus, it can be concluded that the presence of humic acids altered the soil fabric and structure, thereby affecting the soil quality. This study assumes significance in understanding the soil aggregation and the

  7. 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

  8. How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex

    Czech Academy of Sciences Publication Activity Database

    Ovaere, M.; Šponer, Jiří; Šponer, Judit E.; Herdewijn, P.; Van Meervelt, L.

    2012-01-01

    Roč. 40, č. 15 (2012), s. 7573-7583 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GAP208/10/2302; GA ČR(CZ) GA203/09/1476 Institutional research plan: CEZ:AV0Z50040702 Keywords : duplex * atritol nucleic acids * O2' and O4' hydroxyl group Subject RIV: BO - Biophysics Impact factor: 8.278, year: 2012

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

    Science.gov (United States)

    Hwang, Hong-Sik; Winkler-Moser, Jill K

    2017-04-15

    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°C, and the effects of amino acid structure on the antioxidant activity were investigated. Amino acids containing a thiol, a thioether, or an extra amine group such as arginine, cysteine, lysine, methionine, and tryptophan had the strongest antioxidant activities. At 5.5mM, these amino acids had stronger antioxidant activities than 0.02% (1.1mM) tert-butylhydroquinone (TBHQ). A functional group such as an amide, carboxylic acid, imidazole, or phenol appeared to negatively affect amino acid antioxidant activity. Synergism between amino acids and tocopherols was demonstrated, and we found that this synergistic interaction may be mostly responsible for the antioxidant activity that was observed. In a frying study with potato cubes, 5.5mM l-methionine had significantly stronger antioxidant activity than 0.02% TBHQ. Published by Elsevier Ltd.

  10. Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations

    OpenAIRE

    Pande, Vineet; Nilsson, Lennart

    2008-01-01

    Locked nucleic acid (LNA) is a chemically modified nucleic acid with its sugar ring locked in an RNA-like (C3′-endo) conformation. LNAs show extraordinary thermal stabilities when hybridized with DNA, RNA or LNA itself. We performed molecular dynamics simulations on five isosequential duplexes (LNA–DNA, LNA–LNA, LNA–RNA, RNA–DNA and RNA–RNA) in order to characterize their structure, dynamics and hydration. Structurally, the LNA–DNA and LNA–RNA duplexes are found to be similar to regular RNA–D...

  11. 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...

  12. Synthesis and structural evaluation of five coordination complexes of benzenepentacarboxylic acid with aza-donor ligands

    Science.gov (United States)

    Shimpi, Manishkumar R.; Biswas, Sharmita Nandy; Sarkar, Sohini; Pedireddi, V. R.

    2016-06-01

    Synthesis and structural features of five new coordination assemblies, [Co(bpyH)(H2O)5](BPCH)·(bpyH2)0.5·(H2O) (1a), [{Cu(H2O)3}·{Cu0.5(bpy)0.5(H2O)0.5}2(μ-BPCH)] (1b), [{Cd0.5(BPCH)}2·{Cd0.5(bpy)(H2O)2}2]·6(H2O) (1c), [Cu(BPCH2)(bpyeaH)]·2(H2O) (1d) and [Cd2 (bpyea)0.5(oxalate)0.5(μ-BPC) (H2O)]·(bpyeaH2)·2(H2O) (1e), have been reported. All the assemblies were prepared by co-crystallization of benzenepentacarboxylic acid (BPCH5) either with 4,4‧-bipyridine (bpy) or 1,2-bis(4-pyridyl)ethane (bpyea) in the presence of a transition metal ion (either Co(II), Cu(II) or Cd(II)) as the case may be. All the five compounds were synthesized by hydrothermal method and structures were determined by single crystal X-ray diffraction. All the obtained compounds, 1a-1e, exhibit distinct 3-D polymeric architectures either in the form of stacked layers or host-guest networks in which water molecules play a pivotal role providing additional stabilization by coordinate bonds as well as hydrogen bonds. Other non-covalent interactions such as C-H … π and π … π stacking also participate in the formation of exotic 3-D structures of these complexes.

  13. Crystal structures of Lymphocytic choriomeningitis virus endonuclease domain complexed with diketo-acid ligands

    Directory of Open Access Journals (Sweden)

    Magali Saez-Ayala

    2018-03-01

    Full Text Available The Arenaviridae family, together with the Bunyaviridae and Orthomyxoviridae families, is one of the three negative-stranded RNA viral families that encode an endonuclease in their genome. The endonuclease domain is at the N-terminus of the L protein, a multifunctional protein that includes the RNA-dependent RNA polymerase. The synthesis of mRNA in arenaviruses is a process that is primed by capped nucleotides that are `stolen' from the cellular mRNA by the endonuclease domain in cooperation with other domains of the L protein. This molecular mechanism has been demonstrated previously for the endonuclease of the prototype Lymphocytic choriomeningitis virus (LCMV. However, the mode of action of this enzyme is not fully understood as the original structure did not contain catalytic metal ions. The pivotal role played by the cap-snatching process in the life cycle of the virus and the highly conserved nature of the endonuclease domain make it a target of choice for the development of novel antiviral therapies. Here, the binding affinities of two diketo-acid (DKA compounds (DPBA and L-742,001 for the endonuclease domain of LCMV were evaluated using biophysical methods. X-ray structures of the LCMV endonuclease domain with catalytic ions in complex with these two compounds were determined, and their efficacies were assessed in an in vitro endonuclease-activity assay. Based on these data and computational simulation, two new DKAs were synthesized. The LCMV endonuclease domain exhibits a good affinity for these DKAs, making them a good starting point for the design of arenavirus endonuclease inhibitors. In addition to providing the first example of an X-ray structure of an arenavirus endonuclease incorporating a ligand, this study provides a proof of concept that the design of optimized inhibitors against the arenavirus endonuclease is possible.

  14. Structural diversity of solid dispersions of acetylsalicylic acid as seen by solid-state NMR.

    Science.gov (United States)

    Policianova, Olivia; Brus, Jiri; Hruby, Martin; Urbanova, Martina; Zhigunov, Alexander; Kredatusova, Jana; Kobera, Libor

    2014-02-03

    Solid dispersions of active pharmaceutical ingredients are of increasing interest due to their versatile use. In the present study polyvinylpyrrolidone (PVP), poly[N-(2-hydroxypropyl)-metacrylamide] (pHPMA), poly(2-ethyl-2-oxazoline) (PEOx), and polyethylene glycol (PEG), each in three Mw, were used to demonstrate structural diversity of solid dispersions. Acetylsalicylic acid (ASA) was used as a model drug. Four distinct types of the solid dispersions of ASA were created using a freeze-drying method: (i) crystalline solid dispersions containing nanocrystalline ASA in a crystalline PEG matrix; (ii) amorphous glass suspensions with large ASA crystallites embedded in amorphous pHPMA; (iii) solid solutions with molecularly dispersed ASA in rigid amorphous PVP; and (iv) nanoheterogeneous solid solutions/suspensions containing nanosized ASA clusters dispersed in a semiflexible matrix of PEOx. The obtained structural data confirmed that the type of solid dispersion can be primarily controlled by the chemical constitutions of the applied polymers, while the molecular weight of the polymers had no detectable impact. The molecular structure of the prepared dispersions was characterized using solid-state NMR, wide-angle X-ray scattering (WAXS), and differential scanning calorimetry (DSC). By applying various (1)H-(13)C and (1)H-(1)H correlation experiments combined with T1((1)H) and T1ρ((1)H) relaxation data, the extent of the molecular mixing was determined over a wide range of distances, from intimate intermolecular contacts (0.1-0.5 nm) up to the phase-separated nanodomains reaching ca. 500 nm. Hydrogen-bond interactions between ASA and polymers were probed by the analysis of (13)C and (15)N CP/MAS NMR spectra combined with the measurements of (1)H-(15)N dipolar profiles. Overall potentialities and limitations of individual experimental techniques were thoroughly evaluated.

  15. Structural Investigation for Optimization of Anthranilic Acid Derivatives as Partial FXR Agonists by in Silico Approaches

    Science.gov (United States)

    Chen, Meimei; Yang, Xuemei; Lai, Xinmei; Kang, Jie; Gan, Huijuan; Gao, Yuxing

    2016-01-01

    In this paper, a three level in silico approach was applied to investigate some important structural and physicochemical aspects of a series of anthranilic acid derivatives (AAD) newly identified as potent partial farnesoid X receptor (FXR) agonists. Initially, both two and three-dimensional quantitative structure activity relationship (2D- and 3D-QSAR) studies were performed based on such AAD by a stepwise technology combined with multiple linear regression and comparative molecular field analysis. The obtained 2D-QSAR model gave a high predictive ability (R2train = 0.935, R2test = 0.902, Q2LOO = 0.899). It also uncovered that number of rotatable single bonds (b_rotN), relative negative partial charges (RPC−), oprea's lead-like (opr_leadlike), subdivided van der Waal’s surface area (SlogP_VSA2) and accessible surface area (ASA) were important features in defining activity. Additionally, the derived3D-QSAR model presented a higher predictive ability (R2train = 0.944, R2test = 0.892, Q2LOO = 0.802). Meanwhile, the derived contour maps from the 3D-QSAR model revealed the significant structural features (steric and electronic effects) required for improving FXR agonist activity. Finally, nine newly designed AAD with higher predicted EC50 values than the known template compound were docked into the FXR active site. The excellent molecular binding patterns of these molecules also suggested that they can be robust and potent partial FXR agonists in agreement with the QSAR results. Overall, these derived models may help to identify and design novel AAD with better FXR agonist activity. PMID:27070594

  16. Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.

    Directory of Open Access Journals (Sweden)

    James B Howard

    Full Text Available Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification

  17. 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.

  18. 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).

  19. Effects of long-term fertilization on soil humic acid composition and structure in Black Soil.

    Science.gov (United States)

    Zhang, Jiuming; Wang, Jingkuan; An, Tingting; Wei, Dan; Chi, Fengqin; Zhou, Baoku

    2017-01-01

    The composition and structure of humic acid (HA) can be affected by fertilization, but the short-term effects are difficult to detect using traditional analysis methods. Using a 35-year long-term experiment in Black Soil, the molecular structure of HA was analyzed with Fourier transform infrared spectroscopy (FTIR), 13C nuclear magnetic resonance spectroscopy (NMR), and fluorescence spectroscopy. Variation in HA was analyzed after long-term fertilization, including fertilization with manure (M), inorganic N, P and K fertilizer (NPK), manure combined with inorganic N, P, and K fertilizer (MNPK), and a no-fertilizer control (CK). The application of each fertilizer treatment increased crop yields compared with the CK treatment, and the MNPK treatment increased crop yield the most. The ratio of main IR absorption peak of HA at 2,920 cm-1 compared with the peak at 2,850 cm-1 (2920/2850) was higher in the NPK and MNPK treatments compared with the CK treatment. The application of manure (MNPK and M treatments) increased the ratio of hydrogen to carbon (H/C) in HA, and raised the ratio of the main IR absorption peak of HA at 2920 cm-1 to that at 1720 cm-1 (2920/1720). Manure treatments also raised the ratio of aliphatic carbon (C) to aromatic C, alkyl C to alkoxy C and hydrophobic C to hydrophilic C and the fluorescence index (f 450/500), but decreased the degree of aromatization of HA, when compared with the CK treatment. The ratio between each type of C in HA was similar among all the fertilizer treatments, but NPK had a lower ratio of H/C and a lower content of aliphatic C compared with the CK treatment. These results indicated that the molecular structure of HA in Black Soil tends to be aliphatic, simpler, and younger after the application of manure. While the application of inorganic fertilizers increased in the degree of condensation of HA and made HA structure complicated. The application of manure alone or combined with inorganic fertilizers may be an effective way

  20. Theoretical isotopic fractionation between structural boron in carbonates and aqueous boric acid and borate ion

    Science.gov (United States)

    Balan, Etienne; Noireaux, Johanna; Mavromatis, Vasileios; Saldi, Giuseppe D.; Montouillout, Valérie; Blanchard, Marc; Pietrucci, Fabio; Gervais, Christel; Rustad, James R.; Schott, Jacques; Gaillardet, Jérôme

    2018-02-01

    The 11B/10B ratio in calcite and aragonite is an important proxy of oceanic water pH. However, the physico-chemical mechanisms underpinning this approach are still poorly known. In the present study, we theoretically determine the equilibrium isotopic fractionation properties of structural boron species in calcium carbonates, BO33-, BO2(OH)2- and B(OH)4- anions substituted for carbonate groups, as well as those of B(OH)4- and B(OH)3 species in vacuum. Significant variability of equilibrium isotopic fractionation properties is observed among these structural species which is related to their contrasted coordination state, Bsbnd O bond lengths and atomic-scale environment. The isotopic composition of structural boron does not only depend on its coordination number but also on its medium range environment, i.e. farther than its first coordination shell. The isotopic fractionation between aqueous species and their counterparts in vacuum are assessed using previous investigations based on similar quantum-mechanical modeling approaches. At 300 K, the equilibrium isotope composition of structural trigonal species is 7-15‰ lighter than that of aqueous boric acid molecules, whereas substituted tetrahedral borate ions are heavier than their aqueous counterparts by 10-13‰. Although significant uncertainties are known to affect the theoretical prediction of fractionation factors between solids and solutions, the usually assumed lack of isotopic fractionation during borate incorporation in carbonates is challenged by these theoretical results. The present theoretical equilibrium fractionation factors between structural boron and aqueous species differ from those inferred from experiments which may indicate that isotopic equilibrium, unlike chemical equilibrium, was not reached in most experiments. Further research into the isotopic fractionation processes at the interface between calcium carbonates and aqueous solution as well as long duration experiments aimed at

  1. A 1.9 Å Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jui-Hui; Yajima, Rieko; Chadalavada, Durga M.; Chase, Elaine; Bevilacqua, Philip C.; Golden, Barbara L. (Purdue); (Penn)

    2010-11-01

    The hepatitis delta virus (HDV) ribozyme and HDV-like ribozymes are self-cleaving RNAs found throughout all kingdoms of life. These RNAs fold into a double-nested pseudoknot structure and cleave RNA, yielding 2{prime},3{prime}-cyclic phosphate and 5{prime}-hydroxyl termini. The active site nucleotide C75 has a pK{sub a} shifted >2 pH units toward neutrality and has been implicated as a general acid/base in the cleavage reaction. An active site Mg{sup 2+} ion that helps activate the 2{prime}-hydroxyl for nucleophilic attack has been characterized biochemically; however, this ion has not been visualized in any previous structures. To create a snapshot of the ribozyme in a state poised for catalysis, we have crystallized and determined the structure of the HDV ribozyme bound to an inhibitor RNA containing a deoxynucleotide at the cleavage site. This structure includes the wild-type C75 nucleotide and Mg{sup 2+} ions, both of which are required for maximal ribozyme activity. This structure suggests that the position of C75 does not change during the cleavage reaction. A partially hydrated Mg{sup 2+} ion is also found within the active site where it interacts with a newly resolved G {center_dot} U reverse wobble. Although the inhibitor exhibits crystallographic disorder, we modeled the ribozyme-substrate complex using the conformation of the inhibitor strand observed in the hammerhead ribozyme. This model suggests that the pro-RP oxygen of the scissile phosphate and the 2{prime}-hydroxyl nucleophile are inner-sphere ligands to the active site Mg{sup 2+} ion. Thus, the HDV ribozyme may use a combination of metal ion Lewis acid and nucleobase general acid strategies to effect RNA cleavage.

  2. 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

    ]CPP-binding assay (IC50 = 7 +/- 3 microM) and electropharmacologically in the rat cortical wedge model (EC50 = 8 +/- 2 microM). In contrast to this, the tertbutyl analogue 7a of AMAA turned out to be an antagonist at NMDA and AMPA receptors. The conformational characteristics of AMAA and 7a, c were studied...... 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...

  3. A comparison study on polysaccharides extracted from Laminaria japonica using different methods: structural characterization and bile acid-binding capacity.

    Science.gov (United States)

    Gao, Jie; Lin, Lianzhu; Sun, Baoguo; Zhao, Mouming

    2017-09-20

    In this study, the structural characterization and bile acid-binding capacity of Laminaria japonica polysaccharides (LP), obtained by seven different extraction methods, were investigated. The results indicated that extraction methods exhibited significant effects on extraction yield, molecular weight, monosaccharide composition and the content of neutral sugar, fucose, uronic acid and sulfate of LP. AFM analysis indicated that LP extracted by different methods exhibited certain different, flexible and worm-like chains with many branches. Rheological measurements showed that the LP, obtained by pressurized hot water extraction and acid assisted extraction, exhibited lower viscosity due to their lower molecular weight, compared to other extracted polysaccharides. The bile acid-binding capacity of acid assisted extracted LP was significantly higher than other LP samples tested, which was probably ascribed to its highly branched structure, low molecular weight, low viscosity and abundant uronic acid and fucose in total monosaccharides. The present study provides scientific evidence and advances in the preparation technology and a method for evaluating hypolipidemic activities of L. japonica polysaccharides.

  4. Crystal Structure of an Indole-3-Acetic Acid Amido Synthetase from Grapevine Involved in Auxin Homeostasis[W

    Science.gov (United States)

    Peat, Thomas S.; Böttcher, Christine; Newman, Janet; Lucent, Del; Cowieson, Nathan; Davies, Christopher

    2012-01-01

    Auxins are important for plant growth and development, including the control of fruit ripening. Conjugation to amino acids by indole-3-acetic acid (IAA)-amido synthetases is an important part of auxin homeostasis. The structure of the auxin-conjugating Gretchen Hagen3-1 (GH3-1) enzyme from grapevine (Vitis vinifera), in complex with an inhibitor (adenosine-5′-[2-(1H-indol-3-yl)ethyl]phosphate), is presented. Comparison with a previously published benzoate-conjugating enzyme from Arabidopsis thaliana indicates that grapevine GH3-1 has a highly similar domain structure and also undergoes a large conformational change during catalysis. Mutational analyses and structural comparisons with other proteins have identified residues likely to be involved in acyl group, amino acid, and ATP substrate binding. Vv GH3-1 is a monomer in solution and requires magnesium ions solely for the adenlyation reaction. Modeling of IAA and two synthetic auxins, benzothiazole-2-oxyacetic acid (BTOA) and 1-naphthaleneacetic acid (NAA), into the active site indicates that NAA and BTOA are likely to be poor substrates for this enzyme, confirming previous enzyme kinetic studies. This suggests a reason for the increased effectiveness of NAA and BTOA as auxins in planta and provides a tool for designing new and effective auxins. PMID:23136372

  5. Determination of ghrelin structure in the barfin flounder (Verasper moseri and involvement of ingested fatty acids in ghrelin acylation

    Directory of Open Access Journals (Sweden)

    Hiroyuki eKaiya

    2013-09-01

    Full Text Available Ghrelin is a peptide hormone that is acylated with a fatty acid, usually n-octanoic acid, at the third amino acid residue (usually a serine or threonine, and this acylation is known to be essential for ghrelin activity not only in mammals but also in non-mammals, such as fish. However, the modification mechanisms of ghrelin modification in fish are not known. In this study, we elucidated the structure of ghrelin in a teleost, the barfin flounder (Verasper moseri, and determined whether ingested free fatty acids of various chain lengths participated in ghrelin acylation. Complementary DNA cloning revealed the barfin flounder prepro-ghrelin to be a 106-amino acid (aa peptide and the mature ghrelin to be a 20-aa peptide (GSSFLSPSHKPPNKGKPPRA. However, purification of ghrelin peptides from stomach extracts demonstrated that the major form of the hormone was a 19-aa decanoylated peptide (GSS[C10:0]FLSPSHKPPNKGKPPR missing the last alanine of the 20-aa peptide. Ingestion of feed enriched with n-heptanoic acid (C7, n-octanoic acid (C8, or n-nonanoic acid (C9 changed the modification status of the peptide: ingestion of C8 or C9 increased the amount of C8:0 or C9:0 19-aa ghrelin, respectively, but no C7:0 ghrelin was isolated after ingestion of C7. These results indicate that ingested free fatty acids are substrates for ghrelin acylation in the barfin flounder, but the types of free fatty acids utilized as substrates may be limited.

  6. 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.

  7. Consecutive Fragmentation Mechanisms of Protonated Ferulic Acid Probed by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations

    Science.gov (United States)

    Martens, Sabrina M.; Marta, Rick A.; Martens, Jonathan K.; McMahon, Terry B.

    2012-10-01

    Protonated ferulic acid and its principle fragment ion have been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311 + G(d,p) level of theory. Due to its extensively conjugated structure, protonated ferulic acid is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. The first pathway involves proton transfer, resulting in the loss of water and subsequently carbon monoxide, producing fragment ions m/z 177 and 149, respectively. Optimization of m/z 177 yields a species containing an acylium group, which is supported by a diagnostic peak in the IRMPD spectrum at 2168 cm-1. The second pathway involves an alternate proton transfer leading to loss of methanol and rearrangement to a five-membered ring.

  8. Structure-based drug design targeting the cell membrane receptor GPBAR1: exploiting the bile acid scaffold towards selective agonism

    Science.gov (United States)

    di Leva, Francesco Saverio; Festa, Carmen; Renga, Barbara; Sepe, Valentina; Novellino, Ettore; Fiorucci, Stefano; Zampella, Angela; Limongelli, Vittorio

    2015-11-01

    Bile acids can regulate nutrient metabolism through the activation of the cell membrane receptor GPBAR1 and the nuclear receptor FXR. Developing an exogenous control over these receptors represents an attractive strategy for the treatment of enterohepatic and metabolic disorders. A number of dual GPBAR1/FXR agonists are known, however their therapeutic use is limited by multiple unwanted effects due to activation of the diverse downstream signals controlled by the two receptors. On the other hand, designing selective GPBAR1 and FXR agonists is challenging since the two proteins share similar structural requisites for ligand binding. Here, taking advantage of our knowledge of the two targets, we have identified through a rational drug design study a series of amine lithocholic acid derivatives as selective GPBAR1 agonists. The presence of the 3α-NH2 group on the steroidal scaffold is responsible for the selectivity over FXR unveiling unprecedented structural insights into bile acid receptors activity modulation.

  9. Stearoyl-Acyl Carrier Protein Desaturase Mutations Uncover an Impact of Stearic Acid in Leaf and Nodule Structure.

    Science.gov (United States)

    Lakhssassi, Naoufal; Colantonio, Vincent; Flowers, Nicholas D; Zhou, Zhou; Henry, Jason; Liu, Shiming; Meksem, Khalid

    2017-07-01

    Stearoyl-acyl carrier protein desaturase (SACPD-C) has been reported to control the accumulation of seed stearic acid; however, no study has previously reported its involvement in leaf stearic acid content and impact on leaf structure and morphology. A subset of an ethyl methanesulfonate mutagenized population of soybean ( Glycine max ) 'Forrest' was screened to identify mutants within the GmSACPD-C gene. Using a forward genetics approach, one nonsense and four missense Gmsacpd-c mutants were identified to have high levels of seed, nodule, and leaf stearic acid content. Homology modeling and in silico analysis of the GmSACPD-C enzyme revealed that most of these mutations were localized near or at conserved residues essential for diiron ion coordination. Soybeans carrying Gmsacpd-c mutations at conserved residues showed the highest stearic acid content, and these mutations were found to have deleterious effects on nodule development and function. Interestingly, mutations at nonconserved residues show an increase in stearic acid content yet retain healthy nodules. Thus, random mutagenesis and mutational analysis allows for the achievement of high seed stearic acid content with no associated negative agronomic characteristics. Additionally, expression analysis demonstrates that nodule leghemoglobin transcripts were significantly more abundant in soybeans with deleterious mutations at conserved residues of GmSACPD-C. Finally, we report that Gmsacpd-c mutations cause an increase in leaf stearic acid content and an alteration of leaf structure and morphology in addition to differences in nitrogen-fixing nodule structure. © 2017 American Society of Plant Biologists. All Rights Reserved.

  10. 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...

  11. Structure and Electrical Conductivity of Hybrid Langmuir-Blodgett Films from BEDO-TTF and Fatty Acid

    NARCIS (Netherlands)

    Akhtar, Naureen; Gengler, Regis Y. N.; Palstra, Thomas T. M.; Rudolf, Petra

    2012-01-01

    Conducting Langmuir-Blodgett films are one of the candidates for molecular electronics. We investigated the structural and electrical properties of Langmuir-Blodgett films built up as a mixed molecular system of bis(ethylenedioxy)tetrathiafulvalene, in short BEDO-TTF, and fatty acid, as a function

  12. 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

  13. 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.

  14. Influence of phenylacetic acid pulses on anaerobic digestion performance and archaeal community structure in WWTP sewage sludge digesters

    NARCIS (Netherlands)

    Cabrol, L.; Urra, J.; Rosenkranz, F.; Kroff, P.A.; Plugge, C.M.; Lesty, Y.; Chamy, R.

    2015-01-01

    The effect of phenylacetic acid (PAA) pulses on anaerobic digestion (AD) performance and archaeal community structure was evaluated in anaerobic digesters treating sewage sludge from a wastewater treatment plant (WWTP). Four pilot-scale continuous stirred tank reactors were set up at a full-scale

  15. Structure and acidity of individual Fluid Catalytic Cracking catalyst particles studied by synchrotron-based infrared micro-spectroscopy

    NARCIS (Netherlands)

    Buurmans, I.L.C.|info:eu-repo/dai/nl/31406592X; Soulimani, F.|info:eu-repo/dai/nl/313889449; Ruiz Martinez, J.|info:eu-repo/dai/nl/341386405; van der Bij, H.E.|info:eu-repo/dai/nl/328201294; Weckhuysen, B.M.|info:eu-repo/dai/nl/285484397

    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

  16. Diet structure, butyric acid, and fermentable carbohydrates influence growth performance, gut morphology, and cecal fermentation characteristics in broilers

    NARCIS (Netherlands)

    Qaisrani, S.N.; Krimpen, van M.M.; Kwakkel, R.P.; Verstegen, M.W.A.; Hendriks, W.H.

    2015-01-01

    An experiment with 288 male (Ross 308) 1-d-old broilers was conducted to test the hypothesis that a coarse diet supplemented with butyric acid (BA) and fermentable carbohydrates (FC) improves performance of broilers with a poorly digestible protein source. The interaction effects of diet structure

  17. A structural investigation of the interaction of oxalic acid with Cu(110)

    Science.gov (United States)

    White, T. W.; Duncan, D. A.; Fortuna, S.; Wang, Y.-L.; Moreton, B.; Lee, T.-L.; Blowey, P.; Costantini, G.; Woodruff, D. P.

    2018-02-01

    The interaction of oxalic acid with the Cu(110) surface has been investigated by a combination of scanning tunnelling microscopy (STM), low energy electron diffraction (LEED), soft X-ray photoelectron spectroscopy (SXPS), near-edge X-ray absorption fine structure (NEXAFS) and scanned-energy mode photoelectron diffraction (PhD), and density functional theory (DFT). O 1s SXPS and O K-edge NEXAFS show that at high coverages a singly deprotonated monooxalate is formed with its molecular plane perpendicular to the surface and lying in the [ 1 1 bar 0 ] azimuth, while at low coverage a doubly-deprotonated dioxalate is formed with its molecular plane parallel to the surface. STM, LEED and SXPS show the dioxalate to form a (3 × 2) ordered phase with a coverage of 1/6 ML. O 1s PhD modulation spectra for the monooxalate phase are found to be simulated by a geometry in which the carboxylate O atoms occupy near-atop sites on nearest-neighbour surface Cu atoms in [ 1 1 bar 0 ] rows, with a Cusbnd O bondlength of 2.00 ± 0.04 Å. STM images of the (3 × 2) phase show some centred molecules attributed to adsorption on second-layer Cu atoms below missing [001] rows of surface Cu atoms, while DFT calculations show adsorption on a (3 × 2) missing row surface (with every third [001] Cu surface row removed) is favoured over adsorption on the unreconstructed surface. O 1s PhD data from dioxalate is best fitted by a structure similar to that found by DFT to have the lowest energy, although there are some significant differences in intramolecular bondlengths.

  18. Impact of the Fused Deposition (FDM Printing Process on Polylactic Acid (PLA Chemistry and Structure

    Directory of Open Access Journals (Sweden)

    Michael Arthur Cuiffo

    2017-06-01

    Full Text Available Polylactic acid (PLA is an organic polymer commonly used in fused deposition (FDM printing and biomedical scaffolding that is biocompatible and immunologically inert. However, variations in source material quality and chemistry make it necessary to characterize the filament and determine potential changes in chemistry occurring as a result of the FDM process. We used several spectroscopic techniques, including laser confocal microscopy, Fourier transform infrared (FTIR spectroscopy and photoacousitc FTIR spectroscopy, Raman spectroscopy, and X-ray photoelectron spectroscopy (XPS in order to characterize both the bulk and surface chemistry of the source material and printed samples. Scanning electron microscopy (SEM and differential scanning calorimetry (DSC were used to characterize morphology, cold crystallinity, and the glass transition and melting temperatures following printing. Analysis revealed calcium carbonate-based additives which were reacted with organic ligands and potentially trace metal impurities, both before and following printing. These additives became concentrated in voids in the printed structure. This finding is important for biomedical applications as carbonate will impact subsequent cell growth on printed tissue scaffolds. Results of chemical analysis also provided evidence of the hygroscopic nature of the source material and oxidation of the printed surface, and SEM imaging revealed micro- and submicron-scale roughness that will also impact potential applications.

  19. Omega-3 Polyunsaturated Fatty Acids: Structural and Functional Effects on the Vascular Wall

    Directory of Open Access Journals (Sweden)

    Michela Zanetti

    2015-01-01

    Full Text Available Omega-3 polyunsaturated fatty acids (n-3 PUFA consumption is associated with reduced cardiovascular disease risk. Increasing evidence demonstrating a beneficial effect of n-3 PUFA on arterial wall properties is progressively emerging. We reviewed the recent available evidence for the cardiovascular effects of n-3 PUFA focusing on structural and functional properties of the vascular wall. In experimental studies and clinical trials n-3 PUFA have shown the ability to improve arterial hemodynamics by reducing arterial stiffness, thus explaining some of its cardioprotective properties. Recent studies suggest beneficial effects of n-3 PUFA on endothelial activation, which are likely to improve vascular function. Several molecular, cellular, and physiological pathways influenced by n-3 PUFA can affect arterial wall properties and therefore interfere with the atherosclerotic process. Although the relative weight of different physiological and molecular mechanisms and the dose-response on arterial wall properties have yet to be determined, n-3 PUFA have the potential to beneficially impact arterial wall remodeling and cardiovascular outcomes by targeting arterial wall stiffening and endothelial dysfunction.

  20. Structural Analysis and Mechanical Characterization of Hyaluronic Acid-Based Doubly Cross-Linked Networks.

    Science.gov (United States)

    Jha, Amit K; Hule, Rohan A; Jiao, Tong; Teller, Sean S; Clifton, Rodney J; Duncan, Randall L; Pochan, Darrin J; Jia, Xinqiao

    2009-01-01

    We have created a new class of hyaluronic acid (HA)-based hydrogel materials with HA hydrogel particles (HGPs) embedded in and covalently cross-linked to a secondary network. HA HGPs with an average diameter of ∼900 nm and narrow particle size distribution were synthesized using a refined reverse micelle polymerization technique. The average mesh size of the HGPs was estimated to be approximately 5.5 to 7.0 nm by a protein uptake experiment. Sodium periodate oxidation not only introduced aldehyde groups to the particles but also reduced the average particle size. The aldehyde groups generated were used as reactive handles for subsequent cross-linking with an HA derivative containing hydrazide groups. The resulting macroscopic gels contain two distinct hierarchical networks (doubly cross-linked networks, DXNs): one within individual particles and another among different particles. Bulk gels (BGs) formed by direct mixing of HA derivatives with mutually reactive groups were included for comparison. The hydrogel microstructures were collectively characterized by microscopy and neutron scattering techniques. Their viscoelasticity was quantified at low frequencies (0.1-10 Hz) using a controlled stress rheometer and at high frequencies (up to 200 Hz) with a home-built torsional wave apparatus. Both BGs and DXNs are stable elastic gels that become stiffer at higher frequencies. The HA-based DXN offers unique structural hierarchy and mechanical properties that are suitable for soft tissue regeneration.

  1. 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.

  2. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Jose H.; Goh, Ee-Been [Joint BioEnergy Institute, Emeryville, CA 94608 (United States); Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Keasling, Jay D. [Joint BioEnergy Institute, Emeryville, CA 94608 (United States); Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California Berkeley, Berkeley, CA 94720 (United States); Beller, Harry R. [Joint BioEnergy Institute, Emeryville, CA 94608 (United States); Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Adams, Paul D., E-mail: pdadams@lbl.gov [Joint BioEnergy Institute, Emeryville, CA 94608 (United States); Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California Berkeley, Berkeley, CA 94720 (United States)

    2012-10-01

    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.

  4. Structural and Functional Analysis of the Escherichia coli Acid-Sensing Histidine Kinase EvgS.

    Science.gov (United States)

    Sen, Hrishiraj; Aggarwal, Nikhil; Ishionwu, Chibueze; Hussain, Nosheen; Parmar, Chandni; Jamshad, Mohammed; Bavro, Vassiliy N; Lund, Peter A

    2017-09-15

    The EvgS/EvgA two-component system of Escherichia coli is activated in response to low pH and alkali metals and regulates many genes, including those for the glutamate-dependent acid resistance system and a number of efflux pumps. EvgS, the sensor kinase, is one of five unconventional histidine kinases (HKs) in E. coli and has a large periplasmic domain and a cytoplasmic PAS domain in addition to phospho-acceptor, HK and dimerization, internal receiver, and phosphotransfer domains. Mutations that constitutively activate the protein at pH 7 map to the PAS domain. Here, we built a homology model of the periplasmic region of EvgS, based on the structure of the equivalent region of the BvgS homologue, to guide mutagenesis of potential key residues in this region. We show that histidine 226 is required for induction and that it is structurally colocated with a proline residue (P522) at the top of the predicted transmembrane helix that is expected to play a key role in passing information to the cytoplasmic domains. We also show that the constitutive mutations in the PAS domain can be further activated by low external pH. Expression of the cytoplasmic part of the protein alone also gives constitutive activation, which is lost if the constitutive PAS mutations are present. These findings are consistent with a model in which EvgS senses both external and internal pH and is activated by a shift from a tight inactive to a weak active dimer, and we present an analysis of the purified cytoplasmic portion of EvgS that supports this. IMPORTANCE One of the ways bacteria sense their environment is through two-component systems, which have one membrane-bound protein to do the sensing and another inside the cell to turn genes on or off in response to what the membrane-bound protein has detected. The membrane-bound protein must thus be able to detect the stress and signal this detection event to the protein inside the cell. To understand this process, we studied a protein that helps

  5. Prediction of protein structure classes by incorporating different protein descriptors into general Chou's pseudo amino acid composition.

    Science.gov (United States)

    Nanni, Loris; Brahnam, Sheryl; Lumini, Alessandra

    2014-11-07

    Successful protein structure identification enables researchers to estimate the biological functions of proteins, yet it remains a challenging problem. The most common method for determining an unknown protein's structural class is to perform expensive and time-consuming manual experiments. Because of the availability of amino acid sequences generated in the post-genomic age, it is possible to predict an unknown protein's structural class using machine learning methods given a protein's amino-acid sequence and/or its secondary structural elements. Following recent research in this area, we propose a new machine learning system that is based on combining several protein descriptors extracted from different protein representations, such as position specific scoring matrix (PSSM), the amino-acid sequence, and secondary structural sequences. The prediction engine of our system is operated by an ensemble of support vector machines (SVMs), where each SVM is trained on a different descriptor. The results of each SVM are combined by sum rule. Our final ensemble produces a success rate that is substantially better than previously reported results on three well-established datasets. The MATLAB code and datasets used in our experiments are freely available for future comparison at http://www.dei.unipd.it/node/2357. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. 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.

  7. 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.

  8. Inhibition of methane and natural gas hydrate formation by altering the structure of water with amino acids

    Science.gov (United States)

    Sa, Jeong-Hoon; Kwak, Gye-Hoon; Han, Kunwoo; Ahn, Docheon; Cho, Seong Jun; Lee, Ju Dong; Lee, Kun-Hong

    2016-08-01

    Natural gas hydrates are solid hydrogen-bonded water crystals containing small molecular gases. The amount of natural gas stored as hydrates in permafrost and ocean sediments is twice that of all other fossil fuels combined. However, hydrate blockages also hinder oil/gas pipeline transportation, and, despite their huge potential as energy sources, our insufficient understanding of hydrates has limited their extraction. Here, we report how the presence of amino acids in water induces changes in its structure and thus interrupts the formation of methane and natural gas hydrates. The perturbation of the structure of water by amino acids and the resulting selective inhibition of hydrate cage formation were observed directly. A strong correlation was found between the inhibition efficiencies of amino acids and their physicochemical properties, which demonstrates the importance of their direct interactions with water and the resulting dissolution environment. The inhibition of methane and natural gas hydrate formation by amino acids has the potential to be highly beneficial in practical applications such as hydrate exploitation, oil/gas transportation, and flow assurance. Further, the interactions between amino acids and water are essential to the equilibria and dynamics of many physical, chemical, biological, and environmental processes.

  9. 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...

  10. Crystal structure of FAS thioesterase domain with polyunsaturated fatty acyl adduct and inhibition by dihomo-[gamma]-linolenic acid

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Wei; Chakravarty, Bornali; Zheng, Fei; Gu, Ziwei; Wu, Hongmei; Mao, Jianqiang; Wakil, Salih J.; Quiocho, Florante A. (Baylor)

    2012-05-29

    Human fatty acid synthase (hFAS) is a homodimeric multidomain enzyme that catalyzes a series of reactions leading to the de novo biosynthesis of long-chain fatty acids, mainly palmitate. The carboxy-terminal thioesterase (TE) domain determines the length of the fatty acyl chain and its ultimate release by hydrolysis. Because of the upregulation of hFAS in a variety of cancers, it is a target for antiproliferative agent development. Dietary long-chain polyunsaturated fatty acids (PUFAs) have been known to confer beneficial effects on many diseases and health conditions, including cancers, inflammations, diabetes, and heart diseases, but the precise molecular mechanisms involved have not been elucidated. We report the crystal structure of the hFAS TE domain covalently modified and inactivated by methyl {gamma}-linolenylfluorophosphonate. Whereas the structure confirmed the phosphorylation by the phosphonate head group of the active site serine, it also unexpectedly revealed the binding of the 18-carbon polyunsaturated {gamma}-linolenyl tail in a long groove-tunnel site, which itself is formed mainly by the emergence of an {alpha} helix (the 'helix flap'). We then found inhibition of the TE domain activity by the PUFA dihomo-{gamma}-linolenic acid; {gamma}- and {alpha}-linolenic acids, two popular dietary PUFAs, were less effective. Dihomo-{gamma}-linolenic acid also inhibited fatty acid biosynthesis in 3T3-L1 preadipocytes and selective human breast cancer cell lines, including SKBR3 and MDAMB231. In addition to revealing a novel mechanism for the molecular recognition of a polyunsaturated fatty acyl chain, our results offer a new framework for developing potent FAS inhibitors as therapeutics against cancers and other diseases.

  11. Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein.

    Science.gov (United States)

    Arpino, James A J; Rizkallah, Pierre J; Jones, D Dafydd

    2014-08-01

    Single-amino-acid deletions are a common part of the natural evolutionary landscape but are rarely sampled during protein engineering owing to limited and prejudiced molecular understanding of mutations that shorten the protein backbone. Single-amino-acid deletion variants of enhanced green fluorescent protein (EGFP) have been identified by directed evolution with the beneficial effect of imparting increased cellular fluorescence. Biophysical characterization revealed that increased functional protein production and not changes to the fluorescence parameters was the mechanism that was likely to be responsible. The structure EGFP(D190Δ) containing a deletion within a loop revealed propagated changes only after the deleted residue. The structure of EGFP(A227Δ) revealed that a `flipping' mechanism was used to adjust for residue deletion at the end of a β-strand, with amino acids C-terminal to the deletion site repositioning to take the place of the deleted amino acid. In both variants new networks of short-range and long-range interactions are generated while maintaining the integrity of the hydrophobic core. Both deletion variants also displayed significant local and long-range changes in dynamics, as evident by changes in B factors compared with EGFP. Rather than being detrimental, deletion mutations can introduce beneficial structural effects through altering core protein properties, folding and dynamics, as well as function.

  12. Structural characterization of the degradation products of a minor natural sweet diterpene glycoside Rebaudioside M under acidic conditions.

    Science.gov (United States)

    Prakash, Indra; Chaturvedula, Venkata Sai Prakash; Markosyan, Avetik

    2014-01-14

    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.

  13. [Primary structure of the elongation factor G from Escherichia coli. V. Amino acid sequence of the C-terminal domain].

    Science.gov (United States)

    Alakhov, Iu B; Vinokurov, L M; Dovgas, N V; Motuz, L P

    1983-03-01

    The amino acid sequence of the C-terminal domain of the elongation factor G (EF-G) has been studied. The polypeptide chain of the domain consists of 228 amino acid residues, and contains no tryptophan or cysteine residues. To determine its structure, the peptides obtained as a result of the fragment digestion by staphylococcal glutamic protease, cyanogen bromide cleavage, and tryptic hydrolysis of the fragment modified by maleic anhydride have been analyzed, as well as peptides obtained after hydrolyses of cyanogen bromide fragments with chymotrypsin, thermolysin and trypsin.

  14. The amino acid alphabet and the architecture of the protein sequence-structure map. I. Binary alphabets.

    Science.gov (United States)

    Ferrada, Evandro

    2014-12-01

    The correspondence between protein sequences and structures, or sequence-structure map, relates to fundamental aspects of structural, evolutionary and synthetic biology. The specifics of the mapping, such as the fraction of accessible sequences and structures, or the sequences' ability to fold fast, are dictated by the type of interactions between the monomers that compose the sequences. The set of possible interactions between monomers is encapsulated by the potential energy function. In this study, I explore the impact of the relative forces of the potential on the architecture of the sequence-structure map. My observations rely on simple exact models of proteins and random samples of the space of potential energy functions of binary alphabets. I adopt a graph perspective and study the distribution of viable sequences and the structures they produce, as networks of sequences connected by point mutations. I observe that the relative proportion of attractive, neutral and repulsive forces defines types of potentials, that induce sequence-structure maps of vastly different architectures. I characterize the properties underlying these differences and relate them to the structure of the potential. Among these properties are the expected number and relative distribution of sequences associated to specific structures and the diversity of structures as a function of sequence divergence. I study the types of binary potentials observed in natural amino acids and show that there is a strong bias towards only some types of potentials, a bias that seems to characterize the folding code of natural proteins. I discuss implications of these observations for the architecture of the sequence-structure map of natural proteins, the construction of random libraries of peptides, and the early evolution of the natural amino acid alphabet.

  15. Melting properties of some structured lipids native to high stearic acid soybean oil

    Directory of Open Access Journals (Sweden)

    Dunn, R. O.

    2004-06-01

    Full Text Available A number of structured lipids native to high stearic acid soybean oil were synthesized and their physical properties were determined by pulsed nuclear magnetic resonance (NMR, Mettler dropping point and differential scanning calorimetry (DSC. 1,3 Distearo-2-olein (SOS, 1,3 distearo-2-linolein (SLS and1,3 distearo-2-linolenin (SlnS were synthesized from pure 1,3 diacylglycerols and the appropriate fatty acid. Pulsed NMR determinations over the temperature range 10-50 ºC showed that the symmetrical triacylglycerols (SUS: where S = stearic, U = oleic, linoleic or linolenic are high and sharply melting materials, all showing substantial amounts of solids at temperatures up to 33.3 ºC, yet are completely melted at only a few degrees higher. Mettler dropping points for SOS, SLS and SlnS were 44.1, 37.9 and 36.5 ºC respectively. The heats of fusion for the structured triacylglycerols were determined by DSC and shown to be of the order 29-32 cal/gm compared to 45 cal/gm for SSS. The heats of fusion were also calculated from Mettler dropping point determinations as admixtures with soybean oil and showed consistent agreement with the DSC data.Se sintetizaron algunos lípidos estructurados procedentes del aceite de soja con alto contenido en ácido esteárico y sus propiedades físicas se determinaron por resonancia magnética nuclear pulsada (NMR, punto de goteo Mettler y calorimetría diferencial de barrido (DSC. Se sintetizaron 1,3 diestearo-2-oleina (SOS, 1,3 diestearo-2-linoleina (SLS y 1,3 diestearo-2-linolenina (SlnS a partir de 1,3 diacilgliceroles y de los ácidos grasos adecuados puros. Las determinaciones de NMR pulsada en el rango de temperaturas 10- 50 ºC mostraron que los triacilgliceroles simétricos (SUS: donde S = esteárico, U = oleico, linoleico o linolénico funden a mayor temperatura y más bruscamente, todos presentan altos contenidos en sólidos a todas las temperaturas hasta los 33.3 ºC, estando completamente fundidos

  16. Osteogenic activity of titanium surfaces with hierarchical micro/nano-structures obtained by hydrofluoric acid treatment

    Directory of Open Access Journals (Sweden)

    Liang J

    2017-02-01

    Full Text Available Jianfei Liang,1,* Shanshan Xu,1,* Mingming Shen,2,* Bingkun Cheng,3 Yongfeng Li,4 Xiangwei Liu,1 Dongze Qin,1 Anuj Bellare,5 Liang Kong1 1State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Disease & Shaanxi Key Laboratory of Oral Diseases, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi’an, 2Department of Stomatology, Xinhua Hospital of Beijing, Beijing, 3Department of Oral and Maxillofacial Surgery, School of Stomatology, The Second Hospital of Hebei Medical University, Shijiazhuang, 4Department of Stomatology, Chinese PLA 532 Hospital, Huangshan, People’s Republic of China; 5Department of Orthopedic Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA *These authors contributed equally to this work Abstract: An easier method for constructing the hierarchical micro-/nano-structures on the surface of dental implants in the clinic is needed. In this study, three different titanium surfaces with microscale grooves (width 0.5–1, 1–1.5, and 1.5–2 µm and nanoscale nanoparticles (diameter 20–30, 30–50, and 50–100 nm, respectively were obtained by treatment with different concentrations of hydrofluoric acid (HF and at different etching times (1%, 3 min; 0.5%, 12 min; and 1.5%, 12 min, respectively; denoted as groups HF1, HF2, and HF3. The biological response to the three different titanium surfaces was evaluated by in vitro human bone marrow-derived mesenchymal stem cell (hBMMSC experiments and in vivo animal experiments. The results showed that cell adhesion, proliferation, alkaline phosphatase activity, and mineralization of hBMMSCs were increased in the HF3 group. After the different surface implants were inserted into the distal femurs of 40 rats, the bone–implant contact in groups HF1, HF2, and HF3 was 33.17%±2.2%, 33.82%±3.42%, and 41.04%±3.08%, respectively. Moreover, the maximal pullout

  17. Flexible tension sensor based on poly(l-lactic acid) film with coaxial structure

    Science.gov (United States)

    Yoshida, Mitsunobu; Onishi, Katsuki; Tanimoto, Kazuhiro; Nishikawa, Shigeo

    2017-10-01

    We have developed a tension sensor with a coaxial structure using a narrow slit ribbon made of a uniaxially stretched poly(l-lactic acid) (PLLA) film for application to a wearable device. The tension sensor is produced as follows. We used tinsel wire as the center conductor of the sensor. The tinsel wire consists of a yarn of synthetic fibers arranged at the center, with a spirally wound rolled copper foil ribbon on the side surface. Next, slit ribbons obtained from a uniaxially oriented film of PLLA are wound helically on the side surface of the center conductor in the direction of a left-handed screw, at an angle of 45° to the central axis. The rolled copper foil is used as an outer conductor and covers the yarn without a gap. The prototype of the fabricated tension sensor has good flexibility, since the sensor is in the form of a filament and consists of a highly flexible material. For the 1 mm tension sensor, it was found that for a tension of 1 N, a charge of 14 pC was output. It was also found that the sensor maintained its room-temperature sensitivity up to 60 °C. Compared with an existing coaxial line sensor using poly(vinylidene fluoride) (PVDF), the sensor using PLLA does not exhibit pyroelectricity, meaning that no undesirable voltage is generated when in contact with body heat, which is a significant advantage as wearable sensors. The result has demonstrated the potential application of the PLLA film to wearable devices for detecting heartbeat and respiration.

  18. 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

    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...

  19. Structure and rheological properties of acid-induced egg white protein gels

    NARCIS (Netherlands)

    Weijers, M.; Velde, F. van de; Stijnman, A.; Pijpekamp, A. van de; Visschers, R.W.

    2006-01-01

    This study compares the rheological properties of acid-induced gels prepared of industrial spray-dried egg white proteins (EWP) with the acid-induced gels prepared of ovalbumin (OA) and whey protein isolate (WPI). Also we aimed to form transparent gels of EWP by means of the cold-gelation process.

  20. Deprotonation of p-Hydroxybenzoic Acid: Does Electrospray Ionization Sample Solution or Gas-Phase Structures?

    Czech Academy of Sciences Publication Activity Database

    Schröder, Detlef; Buděšínský, Miloš; Roithová, J.

    2012-01-01

    Roč. 134, č. 38 (2012), s. 15897-15905 ISSN 0002-7863 Grant - others:European Research Council(XE) AdG HORIZOMS Institutional support: RVO:61388963 Keywords : mobility-mass-spectrometry * 4-hydroxybenzoic acid * air/water interfase * DFT calculations * aqueous-solution * benzoic-acids Subject RIV: CC - Organic Chemistry Impact factor: 10.677, year: 2012

  1. Aedes aegypti (Diptera: culicidae) biting deterrence: structure-activity relationship of saturated and unsaturated fatty acids

    Science.gov (United States)

    In this study we systematically evaluated for the first time the biting deterrent effects of a series of saturated and unsaturated fatty acids against Aedes aegypti [yellow fever mosquito (Diptera: Culicidae)] using the K & D bioassay system (Klun et al 2005). The saturated fatty acids (C6:0 to C16...

  2. Two dialkylammonium salts of 2-amino-4-nitrobenzoic acid: crystal structures and Hirshfeld surface analysis

    Directory of Open Access Journals (Sweden)

    James L. Wardell

    2016-12-01

    Full Text Available The crystal structures of two ammonium salts of 2-amino-4-nitrobenzoic acid are described, namely dimethylazanium 2-amino-4-nitrobenzoate, C2H8N+·C7H5N2O4−, (I, and dibutylazanium 2-amino-4-nitrobenzoate, C8H20N+·C7H5N2O4−, (II. The asymmetric unit of (I comprises a single cation and a single anion. In the anion, small twists are noted for the carboxylate and nitro groups from the ring to which they are connected, as indicated by the dihedral angles of 11.45 (13 and 3.71 (15°, respectively; the dihedral angle between the substituents is 7.9 (2°. The asymmetric unit of (II comprises two independent pairs of cations and anions. In the cations, different conformations are noted in the side chains in that three chains have an all-trans [(+-antiperiplanar] conformation, while one has a distinctive kink resulting in a (+-synclinal conformation. The anions, again, exhibit twists with the dihedral angles between the carboxylate and nitro groups and the ring being 12.73 (6 and 4.30 (10°, respectively, for the first anion and 8.1 (4 and 12.6 (3°, respectively, for the second. The difference between anions in (I and (II is that in the anions of (II, the terminal groups are conrotatory, forming dihedral angles of 17.02 (8 and 19.0 (5°, respectively. In each independent anion of (I and (II, an intramolecular amino-N—H...O(carboxylate hydrogen bond is formed. In the crystal of (I, anions are linked into a jagged supramolecular chain by charge-assisted amine-N—H...O(carboxylate hydrogen bonds and these are connected into layers via charge-assisted ammonium-N—H...O(carboxylate hydrogen bonds. The resulting layers stack along the a axis, being connected by nitro-N—O...π(arene and methyl-C—H...O(nitro interactions. In the crystal of (II, the anions are connected into four-ion aggregates by charge-assisted amino-N—H...O(carboxylate hydrogen bonding. The formation of ammonium-N—H...O(carboxylate hydrogen bonds, involving

  3. 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.

  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. 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.

  6. 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

  7. 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

  8. 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.

  9. 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 Brandt; 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...

  10. Structural Evolution of Molybdenum Carbides in Hot Aqueous Environments and Impact on Low-Temperature Hydroprocessing of Acetic Acid

    Directory of Open Access Journals (Sweden)

    Jae-Soon Choi

    2015-03-01

    Full Text Available We investigated the structural evolution of molybdenum carbides subjected to hot aqueous environments and their catalytic performance in low-temperature hydroprocessing of acetic acid. While bulk structures of Mo carbides were maintained after aging in hot liquid water, a portion of carbidic Mo sites were converted to oxidic sites. Water aging also induced changes to the non-carbidic carbon deposited during carbide synthesis and increased surface roughness, which in turn affected carbide pore volume and surface area. The extent of these structural changes was sensitive to the initial carbide structure and was lower under actual hydroprocessing conditions indicating the possibility of further improving the hydrothermal stability of Mo carbides by optimizing catalyst structure and operating conditions. Mo carbides were active in acetic acid conversion in the presence of liquid water, their activity being comparable to that of Ru/C. The results suggest that effective and inexpensive bio-oil hydroprocessing catalysts could be designed based on Mo carbides, although a more detailed understanding of the structure-performance relationships is needed, especially in upgrading of more complex reaction mixtures or real bio-oils.

  11. High-resolution NMR reveals secondary structure and folding of amino acid transporter from outer chloroplast membrane.

    Directory of Open Access Journals (Sweden)

    James D Zook

    Full Text Available Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16, an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the (13C, (15N, (2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein.

  12. Modification of ntezi bentonite structure by hydrochloric acid: process kinetics and structural properties of the modified samples

    International Nuclear Information System (INIS)

    Ajemba, R.O.

    2014-01-01

    Bentonite from Ntezi was modified by reacting it with different concentrations of hydrochloric acid solutions. The modified samples were analysed by x-ray fluorescence. The kinetics of the modification reaction was studied by performing the experiment at different temperatures and times. Results of the analysis of the modified samples showed that the octahedral cations were removed which altered the chemical composition of the bentonite. The surface area and adsorptive capacity of the bentonite were improved after the modification. The kinetic studies showed that the acid modification reaction is controlled by the product layer diffusion and can be represented by (1-(l-X)/sup 1/3)/sup 2/ = k t; where, X is the fraction of the bentonite dissolved at time t. The activation energy was determined to be 24.98 kJ/mol. (author)

  13. Comparison of structural effects on Eu(III) complexes with cyclohexyl and benzene polycarboxylic acids

    International Nuclear Information System (INIS)

    Choppin, Gregory R.; Redko, Mikhail Y.

    2003-01-01

    The thermodynamics (β, ΔH, ΔS) of complexation, the residual hydration of the complexed metal ion and the metal-ligand coordination number of the complexes formed by interaction of Eu(III) with 1, 3, 5-cyclohexyltricarboxylic acid, 1, 2, 3- and 1, 2, 4-benzenetricarboxylic acids, cyclohexylhexacarboxylic (CHHS) acid and benzenehexacarboxylic (mellitic) acid have been studied. The 1, 3, 5-cyclohexyltricarboxylate ligand binds by only a single carboxylate while the 1, 2, 3-, and 1, 2, 4-benzene tricarboxylate ligands bind via two carboxylates. The mellitate complexes were found to have bidentate chelation and a residual hydration number, N H 2 O , complexed Eu(III) of ca. 7 in acid-to-neutral solutions. By contrast, in the Eu-CHHS complexation, the coordination number for the ligand binding, CN L , was 2 in acidic to neutral in basic solutions while the residual hydration number of the Eu(III) changed from 6 to 7 in acidic solutions to 2.5 in alkaline solutions. This is interpreted to indicate the formation of [Eu(CHHS)(OH)(H 2 O) 2 ] 4- . The data are discussed in terms of ligand steric effects upon complexation

  14. 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.

  15. Crystal structures and hydrogen bonding in the co-crystalline adducts of 3,5-dinitrobenzoic acid with 4-aminosalicylic acid and 2-hydroxy-3-(1H-indol-3-ylpropenoic acid

    Directory of Open Access Journals (Sweden)

    Graham Smith

    2014-10-01

    Full Text Available The structures of the co-crystalline adducts of 3,5-dinitrobenzoic acid (3,5-DNBA with 4-aminosalicylic acid (PASA, the 1:1 partial hydrate, C7H4N2O6·C7H7NO3·0.2H2O, (I, and with 2-hydroxy-3-(1H-indol-3-ylpropenoic acid (HIPA, the 1:1:1 d6-dimethyl sulfoxide solvate, C7H4N2O6·C11H9NO3·C2D6OS, (II, are reported. The crystal substructure of (I comprises two centrosymmetric hydrogen-bonded R22(8 homodimers, one with 3,5-DNBA, the other with PASA, and an R22(8 3,5-DNBA–PASA heterodimer. In the crystal, inter-unit amine N—H...O and water O—H...O hydrogen bonds generate a three-dimensional supramolecular structure. In (II, the asymmetric unit consists of the three constituent molecules, which form an essentially planar cyclic hydrogen-bonded heterotrimer unit [graph set R32(17] through carboxyl, hydroxy and amino groups. These units associate across a crystallographic inversion centre through the HIPA carboxylic acid group in an R22(8 hydrogen-bonding association, giving a zero-dimensional structure lying parallel to (100. In both structures, π–π interactions are present [minimum ring-centroid separations = 3.6471 (18 Å in (I and 3.5819 (10 Å in (II].

  16. Transmission electron microscopic analysis showing structural changes to bacterial cells treated with electrolyzed water and an acidic sanitizer.

    Science.gov (United States)

    Feliciano, Lizanel; Lee, Jaesung; Pascall, Melvin A

    2012-04-01

    The effects of various sanitizers on the viability and cellular injury to structures of Escherichia coli and Listeria innocua were investigated. A food grade organic acidic formulation (pH 2.5) and acidic, neutral, and basic electrolyzed water [AEW (pH 2.7, oxidation reduction potential; ORP: 1100 mV, free available chlorine; FAC: 150 ppm), NEW (pH 6.9, ORP: 840 mV, FAC: 150 ppm), BEW (pH 11.6, ORP: -810 mV)] were used to treat E. coli and L. innocua cells. After 10 min of exposure to the sanitizers, changes to the bacterial numbers and cell structures were evaluated by plate counting and transmission electron microscopy (TEM), respectively. It was concluded from the results that the sanitizers reduced the E. coli cells between 2 and 3 log CFU/mL. Except for the BEW treatment, reductions in L. innocua population were greater (>1 log CFU/mL) than that of E. coli for all treatments. Data from the TEM showed that all sanitizers caused changes to the cell envelope and cytoplasm of both organisms. However, smaller changes were observed for L. innocua cells. Decrease in the integrity of the cell envelope and aggregation of the cytoplasmic components appeared to be mainly because of exposure to the sanitizers. The organic acid formulation and AEW were the most effective sanitizers against bacterial cells, indicating that penetration of acidic substances effectively caused the cell inactivation. An understanding of the method in which E-water and an acidic sanitizer cause injury to E. coli and L. innocua would be helpful in selecting an effective chemical agent as a food safety tool. This will allow a scientist to target similar microorganisms such as food borne bacteria with structures that are vulnerable to the sanitizer. © 2012 Institute of Food Technologists®

  17. Triple helical structure of acid-soluble collagen derived from Nile tilapia skin as affected by extraction temperature.

    Science.gov (United States)

    Thuanthong, Mantaka; Sirinupong, Nualpun; Youravong, Wirote

    2016-08-01

    Fish skin has become a new source of collagen. It is usually extracted at low temperature. Increasing the extraction temperature can increase the collagen yield. However, high temperature might cause degradation of the triple helical structure of collagen, which is related to its functional biomaterial. This work thus aimed to investigate the effect of extraction temperature on the extraction efficiency and characteristics of acid-soluble collagen (ASC), particularly its triple helical structure. ASC was extracted at 5 ± 1, 15 ± 1 and 25 ± 1 °C for 0-24 h with 0.3 or 0.5 mol L(-1) acetic acid. The results showed that extraction with 0.5 mol L(-1) acetic acid gave a higher extraction efficiency than that in 0.3 mol L(-1) acetic acid (P < 0.5). Extraction at 25 ± 1 °C for 5 h with 0.5 mol L(-1) acetic acid gave a higher extraction efficiency (73.73 ± 1.28%), which is higher than that of 5 ± 1 °C by about 1.7-fold. All ASC obtained were identified as type I collagen and showed similar physicochemical properties. The results showed that extraction temperature strongly affected extraction efficiency. Extraction at 25 °C did not affect the triple helical structure, which was confirmed by the results of Fourier transform infrared, circular dichroism spectrum and collagen self-assembly. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  18. Complexation of trivalent lanthanide cations by different chelation sites of malic and tartric acid (composition, stability and probable structure

    Directory of Open Access Journals (Sweden)

    Mohammed Riri

    2016-11-01

    Full Text Available The formation of colorless gadolinium complexes (x,y,z between x gadolinium ions, y ligands and z protons of some organic acids has been studied in aqueous solution. In this work we shall present the results of investigations on the interaction of the gadolinium ion (Gd3+ with different chelation sites of malic and tartric acid formed in dilute solution for pH values between 5.50 and 7.50. The structures of these new organometallic complexes are Gd3(C4H4O52·(NO33·nH2O and Gd3(C4H4O62·(NO33·nH2O (C4H4O52-: malate ions and C4H4O62-: tartrate ions. These colorless gadolinium complexes of malate and tartrate ions have no absorption band UV–visible, the indirect photometry detection (IPD study; have identified major tri-nuclear complexes of these dicarboxylic acids, giving for these colorless complexes a (3,2,2 and (3,2,3, respectively. Composition and apparent stability constant depends on the acidity of the medium. To complement previous results and to propose probable structures for these new complexes detected in solution FT-IR and FT-Raman spectroscopy have been conducted to identify the different chelation sites for both ligands.

  19. 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.

  20. 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.

  1. Composition, Structural Evolution and the Related Property Variations in Preparation of Mixed Cesium/Ammonium Acidic Salts of Heteropolyacids

    Directory of Open Access Journals (Sweden)

    Heng Zhang

    2016-11-01

    Full Text Available The composition, structural evolution and the related property variations of mixed cesium/ammonium acidic salts of heteropolyacids were investigated in detail by tracking and analyzing the initial precipitates, evaporation residues and the calcined products in their preparation process. Results show that V cannot completely enter the heteropolyanions in the initial precipitates when the Cs+ added amount is low, and the increase in Cs+ adding amount improves the substitution of V for Mo in the heteropolyanions. Both the initial precipitates and the evaporation residues are mixtures of cesium and ammonium salts of heteropolyacids before calcination. Thermal treatment causes the decomposition of the ammonium salts and the formation of single-phase solid solutions from mechanical mixtures. The calcined products of the initial precipitates and the evaporation residues vary greatly in textural properties. The determinants of the catalytic performance for the oxidation of methacrolein to methacrylic acid are acidity and specific surface area of the compounds. The increase in specific surface area mainly improves the conversion of methacrolein, but not the selectivity of methacrylic acid. Insufficient acidity caused by high Cs+ content in the compounds is responsible for the low selectivity.

  2. Structure-function relationships of glucansucrase and fructansucrase enzymes from lactic acid bacteria

    NARCIS (Netherlands)

    Hijum, S.A.F.T. van; Kralj, S.; Ozimek, L.K.; Dijkhuizen, L.; Geel-Schutten, G.H. van

    2006-01-01

    Lactic acid bacteria (LAB) employ sucrase-type enzymes to convert sucrose into homopolysaccharides consisting of either glucosyl units (glucans) or fructosyl units (fructans). The enzymes involved are labeled glucansucrases (GS) and fructansucrases (FS), respectively. The available molecular,

  3. Degradation of Amino Acids and Structure in Model Proteins and Bacteriophage MS2 by Chlorine, Bromine, and Ozone.

    Science.gov (United States)

    Choe, Jong Kwon; Richards, David H; Wilson, Corey J; Mitch, William A

    2015-11-17

    Proteins are important targets of chemical disinfectants. To improve the understanding of disinfectant-protein reactions, this study characterized the disinfectant:protein molar ratios at which 50% degradation of oxidizable amino acids (i.e., Met, Tyr, Trp, His, Lys) and structure were observed during HOCl, HOBr, and O3 treatment of three well-characterized model proteins and bacteriophage MS2. A critical question is the extent to which the targeting of amino acids is driven by their disinfectant rate constants rather than their geometrical arrangement. Across the model proteins and bacteriophage MS2 (coat protein), differing widely in structure, methionine was preferentially targeted, forming predominantly methionine sulfoxide. This targeting concurs with its high disinfectant rate constants and supports its hypothesized role as a sacrificial antioxidant. Despite higher HOCl and HOBr rate constants with histidine and lysine than for tyrosine, tyrosine generally was degraded in preference to histidine, and to a lesser extent, lysine. These results concur with the prevalence of geometrical motifs featuring histidines or lysines near tyrosines, facilitating histidine and lysine regeneration upon Cl[+1] transfer from their chloramines to tyrosines. Lysine nitrile formation occurred at or above oxidant doses where 3,5-dihalotyrosine products began to degrade. For O3, which lacks a similar oxidant transfer pathway, histidine, tyrosine, and lysine degradation followed their relative O3 rate constants. Except for its low reactivity with lysine, the O3 doses required to degrade amino acids were as low as or lower than for HOCl or HOBr, indicating its oxidative efficiency. Loss of structure did not correlate with loss of particular amino acids, suggesting the need to characterize the oxidation of specific geometric motifs to understand structural degradation.

  4. Calculation of Structural Behavior of Indirect NMR Spin-Spin Couplings in the Backbone of Nucleic Acids

    Czech Academy of Sciences Publication Activity Database

    Sychrovský, Vladimír; Vokáčová, Zuzana; Šponer, Jiří; Špačková, Naďa; Schneider, Bohdan

    2006-01-01

    Roč. 110, č. 45 (2006), s. 22894-22902 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GA203/05/0388; GA MŠk(CZ) LC512 Grant - others:NSF(US) DBI 0110076 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507 Keywords : nucleic acids * RNA * DNA * molecular structure Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.115, year: 2006

  5. 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.

  6. In Silico Structure Prediction of Human Fatty Acid Synthase–Dehydratase: A Plausible Model for Understanding Active Site Interactions

    OpenAIRE

    Arun John; Vetrivel Umashankar; A. Samdani; Manoharan Sangeetha; Subramanian Krishnakumar; Perinkulam Ravi Deepa

    2016-01-01

    Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. X-ray crystallographic structures of some of its domains, such as ?-ketoacyl synthase, acetyl transacylase, malonyl transacylase, enoyl reductase, ?-ketoac...

  7. Structural plasticity of green fluorescent protein to amino acid deletions and fluorescence rescue by folding-enhancing mutations.

    Science.gov (United States)

    Liu, Shu-su; Wei, Xuan; Dong, Xue; Xu, Liang; Liu, Jia; Jiang, Biao

    2015-07-25

    Green fluorescent protein (GFP) and its derivative fluorescent proteins (FPs) are among the most commonly used reporter systems for studying gene expression and protein interaction in biomedical research. Most commercially available FPs have been optimized for their oligomerization state to prevent potential structural constraints that may interfere with the native function of fused proteins. Other approach to reducing structural constraints may include minimizing the structure of GFPs. Previous studies in an enhanced GFP variant (EGFP) identified a series of deletions that can retain GFP fluorescence. In this study, we interrogated the structural plasticity of a UV-optimized GFP variant (GFP(UV)) to amino acid deletions, characterized the effects of deletions and explored the feasibility of rescuing the fluorescence of deletion mutants using folding-enhancing mutations. Transposon mutagenesis was used to screen amino acid deletions in GFP that led to fluorescent and nonfluorescent phenotypes. The fluorescent GFP mutants were characterized for their whole-cell fluorescence and fraction soluble. Fluorescent GFP mutants with internal deletions were purified and characterized for their spectral and folding properties. Folding-ehancing mutations were introduced to deletion mutants to rescue their compromised fluorescence. We identified twelve amino acid deletions that can retain the fluorescence of GFP(UV). Seven of these deletions are either at the N- or C- terminus, while the other five are located at internal helices or strands. Further analysis suggested that the five internal deletions diminished the efficiency of protein folding and chromophore maturation. Protein expression under hypothermic condition or incorporation of folding-enhancing mutations could rescue the compromised fluorescence of deletion mutants. In addition, we generated dual deletion mutants that can retain GFP fluorescence. Our results suggested that a "size-minimized" GFP may be developed by

  8. 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.

  9. Mixed-phase PdRu bimetallic structures with high activity and stability for formic acid electrooxidation.

    Science.gov (United States)

    Wu, Dongshuang; Zheng, Zhaoliang; Gao, Shuiying; Cao, Minna; Cao, Rong

    2012-06-14

    Aiming at investigating the effect of structure on electrocatalytic properties, Pd(50)Ru(50) nanoparticles (NPs) with three different structures were carefully designed in a one-pot polyol process for application in formic acid electrooxidation. The three structures are: (1) single-phase PdRu nanodendrites (denoted as PR-1), (2) a mixed-phase mixture of PdRu nanodendrites and monometallic Ru NPs (denoted as PR-2), and (3) a mixed-phase mixture of monometallic Pd and Ru NPs (denoted as PR-3). From PR-1 to PR-3, the structure was varied from single-phase to mixed-phase. The relative position of Ru was altered from completely Pd-connected (PR-1), to a mixture of Pd-connected and monometallic (PR-2), and completely monometallic (PR-3). All PdRu NPs outperform the commercial Pd/C. PR-2 exhibits the highest peak current density, but its stability is slightly lower than that of PR-3. When both the current density and the durability are taken into consideration, PR-2 is the best choice of catalyst for formic acid oxidation. It indicates that both the Pd-connected Ru NPs and monometallic Ru NPs in the mixed-phase PR-2 are essential to improve the electrocatalytic properties. Our study also illustrates that the electrochemical active surface area (ECSA) and hydrogen storage capacity of the as-prepared PdRu NPs are greatly enhanced after several hundred scans in formic acid, indicating the possibility for highly restorable catalysts in direct formic acid fuel cells.

  10. Structure localization relationship of different chain length 1-[C-11]-labeled betamethyl fatty acids

    International Nuclear Information System (INIS)

    Livni, E.; Elmaleh, D.R.; Strauss, H.W.; Brownell, G.L.

    1984-01-01

    Recently, the authors proposed the use of [1-/sup 11/C] betamethyl heptadecanoic acid ([1-/sup 11/C]BMHA) a branched chain fatty acid as a potential myocardial metabolic tracer for positron emission tomography. In this study a series of fatty acids of betamethyl varying chain length was prepared. The compounds synthesized were [1-/sup 11/C] betamethyl undecanoic acid [1-/sup 11/C]BMUA, [1-/sup 11/C] betamethyl palmitic acid ([1/sup 11/C]BMPA), [1-/sup 11/C]BMHA, [1/sup 11/C] betamethyl octadecanoic acid ([1-/sup 11/C]BMOA), and [1-/sup 11/C] betamethyl heneicasanoic acid ([1-/sup 11/C]BMIA). For each compound, biodistribution in rats was performed at various times following intravenous administration. The percentage of radioactivity released as /sup 11/CO/sub 2/ was determined by trapping /sup 11/CO/sub 2/ in KOH solution. The biodistribution study demonstrates that [1-/sup 11/C]BMHA stands out as the compound with highest myocardial uptake and highest ratios of target (heart) to nontarget (blood, lungs and liver), where [1-/sup 11/C] BMUA showed lowest heart uptake at all times. The fact that for all the [C-11] betamethyl fatty acids studies some of the activity is released as /sup 11/CO/sub 2/ suggests that α and or ω-oxidation is taking place to some extent. Imaging studies in dogs with [1-/sup 11/C] BMHA and [1-/sup 11/C]BMPA showed similar behaviour. The syntheses and biodistribution results are reported

  11. The structural analysis of protein sequences based on the quasi-amino acids code

    International Nuclear Information System (INIS)

    Ping, Zhu; Xu-Qing, Tang; Zhen-Yuan, Xu

    2009-01-01

    Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Genome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system (Σ, +, *) is introduced, where Σ is the set of 64 codons. According to the characteristics of (Σ, +, *), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al (2003 J. Anhui Agricultural University 30 439), the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that (ZU, ⊕, ) is a field. Furthermore, the operational results display that the codon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysica Sinica 18(1) 87). The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of 'the 64 codon assignments of mRNA to amino acids is probably completely wrong' proposed by Yang (2006 Progress in Modern Biomedicine 6 3). (cross-disciplinary physics and related areas of science and technology)

  12. The Structure of Fats and Fatty Acid Consumption in Elderly People with Cardiovascular System Diseases.

    Science.gov (United States)

    Skop-Lewandowska, Agata; Kolarzyk, Emilia; Zając, Joanna; Jaworska, Jagoda; Załęska-Żyłka, Izabela

    2016-01-01

    Patients with cardiovascular system diseases having their origin in arteriosclerosis require special dietetic treatment. Among many nutritional components, fats in the diet (both their quantity and quality) play a very important role in primary and secondary prevention of these diseases. The aim of the study was the estimation of total fats participation (saturated fatty acids, mono- and polyunsaturated fatty acids and cholesterol) in the Daily Nutritional Ration (DNR) of elderly people with cardiovascular system diseases. The study included 128 persons (66 women and 62 men, mean age 73.2 ± 6.9) hospitalized in the 1st Clinic of Cardiology and Hypertension, UJCM in Kraków. Daily intakes of energy were estimated using the 24-h nutritional recall and Food Frequency Questionnaire. A higher consumption of fats and fatty acids was observed in men's diet than in women's diet. The percentage of energy from saturated fatty acids (10.6% M and W) was higher than dietary recommendations. The consumption of monounsaturated fatty acids was in accordance with nutritional recommendations. The participation in the diet of polyunsaturated fatty acids was insufficient versus the newest nutritional recommendations and was determined as 4.6% of energy in DNR in men and 4.1% of energy of DNR in women. The excessive amount of saturated fatty acids together with the insufficient amount of polyunsaturated fatty acids in the diet are the result of the excessive consumption of products which are a source of animal fat and insufficient consumption of plant fat, fish and seafood.

  13. Relationship between surface structure and morphology of Fe3O4/silica composite nanospheres and nucleic acid extraction

    International Nuclear Information System (INIS)

    Zeng Wen; Xu Hong; Yang Yongzhe; Gu Hongchen

    2009-01-01

    Fe 3 O 4 /silica composite nanospheres with different surface structure and morphology were synthesized by changing reaction conditions. As-synthesized nanospheres were characterized by high performance particle sizer (HPPS), transmission electron microscopy (TEM), nitrogen adsorption and thermogravimetry (TGA). Besides thoroughly characterization, the particles were used for DNA extraction. We found that the particle surface structure and morphology affected the nucleic acid extraction efficiency. When comparing different samples with the same silanol density (10 18 ), the one with a surface area of 60.37 m 2 /g extracted DNA most effectively. Also, with increasing silanol density per surface area, DNA extraction efficiency increased.

  14. Structure and spectroscopic studies of homo-and heterometallic complexes of adipic acid dihydrazide

    Science.gov (United States)

    Jeragh, Bakir; El-Asmy, Ahmed A.

    A single crystal of adipic acid dihydrazide, ADH, has been analyzed. Its reaction with Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Hg2+, Ag+, Pd2+ and/or Pt2+ gave homometallic and heterometallic complexes which are characterized by partial elemental analysis, spectra (MS, ESR, 1H NMR, electronic; IR), thermal analysis and magnetic measurements. Some complexes: Zn0.73Cu(ADH)Cl4·H2O; Zn0.71Hg0.36(ADH)Cl4·H2O; Zn0.65Cd0.46(ADH)Cl4·½H2O; Zn0.75Co0.41(ADH-2H)Cl2·3H2O; Cd0.85Co0.43(ADH)Cl4·½EtOH were isolated having nonstiochiometric metal ratios. The ligand behaves as a neutral (bidentate or tetradentate) and/or binegative tetradentate. A square-pyramid, square-planar and tetrahedral structures were proposed for the homo Co(II), Cu(II) and Ni(II) complexes, respectively. A similar and different stereochemistry around each metal ion (tetrahedral + tetrahedral; tetrahedral + square-planar; tetrahedral + tetrahedral and/or tetrahedral + octahedral) was suggested for the heterometallic complexes. Some complexes were found highly stable with stability point >240 °C; the most stable is [HgNi(ADH-2H)Cl2]. The presence of diamagnetic atom (Zn, Cd or Hg) reduces the magnetic moments and gave anomalous moments. The degradation steps and the hydrated complexes are confirmed through the TGA study. The order of covalency of [Zn0.73Cu(ADH)Cl4]·H2O, [CdCu(ADH)Cl4]·H2O and [HgCu(ADH-2H)Cl2] matches with the size of the second metal (Zn complex > Cd complex > Hg complex). Some heterometallic complexes were found nonstoichiometric through the analysis of their metal content and supported by TGA.

  15. 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.

  16. 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), enzyme load (E-1, based on substrate), water content (W-c, based on enzyme), and reaction temperature (T-e), the five most important parameters for the reaction, were chosen for the optimization. The range of each parameter was selected as follows: t(r) = 5-17 h; E-1 = 6-14 wt %; T-e = 45-65 degreesC; S......-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...

  17. A Guided Tour of the Structural Biology of Gaucher Disease: Acid-β-Glucosidase and Saposin C

    Directory of Open Access Journals (Sweden)

    Raquel L. Lieberman

    2011-01-01

    Full Text Available Mutations in both acid-β-glucosidase (GCase and saposin C lead to Gaucher disease, the most common lysosomal storage disorder. The past several years have seen an explosion of structural and biochemical information for these proteins, which have provided new insight into the biology and pathogenesis of Gaucher disease, as well as opportunities for new therapeutic directions. Nearly 20 crystal structures of GCase are now available, from different heterologous sources, complexed with different ligands in the active site, in different glycosylation states, as well as one that harbors a prevalent disease-causing mutation, N370S. For saposin C, two NMR and 3 crystal structures have been solved, each with its unique snapshot. This review focuses on the details of these structures to highlight salient common and disparate features that contribute to our current state of knowledge of this complex orphan disease.

  18. Single molecule FRET data analysis procedures for FRET efficiency determination: probing the conformations of nucleic acid structures.

    Science.gov (United States)

    Krüger, Asger Christian; Birkedal, Victoria

    2013-11-01

    Single molecule FRET microscopy is an attractive technique for studying structural dynamics and conformational diversity of nucleic acid structures. Some of its strengths are that it can follow structural changes on a fast time scale and identify conformation distributions arising from dynamic or static population heterogeneity. Here, we give a description of the experiment and data analysis procedures of this method and detail what parameters are needed for FRET efficiency calculation. Using single molecule FRET data obtained on G-quadruplex DNA structures that exhibit large conformation diversity, we illustrate that the shape of the FRET distribution changes depending on what parameters are included in the data analysis procedure. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Influence of phenylacetic acid pulses on anaerobic digestion performance and archaeal community structure in WWTP sewage sludge digesters.

    Science.gov (United States)

    Cabrol, Léa; Urra, Johana; Rosenkranz, Francisca; Kroff, Pablo Araya; Plugge, Caroline M; Lesty, Yves; Chamy, Rolando

    2015-01-01

    The effect of phenylacetic acid (PAA) pulses on anaerobic digestion (AD) performance and archaeal community structure was evaluated in anaerobic digesters treating sewage sludge from a wastewater treatment plant (WWTP). Four pilot-scale continuous stirred tank reactors were set up at a full-scale municipal WWTP in Santiago de Chile, and fed with either primary or mixed sewage sludge. AD performance was evaluated by volatile fatty acid (VFA) and biogas production monitoring. Archaeal community structure was characterized by 16S rRNA denaturing gradient gel electrophoresis and band sequencing. In the primary sludge digester, a single PAA pulse at 200 mg L(-1) was sufficient to affect AD performance and archaeal community structure, resulting in long-term VFA accumulation, reduced biogas production and community shift from dominant acetoclastic (Methanosaeta concilii) to hydrogenotrophic (Methanospirillum hungatei) methanogens. By contrast, AD performance and archaeal community structure in the mixed sludge digester were stable and resistant to repeated PAA pulses at 200 and 600 mg L(-1). This work demonstrated that the effect of PAA pulses on methanogenic activity and archaeal community structure differed according to AD substrate, and suggests that better insights of the correlations between archaeal population dynamics and functional performance could help to better face toxic shocks in AD.

  20. Aedes aegypti (Diptera: Culicidae) biting deterrence: structure-activity relationship of saturated and unsaturated fatty acids.

    Science.gov (United States)

    Ali, Abbas; Cantrell, Charles L; Bernier, Ulrich R; Duke, Stephen O; Schneider, John C; Agramonte, Natasha M; Khan, Ikhlas

    2012-11-01

    In this study we evaluated the biting deterrent effects of a series of saturated and unsaturated fatty acids against Aedes aegypti (L), yellow fever mosquito (Diptera: Culicidae) using the K & Dbioassay module system. Saturated (C6:0 to C16:0 and C18:0) and unsaturated fatty acids (C11:1 to C14:1, C16:1, C18:1, and C18:2) showed biting deterrence index (BDI) values significantly greater than ethanol, the negative control. Among the saturated fatty acids, mid chain length acids (C10:0 to C13:0) showed higher biting deterrence than short (C6:0 to C9:0) and long chain length acids (C14:0 to C18:0), except for C8:0 and C16:0 that were more active than the other short and long chain acids. The BDI values of mid chain length acids (C10:0 to C13:0) were not significantly less than N, N-diethyl-meta-toluamide (DEET), the positive control. Among the unsaturated fatty acids, C11:1 showed the highest activity (BDI = 1.05) and C18:2 had the lowest activity (BDI = 0.7). In C11:1, C12:1, and C14:1 BDI values were not significantly less than DEET. After the preliminary observations, residual activity bioassays were performed on C11:0, C12:0, C11:1, and C12:1 over a 24-h period. All the fatty acids (C11:0, C12:0, C11:1, and C12:1) and DEET showed significantly higher activity at all test intervals than the solvent control. At treatment and 1-h posttreatment, all fatty acids showed proportion not biting (PNB) values not significantly less than DEET. At 3-, 6-, and 12-h posttreatment, all fatty acids showed PNB values significantly greater than DEET. At 24-h posttreatment, only the PNB value for C12:0 was significantly higher than DEET. The dose-responses of C12:0 and DEET were determined at concentrations of 5-25 nmol/cm2. As in the residual activity bioassays, the PNB values for C12:0 and DEET at 25 nmol/cm(2) were not significantly different. However, at lower concentrations, the PNB values for C12:0 were significantly greater than DEET. These results clearly indicate that mid

  1. 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.

  2. 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...... screened for their ability to incorporate caprylic acid into the canola oil. The sn-1,3 regiospecificity toward the glycerol backbone of canola oil of the lipases with relatively higher acidolysis activity was compared by investigating the fatty acid profiles of the products. The results showed...

  3. Structure/Property Relationships of Poly(L-lactic Acid/Mesoporous Silica Nanocomposites

    Directory of Open Access Journals (Sweden)

    Javier Gudiño-Rivera

    2013-01-01

    Full Text Available Biodegradable poly(L-lactic acid (PLLA/mesoporous silica nanocomposites were prepared by grafting L-lactic acid oligomer onto silanol groups at the surface of mesoporous silica (SBA-15. The infrared results showed that the lactic acid oligomer was grafted onto the mesoporous silica. Surface characterization of mesoporous silica proved that the grafted oligomer blocked the entry of nitrogen into the mesopores. Thermal analysis measurements showed evidence that, once mixed with PLLA, SBA-15 not only nucleated the PLLA but also increased the total amount of crystallinity. Neat PLLA and its nanocomposites crystallized in the same crystal habit and, as expected, PLLA had a defined periodicity compared with the nanocomposites. This was because the grafted macromolecules on silica tended to cover the lamellar crystalline order. The g-SBA-15 nanoparticles improved the tensile moduli, increasing also the tensile strength of the resultant nanocomposites. Overall, the silica concentration tended to form a brittle material.

  4. Crystal structure of olivetolic acid: a natural product from Cetrelia sanguinea (Schaer.).

    Science.gov (United States)

    Ismed, Friardi; Farhan, Aulia; Bakhtiar, Amri; Zaini, Erizal; Nugraha, Yuda Prasetya; Dwichandra Putra, Okky; Uekusa, Hidehiro

    2016-11-01

    The title compound, C 12 H 16 O 4 (systematic name: 2,4-dihy-droxy-6-pentyl-benzoic acid) is a natural product isolated from C. sanguinea (Schaer.) and is reported to have various pharmacological activities. The mol-ecule is approximately planar (r.m.s. deviation for the non-H atoms = 0.096 Å) and features an intra-molecular O-H⋯O hydrogen bond. In the crystal, each olivetolic acid mol-ecule is connected to three neighbours via O-H⋯O hydrogen bonds, generating (10-1) sheets. This crystal is essentially isostructural with a related resorcinolic acid with a longer alkyl chain.

  5. Semi-Empirical Predictions on the Structure and Properties of ent-Kaurenoic Acid and Derivatives

    Directory of Open Access Journals (Sweden)

    Jose Isagani B. Janairo

    2011-01-01

    Full Text Available The physicochemical properties of ent- kaurenoic acid model derivatives, which possibly influence its therapeutic application, were calculated. Results revealed that the molecule possess favourable attributes which renders it possible to be considered as a drug lead only that its very hydrophobic nature can result to poor bioavailabilty, low absorption and poor systemic circulation. In silico simulations revealed that this setback can be overcome by introduction of hydroxyl group to the tertiary carbon of ent-kaurenoic acid employing m-CPBA catalyzed hydroxylation, thus, unleashing its full drug potency. Moreover, molecular similarity analyses derived from semi-empirical calculations between ent-kaurenoic acid and a set of kaurane diterpenoids showed differences in hydrophobic complementarity, size and electronic properties despite possessing nearly identical molecular frameworks, thus, arriving in a generalization for their observed mechanistic differences on acting on different targets.

  6. 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.

  7. 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.

  8. A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution

    Science.gov (United States)

    Zhou, J.; Krueger, S.; Gregurick, S. K.

    2005-01-01

    We present a theoretical method to calculate the small angle neutron scattering profile of nucleic acid structures in solution. Our approach is sensitive to the sequence and the structure of the nucleic acid. In order to test our approach, we apply this method to the calculation of the experimental scattered intensity of the decamer d(CCAACGTTGG)2 in H2O. This sequence was specifically chosen for this study as it is believed to adopt a canonical B-form structure in 0.3 M NaCl. We find that not only will our methodology reproduce the experimental scattered intensity for this sequence, but our method will also discriminate between B-, A- and Z-form DNA. By studying the scattering profile of this structure in 0.5 and 1.0 M NaCl, we are also able to identify tetraplex and other similar oligomers formation and to model the complex using the experimental scattering data in conjunction with our methodology. PMID:16282586

  9. Aedes aegypti (Diptera: Culicidae) Biting Deterrence: Structure-Activity Relationship of Saturated and Unsaturated Fatty Acids

    Science.gov (United States)

    2012-11-01

    C18:0), oleic acid (C18:1), and linoleic acid (C18:2) were all purchased from SigmaÐAldrich (St. Louis, MO). Insects . Ae. aegypti used in Klun...place where the insects feed in its absence. This is contrasted by re- pellent,which is achemical that causes insects tomake oriented movement away...after which they were collected back into the module. Mosquitoes were squashed and the presence of red dye (or not) in the gut was used as an indicator

  10. 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.

  11. 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.

  12. Numerical simulation of the solvate structures of acetylsalicylic acid in supercritical carbon dioxide containing polar co-solvents

    Science.gov (United States)

    Petrenko, V. E.; Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.; Kumeev, R. S.; Golubev, V. A.

    2016-07-01

    Hydrogen-bonded complexes of acetylsalicylic acid with polar co-solvents in supercritical carbon dioxide, modified by methanol, ethanol, and acetone of 0.03 mole fraction concentration, are studied by numerical methods of classical molecular dynamics simulation and quantum chemical calculations. The structure, energy of formation, and lifetime of hydrogen-bonded complexes are determined, along with their temperature dependences (from 318 to 388 K at constant density of 0.7 g cm-3). It is shown that the hydrogen bonds between acetylsalicylic acid and methanol are most stable at 318 K and are characterized by the highest value of absolute energy. At higher supercritical temperatures, however, the longest lifetime is observed for acetylsalicylic acid-ethanol complexes. These results correlate with the known literature experimental data showing that the maximum solubility of acetylsalicylic acid at density values close to those considered in this work and at temperatures of 318 and 328 K is achieved when using methanol and ethanol as co-solvents, respectively.

  13. Changes in the structure of water in aqueous solutions of acetic acid, depending on concentration and temperature according to densitometry, viscosimetry, and IR spectroscopy data

    Science.gov (United States)

    Masimov, E. A.; Khasanov, G. Sh.; Pashaev, B. G.

    2013-06-01

    The structural features of aqueous solutions of acetic acid are studied by means of viscosimetry, densimetry, and IR spectroscopy within the temperature range of 283.15-333.15 K and a concentration range of 0-80%. The results from our experiments are used to calculate the parameters of viscous flow activation, the structural temperature, the partial molar volume of acetic acid in the solution, the thermal expansion coefficient, and the energies and lengths of the hydrogen bonds between water molecules. The concentration dependences of these parameters are analyzed. Based on the obtained results, we conclude that acetic acid disrupts the structure of water.

  14. Corrosion behaviour and structure of the surface layer formed on austempered ductile iron in concentrated sulphuric acid

    Energy Technology Data Exchange (ETDEWEB)

    Krawiec, H. [AGH University of Science and Technology, Department of Foundry Engineering, ul. Reymonta 23, 30-059 Cracow (Poland)]. E-mail: krawiec@uci.agh.edu.pl; Stypula, B. [AGH University of Science and Technology, Department of Foundry Engineering, ul. Reymonta 23, 30-059 Cracow (Poland); Stoch, J. [Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences (PAS), ul. Niezapominajek 8, 30-239 Cracow (Poland); Mikolajczyk, M. [Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences (PAS), ul. Niezapominajek 8, 30-239 Cracow (Poland)

    2006-03-15

    The aim of this paper is to investigate the structure of the surface layer formed on austempered ductile iron (ADI) after exposure to hot concentrated sulphuric acid at the open circuit potential value (OCP). The results derived from polarization measurements carried out in sulphuric acid at a temperature of 90 deg. C show that anodic dissolution of ADI is divided into three stages (corresponding to three anodic dissolution peaks). The structure of the layer formed on alloys at 90 deg. C at OCP was investigated using X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). SEM analysis shows that the main elements of the surface layer are iron, silicon, oxygen, sulphur, and carbon. The binding energy recorded in individual bands indicates that the surface layer includes mainly SiO{sub 2} and FeOOH. The presence of sulphur at the lower oxidation state (S{sup 2-}) indicates that sulphuric acid undergoes reduction during this process. The corrosion resistance of these alloys is connected with the presence of SiO{sub 2} in the surface layer.

  15. Influence of Poly(styrene-co-maleic acid) Copolymer Structure on the Properties and Self-Assembly of SMALP Nanodiscs.

    Science.gov (United States)

    Hall, Stephen C L; Tognoloni, Cecilia; Price, Gareth J; Klumperman, Bert; Edler, Karen J; Dafforn, Tim R; Arnold, Thomas

    2018-01-16

    Polymer stabilized nanodiscs are self-assembled structures composed of a polymer belt that wraps around a segment of lipid bilayer, and as such are capable of encapsulating membrane proteins directly from the cell membrane. To date, most studies on these nanodiscs have used poly(styrene-co-maleic acid) (SMA) with the term SMA-lipid particles (SMALPs) coined to describe them. In this study, we have determined the physical and thermodynamic properties of such nanodiscs made with two different SMA copolymers. These include a widely used and commercially available statistical poly(styrene-co-maleic acid) copolymer (coSMA) and a reversible addition-fragmentation chain transfer synthesized copolymer with narrow molecular weight distribution and alternating styrene and maleic acid groups with a polystyrene tail, (altSMA). We define phase diagrams for each polymer, and show that, regardless of polymer topological structure, self-assembly is driven by the free energy change associated with the polymers. We also show that nanodisc size is polymer dependent, but can be modified by varying polymer concentration. The thermal stability of each nanodisc type is similar, and both can effectively solubilize proteins from the E. coli membrane. These data show the potential for the development of different SMA polymers with controllable properties to produce nanodiscs that can be optimized for specific applications and will enable more optimized and widespread use of the SMA-based nanodiscs in membrane protein research.

  16. 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.

  17. 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

  18. A Novel Coordination Polymer Based on 4,4'-(Hexauoroisopropylidene)diphthalic Acid: Synthesis, Structure and Physical Properties

    International Nuclear Information System (INIS)

    Wang, Jun; Tao, Jianqing; Xu, Xiaojuan; Tan, Chunyun

    2012-01-01

    The design and synthesis of coordination polymers is an attractive area of research, not only owing to their diverse topology and intriguing structures but also due to their potential applications in many fields, such as ion-exchange, catalysis, luminescence, magnets, and gas storage. The mainstream method of constructing such coordination polymers is to utilize organic ligands with aromatic polycarboxylate groups, because of their excellent coordination capability and flexible coordination patterns. Among them, aromatic polycarboxylic derivatives, such as 1,2,4,5-benzenetetracarboxylic acid, 4,4'-oxydiphthalic acid, 4,4'-(hexauoroisopropylidene) diphthalic acid (H 4 FA), and so on, have been extensively used to prepare coordination polymers. Meanwhile, the flexible 1,4-bis(1,2,4-triazol-1-ylmethyl)-benzene (BTX) as an excellent derivative of triazole not only possesses the merits of triazole, but also can adopt different conformations compared with the corresponding 1,2,4-triazole ligand on the basis of the relative orientations of its CH 2 groups.10 Taking these into consideration, we explored the self-assembly of Cd(II) ion, H 4 FA, and BTX under hydrothermal conditions, and obtained a novel 3D coordination polymer: [Cd 3 (BTX) 2 (HFA) 2 · 2 H 2 O] n . Herein, we report the synthesis, crystal structure, and physical properties

  19. Pulse electrodeposition to prepare core-shell structured AuPt@Pd/C catalyst for formic acid fuel cell application

    Science.gov (United States)

    Lu, Xueyi; Luo, Fan; Song, Huiyu; Liao, Shijun; Li, Hualing

    2014-01-01

    A novel core-shell structured AuPt@Pd/C catalyst for the electrooxidation of formic acid is synthesized by a pulse electrodeposition process, and the AuPt core nanoparticles are obtained by a NaBH4 reduction method. The catalyst is characterized with X-ray powder diffraction and transmission electron microscopy, thermogravimetric analysis, cyclic voltammetry, CO stripping and X-ray photoelectron spectroscopy. The core-shell structure of the catalyst is revealed by the increase in particle size resulting from a Pd layer covering the AuPt core, and by a negative shift in the CO stripping peaks. The addition of a small amount of Pt improves the dispersion of Au and results in smaller core particles. The catalyst's activity is evaluated by cyclic voltammetry in formic acid solution. The catalyst shows excellent activity towards the anodic oxidation of formic acid, the mass activity reaches 4.4 A mg-1Pd and 0.83 A mg-1metal, which are 8.5 and 1.6 times that of commercial Pd/C. This enhanced electrocatalytic activity could be ascribed to the good dispersion of Au core particles resulting from the addition of Pt, as well as to the interaction between the Pd shell layer and the Au and Pt in the core nanoparticles.

  20. Crystal structures of serum albumins from domesticated ruminants and their complexes with 3,5-diiodosalicylic acid.

    Science.gov (United States)

    Bujacz, Anna; Talaj, Julita A; Zielinski, Kamil; Pietrzyk-Brzezinska, Agnieszka J; Neumann, Piotr

    2017-11-01

    Serum albumin (SA) is the most abundant protein in plasma and is the main transporter of molecules in the circulatory system of all vertebrates, with applications in medicine, the pharmaceutical industry and molecular biology. It is known that albumins from different organisms vary in sequence; thus, it is important to know the impact of the amino-acid sequence on the three-dimensional structure and ligand-binding properties. Here, crystal structures of ovine (OSA) and caprine (CSA) serum albumins, isolated from sheep and goat blood, are described, as well those of their complexes with 3,5-diiodosalicylic acid (DIS): OSA-DIS (2.20 Å resolution) and CSA-DIS (1.78 Å resolution). The ligand-free OSA structure was determined in the trigonal space group P3 2 21 at 2.30 Å resolution, while that of CSA in the orthorhombic space group P2 1 2 1 2 1 was determined at 1.94 Å resolution. Both albumins are also capable of crystallizing in the triclinic space group P1, giving isostructural crystals that diffract to around 2.5 Å resolution. A comparison of OSA and CSA with the closely related bovine serum albumin (BSA) shows both similarities and differences in the distribution of DIS binding sites. The investigated serum albumins from domesticated ruminants in their complexes with DIS are also compared with the analogous structures of equine and human serum albumins (ESA-DIS and HSA-DIS). Surprisingly, despite 98% sequence similarity, OSA binds only two molecules of DIS, whereas CSA binds six molecules of this ligand. Moreover, the binding of DIS to OSA and CSA introduced changes in the overall architecture of the proteins, causing not only different conformations of the amino-acid side chains in the binding pockets, but also a significant shift of the whole helices, changing the volume of the binding cavities.

  1. Phase Structure Transition and Properties of Salt-Free Phosphoric Acid/Non-ionic Surfactants in Water.

    Science.gov (United States)

    Wang, Lihuan; Zhao, Wenrong; Dong, Renhao; Hao, Jingcheng

    2016-08-23

    Precise control of phase structure transition for the synthesis of multi-dimensional soft materials is a fascinating target in amphiphilic molecule self-assembly. Here, we demonstrate a spontaneous formation of a closely packed lamellar phase consisting of uni- and multi-lamellar vesicles through the incorporation of a small amount of an extractant, di(2-ethylhexyl)phosphoric acid (DEHPA), into the highly swollen, planar lamellar phase of a non-ionic tetraethylene glycol monododecyl ether (C12EO4) surfactant in water. It is figured out that the introduction of negative membrane charges results in the electrostatic repulsion among the lamellae, which suppresses the Helfrich undulation and induces a phase structure transition from planar lamellae to closely packed vesicles. Our results provide important insight into amphiphilic molecule self-assembly, where additives and pH can satisfy the opportunities for the precise tuning of the lamellar structures, which makes a way for the development of lamellar soft materials.

  2. Structural Insights into Maize Viviparous14, a Key Enzyme in the Biosynthesis of the Phytohormone Abscisic Acid W

    Energy Technology Data Exchange (ETDEWEB)

    Messing, S.; Gabelli, S; Echeverria, I; Vogel, J; Guan, J; Tan, B; Klee, H; McCarty, D; Amzela, M

    2010-01-01

    The key regulatory step in the biosynthesis of abscisic acid (ABA), a hormone central to the regulation of several important processes in plants, is the oxidative cleavage of the 11,12 double bond of a 9-cis-epoxycarotenoid. The enzyme viviparous14 (VP14) performs this cleavage in maize (Zea mays), making it a target for the rational design of novel chemical agents and genetic modifications that improve plant behavior through the modulation of ABA levels. The structure of VP14, determined to 3.2-{angstrom} resolution, provides both insight into the determinants of regio- and stereospecificity of this enzyme and suggests a possible mechanism for oxidative cleavage. Furthermore, mutagenesis of the distantly related CCD1 of maize shows how the VP14 structure represents a template for all plant carotenoid cleavage dioxygenases (CCDs). In addition, the structure suggests how VP14 associates with the membrane as a way of gaining access to its membrane soluble substrate.

  3. Structural Insights into Maize Viviparous14, a Key Enzyme in the Biosynthesis of the Phytohormone Abscisic Acid

    Energy Technology Data Exchange (ETDEWEB)

    Messing, Simon A.J.; Gabelli, Sandra B.; Echeverria, Ignacia; Vogel, Jonathan T.; Guan, Jiahn Chou; Tan, Bao Cai; Klee, Harry J.; McCarty, Donald R.; Amzel, L. Mario (JHU); (Florida)

    2011-09-06

    The key regulatory step in the biosynthesis of abscisic acid (ABA), a hormone central to the regulation of several important processes in plants, is the oxidative cleavage of the 11,12 double bond of a 9-cis-epoxycarotenoid. The enzyme viviparous14 (VP14) performs this cleavage in maize (Zea mays), making it a target for the rational design of novel chemical agents and genetic modifications that improve plant behavior through the modulation of ABA levels. The structure of VP14, determined to 3.2-{angstrom} resolution, provides both insight into the determinants of regio- and stereospecificity of this enzyme and suggests a possible mechanism for oxidative cleavage. Furthermore, mutagenesis of the distantly related CCD1 of maize shows how the VP14 structure represents a template for all plant carotenoid cleavage dioxygenases (CCDs). In addition, the structure suggests how VP14 associates with the membrane as a way of gaining access to its membrane soluble substrate.

  4. Synthesis of Framework Isomer MOFs Containing Zinc and 4-Tetrazolyl Benzenecarboxylic Acid via a Structure Directing Solvothermal Approach

    Directory of Open Access Journals (Sweden)

    Carlos Ordonez

    2015-04-01

    Full Text Available The solvothermal synthesis of framework isomers was carried out using the hybrid carboxylate and tetrazolate functional ligand, 4-tetrazolyl benzenecarboxylic acid (H2TBC, TBC = 4-tetrazolyl benzenecarboxylate and zinc. H2TBC was also synthesized with the solvothermal approach, and is referred herein as structure 1. Using single-crystal X-ray diffraction, we found that the tetrazolate groups of TBC show an unusual “opposite-on” coordination mode with zinc. Three previously characterized metal-organic frameworks (MOFs were obtained by systematically changing the solvents of the H2TBC-Zn reaction, (1 ZnTBC, 2, which has a non-porous structure; (2 Zn2(TBC2(H2O, 3, which has an amphiphilic pore structure and (3 Zn2(TBC2{guest}, 4, which is porous and has channels containing uncoordinated N heteroatoms. Fluorescence spectra of 4 reveal a strong blue emission mainly from the TBC ligands.

  5. Bioreduction of Uranium(VI) Complexed with Citric Acid by Clostridia Affects its Structure and Mobility

    International Nuclear Information System (INIS)

    Francis, A.; Dodge, C.

    2008-01-01

    Uranium contamination of the environment from mining and milling operations, nuclear-waste disposal, and ammunition use is a widespread global problem. Natural attenuation processes such as bacterial reductive precipitation and immobilization of soluble uranium is gaining much attention. However, the presence of naturally occurring organic ligands can affect the precipitation of uranium. Here, we report that the anaerobic spore-forming bacteria Clostridia, ubiquitous in soils, sediments, and wastes, capable of reduction of Fe(III) to Fe(II), Mn(IV) to Mn(II), U(VI) to U(IV), Pu(IV) to Pu(III), and Tc(VI) to Tc(IV); reduced U(VI) associated with citric acid in a dinuclear 2:2 U(VI):citric acid complex to a biligand mononuclear 1:2 U(IV):citric acid complex, which remained in solution, in contrast to reduction and precipitation of uranium. Our findings show that U(VI) complexed with citric acid is readily accessible as an electron acceptor despite the inability of the bacterium to metabolize the complexed organic ligand. Furthermore, it suggests that the presence of organic ligands at uranium-contaminated sites can affect the mobility of the actinide under both oxic and anoxic conditions by forming such soluble complexes.

  6. Structural diversity of solid dispersions of acetylsalicylic acid as seen by solid-state NMR

    Czech Academy of Sciences Publication Activity Database

    Policianová, Olivia; Brus, Jiří; Hrubý, Martin; Urbanová, Martina; Zhigunov, Alexander; Kredatusová, Jana; Kobera, Libor

    2014-01-01

    Roč. 11, č. 2 (2014), s. 516-530 ISSN 1543-8384 R&D Projects: GA ČR GPP106/11/P426 Institutional support: RVO:61389013 Keywords : solid dispersions * acetylsalicylic acid * polymers Subject RIV: FR - Pharmacology ; Medidal Chemistry Impact factor: 4.384, year: 2014

  7. Ammonia-oxidizing activity and microbial community structure in acid tea (Camellia sinensis) orchard soil

    Science.gov (United States)

    Okamura, K.; Takanashi, A.; Yamada, T.; Hiraishi, A.

    2012-03-01

    The purpose of this study was to determine the ammonia-oxidizing activity and the phylogentic composition of microorganisms involved in acid tea (Camellia sinensis) orchard soil. All soil samples were collected from three sites located in Tahara and Toyohashi, Aichi Prefecture, Japan. The potential nitrification rate (PNR) was measured by the chlorate inhibition method. The soil pH of tea orchards studied ranged from 2.78 to 4.84, differing significantly from sample to sample, whereas that of meadow and unplanted fields ranged from 5.78 to 6.35. The PNR ranged from 0.050 to 0.193 μg NO2--Ng-1 h-1 and were positively correlated with the soil pH (r2 = 0.382, p<0.001). Bulk DNA was extracted from a tea orchard soil (pH 4.8; PNR, 0.078 μg NO2--Ng-1 h-1) and subjected to PCR-aided clone library analyses targeting archaeal and bacterial amoA genes. The detected archaeal clones separated from the cluster of the 'Soil clones' and tightly clustered with the clones originating from other acidic soil environments including the Chinese tea orchard soil. These results suggest that the specific archaeal populations dominate as the ammonia oxidizers in acid tea-orchard soils and possibly other acid soils, independent of geographic locations, which results from the adaptation to specific ecological niches.

  8. Ammonia-oxidizing activity and microbial community structure in acid tea (Camellia sinensis) orchard soil

    International Nuclear Information System (INIS)

    Okamura, K; Yamada, T; Hiraishi, A; Takanashi, A

    2012-01-01

    The purpose of this study was to determine the ammonia-oxidizing activity and the phylogentic composition of microorganisms involved in acid tea (Camellia sinensis) orchard soil. All soil samples were collected from three sites located in Tahara and Toyohashi, Aichi Prefecture, Japan. The potential nitrification rate (PNR) was measured by the chlorate inhibition method. The soil pH of tea orchards studied ranged from 2.78 to 4.84, differing significantly from sample to sample, whereas that of meadow and unplanted fields ranged from 5.78 to 6.35. The PNR ranged from 0.050 to 0.193 μg NO 2 - -Ng -1 h -1 and were positively correlated with the soil pH (r 2 0.382, p 2 - -Ng -1 h -1 ) and subjected to PCR-aided clone library analyses targeting archaeal and bacterial amoA genes. The detected archaeal clones separated from the cluster of the 'Soil clones' and tightly clustered with the clones originating from other acidic soil environments including the Chinese tea orchard soil. These results suggest that the specific archaeal populations dominate as the ammonia oxidizers in acid tea-orchard soils and possibly other acid soils, independent of geographic locations, which results from the adaptation to specific ecological niches.

  9. Volatile fatty acids influence on the structure of microbial communities producing PHAs

    Directory of Open Access Journals (Sweden)

    Slawomir Ciesielski

    2014-06-01

    Full Text Available Polyhydroxyalkanoates (PHAs can be produced by microorganisms and are a biodegradable alternative to fossil-fuel based plastics. Currently, the focus is on reducing production costs by exploring alternative substrates for PHAs production, and on producing copolymers which are less brittle than monomers. Accordingly, this study used a substrate consisting of wastewater from waste-glycerol fermentation, supplemented with different amounts of acetic and propionic acids. These substrates were used to feed mixed microbial communities enriched from activated sludge in a sequencing batch reactor. A reactor supplemented with 2 mL of acetic acid produced 227.8 mg/L of a homopolymer of hydroxybutyrate (3HB; 4 mL of acetic acid produced 279.8 mg/L 3HB; whereas 4 mL of propionic acid produced 673.0 mg/L of a copolymer of 3HB and 3HV (hydroxyvalerate. Ribosomal Intergenic Spacer Analysis (RISA was used to show the differences between the communities created in the reactors. Thauera species predominated in biomass that produced 3HB; Paracoccus denitrificans in the biomass that produced 3HB-co-3HV. Because P. denitrificans produced the more desirable copolymer, it may be advantageous to promote its growth in PHAs-producing reactors by adding propionate.

  10. Volatile fatty acids influence on the structure of microbial communities producing PHAs.

    Science.gov (United States)

    Ciesielski, Slawomir; Przybylek, Grzegorz

    2014-01-01

    Polyhydroxyalkanoates (PHAs) can be produced by microorganisms and are a biodegradable alternative to fossil-fuel based plastics. Currently, the focus is on reducing production costs by exploring alternative substrates for PHAs production, and on producing copolymers which are less brittle than monomers. Accordingly, this study used a substrate consisting of wastewater from waste-glycerol fermentation, supplemented with different amounts of acetic and propionic acids. These substrates were used to feed mixed microbial communities enriched from activated sludge in a sequencing batch reactor. A reactor supplemented with 2 mL of acetic acid produced 227.8 mg/L of a homopolymer of hydroxybutyrate (3 HB); 4 mL of acetic acid produced 279.8 mg/L 3 HB; whereas 4 mL of propionic acid produced 673.0 mg/L of a copolymer of 3 HB and 3 HV (hydroxyvalerate). Ribosomal Intergenic Spacer Analysis (RISA) was used to show the differences between the communities created in the reactors. Thauera species predominated in biomass that produced 3 HB; Paracoccus denitrificans in the biomass that produced 3 HB-co-3 HV. Because P. denitrificans produced the more desirable copolymer, it may be advantageous to promote its growth in PHAs-producing reactors by adding propionate.

  11. Structure of Acidic pH Dengue Virus Showing the Fusogenic Glycoprotein Trimers

    NARCIS (Netherlands)

    Zhang, Xinzheng; Sheng, Ju; Austin, S. Kyle; Hoornweg, Tabitha E.; Smit, Jolanda M.; Kuhn, Richard J.; Diamond, Michael S.; Rossmann, Michael G.

    Flaviviruses undergo large conformational changes during their life cycle. Under acidic pH conditions, the mature virus forms transient fusogenic trimers of E glycoproteins that engage the lipid membrane in host cells to initiate viral fusion and nucleocapsid penetration into the cytoplasm. However,

  12. Some aspects of lamellar structure in various green leaf particles, indicated by oleic acid effects

    NARCIS (Netherlands)

    Terpstra, Willem

    1. (1) The influence of oleic acid on “whole chloroplasts and large fragments”, isolated from spinach or endive leaves, was compared to that on Photosystem I (PS I) and PS I+II particles, probably stroma lamellae, isolated from the same leaves. 2. (2) Photochemical activity (Hill reaction and

  13. Determination of the Nucleic Acid Adducts Structure at the Nucleoside/Nucleotide Level by NMR Spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Dračínský, Martin; Pohl, Radek

    2015-01-01

    Roč. 28, č. 2 (2015), s. 155-165 ISSN 0893-228X R&D Projects: GA ČR GA13-24880S Institutional support: RVO:61388963 Keywords : NMR spectroscopy * nucleic acids * nucleotides Subject RIV: CC - Organic Chemistry Impact factor: 3.025, year: 2015

  14. Radiochemically pure [1-14C]valproic acid--a mixture of labeled structural isomers

    International Nuclear Information System (INIS)

    Dickinson, R.G.; Wood, B.T.; Kluck, R.M.; Hooper, W.D.

    1986-01-01

    Ongoing studies of the disposition of valproic acid (VPA) and its glucuronide conjugate required the radiolabeled drug for greater sensitivity and tracing of oxidation metabolites. [1- 14 C]VPA hereinafter called LABEL (radiochemical purity greater than 98% as determined by paper and thin layer chromatography) was purchased from Amersham International, U.K. Quantitative analysis of VPA and VPA-glucuronide in bile and urine samples from rats given VPA and tracer LABEL by our standard gas chromatographic assay showed gross discrepancies with the results obtained by liquid scintillation counting of the same extracts. Examination of the purity of LABEL was therefore undertaken. Equilibration of LABEL between various organic-aqueous solvent pairs was identical to that of authentic VPA. However, gas chromatographic-mass spectrometric analysis of the trimethylsilyl derivative of LABEL revealed it to be a mixture of labeled 2-methylheptanoic acid (approximately 60%), 2-ethylhexanoic acid (approximately 30%), and 2-propylpentanoic acid (i.e., VPA, 5-10%). The origin of the isomers of VPA in LABEL was logically traced to the synthetic procedure--coupling of the Grignard reagent of (an isomeric mixture of 2-, 3-, and 4-) chloroheptane(s) with [ 14 C]carbon dioxide. This result highlights the inadequacy of the quality control procedures used and reinforces the necessity for caution in accepting the quoted purity of radiolabeled drugs

  15. Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.

    Science.gov (United States)

    Billoud, B; Kontic, M; Viari, A

    1996-01-01

    At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usually dedicated to particular structures and are written using general purpose programming languages through a complex and time consuming process where the biological problem of defining the structure and the computer engineering problem of looking for it are intimately intertwined. In this paper, we describe a general representation of structures, suitable for database scanning, together with a programming language, Palingol, designed to manipulate it. Palingol has specific data types, corresponding to structural elements-basically helices-that can be arranged in any way to form a complex structure. As a consequence of the declarative approach used in Palingol, the user should only focus on 'what to search for' while the language engine takes care of 'how to look for it'. Therefore, it becomes simpler to write a scanning program and the structural constraints that define the required structure are more clearly identified. PMID:8628670

  16. Very long-chain fatty acids support synaptic structure and function in the mammalian retina

    Directory of Open Access Journals (Sweden)

    Hopiavuori Blake R.

    2016-01-01

    Full Text Available Elongation of Very Long chain fatty acids-like 4 (ELOVL4 is a fatty acid elongase responsible for the biosynthesis of very long chain (VLC; ≥ C26 fatty acids in the retina, brain, skin, Meibomian gland, and testes. Heterozygous inheritance of mutant ELOVL4 causes juvenile macular degeneration in autosomal dominant Stargardt-like macular dystrophy (STGD3. Retinal photoreceptors are enriched with VLC polyunsaturated fatty acids (VLC-PUFAs, which have been shown by our group and others to be necessary for the survival of rod photoreceptors. Our group performed a series of studies using mice conditionally depleted of retinal Elovl4 (KO aimed at understanding the role of VLC-PUFAs in long-term retinal health and function, focusing on the role of these fatty acids in mediating synaptic function between the photoreceptors and the rest of the neural retina. The absence of VLC-PUFA from the retina of KO mice resulted in a marked decrease in retinal b-wave responses of the electroretinogram as well as a decrease in the amplitude of the oscillatory potentials mediated by the neural retina. Although there were no measureable differences between KO and wild type (WT mice in either pre-synaptic rod calcium channel function or post-synaptic bipolar cell glutamate receptor responses, ultrastructural analysis revealed a marked decrease in the diameter of synaptic vesicles in rod terminals. Recent quantification suggests that this decrease in synaptic vesicle size due to the absence of VLC-PUFAs in KO mice, and the consequent decrease in glutamate content, could account for the decrease in b-wave response amplitudes that were previously measured in these animals.

  17. 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.

  18. 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...

  19. 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.

  20. 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

  1. 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.

  2. Campylobacter jejuni fatty acid synthase II: Structural and functional analysis of [beta]-hydroxyacyl-ACP dehydratase (FabZ)

    Energy Technology Data Exchange (ETDEWEB)

    Kirkpatrick, Andrew S.; Yokoyama, Takeshi; Choi, Kyoung-Jae; Yeo, Hye-Jeong; (Houston)

    2009-08-14

    Fatty acid biosynthesis is crucial for all living cells. In contrast to higher organisms, bacteria use a type II fatty acid synthase (FAS II) composed of a series of individual proteins, making FAS II enzymes excellent targets for antibiotics discovery. The {beta}-hydroxyacyl-ACP dehydratase (FabZ) catalyzes an essential step in the FAS II pathway. Here, we report the structure of Campylobacter jejuni FabZ (CjFabZ), showing a hexamer both in crystals and solution, with each protomer adopting the characteristic hot dog fold. Together with biochemical analysis of CjFabZ, we define the first functional FAS II enzyme from this pathogen, and provide a framework for investigation on roles of FAS II in C. jejuni virulence

  3. 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.

  4. 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.

  5. 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

  6. Effects of synthesis conditions on chemical structures and physical properties of copolyesters from lactic acid, ethylene glycol and dimethyl terephthalate

    Directory of Open Access Journals (Sweden)

    2009-07-01

    Full Text Available Lactic acid/ethylene terephthalate copolyesters were synthesized by the standard melt polycondensation of lactic acid (L, ethylene glycol (EG and dimethyl-terephthalate (DMT. Effects of reaction temperatures and types of catalysts on the structures and properties of the copolymers were examined. In addition, feasibility of promoting the copolymerization process by a novel synthesis step of using thermo-stabilizers was investigated. The results show that a reaction temperature of higher than 180°C is necessary to produce copolymers with appreciable molecular weight. However, degradation was observed when the reaction temperature is higher than 220°C. Triphenyl phosphate (TPP shows promising results as a potential thermo-stabilizer to minimize this problem. It was found that Sb2O3 and Tin(II octoate are most effective among 4 types of catalysts employed in this study. 1H-NMR results indicate that copolymers have a random microstructure composed mainly of single L units alternately linked with ET blocks at various sequential lengths. The longer ET sequence in the chain structure leads to the increase in melting temperature of the copolymer. TGA results show that the resulting copolymers possessed greater thermal stability than commercially-available aliphatic PLA, as a result of the inclusion of T (terephthalate units in the chain structure.

  7. 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.

  8. 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

  9. Effect of the structural features of hydrochloric acid-deamidated wheat gluten on its susceptibility to enzymatic hydrolysis.

    Science.gov (United States)

    Cui, Chun; Hu, Qingling; Ren, Jiaoyan; Zhao, Haifeng; You, Lijun; Zhao, Mouming

    2013-06-19

    The effect of the structural features of hydrochloric acid-deamidated wheat gluten with different degrees of deamidation (DDs) on the susceptibility to enzymatic hydrolysis by pancreatin was investigated. The wheat gluten deamidated by hydrochloric acid with a DD of 55% revealed the highest susceptibility to enzymatic hydrolysis as evaluated by the hydrolysis degree and nitrogen solubility index of the hydrolysates. An increase of peptides with MW below 3000 Da was observed as the DD increased. Raman spectra in the 1740-1800 cm⁻¹ and 521-530 cm⁻¹ range suggested that wheat gluten had taken off the deamidation with different DDs and that the disulfide bond had disrupted the sulfhydryl groups with different intensities, respectively. Results from the deconvolution of the amide I region of FTIR spectra in the 1600-1700 cm⁻¹ range showed that the content of the α-helix decreased and that the content of the β-turn and β-sheet increased with increasing DDs, which improved the molecular structure and flexibility of wheat gluten. A scanning electron microscope (SEM) revealed that the image of HDG-55% presented the smoothest surface and the least uniform pore, enabling the sample to be more susceptible to enzymatic hydrolysis. The above information will enable us to better understand the effect of structure on the susceptibility of deamidated wheat gluten.

  10. Characterization of gene-activated human acid-beta-glucosidase: crystal structure, glycan composition, and internalization into macrophages.

    Science.gov (United States)

    Brumshtein, Boris; Salinas, Paul; Peterson, Brian; Chan, Victor; Silman, Israel; Sussman, Joel L; Savickas, Philip J; Robinson, Gregory S; Futerman, Anthony H

    2010-01-01

    Gaucher disease, the most common lysosomal storage disease, can be treated with enzyme replacement therapy (ERT), in which defective acid-beta-glucosidase (GlcCerase) is supplemented by a recombinant, active enzyme. The X-ray structures of recombinant GlcCerase produced in Chinese hamster ovary cells (imiglucerase, Cerezyme) and in transgenic carrot cells (prGCD) have been previously solved. We now describe the structure and characteristics of a novel form of GlcCerase under investigation for the treatment of Gaucher disease, Gene-Activated human GlcCerase (velaglucerase alfa). In contrast to imiglucerase and prGCD, velaglucerase alfa contains the native human enzyme sequence. All three GlcCerases consist of three domains, with the active site located in domain III. The distances between the carboxylic oxygens of the catalytic residues, E340 and E235, are consistent with distances proposed for acid-base hydrolysis. Kinetic parameters (K(m) and V(max)) of velaglucerase alfa and imiglucerase, as well as their specific activities, are similar. However, analysis of glycosylation patterns shows that velaglucerase alfa displays distinctly different structures from imiglucerase and prGCD. The predominant glycan on velaglucerase alfa is a high-mannose type, with nine mannose units, while imiglucerase contains a chitobiose tri-mannosyl core glycan with fucosylation. These differences in glycosylation affect cellular internalization; the rate of velaglucerase alfa internalization into human macrophages is at least 2-fold greater than that of imiglucerase.

  11. Structural elucidation of the hormonal inhibition mechanism of the bile acid cholate on human carbonic anhydrase II

    International Nuclear Information System (INIS)

    Boone, Christopher D.; Tu, Chingkuang; McKenna, Robert

    2014-01-01

    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 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

  12. 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.

  13. Structure of rat acidic fibroblast growth factor at 1.4 A resolution

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Artur

    2007-01-01

    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 A resolution X-ray structure of rat FGF1 is presented. Two molecules are present...

  14. Crystal structure of (E-4-{2-[4-(allyloxyphenyl]diazenyl}benzoic acid

    Directory of Open Access Journals (Sweden)

    Md. Lutfor Rahman

    2014-12-01

    Full Text Available The title compound, C16H14N2O3, has an E conformation about the azobenzene [—N=N– = 1.2481 (16 Å] linkage. The benzene rings are almost coplanar [dihedral angle = 1.36 (7°]. The O atoms of the carboxylic acid group are disordered over two sets of sites and were refined with an occupancy ratio of 0.5:0.5. The two disordered components of the carboxylic acid group make dihedral angles of 1.5 (14 and 3.8 (12° with the benzene ring to which they are attached. In the crystal, molecules are linked via pairs of O—H...O hydrogen bonds, forming inversion dimers. The dimers are connected via C—H...O hydrogen bonds, forming ribbons lying parallel to [120]. These ribbons are linked via C—H...π interactions, forming slabs parallel to (001.

  15. Organophosphorus acid anhydrolase from Alteromonas macleodii: structural study and functional relationship to prolidases

    Czech Academy of Sciences Publication Activity Database

    Štěpánková, Andrea; Dušková, Jarmila; Skálová, Tereza; Hašek, Jindřich; Koval, Tomáš; Ostergaard, L. H.; Dohnálek, Jan

    2013-01-01

    Roč. 69, č. 4 (2013), s. 346-354 ISSN 1744-3091 R&D Projects: GA ČR GA310/09/1407; GA ČR GA305/07/1073; GA MŠk EE2.3.30.0029 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : organophosphorus acid anhydrolase * prolidases * bifunctional Subject RIV: CE - Biochemistry Impact factor: 0.568, year: 2013

  16. Impact of the Fused Deposition (FDM) Printing Process on Polylactic Acid (PLA) Chemistry and Structure

    OpenAIRE

    Michael Arthur Cuiffo; Jeffrey Snyder; Alicia M. Elliott; Nicholas Romero; Sandhiya Kannan; Gary P. Halada

    2017-01-01

    Polylactic acid (PLA) is an organic polymer commonly used in fused deposition (FDM) printing and biomedical scaffolding that is biocompatible and immunologically inert. However, variations in source material quality and chemistry make it necessary to characterize the filament and determine potential changes in chemistry occurring as a result of the FDM process. We used several spectroscopic techniques, including laser confocal microscopy, Fourier transform infrared (FTIR) spectroscopy and pho...

  17. Effects of brief milling and acid treatment on two ordered and disordered kaolinite structures

    Czech Academy of Sciences Publication Activity Database

    Valášková, M.; Barabaszová, K.; Hundáková, M.; Ritz, M.; Plevová, Eva

    2011-01-01

    Roč. 54, č. 1 (2011), s. 70-76 ISSN 0169-1317 R&D Projects: GA ČR GA105/08/1398 Grant - others:GA ČR(CZ) GA205/09/0352 Institutional research plan: CEZ:AV0Z30860518 Keywords : kaolinite * milling * hydrochloric acid Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.474, year: 2011 http://www.sciencedirect.com/science/article/pii/S0169131711002675

  18. Acidity and Structure of Isosaccharinate in Aqueous Solution: A Nuclear Magnetic Resonance Study

    International Nuclear Information System (INIS)

    Cho, Herman M.; Rai, Dhanpat; Hess, Nancy J.; Xia, Yuanxian; Rao, Linfeng

    2003-01-01

    Dilute aqueous solutions of the calcium and sodium salts of -D-isosaccharinate (ISA) have been analyzed by 13C and 1H NMR spectroscopy. The positions of the six 13C ISA NMR lines show a pH dependence that can be used to infer that the most acidic proton is the one associated with the carboxylate group, with a log k0 of -3.27 - -3.36 for the reaction H(ISA) H+ K ISA-

  19. A measure of bending in nucleic acids structures applied to A-tract DNA

    Czech Academy of Sciences Publication Activity Database

    Lankaš, Filip; Špačková, Naďa; Moakher, M.; Enkhbayar, P.; Šponer, Jiří

    2010-01-01

    Roč. 38, č. 10 (2010), s. 3414-3422 ISSN 0305-1048 R&D Projects: GA MŠk(CZ) LC06030 Grant - others:GA MŠk(CZ) LC512 Program:LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506 Keywords : nucleic acids * DNA * molecular dynamics Subject RIV: BO - Biophysics Impact factor: 7.836, year: 2010

  20. 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

  1. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.

    Science.gov (United States)

    Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll

    2016-01-04

    Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Synthesis and structural elucidation of glutathione and N-aceyl-cysteine conjugates of 5-aminosalicylic acid

    DEFF Research Database (Denmark)

    Jensen, J.; Cornett, Claus; Olsen, C. E.

    1993-01-01

    conjugates of 5-ASA and GSH were found to be formed. 5-ASA was initially oxidized by PbO2 in a solution of TRIS-HCl buffer pH 9.3 followed by the in situ addition of N-acetyl-cysteine or glutathione to the oxidized 5-ASA at pH 7.5. The resulting conjugates were N-acetylated at the aromatic amino group......The ability of 5-aminosalicylic acid (5-ASA) to be oxidized to a quinone monoimine compound capable of conjugating with nucleophilic compounds such as N-acetyl-cysteine (NAC) and glutathione (GSH) has been investigated in vitro. Three isomeric conjugates of 5-ASA and NAC as well as three isomeric...... dose of 5-ASA into mercapturic acids of 5-ASA, when 1 g of 5-ASA was ingested. In spite of the low detection limits, none of the mercapturic acid conjugates was detected in the urine from persons treated with 5-ASA....

  3. Biological and structural effects of the conjugation of an antimicrobial decapeptide with saturated, unsaturated, methoxylated and branched fatty acids.

    Science.gov (United States)

    Húmpola, María Verónica; Rey, María Carolina; Carballeira, Nestor M; Simonetta, Arturo Carlos; Tonarelli, Georgina Guadalupe

    2017-01-01

    The increasing bacterial resistance against conventional antibiotics has led to the search for new antimicrobial drugs with different modes of action. Cationic antimicrobial peptides (AMPs) and lipopeptides are promising candidates to treat infections because they act on bacterial membranes causing rapid destruction of sensitive bacteria. In this study, a decapeptide named A2 (IKQVKKLFKK) was conjugated at the N-terminus with saturated, unsaturated, methoxylated and methyl -branched fatty acids of different chain lengths (C8 - C20), the antimicrobial and structural properties of the lipopeptides being then investigated. The attachment of the fatty acid chain significantly improved the antimicrobial activity of A2 against bacteria, and so, endowed it with moderated antifungal activity against yeast strains belonging to genus Candida. Lipopeptides containing hydrocarbon chain lengths between C8 and C14 were the best antibacterial compounds (MIC = 0.7 to 5.8 μM), while the most active compounds against yeast were A2 conjugated with methoxylated and enoic fatty acids (11.1 to 83.3 μM). The improvement in antimicrobial activity was mainly related to the amphipathic secondary structure adopted by A2 lipopeptides in the presence of vesicles that mimic bacterial membranes. Peptide conjugation with long hydrocarbon chains (C12 or more), regardless of their structure, significantly increased toxicity towards eukaryotic cells, resulting in a loss of selectivity. These findings suggest that A2-derived lipopeptides are potential good candidates for the treatment of infectious diseases caused by bacteria and opportunistic pathogenic yeast belonging to genus Candida. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

  4. ESTIMATION OF HYDROLYSIS RATE CONSTANTS OF CARBOXYLIC ACID ESTER AND PHOSPHATE ESTER COMPOUNDS IN AQUEOUS SYSTEMS FROM MOLECULAR STRUCTURE BY SPARC

    Science.gov (United States)

    SPARC (SPARC Performs Automated Reasoning in Chemistry) chemical reactivity models were extended to calculate hydrolysis rate constants for carboxylic acid ester and phosphate ester compounds in aqueous non- aqueous and systems strictly from molecular structure. The energy diffe...

  5. 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.

  6. Electronic structure and spectroscopy of nucleic acid bases: Ionization energies, ionization-induced structural changes, and photoelectron spectra

    Energy Technology Data Exchange (ETDEWEB)

    Bravaya, Ksenia B.; Kostko, Oleg; Dolgikh, Stanislav; Landau, Arie; Ahmed, Musahid; Krylov, Anna I.

    2010-08-02

    We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra.

  7. Effects of organic wastes on structural characterizations of humic acid in semiarid soil under plastic mulched drip irrigation.

    Science.gov (United States)

    Hu, Juan; Wu, Jinggui; Qu, Xiaojing; Li, Jianming

    2018-02-22

    The objective of this work was to evaluate the variation in the amount and structure of humic acid (HA) after the application of organic wastes (OWs) in semiarid soil under plastic mulched drip irrigation, measured by elemental composition, excitation-emission matrix (EEM) fluorescence, and carbon 13 nuclear magnetic resonance ( 13 C CPMAS NMR). The experiment involved chemical fertilizer combined with chicken manure (CM), sheep manure (SM), maize straw (MS), fodder grass (FG), and tree leaves (TL), while chemical fertilizer only was used as control (CK). The highest cation exchange capacity (CEC), soil organic carbon (SOC), and HA contents (P plastic mulched drip irrigation conditions. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Use of a (Quantitative) Structure-Activity Relationship [(Q)SAR] model to predict the toxicity of naphthenic acids

    DEFF Research Database (Denmark)

    Frank, Richard; Sanderson, Hans; Kavanagh, Richard

    2010-01-01

    as the principal toxic components of oil sands process-affected water (OSPW), and microbial degradation of lower molecular weight (MW) NAs decreases the toxicity of NA mixtures in OSPW.  Analysis by proton nuclear magnetic resonance spectroscopy indicated that larger, more cyclic NAs contain greater carboxylic...... acid content, thereby decreasing their hydrophobicity and acute toxicity in comparison to lower MW NAs.  The relationship between the acute toxicity of NAs and hydrophobicity suggests that narcosis is the probable mode of acute toxic action.  The applicability of a (Quantitative) Structure...

  9. Crystal growth, structure analysis and characterisation of 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Sankari, R. Siva, E-mail: sivasankari.sh@act.edu.in [Department of Physics, Agni College of Technology, Thalambur, Chennai-603103 (India); Perumal, Rajesh Narayana [Department of Physics, SSN College of Engineering, Kalavakkam, Chennai-603110 (India)

    2014-04-24

    Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.

  10. Effect of structured lipids based on fish oil on the growth and fatty acid composition in Rainbow Trout (Oncorhynchus mykiss)

    DEFF Research Database (Denmark)

    Nielsen, Nina Skall; Gøttsche, Jesper; Holm, Jørgen

    2005-01-01

    containing DAG. A feeding experiment where groups of rainbow trout were fed six diets containing different types of oils for 61 days was performed. The lipid fraction of the six diets was as follows: 1) Fish oil and rapeseed oil (FO diet), 2) Specific structured lipid and rapeseed oil (SL diet), 3....... There was no additional effect of incorporating the medium chain fatty acids in specific positions and no weight reducing effect of adding DAG to the diets. (C) 2005 Elsevier B.V. All rights reserved....

  11. 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.

  12. Multifunctional electroactive electrospun nanofiber structures from water solution blends of PVA/ODA-MMT and poly(maleic acid-alt-acrylic acid): effects of Ag, organoclay, structural rearrangement and NaOH doping factors

    Science.gov (United States)

    Şimşek, Murat; Rzayev, Zakir M. O.; Bunyatova, Ulviya

    2016-06-01

    Novel multifunctional colloidal polymer nanofiber electrolytes were fabricated by green reactive electrospinning nanotechnology from various water solution/dispersed blends of poly (vinyl alcohol-co-vinyl acetate) (PVA)/octadecyl amine-montmorillonite (ODA-MMT) as matrix polymer nanocomposite and poly(maleic acid-alt-acrylic acid) (poly(MAc-alt-AA) and/or its Ag-carrying complex as partner copolymers. Polymer nanofiber electrolytes were characterized using FTIR, XRD, thermal (DSC, TGA-DTG), SEM, and electrical analysis methods. Effects of partner copolymers, organoclay, in situ generated silver nanoparticles (AgNPs), and annealing procedure on physical and chemical properties of polymer composite nanofibers were investigated. The electrical properties (resistance, conductivity, activation energy) of nanofibers with/without NaOH doping agent were also evaluated. This work presented a structural rearrangement of nanofiber mats by annealing via decarboxylation of anhydride units with the formation of new conjugated double bond sites onto partner copolymer main chains. It was also found that the semiconductor behaviors of nanofiber structures were essentially improved with increasing temperature and fraction of partner copolymers as well as presence of organoclay and AgNPs in nanofiber composite.

  13. Structure formation of soil dispersions in the presence of polyelectrolytes on the basis of allyl alcohol and acryl acid derivatives

    Directory of Open Access Journals (Sweden)

    Amankait Asanov

    2015-09-01

    Full Text Available Some changes of structural composition and surface properties of soil dispersions in the presence of polyelectrolytes, based on allyl alcohol and acryl acid derivatives, have been studied. The results show, that the changes in the structure of soil dispersions composition are connected with the added concentration and pH value, that depend on mole ratio and nature of functional groups, as well as on the nature of counterions and concomitant electrolytes, changing with the conditions of polymer analogous conversion and neutralization reaction. Experimental data show, that the change in the conformational state and the length of the macromolecule has a significant impact on the structure-forming effect and the amount of polyelectrolyte, needed to achieve the same degree of structure-forming effect of soil dispersions. The causes for the revealed reasons are shown on the basis of the results of the experiment. Along with this, it was found that particular changes of structural composition and surface properties of the soil dispersions depend on the type and concentration of the added polyelectrolyte.

  14. Structure-performance relationships of phenyl cinnamic acid derivatives as MALDI-MS matrices for sulfatide detection.

    Science.gov (United States)

    Tambe, Suparna; Blott, Henning; Fülöp, Annabelle; Spang, Nils; Flottmann, Dirk; Bräse, Stefan; Hopf, Carsten; Junker, Hans-Dieter

    2017-02-01

    A key aspect for the further development of matrix-assisted laser desorption ionization (MALDI)-mass spectrometry (MS) is a better understanding of the working principles of MALDI matrices. To address this issue, a chemical compound library of 59 structurally related cinnamic acid derivatives was synthesized. Potential MALDI matrices were evaluated with sulfatides, a class of anionic lipids which are abundant in complex brain lipid mixtures. For each matrix relative mean S/N ratios of sulfatides were determined against 9-aminoacridine as a reference matrix using negative ion mass spectrometry with 355 and 337 nm laser systems. The comparison of matrix features with their corresponding relative mean S/N ratios for sulfatide detection identified correlations between matrix substitution patterns, their chemical functionality, and their MALDI-MS performance. Crystal structures of six selected matrices provided structural insight in hydrogen bond interactions in the solid state. Principal component analysis allowed the additional identification of correlation trends between structural and physical matrix properties like number of exchangeable protons at the head group, MW, logP, UV-Vis, and sulfatide detection sensitivity. Graphical abstract Design, synthesis and mass spectrometric evaluation of MALDI-MS matrix compound libraries allows the identification of matrix structure - MALDI-MS performance relationships using multivariate statistics as a tool.

  15. Flexible poly(amic acid) conducting polymers: effect of chemical composition on structural, electrochemical, and mechanical properties.

    Science.gov (United States)

    Du, Nian; Wong, Cheuk; Feurstein, Michael; Sadik, Omowunmi A; Umbach, Christopher; Sammakia, Bahgat

    2010-09-07

    A new approach for creating flexible, mechanically strong poly(amic acid) (PAA) hybrid copolymers is described. The reduction of gold salts to gold nanoparticles by PAA coupled with its copolymerization in the presence of various silanes (e.g., N-[3-(trimethoxysilyl)-propyl] aniline (TMOSPA), 3-aminopropyl-trimethoxysilane (APTMOS), dichlorodimethylsilane (DCMS), and tetramethoxysilane (TMOS)) has enabled the design of a series of polymeric films. The resulting poly(amic acid), silane, and gold (PSG) solutions were employed for the fabrication of flexible, ternary polymers with a minimum bend ratio of 3 mm using thermal desolvation and/or wet-phase inversion techniques. By controlling the composition and synthesis conditions, porous PSG films were produced that are flexible or rigid, transparent or opaque, and/or mechanically strong. (1)H NMR, (13)C NMR, and Fourier transform infrared spectroscopy (FTIR) characterization results showed that the carboxylic acid moieties were retained in the PSG copolymer. Thermal stabilities with degradation characteristics of the polymers were determined using thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). Although structurally and morphologically different from the parent PAA, copolymerization with silanes had significantly improved the mechanical and interfacial property of the PSG class of films.

  16. Syntheses, structures, and photoluminescence of three-dimensional lanthanide coordination polymers with 2,5-pyridinedicarboxylic acid

    International Nuclear Information System (INIS)

    Huang Yan; Song Yishan; Yan, Bing; Shao Min

    2008-01-01

    Four new open-framework coordination polymers of lanthanide 2,5-pyridinedicarboxylates, with the formulas Pr2(pydc) 3 (H 2 O) 2 (1), Ln(pydc)(Hpydc) (Ln=Tb (2), Er (3), Eu (5)), and Gd(pydc)(nic)(H 2 O) (4) (H 2 pydc=2,5-pyridinedicarboxylic acid, Hnic=nicotinic acid), have been hydrothermally synthesized and four of them (except Eu (5)) have been structurally characterized. Complex 1 consists of two types of ligand-binding modes contributing to link the PrO 7 N(H 2 O) polyhedral chains to three-dimensional (3D) open-framework architecture. Complexes 2 and 3 are isostructural and feature unique 3D cage-like supramolecular frameworks remarkably different from that of 1, owing to the different ligand-bridging pattern. Complex 4, however, has the distinct 3D open-framework architecture due to the presence of unexpected nicotinate ligands, which may be derived from pydc ligands via in-situ decarboxylation under the hydrothermal condition. - Graphical abstract: Four new lanthanide coordination polymers have been hydrothermally synthesized by the reaction of 2,5-pyridinedicarboxylic acid with the corresponding lanthanide nitrates, and they show three types of 3D open-framework architecture. Complexes 2 and 5 show strong characteristic green (or red) luminescence and long lifetimes

  17. Augmenting the activity of antifungal agents against aspergilli using structural analogues of benzoic acid as chemosensitizing agents.

    Science.gov (United States)

    Kim, Jong H; Campbell, Bruce C; Mahoney, Noreen; Chan, Kathleen L; Molyneux, Russell J; Balajee, Arunmozhi

    2010-10-01

    A number of benzoic acid analogues showed antifungal activity against strains of Aspergillus flavus, Aspergillus fumigatus and Aspergillus terreus, causative agents of human aspergillosis, in in vitro bioassays. Structure-activity analysis revealed that antifungal activities of benzoic and gallic acids were increased by addition of a methyl, methoxyl or chloro group at position 4 of the aromatic ring, or by esterification of the carboxylic acid with an alkyl group, respectively. Thymol, a natural phenolic compound, was a potent chemosensitizing agent when co-applied with the antifungal azole drugs fluconazole and ketoconazole. The thymol-azole drug combination demonstrated complete inhibition of fungal growth at dosages far lower than the drugs alone. Co-application of thymol with amphotericin B had an additive effect on all strains of aspergilli tested with the exception of two of three strains of A. terreus, where there was an antagonistic effect. Use of two mitogen-activated protein kinase (MAPK) mutants of A. fumigatus, sakAΔ and mpkCΔ, having gene deletions in the oxidative stress response pathway, indicated antifungal and/or chemosensitization activity of the benzo analogues was by disruption of the oxidative stress response system. Results showed that both these genes play overlapping roles in the MAPK system in this fungus. The potential of safe, natural compounds or analogues to serve as chemosensitizing agents to enhance efficacy of commercial antifungal agents is discussed. Published by Elsevier Ltd.

  18. 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

  19. X-ray structure characterization of palladium(II) ternary complexes of pyridinedicarboxylic and phthalic acid with phenanthroline and bipyridine.

    Science.gov (United States)

    Wang, Yue; Okabe, Nobuo

    2005-04-01

    The crystal structures of the series of four ternary complexes, [Pd(phen)(2,6-PDCA)].4H(2)O (1) (phen=1,10-phenanthroline; 2,6-PDCA=2,6-pyridinedicarboxylic acid), [Pd(bpy)(2,3-PDCA)].3H(2)O (2) (bpy=2,2'-bipyridineand; 2,3-PDCA=2,3-pyridinedicarboxylic acid) and [Pd(phen)(PHT)].2.5H(2)O (3) (PHT=o-phthalic acid ) and [Pd(bpy)(PHT)].1.5H(2)O (4), are determined and the coordination modes of palladium(II) ternary complexes are characterized. All complexes take the mononuclear Pd(II) complexes, in which central Pd(II) atom of each complex has a similar distorted square-planar four coordination geometry. In all complexes, the aromatic heterocyclic compounds, phen and bpy, behave as a bidentate N, N' ligand. In the complex 1 and 2, 2,6-PDCA and 2,3-PDCA behave as a bidentate N, O ligand, and in complex 3 and 4, PHT behaves as a bidentate O, O' ligand.

  20. Structure-Processing-Property Relationship of Poly(Glycolic Acid for Drug Delivery Systems 1: Synthesis and Catalysis

    Directory of Open Access Journals (Sweden)

    Vineet Singh

    2010-01-01

    Full Text Available Till date, market is augmented with a huge number of improved drug delivery systems. The success in this area is basically due to biodegradable polymers. Although conventional systems of drug delivery utilizing the natural and semisynthetic polymers so long but synthetic polymer gains success in the controlled drug delivery area due to better degradation profile and controlled network and functionality. The polyesters are the most studied class group due the susceptible ester linkage in their backbone. The Poly(glycolic Acid (PGA, Poly(lactic acid (PLA, and Polylactide-co-glycolide (PLGA are the best profiled polyesters and are most widely used in marketed products. These polymers, however, still are having drawbacks which failed them to be used in platform technologies like matrix systems, microspheres, and nanospheres in some cases. The common problems arose with these polymers are entrapment inefficiency, inability to degrade and release drugs with required profile, and drug instability in the microenvironment of the polymers. These problems are forcing us to develop new polymers with improved physicochemical properties. The present review gave us an insight in the various structural elements of Poly(glycolic acid, polyester, with in depth study. The first part of the review focuses on the result of studies related to synthetic methodologies and catalysts being utilized to synthesize the polyesters. However the author will also focus on the effect of processing methodologies but due some constraints those are not included in the preview of this part of review.

  1. Structures, Hydration, and Electrical Mobilities of Bisulfate Ion-Sulfuric Acid-Ammonia/Dimethylamine Clusters: A Computational Study.

    Science.gov (United States)

    Tsona, Narcisse T; Henschel, Henning; Bork, Nicolai; Loukonen, Ville; Vehkamäki, Hanna

    2015-09-17

    Despite the well-established role of small molecular clusters in the very first steps of atmospheric particle formation, their thermochemical data are still not completely available due to limitation of the experimental techniques to treat such small clusters. We have investigated the structures and the thermochemistry of stepwise hydration of clusters containing one bisulfate ion, sulfuric acid, base (ammonia or dimethylamine), and water molecules using quantum chemical methods. We found that water facilitates proton transfer from sulfuric acid or the bisulfate ion to the base or water molecules, and depending on the hydration level, the sulfate ion was formed in most of the base-containing clusters. The calculated hydration energies indicate that water binds more strongly to ammonia-containing clusters than to dimethylamine-containing and base-free clusters, which results in a wider hydrate distribution for ammonia-containing clusters. The electrical mobilities of all clusters were calculated using a particle dynamics model. The results indicate that the effect of humidity is negligible on the electrical mobilities of molecular clusters formed in the very first steps of atmospheric particle formation. The combination of the results of this study with those previously published on the hydration of neutral clusters by our group provides a comprehensive set of thermochemical data on neutral and negatively charged clusters containing sulfuric acid, ammonia, or dimethylamine.

  2. Biochemical and structural characterization of Klebsiella pneumoniae oxamate amidohydrolase in the uric acid degradation pathway

    Energy Technology Data Exchange (ETDEWEB)

    Hicks, Katherine A.; Ealick, Steven E.

    2016-05-25

    HpxW from the ubiquitous pathogenKlebsiella pneumoniaeis involved in a novel uric acid degradation pathway downstream from the formation of oxalurate. Specifically, HpxW is an oxamate amidohydrolase which catalyzes the conversion of oxamate to oxalate and is a member of the Ntn-hydrolase superfamily. HpxW is autoprocessed from an inactive precursor to form a heterodimer, resulting in a 35.5 kDa α subunit and a 20 kDa β subunit. Here, the structure of HpxW is presented and the substrate complex is modeled. In addition, the steady-state kinetics of this enzyme and two active-site variants were characterized. These structural and biochemical studies provide further insight into this class of enzymes and allow a mechanism for catalysis consistent with other members of the Ntn-hydrolase superfamily to be proposed.

  3. Laboratory Investigation of the Growth and Crystal Structure of Nitric Acid Hydrates by Transmission Electron Microscopy (TEM)

    Science.gov (United States)

    Blake, David F.; Chang, Sherwood (Technical Monitor)

    1994-01-01

    A great deal of recent laboratory work has focussed on the characterization of the nitric acid hydrates, thought to be present in type I Polar Stratospheric Clouds (PSCs). Phase relationships and vapor pressure measurements (1-3) and infrared characterizations (4-5) have been made. However, the observed properties of crystalline solids (composition, melting point, vapor pressure, surface reactivity, thermodynamic stability, extent of solid solution with other components, etc.) are controlled by their crystal structure. The only means of unequivocal structural identification for crystalline solids is diffraction (using electrons, X-rays, neutrons, etc.). Other observed properties of crystalline solids, such as their infrared spectra, their vapor pressure as a function of temperature, etc. yield only indirect information about what phases are present, their relative proportions, or whether they are crystalline or amorphous.

  4. Synthesis and structural studies of some trivalent lanthanide complexes of isonicotinic acid hydrazide

    International Nuclear Information System (INIS)

    Rao, T.R.; Khan, I.A.; Aggarwal, R.C.

    1985-01-01

    Trivalent lanthanides have been found to form complexes with isonicotinic acid hydrazide (INH) of the type M(INH) 3 X 3 [X=Cl, SCN; M=La(III), Pr(III), Nd(III), Sm(III) and Gd(III)]. The complexes have been characterized by elemental analysis, molar conductance, magnetic susceptibility, infrared and electronic spectral studies. The nephelauxetic ratio (β), covalency (δ) and bonding parameter (b 1/1 ) have been calculated from the electronic spectra. Infrared spectral studies reveal that INH acts as a neutral bidentate chelating ligand in all the complexes and that thiocyanate is N-bonded. (author)

  5. Structural dynamic of a self-assembling peptide d-EAK16 made of only D-amino acids.

    Directory of Open Access Journals (Sweden)

    Zhongli Luo

    Full Text Available We here report systematic study of structural dynamics of a 16-residue self-assembling peptide d-EAK16 made of only D-amino acids. We compare these results with its chiral counterpart L-form, l-EAK16. Circular dichroism was used to follow the structural dynamics under various temperature and pH conditions. At 25 degrees C the d-EAK16 peptide displayed a typical beta-sheet spectrum. Upon increasing the temperature above 70 degrees C, there was a spectrum shift as the 218 nm valley widens toward 210 nm. Above 80 degrees C, the d-EAK16 peptide transformed into a typical alpha-helix CD spectrum without going through a detectable random-coil intermediate. When increasing the temperature from 4 degrees C to 110 degrees C then cooling back from 110 degrees C to 4 degrees C, there was a hysteresis: the secondary structure from beta-sheet to alpha-helix and then from alpha-helix to beta-sheet occurred. d-EAK16 formed an alpha-helical conformation at pH0.76 and pH12 but formed a beta-sheet at neutral pH. The effects of various pH conditions, ionic strength and denaturing agents were also noted. Since D-form peptides are resistant to natural enzyme degradation, such drastic structural changes may be exploited for fabricating molecular sensors to detect minute environmental changes. This provides insight into the behaviors of self-assembling peptides made of D-amino acids and points the way to designing new peptide materials for biomedical engineering and nanobiotechnology.

  6. Fatty acid composition in fractions of structural and storage lipids in liver and skeletal muscle of hereditary hypertriglyceridemic rats.

    Science.gov (United States)

    Bohov, P; Seböková, E; Gasperíková, D; Langer, P; Klimes, I

    1997-09-20

    The fatty acid (FA) compositions of liver and skeletal muscle structural lipids, overall phospholipids and phosphatidylcholine, and triglycerides (TG) were determined in the hereditary hypertriglyceridemic (HTG) rat, a nonobese animal model of the insulin resistance syndrome. Four groups of HTG rats and four groups of control animals were fed equal-energy diets for two weeks: basal (B), high-sucrose (HS), or fish oil-supplemented basal (BFO) or high-sucrose (HSFO) diets. In the liver of HTG rats, a decrease of n-6 long-chain polyunsaturated FA (PUFA), especially in 20:4n-6, in comparison with controls was found. Moreover, a concomitant accumulation of 18:2n-6 in structural lipids was observed. These differences were more pronounced in liver than in skeletal muscle. HS feeding raised the proportion of 18:1n-9 and decreased 18:2n-6 in lipid fractions. In both tissues and in both strains, the amounts of long-chain n-3 PUFA, as well as the level of total C20-22 PUFA, went up after fish oil feeding. However, the effects were somewhat less pronounced in the HTG rats. The increase in n-3 PUFA occurred mainly at the expense of reduced levels of 18:2n-6 in structural lipids and of 18:1n-9 in triglycerides. These changes were associated, in companion studies reported in this volume, with improved insulin action in HTG rats. In conclusion, the FA composition in lipid subclasses of HTG rats differs significantly from the controls mainly in liver structural lipids, suggesting the impairment of PUFA desaturation. Dietary change effected a similar modulation of FA profile across both strains, with fish oil increasing the levels of long-chain PUFA toward control values in the NTG rats. The HTG rat thus provides an interesting animal model for the study of impaired fatty acid metabolism.

  7. Using analyses of amino Acid coevolution to understand protein structure and function.

    Science.gov (United States)

    Ashenberg, Orr; Laub, Michael T

    2013-01-01

    Determining which residues of a protein contribute to a specific function is a difficult problem. Analyses of amino acid covariation within a protein family can serve as a useful guide by identifying residues that are functionally coupled. Covariation analyses have been successfully used on several different protein families to identify residues that work together to promote folding, enable protein-protein interactions, or contribute to an enzymatic activity. Covariation is a statistical signal that can be measured in a multiple sequence alignment of homologous proteins. As sequence databases have expanded dramatically, covariation analyses have become easier and more powerful. In this chapter, we describe how functional covariation arises during the evolution of proteins and how this signal can be distinguished from various background signals. We discuss the basic methodology for performing amino acid covariation analysis, using bacterial two-component signal transduction proteins as an example. We provide practical suggestions for each step of the process including assembly of protein sequences, construction of a multiple sequence alignment, measurement of covariation, and analysis of results. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Synthesis, structural studies, and cytotoxic evaluation of novel ursolic acid hybrids with capabilities to arrest breast cancer cells in mitosis.

    Science.gov (United States)

    Pattnaik, Banita; Lakshmi, Jerripothula K; Kavitha, Rachineni; Jagadeesh, Bharatam; Bhattacharjee, Debanjan; Jain, Nishant; Mallavadhani, Uppuluri V

    2017-03-01

    Some novel chemically modified frameworks of ursolic acid have been designed and synthesized. The key step was the cycloaddition of azidopropyl-3β-hydroxy-urs-12-en-28-oate with the appropriate C28 propargyl esters of ursolic, corosolic, asiatic, oleanolic, and betulinic acid under Click reaction conditions, and the products were obtained in 74-84% yields. In view of their intriguing structural diversity, they have been subjected to detailed 1D and 2D NMR studies and their structures are thoroughly assigned. The synthesized compounds were screened for their anticancer potential against two human breast cancer cell lines (MCF-7 & MDA-MB-231) using sulforhodamine B cell proliferation assay. The GI 50 data revealed that the synthesized compounds exhibit highly potent activities against the two tested cell lines. Interestingly, the synthesized compounds showed selectivity and higher activity against MDA-MB-231 cell line than MCF-7. Among the tested compounds, compound 17 is the most potent one with GI 50 value of 1.4 ± 0.1 μM and showed 2.9 times more activity than the standard doxorubicin against MDA-MB-231. In addition, 17 arrests cells in mitotic phase of cell cycle, resulting in a change in cell phenotype. In view of the selective and highly promising activity against breast cancer cell lines, these compounds can serve as promising leads for further development.

  9. Synthesis, crystal structure and DFT studies of a novel dinuclear copper(I) complex with triphenylphosphine and 2-mercaptonicotinic acid

    Science.gov (United States)

    Ahmad, Tayyaba; Mahmood, Rashid; Georgieva, Ivelina; Zahariev, Tsvetan; Tahir, Muhammad Nawaz; Shaheen, Muhammad Ashraf; Gilani, Mazhar Amjad; Ahmad, Saeed

    2018-02-01

    A novel dinuclear copper(I) complex, {[Cu2(Mnt)2(PPh3)2Cl2].2H2O.CH3CN}2 (1) (Mnt = Mercaptonicotinic acid, PPh3 = triphenylphosphine) was prepared and its structure was determined by X-ray crystallography. The complex 1 consists of two dinuclear molecules and in each molecule, the two copper atoms are bridged by S atoms of N-protonated mercaptonicotinic acid forming a four-membered ring. The planar Cu2S2 core is characterized by significant cuprophilic interactions (Cusbnd Cu distance = 2.7671(8), 2.8471(8) Å). Each copper atom in 1 is coordinated by two sulfur atoms of Mnt, one phosphorus atom of PPh3 and a chloride ion adopting a tetrahedral geometry. The calculated Gibbs energies for reaction in CH3CN supported the experimental structure and predicted more favorable formation of dinuclear Cu(I) complex as compared to the mononuclear Cu(I) complex. The dinuclear complex is stabilized by 65.98 kJ mol-1 by coupling of two mononuclear Cu(I) complexes. The IR spectra of 1 and Mnt ligand were reliably interpreted and the Mnt vibrations, which are sensitive to the ligand coordination to Cu(I) ion in 1 were selected with the help of DFT/ωB97XD calculations.

  10. On the Origin of the Methyl Radical Loss from Deprotonated Ferulic and Isoferulic Acids: Electronic Excitation of a Transient Structure

    Science.gov (United States)

    Zhang, Xiaoping; Li, Fei; Lv, Huiqing; Wu, Yanqing; Bian, Gaofeng; Jiang, Kezhi

    2013-06-01

    Formation of radical fragments from even-electron ions is an exception to the "even-electron rule". In this work, ferulic acid (FA) and isoferulic acid (IFA) were used as the model compounds to probe the fragmentation mechanisms and the isomeric effects on homolytic cleavage. Elimination of methyl radical and CO2 are the two competing reactions observed in the CID-MS of [FA - H]- and [IFA - H]-, of which losing methyl radical violates the "even-electron rule". The relative intensity of their product ions is significantly different, and thereby the two isomeric compounds can be differentiated by tandem MS. Theoretical calculations indicate that both the singlet-triplet gap and the excitation energy decrease in the transient structures, as the breaking C-O bond is lengthened. The methyl radical elimination has been rationalized as the intramolecular electronic excitation of a transient structure with an elongating C-O bond. The potential energy diagrams, completed by the addition of the energy barrier of the radical elimination, have provided a reasonable explanation of the different CID-MS behaviors of [FA - H]- and [IFA - H]-.

  11. 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.

  12. 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.

  13. Production of trans-free margarine with stearidonic acid soybean and high-stearate soybean oils-based structured lipid.

    Science.gov (United States)

    Pande, Garima; Akoh, Casimir C; Shewfelt, Robert L

    2012-11-01

    Omega-3 fatty acids (n-3 FAs) have been positively associated with prevention and treatment of chronic diseases. Intake of high amounts of trans fatty acids (TFAs) is correlated with increased risk of coronary heart disease, inflammation, and cancer. Structured lipid (SL) was synthesized using stearidonic acid (SDA) soybean oil and high-stearate soybean oil catalyzed by Lipozyme(®) TLIM lipase. The SL was compared to extracted fat (EF) from a commercial brand for FA profile, sn-2 positional FAs, triacylglycerol (TAG) profile, polymorphism, thermal behavior, oxidative stability, and solid fat content (SFC). Both SL and EF had similar saturated FA (about 31 mol%) and unsaturated FA (about 68 mol%), but SL had a much lower n-6/n-3 ratio (1.1) than EF (5.8). SL had 10.5 mol% SDA. After short-path distillation, a loss of 53.9% was observed in the total tocopherol content of SL. The tocopherols were lost as free tocopherols. SL and EF had similar melting profile, β' polymorph, and oxidative stability. Margarine was formulated using SL (SLM) and EF (RCM, reformulated commercial margarine). No sensory difference was observed between the 2 margarines. The SL synthesized in this study contained no TFA and possessed desirable polymorphism, thermal properties, and SFC for formulation of soft margarine. The margarine produced with this SL was trans-free and SDA-enriched. The current research increases the food applications of stearidonic acid (SDA) soybean oil. trans-Free SDA containing SL was synthesized with desirable polymorph, thermal properties, and SFC for formulation of soft margarine. The margarine produced with this SL had no trans fat and had a low n-6/n-3 ratio. This may help in reducing trans fat intake in our diet while increasing n-3 FA intake. © 2012 Institute of Food Technologists®

  14. Syntheses, structures, photoluminescence and photocatalysis of 2D layered lanthanide-carboxylates with 2, 2′-dithiodibenzoic acid

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Ling; Zhong, Jie-Cen; Qiu, Xing-Tai; Sun, Yan-Qiong, E-mail: sunyq@fzu.edu.cn; Chen, Yi-Ping

    2017-02-15

    Two series of lanthanide-carboxylates, [Ln(2,2′-dtba)(2,2′-Hdtba)(EtOH)]{sub n} (I:Ln=Eu(1a), Dy(1b)) and [Ln(2,2′-dtba)(2,2′-Hdtba)(4,4′-bpy){sub 0.5}]{sub n} (II:Ln=Eu(2a), Dy(2b), Tb(2c) 2,2′-H{sub 2}dtba=2,2′-dithiodibenzoic acid, 4,4′-bpy=4,4′-bipyridine) have been synthesized under hydrothermal conditions. Interestingly, the H{sub 2}dtba organic ligand was generated by in situ S–S reaction of 2-mercaptobenzoic acid. Compounds I and II possess different 2D layered structures based on similar 1D [Ln(2,2′-dtba)]{sup +} chains. Photoluminescence studies reveal that compounds I and II exhibit strong lanthanide characteristic emission bands. Remarkably, Compounds 1b and 2a both exhibit good photocatalytic activity for degradation of Rhodamine-B (Rh-B) under the simulated sunlight irradiation. - Graphical abstract: Two series of lanthanide-carboxylates have been in situ synthesized under hydrothermal conditions. The lanthanide-carboxylates exhibit strong lanthanide characteristic emission bands and good photocatalytic activity for degradation of Rhodamine-B. - Highlights: • 2D layered lanthanide-carboxylates with 2,2′-dithiodibenzoic acid. • In situ S–S reaction of 2-mercaptobenzoic acid under hydrothermal condition. • The Emission spectra of I and II exhibit the characteristic transition of lanthanide ions. • Compounds 1b and 2a exhibit good photocatalytic activity for degradation of Rhodamine-B.

  15. Microhardness, Structure, and Morphology of Primary Enamel after Phosphoric Acid, Self-Etching Adhesive, and Er:YAG Laser Etching

    Directory of Open Access Journals (Sweden)

    María del Carmen Zoila Alcantara-Galeana

    2017-01-01

    Full Text Available Background. Phosphoric acid is the traditional etching agent; self-etching adhesives and Er:YAG laser are alternative methods. Knowledge of deciduous enamel etching is required. Aim. To evaluate primary enamel microhardness, structure, and morphology after phosphoric acid, self-etching, and Er:YAG laser etching. Design. Seventy primary incisors were assigned to five groups (n=14: I (control, II (35% phosphoric acid, III (self-etching adhesive, IV (Er:YAG laser at 15 J/cm2, and V (Er:YAG laser at 19.1 J/cm2. Microhardness was evaluated by Vickers indentation. Chemical composition was analyzed by energy dispersive X-ray spectroscopy and morphological changes by scanning electron microscopy. One-way ANOVA, Kruskal–Wallis, Mann–Whitney U, and Pearson bivariate correlation were employed (α=0.05. Results. Vickers microhardness showed differences and no correlation with Ca/P ratio. Group II showed differences in carbon, oxygen, and phosphorus atomic percent and group V in Ca/P ratio. Morphological changes included exposed prisms, fractures, craters, and fusion. Conclusions. Enamel treated with phosphoric acid showed different chemical characterization among groups. Self-etching and Er:YAG laser irradiation at 19.1 J/cm2 showed similar microhardness and chemical characterization. Er:YAG laser irradiation at 15 J/cm2 maintained microhardness as untreated enamel. Er:YAG laser irradiation at 19.1 J/cm2 enhanced mineral content. Morphological retentive changes were specific to each type of etching protocol.

  16. Influence of pH and ozone dose on the content and structure of haloacetic acid precursors in groundwater.

    Science.gov (United States)

    Molnar, Jelena; Agbaba, Jasmina; Dalmacija, Božo; Rončević, Srđan; Prica, Miljana; Tubić, Aleksandra

    2012-09-01

    This study investigated the effects of pH (6-10) and ozone dose [0.4-3.0 mg O(3)/mg dissolved organic carbon (DOC)] on the content and structure of haloacetic acid (HAA) precursors in groundwater rich in natural organic matter (NOM; DOC 9.85 ± 0.18 mg/L) during drinking water treatment. The raw water was ozonated in a 2 L glass column. NOM fractionation was carried out using XAD resins. HAA formation potential (HAAFP) was determined according to standard EPA Method 552. NOM characterization revealed it is mostly hydrophobic (65 % fulvic and 14 % humic acids). Hydrophobic NOM significantly influences HAA formation, as confirmed by the high HAAFP (309 ± 15 μg/L). Ozonation at pH 6-10 led to changes in NOM structure, i.e. complete humic acid oxidation, and increased the hydrophilic NOM fraction content (65-90 % achieved using 3.0 mg O(3)/mg DOC). The highest degree of NOM oxidation and HAA precursor removal was achieved at pH 10 (up to 68 % HAAFP). Ozonation pH influenced the distribution of HAA precursor content, as increasing the pH from 6 to 10 increased the reactivity of the hydrophilic fraction, with the HAAFP increasing from 19.1 ± 6.0 μg/mg DOC in raw water to 152 ± 8 μg/mg DOC in ozonated water. The degree of HAA precursor removal depends on the dominant oxidation mechanism, which is related to the applied ozone dose and the pH of the oxidation process. Ozonation at pH 10 favours the mechanism of radical NOM oxidation and was the most effective for HAAFP reduction, with the efficacy of the process improving with increasing ozone dose.

  17. Fabrication of the micro/nano-structure superhydrophobic surface on aluminum alloy by sulfuric acid anodizing and polypropylene coating.

    Science.gov (United States)

    Wu, Ruomei; Liang, Shuquan; Liu, Jun; Pan, Anqiang; Yu, Y; Tang, Yan

    2013-03-01

    The preparation of the superhydrophobic surface on aluminum alloy by anodizing and polypropylene (PP) coating was reported. Both the different anodizing process and different PP coatings of aluminum alloy were investigated. The effects of different anodizing conditions, such as electrolyte concentration, anodization time and current on the superhydrophobic surface were discussed. By PP coating after anodizing, a good superhydrophobic surface was facilely fabricated. The optimum conditions for anodizing were determined by orthogonal experiments. After the aluminium-alloy was grinded with 600# sandpaper, pretreated by 73 g/L hydrochloric acid solution at 1 min, when the concentration of sulfuric acid was 180 g/L, the concentration of oxalic acid was 5 g/L, the concentration of potassium dichromate was 10 g/L, the concentration of chloride sodium was 50 g/L and 63 g/L of glycerol, anodization time was 20 min, and anodization current was 1.2 A/dm2, anodization temperature was 30-35 degrees C, the best micro-nanostructure aluminum alloy films was obtained. On the other hand, the PP with different concentrations was used to the PP with different concentrations was used to coat the aluminum alloy surface after anodizing. The results showed that the best superhydrophobicity was achieved by coating PP, and the duration of the superhydrophobic surface was improved by modifying the coat the aluminum alloy surface after anodizing. The results showed that the best superhydrophobicity was surface with high concentration PP. The morphologies of micro/nano-structure superhydrophobic surface were further confirmed by scanning electron microscope (SEM). The material of PP with the low surface free energy combined with the micro/nano-structures of the surface resulted in the superhydrophobicity of the aluminum alloy surface.

  18. Secondary structure of prokaryotic 5S ribosomal ribonucleic acids: a study with ribonucleases

    DEFF Research Database (Denmark)

    Douthwaite, S; Garrett, R A

    1981-01-01

    The structures of 5S ribosomal RNAs from Escherichia coli and Bacillus stearothermophilus were examined by using ribonucleases A, T1, and T2 and a double helix specific cobra venom ribonuclease. By using both 5' and 3'-32P-end labeling methods and selecting for digested but intact 5S RNA molecules...... evidence for three of the helical regions of the Fox and Woese model of 5S RNA [Fox, G. E., & Woese, C. (1975) Nature (London) 256, 505] and support other important structural features which include a nucleotide looped out from a helical region which has been proposed as a recognition site for protein L18....

  19. Organic salts formed by 2,4,6-triaminopyrimidine and selected carboxylic acids