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...

Silica promoted self-assembled mesoporous aluminas. Impact of the silica precursor on the structural, textural and acidic properties

NARCIS (Netherlands)

Perez, Lidia Lopez; Zarubina, Valeriya; Mayoral, Alvaro; Melian-Cabrera, Ignacio

2015-01-01

This paper investigates the effect of silica addition on the structural, textural and acidic properties of an evaporation induced self-assembled (EISA) mesoporous alumina. Two silica addition protocols were applied while maintaining the EISA synthesis route. The first route is based on the addition

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.

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.

A Standard Structure for Bile Acids and Derivatives

Directory of Open Access Journals (Sweden)

Francisco Meijide

2018-02-01

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

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.

Reliability analysis applied to structural tests

Science.gov (United States)

Diamond, P.; Payne, A. O.

1972-01-01

The application of reliability theory to predict, from structural fatigue test data, the risk of failure of a structure under service conditions because its load-carrying capability is progressively reduced by the extension of a fatigue crack, is considered. The procedure is applicable to both safe-life and fail-safe structures and, for a prescribed safety level, it will enable an inspection procedure to be planned or, if inspection is not feasible, it will evaluate the life to replacement. The theory has been further developed to cope with the case of structures with initial cracks, such as can occur in modern high-strength materials which are susceptible to the formation of small flaws during the production process. The method has been applied to a structure of high-strength steel and the results are compared with those obtained by the current life estimation procedures. This has shown that the conventional methods can be unconservative in certain cases, depending on the characteristics of the structure and the design operating conditions. The suitability of the probabilistic approach to the interpretation of the results from full-scale fatigue testing of aircraft structures is discussed and the assumptions involved are examined.

Lymphatic fatty acids in canine with pharmaceutical formulations containing structured triacylglycerols

DEFF Research Database (Denmark)

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

2006-01-01

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

Anti-reflection coatings applied by acid leaching process

Science.gov (United States)

Pastirik, E.

1980-01-01

The Magicote C process developed by S.M. Thompsen was evaluated for use in applying an antireflective coating to the cover plates of solar panels. The process uses a fluosilicic acid solution supersaturated with silica at elevated temperature to selectively attack the surface of soda-lime glass cover plates and alter the physical and chemical composition of a thin layer of glass. The altered glass layer constitutes an antireflective coating. The process produces coatings of excellent optical quality which possess outstanding resistance to soiling and staining. The coatings produced are not resistant to mechanical abrasion and are attacked to some extent by glass cleansers. Control of the filming process was found to be difficult.

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).

Path Integration Applied to Structural Systems with Uncertain Properties

DEFF Research Database (Denmark)

Nielsen, Søren R.K.; Köylüoglu, H. Ugur

Path integration (cell-to-cell mapping) method is applied to evaluate the joint probability density function (jpdf) of the response of the structural systems, with uncertain properties, subject to white noise excitation. A general methodology to deal with uncertainties is outlined and applied...... to the friction controlled slip of a structure on a foundation where the friction coefficient is modelled as a random variable. Exact results derived using the total probability theorem are compared to the ones obtained via path integration....

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

Science.gov (United States)

Rose, Peter W; Prlić, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F; Christie, Cole H; Dutta, Shuchismita; Green, Rachel Kramer; Goodsell, David S; Westbrook, John D; Woo, Jesse; Young, Jasmine; Zardecki, Christine; Berman, Helen M; Bourne, Philip E; Burley, Stephen K

2015-01-01

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

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.

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

Science.gov (United States)

Tikhonova, Irina G

2017-01-01

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

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.

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

Science.gov (United States)

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

2018-05-02

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

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

Science.gov (United States)

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

2008-08-01

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

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

Science.gov (United States)

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

2002-01-01

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

Resonant coupling applied to superconducting accelerator structures

International Nuclear Information System (INIS)

Potter, James M.; Krawczyk, Frank L.

2013-01-01

The concept of resonant coupling and the benefits that accrue from its application is well known in the world of room temperature coupled cavity linacs. Design studies show that it can be applied successfully between sections of conventional elliptical superconducting coupled cavity accelerator structures and internally to structures with spoked cavity resonators. The coupling mechanisms can be designed without creating problems with high field regions or multipactoring. The application of resonant coupling to superconducting accelerators eliminates the need for complex cryogenic mechanical tuners and reduces the time needed to bring a superconducting accelerator into operation.

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 ...

Acetaldehyde stimulation of net gluconeogenic carbon movement from applied malic acid in tomato fruit pericarp tissue

International Nuclear Information System (INIS)

Halinska, A.; Frenkel, C.

1991-01-01

Applied acetaldehyde is known to lead to sugar accumulation in fruit including tomatoes (Lycopersicon esculentum) presumably due to stimulation of gluconeogenesis. This conjecture was examined using tomato fruit pericarp discs as a test system and applied l-[U- 14 C]malic acid as the source for gluconeogenic carbon mobilization. Results indicate that malic and perhaps other organic acids are carbon sources for gluconeogenesis occurring normally in ripening tomatoes. The process is stimulated by acetaldehyde apparently by attenuating the fructose-2,6-biphosphate levels. The mode of the acetaldehyde regulation of fructose-2,6-biphosphate metabolism awaits clarification

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.

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

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

International Nuclear Information System (INIS)

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

2010-01-01

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

Toxicological studies on the Use of acid applied or combined with gamma radiation for controlling the mediterranean fruit fly Ceratitis Capitata Wied

International Nuclear Information System (INIS)

Fadel, A.M.; Othman, K.S.A.

1997-01-01

Biological studies were conducted to determine the effect of boric acid applied alone to different stages of ceratitis capitata or combined with gamma radiation of the produced treated pupae (9 days old). At a concentration range of 200-2000 ppm of boric acid per gm larval diet, larval and pupal durations were insignificantly affected. Pupation significantly decreased with increasing concentration, and adult emergence significantly increased at higher concentrations. Lc50 value of boric acid applied to the larval diet was 250 ppm. Applying boric acid as a powder mixed with pupal medium, the Lc50 was 96 mg/gm sand. Male and emergence significantly decreased. Significant mortality was obtained in adults of C capitata after applying boric acid as a thin film on the inner surface of the experimental cages where the adults were kept or when mixed with their food or as powder on the cage bottom. Applying boric acid to larval diet and gamma radiation to the produced pupae (9 days old) insignificantly affected larval and durations, percent pupation, adult emergence or adult survival. In cross-mating experiments, egg hatch ability was significantly reduced in the combination treatments of boric acid (500, 1000 ppm) and gamma radiation (90 Gy). On the other hand gamma radiation combined with boric acid treatments significantly increased male mating competitiveness at the concentration of 1000 ppm of boric acid followed by gamma irradiation (90 Gy). 2 figs., 5 tabs

[Apply fourier transform infrared spectra coupled with two-dimensional correlation analysis to study the evolution of humic acids during composting].

Science.gov (United States)

Bu, Gui-jun; Yu, Jing; Di, Hui-hui; Luo, Shi-jia; Zhou, Da-zhai; Xiao, Qiang

2015-02-01

The composition and structure of humic acids formed during composting play an important influence on the quality and mature of compost. In order to explore the composition and evolution mechanism, municipal solid wastes were collected to compost and humic and fulvic acids were obtained from these composted municipal solid wastes. Furthermore, fourier transform infrared spectra and two-dimensional correlation analysis were applied to study the composition and transformation of humic and fulvic acids during composting. The results from fourier transform infrared spectra showed that, the composition of humic acids was complex, and several absorbance peaks were observed at 2917-2924, 2844-2852, 2549, 1662, 1622, 1566, 1454, 1398, 1351, 990-1063, 839 and 711 cm(-1). Compared to humic acids, the composition of fulvci acids was simple, and only three peaks were detected at 1725, 1637 and 990 cm(-1). The appearance of these peaks showed that both humic and fulvic acids comprised the benzene originated from lignin and the polysaccharide. In addition, humic acids comprised a large number of aliphatic and protein which were hardly detected in fulvic acids. Aliphatic, polysaccharide, protein and lignin all were degraded during composting, however, the order of degradation was different between humic and fulvci acids. The result from two-dimensional correlation analysis showed that, organic compounds in humic acids were degraded in the following sequence: aliphatic> protein> polysaccharide and lignin, while that in fulvic acids was as following: protein> polysaccharide and aliphatic. A large number of carboxyl, alcohols and ethers were formed during the degradation process, and the carboxyl was transformed into carbonates. It can be concluded that, fourier transform infrared spectra coupled with two-dimensional correlation analysis not only can analyze the function group composition of humic substances, but also can characterize effectively the degradation sequence of these

Study on structural design technique of silicon carbide applied for thermochemical hydrogen production IS process

International Nuclear Information System (INIS)

Takegami, Hiroaki; Terada, Atsuhiko; Inagaki, Yoshiyuki; Ishikura, Syuichi

2011-03-01

The IS process is the hydrogen production method which used the thermochemical reaction cycle of sulfuric acid and iodyne. Therefore, the design to endure the high temperature and moreover corrode-able environment is required to the equipment. Specifically, the sulfuric acid decomposer which is one of the main equipment of the IS process is the equipment to heat with hot helium and for the sulfuric acid of 90 wt% to evaporate. Moreover, it is the important equipment to supply the SO 3 decomposer which is the following process, resolving the part of sulfuric acid vapor into SO 3 with. The heat exchanger that sulfuric acid evaporates must be made pressure-resistant structure because it has the high-pressure helium of 4 MPa and the material that the high temperature and the corrosion environment of equal to or more than 700degC can be endured must be used. As the material, it is selected from the corrosion experiment and so on when SiC which is carbonization silicone ceramics is the most excellent material. However, even if it damages the ceramic block which is a heat exchanger because it becomes the structure which is stored in pressure-resistant metallic container, fluid such as sulfuric acid becomes the structure which doesn't leak out outside. However, the structure design technique to have been unified when using ceramics as the structure part isn't serviced as the standard. This report is the one which was studied about the structural design technique to have taken the material strength characteristic of the ceramics into consideration, refer to existing structural design standard. (author)

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

International Nuclear Information System (INIS)

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

2014-01-01

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

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

Science.gov (United States)

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

2014-08-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1993-04-01

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

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

Science.gov (United States)

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

1993-04-01

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

Nucleic acid helix structure determination from NMR proton chemical shifts

Energy Technology Data Exchange (ETDEWEB)

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

2013-06-15

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

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

OpenAIRE

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

1993-01-01

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

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

Science.gov (United States)

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

2018-06-01

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

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

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.

Test fabrication of sulfuric acid decomposer applied for thermochemical hydrogen production IS process

International Nuclear Information System (INIS)

Noguchi, Hiroki; Terada, Atsuhiko; Kubo, Shinji; Onuki, Kaoru; Hino, Ryutaro; Ota, Hiroyuki

2007-07-01

Thermo-chemical Iodine-Sulfur (IS) process produces large amount of hydrogen effectively without carbon dioxide emission. Since the IS process uses strong acids such as sulfuric acid and hydriodic acid, it is necessary to develop large-scale chemical reactors featuring materials that exhibit excellent heat and corrosion resistance. A sulfuric acid decomposer is one of the key components of the IS process plant, in which sulfuric acid is evaporated and decomposed into water and sulfur trioxide under temperature range from 300degC to 500degC using the heat supplied by high temperature helium gas. The decomposer is exposed to severe corrosion condition of sulfuric acid boiling flow, where only the SiC ceramics shows good corrosion resistance. However, at the current status, it is very difficult to manufacture the large-scale SiC ceramics structure required in the commercial plant. Therefore, we devised a new concept of the decomposer, which featured a counter flow type heat exchanger consisting of cylindrical blocks made of SiC ceramics. Scale up can be realized by connecting the blocks in parallel and/or in series. This paper describes results of the design work and the test-fabrication study of the sulfuric acid decomposer, which was carried out in order to confirm its feasibility. (author)

Applied structural and solid mechanics section: 1983 review and 1984 programs

International Nuclear Information System (INIS)

Chadha, J.A.

1984-01-01

This report reviews briefly the applied research and problem solving work carried out by the Applied Structural and Solid Mechanics Section during 1983. In 1983 there was a strong demand for services in the areas of theroretical and experimental stress analysis, heat transfer analysis, nonlinear analysis, and general structural analyses related to nuclear and thermal power plant, and transmission line components. Development of capabilities in these areas progressed well. Proposed work programs for 1984 are outlined in this report

The effects of surface-applied jasmonic and salicylic acids on caterpillar growth and damage to tomato plants

Science.gov (United States)

Aaron L. Iverson; Louis R. Iverson; Steve Eshita

2001-01-01

We tested the role of salicylic acid (SA) and jasmonic acid (JA) in altering the tomato plant's defense against herbivory by tobacco hornworm. Treatments of SA or JA were topically applied to tomato plants, hornworm consumption was allowed to proceed for 12 days, and harvest analyses were performed Measurements taken included a subjective plant rating (1-10 score...

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

Quantitative Analysis of Mixtures of Monoprotic Acids Applying Modified Model-Based Rank Annihilation Factor Analysis on Variation Matrices of Spectrophotometric Acid-Base Titrations

Directory of Open Access Journals (Sweden)

Ebrahim Ghorbani-Kalhor

2015-04-01

Full Text Available In the current work, a new version of rank annihilation factor analysis was developedto circumvent the rank deficiency problem in multivariate data measurements.Simultaneous determination of dissociation constant and concentration of monoprotic acids was performed by applying model-based rank annihilation factor analysis on variation matrices of spectrophotometric acid-base titrations data. Variation matrices can be obtained by subtracting first row of data matrix from all rows of the main data matrix. This method uses variation matrices instead of multivariate spectrophotometric acid-base titrations matrices to circumvent the rank deficiency problem in the rank quantitation step. The applicability of this approach was evaluated by simulated data at first stage, then the binary mixtures of ascorbic and sorbic acids as model compounds were investigated by the proposed method. At the end, the proposed method was successfully applied for resolving the ascorbic and sorbic acid in an orange juice real sample. Therefore, unique results were achieved by applying rank annihilation factor analysis on variation matrix and using hard soft model combination advantage without any problem and difficulty in rank determination. Normal 0 false false false EN-US X-NONE AR-SA /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Arial; mso-bidi-theme-font:minor-bidi; mso-bidi-language:AR-SA;}    

Tailoring the Synergistic Bronsted-Lewis acidic effects in Heteropolyacid catalysts: Applied in Esterification and Transesterification Reactions

OpenAIRE

Tao, Meilin; Xue, Lifang; Sun, Zhong; Wang, Shengtian; Wang, Xiaohong; Shi, Junyou

2015-01-01

In order to investigate the influences of Lewis metals on acidic properties and catalytic activities, a series of Keggin heteropolyacid (HPA) catalysts, HnPW11MO39 (M = TiIV, CuII, AlIII, SnIV, FeIII, CrIII, ZrIV and ZnII; for Ti and Zr, the number of oxygen is 40), were prepared and applied in the esterification and transesterification reactions. Only those cations with moderate Lewis acidity had a higher impact. Ti Substituted HPA, H5PW11TiO40, posse lower acid content compared with TixH3−4...

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

International Nuclear Information System (INIS)

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

2013-01-01

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

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

Directory of Open Access Journals (Sweden)

SNEZANA BREZOVSKA

2005-02-01

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

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.

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

Science.gov (United States)

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

2011-07-01

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

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.

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.

Vine-shoot waste aqueous extract applied as foliar fertilizer to grapevines: Effect on amino acids and fermentative volatile content.

Science.gov (United States)

Sánchez-Gómez, R; Garde-Cerdán, T; Zalacain, A; Garcia, R; Cabrita, M J; Salinas, M R

2016-04-15

The aim of this work was to study the influence of foliar applications of different wood aqueous extracts on the amino acid content of musts and wines from Airén variety; and to study their relationship with the volatile compounds formed during alcoholic fermentation. For this purpose, the foliar treatments proposed were a vine-shoot aqueous extract applied in one and two times, and an oak extract which was only applied once. Results obtained show the potential of Airén vine-shoot waste aqueous extracts to be used as foliar fertilizer, enhancing the wine amino acid content especially when they were applied once. Similar results were observed with the aqueous oak extract. Regarding wine fermentative volatile compounds, there is a close relationship between musts and their wines amino acid content allowing us to discuss about the role of proline during the alcoholic fermentation and the generation of certain volatiles. Copyright © 2015 Elsevier Ltd. All rights reserved.

Investigation of Micro Square Structure Fabrication by Applying Textured Cutting Tool in WEDM

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Jianguo Zhang

2015-09-01

Full Text Available This paper studies micro structure fabrication by means of a textured tool cutting edge, which is manufactured by applying the wire cut electrical discharge machining (WEDM. Machining performance of the square structure fabrication on the tool cutting edge is investigated in the WEDM process, and the machining accuracy is explored in experimental analyses. In this proposed method, undesired overcut comes from the discharge between the processing debris and the side wall of the target structure. Furthermore, by applying the textured cutting tool, the target square structure is directly fabricated on the alumina workpiece with just a simple turning process, which verifies the feasibility of the proposed tool cutting edge textured method by applying the WEDM. This technology is expected to become a potential method for the mass production of micro structure surfaces in the future.

Prospect of Ti-Ni shape memory alloy applied in reactor structures

International Nuclear Information System (INIS)

Duan Yuangang

1995-01-01

Shape memory effect mechanism, physical property, composition, manufacturing process and application in mechanical structure of Ti-Ni shape memory alloy are introduced. Applications of Ti-Ni shape memory alloy in reactor structure are prospected and some necessary technical conditions of shape memory alloy applied in the reactor structure are put forward initially

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...

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

Science.gov (United States)

Ahmed, Sahar; Sprules, Tara; Kaur, Kamaljit

2014-07-01

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

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

Directory of Open Access Journals (Sweden)

Zhou Yuan Wu

2013-07-01

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

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

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

DEFF Research Database (Denmark)

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

2003-01-01

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

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...

The hybrid thermography approach applied to architectural structures

Science.gov (United States)

Sfarra, S.; Ambrosini, D.; Paoletti, D.; Nardi, I.; Pasqualoni, G.

2017-07-01

This work contains an overview of infrared thermography (IRT) method and its applications relating to the investigation of architectural structures. In this method, the passive approach is usually used in civil engineering, since it provides a panoramic view of the thermal anomalies to be interpreted also thanks to the use of photographs focused on the region of interest (ROI). The active approach, is more suitable for laboratory or indoor inspections, as well as for objects having a small size. The external stress to be applied is thermal, coming from non-natural apparatus such as lamps or hot / cold air jets. In addition, the latter permits to obtain quantitative information related to defects not detectable to the naked eyes. Very recently, the hybrid thermography (HIRT) approach has been introduced to the attention of the scientific panorama. It can be applied when the radiation coming from the sun, directly arrives (i.e., possibly without the shadow cast effect) on a surface exposed to the air. A large number of thermograms must be collected and a post-processing analysis is subsequently applied via advanced algorithms. Therefore, an appraisal of the defect depth can be obtained passing through the calculation of the combined thermal diffusivity of the materials above the defect. The approach is validated herein by working, in a first stage, on a mosaic sample having known defects while, in a second stage, on a Church built in L'Aquila (Italy) and covered with a particular masonry structure called apparecchio aquilano. The results obtained appear promising.

Zinc oxide modified with benzylphosphonic acids as transparent electrodes in regular and inverted organic solar cell structures

Energy Technology Data Exchange (ETDEWEB)

Lange, Ilja; Reiter, Sina; Kniepert, Juliane; Piersimoni, Fortunato; Brenner, Thomas; Neher, Dieter, E-mail: neher@uni-potsdam.de [Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam (Germany); Pätzel, Michael; Hildebrandt, Jana; Hecht, Stefan [Department of Chemistry and IRIS Adlershof, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin (Germany)

2015-03-16

An approach is presented to modify the work function of solution-processed sol-gel derived zinc oxide (ZnO) over an exceptionally wide range of more than 2.3 eV. This approach relies on the formation of dense and homogeneous self-assembled monolayers based on phosphonic acids with different dipole moments. This allows us to apply ZnO as charge selective bottom electrodes in either regular or inverted solar cell structures, using poly(3-hexylthiophene):phenyl-C71-butyric acid methyl ester as the active layer. These devices compete with or even surpass the performance of the reference on indium tin oxide/poly(3,4-ethylenedioxythiophene) polystyrene sulfonate. Our findings highlight the potential of properly modified ZnO as electron or hole extracting electrodes in hybrid optoelectronic devices.

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

Science.gov (United States)

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

1992-02-01

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

Influence of media with different acidity on structure of FeNi nanotubes

Science.gov (United States)

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

2018-04-01

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

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.

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

Science.gov (United States)

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

1995-07-01

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

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.

Influence of media with different acidity on structure of FeNi nanotubes

Directory of Open Access Journals (Sweden)

Shumskaya Alena

2018-01-01

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

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.

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.

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

Science.gov (United States)

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

2017-07-01

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

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

International Nuclear Information System (INIS)

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

1986-01-01

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

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.

Study of endogenic abscisic acids and cytokinin content in soybean crops of variable salt sensitivity as well as the effect of exogenically applied abscisic acid on Cl/sup -/ translocation. [in German

Energy Technology Data Exchange (ETDEWEB)

Roeb, G.

1981-05-01

A study of the phytohormones abscisic acid and cytokinin with respect to plant salt stress and its relationship to genetic control over endogen content. An analysis is made of the acid cytokinin content, and an investigation is made of the influence exerted by exogenic applied synthetic abscisic acid on Cl/sup -/ uptake and accumulation. 275 references, 14 figures, 11 tables.

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.

Structure, stability and behaviour of nucleic acids in ionic liquids

Science.gov (United States)

Tateishi-Karimata, Hisae; Sugimoto, Naoki

2014-01-01

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

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

Science.gov (United States)

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

2015-09-01

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

Polyurethane structural adhesives applied in automotive composite joints

Directory of Open Access Journals (Sweden)

Josue Garcia Quini

2012-06-01

Full Text Available In recent years structural adhesives technology has demonstrated great potential for application due to its capacity to transform complex structures into solid unitary and monolithic assemblies using different materials. Thus, seams or joints integrate these structures providing, besides a reduction in weight, a considerable increase in the mechanical resistance and stiffness. The increase in the industrial use of structural adhesives is mainly due to their ability to efficiently bond different materials in an irreversible manner, even replacing systems involving mechanical joints. In the automobile industry structural adhesives have been widely used for the bonding of metal substrates, thermoplastics and composites, frequently employing these in combination, particularly glass fiber and polyester resin composites molded using RTM and SMC processes. However, the use of urethane structural adhesives in applications involving composites and thermoplastics has been the subject of few investigations. In this study the effects of temperature and time on the shear strength of RTM, SMC and ABS joints, applying temperatures of -40, 25, 80, 120 and 177 °C and times of 20 minutes and 500 hours, were determined. The objective was to evaluate the performance under extreme conditions of use in order to assess whether these joints could be used in passenger or off-road vehicles. The results showed that the urethane structural adhesive promoted the efficient bonding of these materials, considering that due to the high adhesive strength the failures occurred in the substrates without adversely affecting the bonded area. For each test condition the joint failure modes were also determined.

Coda Wave Interferometry Method Applied in Structural Monitoring to Assess Damage Evolution in Masonry and Concrete Structures

International Nuclear Information System (INIS)

Masera, D; Bocca, P; Grazzini, A

2011-01-01

In this experimental program the main goal is to monitor the damage evolution in masonry and concrete structures by Acoustic Emission (AE) signal analysis applying a well-know seismic method. For this reason the concept of the coda wave interferometry is applied to AE signal recorded during the tests. Acoustic Emission (AE) are very effective non-destructive techniques applied to identify micro and macro-defects and their temporal evolution in several materials. This technique permits to estimate the velocity of ultrasound waves propagation and the amount of energy released during fracture propagation to obtain information on the criticality of the ongoing process. By means of AE monitoring, an experimental analysis on a set of reinforced masonry walls under variable amplitude loading and strengthening reinforced concrete (RC) beams under monotonic static load has been carried out. In the reinforced masonry wall, cyclic fatigue stress has been applied to accelerate the static creep and to forecast the corresponding creep behaviour of masonry under static long-time loading. During the tests, the evaluation of fracture growth is monitored by coda wave interferometry which represents a novel approach in structural monitoring based on AE relative change velocity of coda signal. In general, the sensitivity of coda waves has been used to estimate velocity changes in fault zones, in volcanoes, in a mining environment, and in ultrasound experiments. This method uses multiple scattered waves, which travelled through the material along numerous paths, to infer tiny temporal changes in the wave velocity. The applied method has the potential to be used as a 'damage-gauge' for monitoring velocity changes as a sign of damage evolution into masonry and concrete structures.

Coda Wave Interferometry Method Applied in Structural Monitoring to Assess Damage Evolution in Masonry and Concrete Structures

Energy Technology Data Exchange (ETDEWEB)

Masera, D; Bocca, P; Grazzini, A, E-mail: davide.masera@polito.it [Department of Structural and Geotechnical Engineering - Politecnico di Torino, corso Duca degli Abruzzi 24, 10129 Turin (Italy)

2011-07-19

In this experimental program the main goal is to monitor the damage evolution in masonry and concrete structures by Acoustic Emission (AE) signal analysis applying a well-know seismic method. For this reason the concept of the coda wave interferometry is applied to AE signal recorded during the tests. Acoustic Emission (AE) are very effective non-destructive techniques applied to identify micro and macro-defects and their temporal evolution in several materials. This technique permits to estimate the velocity of ultrasound waves propagation and the amount of energy released during fracture propagation to obtain information on the criticality of the ongoing process. By means of AE monitoring, an experimental analysis on a set of reinforced masonry walls under variable amplitude loading and strengthening reinforced concrete (RC) beams under monotonic static load has been carried out. In the reinforced masonry wall, cyclic fatigue stress has been applied to accelerate the static creep and to forecast the corresponding creep behaviour of masonry under static long-time loading. During the tests, the evaluation of fracture growth is monitored by coda wave interferometry which represents a novel approach in structural monitoring based on AE relative change velocity of coda signal. In general, the sensitivity of coda waves has been used to estimate velocity changes in fault zones, in volcanoes, in a mining environment, and in ultrasound experiments. This method uses multiple scattered waves, which travelled through the material along numerous paths, to infer tiny temporal changes in the wave velocity. The applied method has the potential to be used as a 'damage-gauge' for monitoring velocity changes as a sign of damage evolution into masonry and concrete structures.

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

Science.gov (United States)

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

2001-08-20

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

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)

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

Directory of Open Access Journals (Sweden)

Aaron M. Chesna

2017-03-01

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

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.

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

Directory of Open Access Journals (Sweden)

Dan-Andrei Catana

2012-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2013-11-01

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

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

International Nuclear Information System (INIS)

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

2013-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Pobul, L; Mannik, A

1974-01-01

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

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

Science.gov (United States)

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

2018-04-10

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

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

Science.gov (United States)

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

2016-06-09

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

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.

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.

Guidelines for Applying Cohesive Models to the Damage Behaviour of Engineering Materials and Structures

CERN Document Server

Schwalbe, Karl-Heinz; Cornec, Alfred

2013-01-01

This brief provides guidance for the application of cohesive models to determine damage and fracture in materials and structural components. This can be done for configurations with or without a pre-existing crack. Although the brief addresses structural behaviour, the methods described herein may also be applied to any deformation induced material damage and failure, e.g. those occurring during manufacturing processes. The methods described are applicable to the behaviour of ductile metallic materials and structural components made thereof. Hints are also given for applying the cohesive model to other materials.

Discovery of novel histidine-derived lipo-amino acids: applied in the synthesis of ultra-short antimicrobial peptidomimetics having potent antimicrobial activity, salt resistance and protease stability.

Science.gov (United States)

Ahn, Mija; Murugan, Ravichandran N; Jacob, Binu; Hyun, Jae-Kyung; Cheong, Chaejoon; Hwang, Eunha; Park, Hyo-Nam; Seo, Ji-Hyung; Srinivasrao, G; Lee, Kyung S; Shin, Song Yub; Bang, Jeong Kyu

2013-10-01

Here we report for the first time the synthesis of Histidine (His) derived lipo-amino acids having pendant lipid tails at N(τ)- and N(π)-positions on imidazole group of His and applied it into synthesis of lipo-peptides. The attachment of His-derived lipo-amino acid into the very short inactive cationic peptides endows potent antimicrobial activity against Gram-positive and Gram-negative bacteria without hemolytic activity. Furthermore, our designed His-derived lipo-peptidomimetics (HDLPs) consisting of two or three residues displayed strong anti-MRSA activity and protease stability as well as retained potent antimicrobial activity under high salt concentration. Our results demonstrate that the novel lipo-amino acid is highly flexible to synthesize and carry out the extensive structure-activity relationship (SAR) on lipo-antimicrobial peptidomimetics and represents a unique amenable platform for modifying parameters important for antimicrobial activity. Through this study, we proved that the discovery of His-derived lipo-amino acid and the corresponding HDLPs are an excellent candidate as a lead compound for the development of novel antimicrobial agents. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Applying Limestone or Basalt in Combination with Bio-Fertilizer to Sustain Rice Production on an Acid Sulfate Soil in Malaysia

Directory of Open Access Journals (Sweden)

Qurban Ali Panhwar

2016-07-01

Full Text Available A study was conducted to determine the efficacy of applying ground magnesium limestone (GML or ground basalt in combination with bio-fertilizer to sustain rice production on an acid sulfate soil in Malaysia. Soils from Kelantan Plains, Malaysia, were treated with GML, ground basalt, bio-fertilizer, GML + bio-fertilizer, and ground basalt + bio-fertilizer (4 t·ha−1 each. Results showed that soil fertility was improved by applying the soil amendments. GML and basalt contain some Zn and Cu; thus, application of these amendments would increase their contents in the soil needed for the healthy growth of rice. Basalt applied in combination with bio-fertilizer appeared to be the best agronomic option to improve the fertility of acid sulfate soils for sustainable rice production in the long run. In addition to increasing Ca, Mg, Zn, and Cu reserves in the soil, water pH increased and precipitated Al3+ and/or Fe2+. Ground basalt is cheaper than GML, but basalt dissolution in the acidic soil was slow. As such, its ameliorative effects could only be seen significantly from the second season onwards. The specially-formulated bio-fertilizer for alleviating the infertility of acid sulfate soil could also enhance rice growth. The use of the bio-fertilizer fortified with N2-fixing bacteria is a green technology that would help reduce NO3− and/or NO2− pollution and reduce the cost of rice production. The phosphate-solubilizing bacteria (PSB present in the bio-fertilizer not only increased the available P, but also helped release organic acids that would inactivate Al3+ and/or Fe2+ via the process of chelation.

Effects of Fatty Acid Inclusion in a DMPC Bilayer Membrane

DEFF Research Database (Denmark)

Peters, Günther H.J.; Hansen, Flemming Yssing; Møller, Martin S.

2009-01-01

Free fatty acids in biomembranes have been proposed to be a central component in several cellular control and regulatory mechanisms. To elucidate some fundamental elements underlying this, we have applied molecular dynamics simulations and experimental density measurements to study the molecular...... packing and structure of oleic acid (HOA) and stearic acid (HSA) in fluid bilayers of dimyristoylphosphatidylcholine (DMPC). The experimental data show a small but consistent positive excess volume for fatty acid concentrations below 10 mol %. At higher concentrations the fatty acids mix ideally...... with fluid DMPC. The simulations, which were benchmarked against the densitometric data, revealed interesting differences in the structure and location of the fatty acids depending on their protonation status. Thus, the protonated (uncharged) acid is located rather deeply in the membrane with an average...

Overview of experimental research on nuclear structure in department of modern applied physics

International Nuclear Information System (INIS)

Zhu Shengjiang

1999-01-01

The experimental research on nuclear structure in Department of Modern Applied Physics, Tsinghua University has been summarized. The main research results in high spin states of nuclear structure, as well as some low spin states, have been reported

In-situ Spectroscopic Studies and Modelling of Crystallization Processes of Sulphuric Acid Catalysts

DEFF Research Database (Denmark)

Oehlers, C.; Fehrmann, Rasmus; Masters, Stephen Grenville

1996-01-01

Deactivation of commercial and prototype sulphuric acid catalysts has been investigated in-situ by ESR spectroscopy. The influence of support pore structure,and the chemical composition of the catalyst and the gas phase was dicussed.A statistical lattice model was applied to describe the crystall......Deactivation of commercial and prototype sulphuric acid catalysts has been investigated in-situ by ESR spectroscopy. The influence of support pore structure,and the chemical composition of the catalyst and the gas phase was dicussed.A statistical lattice model was applied to describe...

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

Science.gov (United States)

SilRoy, Sumita; Ghosh, Mahua

2011-01-01

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

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

Science.gov (United States)

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

2018-04-01

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

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.

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.

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

DEFF Research Database (Denmark)

Norrild, Jens Chr.; Søtofte, Inger

2002-01-01

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

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

Science.gov (United States)

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

2014-01-01

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

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

International Nuclear Information System (INIS)

Guoxin Tian; Linfeng Rao

2006-01-01

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

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.

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

Science.gov (United States)

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

2007-10-01

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

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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

DEFF Research Database (Denmark)

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

2004-01-01

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

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

Science.gov (United States)

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

2016-07-01

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

The effect of physically applied alpha hydroxyl acids on the skin pore and comedone.

Science.gov (United States)

Kim, S J; Baek, J H; Koh, J S; Bae, M I; Lee, S J; Shin, M K

2015-10-01

Alpha hydroxy acids (AHA) have been recognized as commonly used therapy for acne. Our studies examined whether an additional effect of physical treatment using chemical peeling combined with negative pressure and compared with AHA treatment only occurs in acne-prone subjects. The chemical peeling agent used 4% of an AHA solution (mixture of 1000 mL of carbonated water, 20 mL of glycolic acid and 20 mL of lactic acid). All subjects' faces were randomly divided into test and control groups. The test group was treated with chemical peeling combined with a physical effect, and the control group applied chemical peeling alone. For the 23 healthy females (average age: 30.17 ± 5.06 year), we measured sebum output level by light transmission, pore area and number by optical image analyser, and comedone counting before treatment and at 1, 2 and 4 weeks after a single treatment. Compared to the before treatment, whiteheads and blackheads were significantly decreased at 1, 2 and 4 weeks in the test group (P Pore area and number significantly decreased at 1 week (P pore size and seborrhoea. © 2015 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

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.

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

DEFF Research Database (Denmark)

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

2001-01-01

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

A rapid NMR-based method for discrimination of strain-specific cell wall teichoic acid structures reveals a third backbone type in Lactobacillus plantarum.

Science.gov (United States)

Tomita, Satoru; Tanaka, Naoto; Okada, Sanae

2017-03-01

The lactic acid bacterium Lactobacillus plantarum is capable of producing strain-specific structures of cell wall teichoic acid (WTA), an anionic polysaccharide found in the Gram-positive bacterial cell wall. In this study, we established a rapid, NMR-based procedure to discriminate WTA structures in this species, and applied it to 94 strains of L. plantarum. Six previously reported glycerol- and ribitol-containing WTA subtypes were successfully identified from 78 strains, suggesting that these were the dominant structures. However, the level of structural variety differed markedly among bacterial sources, possibly reflecting differences in strain-level microbial diversity. WTAs from eight strains were not identified based on NMR spectra and were classified into three groups. Structural analysis of a partial degradation product of an unidentified WTA produced by strain TUA 1496L revealed that the WTA was 1-O-β-d-glucosylglycerol. Two-dimensional NMR analysis of the polymer structure showed phosphodiester bonds between C-3 and C-6 of the glycerol and glucose residues, suggesting a polymer structure of 3,6΄-linked poly(1-O-β-d-glucosyl-sn-glycerol phosphate). This is the third WTA backbone structure in L. plantarum, following 3,6΄-linked poly(1-O-α-d-glucosyl-sn-glycerol phosphate) and 1,5-linked poly(ribitol phosphate). © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

Science.gov (United States)

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

2006-07-01

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

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

International Nuclear Information System (INIS)

Galasso, V.

2010-01-01

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

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.

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.

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

Old and new approaches to the interpretation of acid-base metabolism, starting from historical data applied to diabetic acidosis.

Science.gov (United States)

Mioni, Roberto; Marega, Alessandra; Lo Cicero, Marco; Montanaro, Domenico

2016-11-01

The approach to acid-base chemistry in medicine includes several methods. Currently, the two most popular procedures are derived from Stewart's studies and from the bicarbonate/BE-based classical formulation. Another method, unfortunately little known, follows the Kildeberg theory applied to acid-base titration. By using the data produced by Dana Atchley in 1933, regarding electrolytes and blood gas analysis applied to diabetes, we compared the three aforementioned methods, in order to highlight their strengths and their weaknesses. The results obtained, by reprocessing the data of Atchley, have shown that Kildeberg's approach, unlike the other two methods, is consistent, rational and complete for describing the organ-physiological behavior of the hydrogen ion turnover in human organism. In contrast, the data obtained using the Stewart approach and the bicarbonate-based classical formulation are misleading and fail to specify which organs or systems are involved in causing or maintaining the diabetic acidosis. Stewart's approach, despite being considered 'quantitative', does not propose in any way the concept of 'an amount of acid' and becomes even more confusing, because it is not clear how to distinguish between 'strong' and 'weak' ions. As for Stewart's approach, the classical method makes no distinction between hydrogen ions managed by the intermediate metabolism and hydroxyl ions handled by the kidney, but, at least, it is based on the concept of titration (base-excess) and indirectly defines the concept of 'an amount of acid'. In conclusion, only Kildeberg's approach offers a complete understanding of the causes and remedies against any type of acid-base disturbance.

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.

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

Science.gov (United States)

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

2009-09-01

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

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.

A new approach for structural health monitoring by applying anomaly detection on strain sensor data

Science.gov (United States)

Trichias, Konstantinos; Pijpers, Richard; Meeuwissen, Erik

2014-03-01

Structural Health Monitoring (SHM) systems help to monitor critical infrastructures (bridges, tunnels, etc.) remotely and provide up-to-date information about their physical condition. In addition, it helps to predict the structure's life and required maintenance in a cost-efficient way. Typically, inspection data gives insight in the structural health. The global structural behavior, and predominantly the structural loading, is generally measured with vibration and strain sensors. Acoustic emission sensors are more and more used for measuring global crack activity near critical locations. In this paper, we present a procedure for local structural health monitoring by applying Anomaly Detection (AD) on strain sensor data for sensors that are applied in expected crack path. Sensor data is analyzed by automatic anomaly detection in order to find crack activity at an early stage. This approach targets the monitoring of critical structural locations, such as welds, near which strain sensors can be applied during construction and/or locations with limited inspection possibilities during structural operation. We investigate several anomaly detection techniques to detect changes in statistical properties, indicating structural degradation. The most effective one is a novel polynomial fitting technique, which tracks slow changes in sensor data. Our approach has been tested on a representative test structure (bridge deck) in a lab environment, under constant and variable amplitude fatigue loading. In both cases, the evolving cracks at the monitored locations were successfully detected, autonomously, by our AD monitoring tool.

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

International Nuclear Information System (INIS)

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

1994-01-01

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

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

Science.gov (United States)

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

2012-02-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1986-01-01

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

The relationship between the applied torque and stresses in post-tension structures

International Nuclear Information System (INIS)

Liew, F.K.; Hamdan, S.; Osman, M.S.

2008-01-01

This paper presents the nondestructive testing (NDT) method to determine the resultant stresses in mild steel bar usually employed in structures. The technique utilized ultrasonic pulse-echo that determined the wave velocity change due to torque applied between bolt and nut. Mild steel bar with nominal diameter of 19 and 25mm were used. The specimen was loaded by means of a torque wrench that gave the required amount of moment (∼300Nm). This was carefully achieved manually. In order to measure the strain, strain gauges were employed. The direct strain gauge method gives the strain values. This strain is used to calculate the stress due to the applied load. The experiment had been carried out in a control environment with constant temperature. The relationship between torque-velocity, torque-strain and stress-strain is obtained and compared. The test results indicate that ultrasonic wave velocity decrease with the applied torque. This is due to degradation or loss of strength of the material. The potential of this NDT method to obtain structure quality and strength determination is discussed. (author)

The relationship between the applied torque and stresses in post-tension structures

Energy Technology Data Exchange (ETDEWEB)

Liew, F.K.; Hamdan, S.; Osman, M.S. [Univ. Malaysia Sarawak, Faculty of Engineering, Kota Samarahan, Sarawak (Malaysia)

2008-09-15

This paper presents the nondestructive testing (NDT) method to determine the resultant stresses in mild steel bar usually employed in structures. The technique utilized ultrasonic pulse-echo that determined the wave velocity change due to torque applied between bolt and nut. Mild steel bar with nominal diameter of 19 and 25mm were used. The specimen was loaded by means of a torque wrench that gave the required amount of moment (∼300Nm). This was carefully achieved manually. In order to measure the strain, strain gauges were employed. The direct strain gauge method gives the strain values. This strain is used to calculate the stress due to the applied load. The experiment had been carried out in a control environment with constant temperature. The relationship between torque-velocity, torque-strain and stress-strain is obtained and compared. The test results indicate that ultrasonic wave velocity decrease with the applied torque. This is due to degradation or loss of strength of the material. The potential of this NDT method to obtain structure quality and strength determination is discussed. (author)

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

DEFF Research Database (Denmark)

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

2006-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2009-05-15

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

Structural and electronic properties of L-amino acids

Science.gov (United States)

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

2005-05-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2010-12-15

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

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

Science.gov (United States)

Holmes, D. S.

2016-12-01

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

Synthesis and conductivity of heptadecatungstovanadodiphosphoric heteropoly acid with Dawson structure

Energy Technology Data Exchange (ETDEWEB)

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

2011-07-21

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

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.

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.

Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2)

Science.gov (United States)

Anderson, Lissa C.; Håkansson, Maria; Walse, Björn; Nilsson, Carol L.

2017-09-01

Structural technologies are an essential component in the design of precision therapeutics. Precision medicine entails the development of therapeutics directed toward a designated target protein, with the goal to deliver the right drug to the right patient at the right time. In the field of oncology, protein structural variants are often associated with oncogenic potential. In a previous proteogenomic screen of patient-derived glioblastoma (GBM) tumor materials, we identified a sequence variant of human mitochondrial branched-chain amino acid aminotransferase 2 as a putative factor of resistance of GBM to standard-of-care-treatments. The enzyme generates glutamate, which is neurotoxic. To elucidate structural coordinates that may confer altered substrate binding or activity of the variant BCAT2 T186R, a 45 kDa protein, we applied combined ETD and CID top-down mass spectrometry in a LC-FT-ICR MS at 21 T, and X-Ray crystallography in the study of both the variant and non-variant intact proteins. The combined ETD/CID fragmentation pattern allowed for not only extensive sequence coverage but also confident localization of the amino acid variant to its position in the sequence. The crystallographic experiments confirmed the hypothesis generated by in silico structural homology modeling, that the Lys59 side-chain of BCAT2 may repulse the Arg186 in the variant protein (PDB code: 5MPR), leading to destabilization of the protein dimer and altered enzyme kinetics. Taken together, the MS and novel 3D structural data give us reason to further pursue BCAT2 T186R as a precision drug target in GBM. [Figure not available: see fulltext.

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).

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

International Nuclear Information System (INIS)

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

1986-01-01

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

Quantitative structure-cytotoxicity relationship of piperic acid amides.

Science.gov (United States)

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

2014-09-01

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

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.

Utilization of applied zinc by rice crop in wetland acidic soils

International Nuclear Information System (INIS)

Singh, A.K.; Nongkynrih, P.; Sachdev, P.; Sachdev, M.S.

2001-01-01

A greenhouse experiment was conducted to study the response of rice plant to zinc fertilizer under submerged condition using 65 Zn-labelled ZnSO 4 in 13 wetland acidic soils of Meghalaya. Application of Zn significantly increased the dry matter yield. Dry matter yield, total Zn content and per cent Zndff of rice plant at 2.5 and 5 mg Zn kg -1 increased significantly from 7.05 to 8.47 g/pot, 66 g/pot to 78 mg/pot and 7.56 to 8.73 per cent, respectively. Per cent Zn utilization declined significantly from 0.188 to 0.131 on enhancing the levels of Zn from 2.5 to 5 mg kg -1 . On an average, per cent utilization of added Zn by rice plant was only a fraction of total quantity of applied Zn. Most of the soil characteristics analysed play important role in regulating the availability of added Zn in these soils. (author)

[Teichoic acids from lactic acid bacteria].

Science.gov (United States)

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

2012-01-01

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

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

Science.gov (United States)

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

2016-03-01

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

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

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

Group I mGlu receptors potentiate synaptosomal [3H]glutamate release independently of exogenously applied arachidonic acid

International Nuclear Information System (INIS)

Reid, M.E.; Toms, N.J.; Bedingfield, J.S.; Roberts, P.J.

1999-01-01

In the current study, we have characterized group I metabotropic glutamate (mGlu) receptor enhancement of 4-aminopyridine (4AP)-evoked [ 3 H]glutamate release from rat cerebrocortical synaptosomes. The broad spectrum mGlu receptor agonist (1S,3R)-1-aminocyclopentane-1,3-dicarboxylic acid ((1S,3R)-ACPD, 10 μM) increased 4AP-evoked [ 3 H]glutamate release (143.32±2.73% control) only in the presence of exogenously applied arachidonic acid; an effect reversed by the inclusion of bovine serum albumin (BSA, fatty acid free). In contrast, the selective group I mGlu receptor agonist (S)-3,5-dihydroxyphenylglycine (DHPG) potentiated (EC 50 =1.60±0.25 μM; E max =147.61±10.96% control) 4AP-evoked [ 3 H]glutamate release, in the absence of arachidonic acid. This potentiation could be abolished by either the selective mGlu 1 receptor antagonist (R,S)-1-aminoindan-1,5-dicarboxylic acid (AIDA, 1 mM) or the selective PKC inhibitor (Ro 31-8220, 10 μM) and was BSA-insensitive. The selective mGlu 5 receptor agonist (R,S)-2-chloro-5-hydroxyphenylglycine (CHPG, 300μM) was without effect. DHPG (100 μM) also potentiated both 30 mM and 50 mM K + -evoked [ 3 H]glutamate release (121.60±12.77% and 121.50±4.45% control, respectively). DHPG (100 μM) failed to influence both 4AP-stimulated 45 Ca 2+ influx and 50 mM K + -induced changes in synaptosomal membrane potential. Possible group I mGlu receptor suppression of tonic adenosine A 1 receptor, group II/III mGlu receptors or GABA B receptor activity is unlikely since 4AP-evoked [ 3 H]glutamate release was insensitive to the selective inhibitory receptor antagonists 8-cyclopentyl-1,3-dimethylxanthine, (R,S)-α-cyclopropyl-4-phosphonophenylglycine or CGP55845A, respectively. These data suggest an 'mGlu 1 receptor-like' receptor potentiates [ 3 H]glutamate release from cerebrocortical synaptosomes in the absence of exogenously applied arachidonic acid. This PKC dependent effect is unlikely to be via modulation of synaptosomal membrane

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.

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.

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

Energy Technology Data Exchange (ETDEWEB)

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

2006-06-10

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

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.

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

Science.gov (United States)

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

2016-06-07

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

Assessment for Melting Temperature Measurement of Nucleic Acid by HRM.

Science.gov (United States)

Wang, Jing; Pan, Xiaoming; Liang, Xingguo

2016-01-01

High resolution melting (HRM), with a high sensitivity to distinguish the nucleic acid species with small variations, has been widely applied in the mutation scanning, methylation analysis, and genotyping. For the aim of extending HRM for the evaluation of thermal stability of nucleic acid secondary structures on sequence dependence, we investigated effects of the dye of EvaGreen, metal ions, and impurities (such as dNTPs) on melting temperature ( T m ) measurement by HRM. The accuracy of HRM was assessed as compared with UV melting method, and little difference between the two methods was found when the DNA T m was higher than 40°C. Both insufficiency and excessiveness of EvaGreen were found to give rise to a little bit higher T m , showing that the proportion of dye should be considered for precise T m measurement of nucleic acids. Finally, HRM method was also successfully used to measure T m s of DNA triplex, hairpin, and RNA duplex. In conclusion, HRM can be applied in the evaluation of thermal stability of nucleic acid (DNA or RNA) or secondary structural elements (even when dNTPs are present).

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....

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

Science.gov (United States)

Hogsden, Kristy L; Harding, Jon S

2012-03-01

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

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

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

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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.

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

Science.gov (United States)

Goodger, Jason Q D; Woodrow, Ian E

2011-12-01

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

Electrodeposited Fe-Co films prepared from a citric-acid-based plating bath

OpenAIRE

Yanai, Takeshi; Uto, H.; Shimokawa, Takaya; Nakano, Masaki; Fukunaga, Hirotoshi; Suzuki, K.

2013-01-01

Electrodeposited Fe-Co films are commonly prepared in a boric-acid-based bath. In this research, we applied citric acid instead of boric acid for the plating of Fe-Co films because boron in the waste bath is restricted by environmental-protection regulations in Japan. We evaluated the effect of citric acid on the magnetic and structural properties of the films. The saturation magnetization of the Fe-Co films slightly increased while the Fe content in the Fe-Co films decreased with increasing ...

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

Science.gov (United States)

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

2018-03-01

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

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).

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).

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...

Facile Synthesis of Oleanolic Acid Monoglycosides and Diglycosides

Directory of Open Access Journals (Sweden)

Mao-Sheng Cheng

2008-07-01

Full Text Available Oleanolic acid and its glycosides are important natural products, possessing various attractive biological activities such as antitumor, antivirus and anti-inflammatory properties. In the present work, fifteen oleanolic acid saponins bearing various saccharide moieties, including 3-monoglycoside, 28-monoglycoside and 3,28-diglycoside, were easily synthesized in high yields. Benzyl was chosen as the protective group for the COOH(28 group, instead of commonly used methyl and allyl, to avoid difficulties in the final deprotection. Alkali-promoted condensation of the carboxylic acid with bromoglycosides was found to be more efficient in the synthesis of 28-glycosides. Two approaches were investigated and proved practicable in the preparation of 3,28- diglycosides. This method is suitable for preparing oleanolic acid glycosides with structural diversity for extensive biological evaluation and structure-activity relationship study, and it also apply new idea for the corresponding synthetic methods to the glycoside derivatives of other triterpenoid.

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

Science.gov (United States)

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

2018-06-25

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

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

Science.gov (United States)

Jelínek, Jan; Škoda, Petr; Hoksza, David

2017-12-06

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

Structure of rat acidic fibroblast growth factor at 1.4 Å resolution

International Nuclear Information System (INIS)

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

2007-01-01

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

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

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.

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.

New Acid Combination for a Successful Sandstone Acidizing

Science.gov (United States)

Shafiq, M. U.; Mahmud, H. K. B.; Rezaee, R.

2017-05-01

With the development of new enhanced oil recovery techniques, sandstone acidizing has been introduced and played a pivotal role in the petroleum industry. Different acid combinations have been applied, which react with the formation, dissolve the soluble particles; thus increase the production of hydrocarbons. To solve the problems which occurred using current preflush sandstone acidizing technology (hydrochloric acid); a new acid combination has been developed. Core flooding experiments on sandstone core samples with dimensions 1.5 in. × 3 in. were conducted at a flow rate of 2 cm3/min. A series of hydrochloric-acetic acid mixtures with different ratios were tested under 150°F temperature. The core flooding experiments performed are aimed to dissolve carbonate, sodium, potassium and calcium particles from the core samples. These experiments are followed by few important tests which include, porosity-permeability, pH value, Inductively Coupled Plasma (ICP) analysis and Nuclear Magnetic Resonance (NMR measurements). All the results are compared with the results of conventional hydrochloric acid technology. NMR and porosity analysis concluded that the new acid combination is more effective in creating fresh pore spaces and thus increasing the reservoir permeability. It can be seen from the pore distribution before and after the acidizing. Prior applying acid; the large size of pores appears most frequently in the pore distribution while with the applied acid, it was found that the small pore size is most the predominant of the pore distribution. These results are validated using ICP analysis which shows the effective removal of calcium and other positive ions from the core sample. This study concludes that the combination of acetic-hydrochloric acid can be a potential candidate for the preflush stage of sandstone acidizing at high temperature reservoirs.

Excitation of plane Lamb wave in plate-like structures under applied surface loading

Science.gov (United States)

Zhou, Kai; Xu, Xinsheng; Zhao, Zhen; Yang, Zhengyan; Zhou, Zhenhuan; Wu, Zhanjun

2018-02-01

Lamb waves play an important role in structure health monitoring (SHM) systems. The excitation of Lamb waves has been discussed for a long time with absorbing results. However, little effort has been made towards the precise characterization of Lamb wave excitation by various transducer models with mathematical foundation. In this paper, the excitation of plane Lamb waves with plane strain assumption in isotropic plate structures under applied surface loading is solved with the Hamiltonian system. The response of the Lamb modes excited by applied loading is expressed analytically. The effect of applied loading is divided into the product of two parts as the effect of direction and the effect of distribution, which can be changed by selecting different types of transducer and the corresponding transducer configurations. The direction of loading determines the corresponding displacement of each mode. The effect of applied loading on the in-plane and normal directions depends on the in-plane and normal displacements at the surface respectively. The effect of the surface loading distribution on the Lamb mode amplitudes is mainly reflected by amplitude versus frequency or wavenumber. The frequencies at which the maxima and minima of the S0 or A0 mode response occur depend on the distribution of surface loading. The numerical results of simulations conducted on an infinite aluminum plate verify the theoretical prediction of not only the direction but also the distribution of applied loading. A pure S0 or A0 mode can be excited by selecting the appropriate direction and distribution at the corresponding frequency.

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

International Nuclear Information System (INIS)

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

2012-01-01

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

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

Science.gov (United States)

Kulandaisamy, Arockia Jayalatha; Rayappan, John Bosco Balaguru

2018-08-01

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

Computer Aided Synthesis of Innovative Processes: Renewable Adipic Acid Production

DEFF Research Database (Denmark)

Rosengarta, Alessandro; Bertran, Maria-Ona; Manenti, Flavio

2017-01-01

A promising biotechnological route for the production of adipic acid from renewables has been evaluated, applying a systematic methodology for process network synthesis and optimization. The method allows organizing in a structured database the available knowledge from different sources (prelimin...

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

Science.gov (United States)

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

2016-12-15

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

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)

Releasing Pattern of Applied Phosphorus and Distribution Change of Phosphorus Fractions in the Acid Upland Soils with Successive Resin Extraction

Directory of Open Access Journals (Sweden)

Arief Hartono

2008-05-01

Full Text Available The releasing pattern of applied P in the acid upland soils and the soil properties influencing the pattern were studied. Surface horizons of six acid upland soils from Sumatra, Java and Kalimantan were used in this study. The releasing pattern of applied P (300 mg P kg-1 of these soils were studied by successive resin extraction. P fractionation was conducted to evaluate which fractions released P to the soil solution after successive resin extraction. The cumulative of resin-Pinorganic (Pi release of soils was fitted to the first order kinetic. Regression analyses using factor scores obtained from the previous principal components analyses was applied to determine soil properties influencing P releasing pattern. The results suggested that the maximum P release was significantly (P < 0.05 increased by acidity plus 1.4 nm mineral-related factor (PC2 i.e. exchangeable Al and 1.4 nm minerals (smectite and vermiculite and decreased by oxide related factor (PC1 i.e. aluminum (Al plus 1/2 iron (Fe (by ammonium oxalate, crystalline Al and Fe oxides, cation exchange capacity, and clay content. P fractionation analysis after successive resin extraction showed that both labile and less labile in the form of NaHCO3-Pi and NaOH-Pi fractions, respectively, can be transformed into resin-Pi when in the most labile resin-Pi is depleted. Most of P released in high oxides soils were from NaOH-Pi fraction while in low oxides soils were from NaHCO3-Pi. P release from the former fraction resulted in the maximum P release lower than that of the latter one. When NaHCO3-Pi was high, NaOH-Pi was relatively more stable than NaHCO3-Pi despite resin-Pi removal. NaHCO3-Pi and NaOH-Pi are very important P fractions in replenishing resin-Pi in these acid upland soils.

Innovations in structuring article introductions: The case of Applied Linguistics

Directory of Open Access Journals (Sweden)

Ling Lin

2014-10-01

Full Text Available This study explores the rhetorical structure of introductions that are followed by an independent Literature Review (L section. It is motivated by an increasing use or even the prevalent use of both the introduction and L sections in the opening phase of empirical research articles in many disciplines and the lack of systematic genre-based investigation of introductions with a following L section. Based on a detailed examination of 30 introductions with a subsequent L section in Applied Linguistics, this study found that they generally can be classified into two categories according to their communicative functions and structures. They are the traditional CARS type that largely follows the classic “Create a Research Space” (CARS model and the innovative Two-move Orientation type. Some featured elements used in the introductions with a subsequent L are identified and the “Two-move Orientation” approach is formulated for the rhetorical structure of this new type of introductions. The interesting links between introduction and L are also suggested. The study contributes to our understanding of the structure and function of this important part-genre in a new generic context (that is, introductions being followed by an independent L section and illuminates the current genre-based teaching of introduction writing.

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.

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.

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.

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.

Gustatory sensation of (L)- and (D)-amino acids in humans.

Science.gov (United States)

Kawai, Misako; Sekine-Hayakawa, Yuki; Okiyama, Atsushi; Ninomiya, Yuzo

2012-12-01

Amino acids are known to elicit complex taste, but most human psychophysical studies on the taste of amino acids have focused on a single basic taste, such as umami (savory) taste, sweetness, or bitterness. In this study, we addressed the potential relationship between the structure and the taste properties of amino acids by measuring the human gustatory intensity and quality in response to aqueous solutions of proteogenic amino acids in comparison to D-enantiomers. Trained subjects tasted aqueous solution of each amino acid and evaluated the intensities of total taste and each basic taste using a category-ratio scale. Each basic taste of amino acids showed the dependency on its hydrophobicity, size, charge, functional groups on the side chain, and chirality of the alpha carbon. In addition, the overall taste of amino acid was found to be the combination of basic tastes according to the partial structure. For example, hydrophilic non-charged middle-sized amino acids elicited sweetness, and L-enantiomeric hydrophilic middle-sized structure was necessary for umami taste. For example, L-serine had mainly sweet and minor umami taste, and D-serine was sweet. We further applied Stevens' psychophysical function to relate the total-taste intensity and the concentration, and found that the slope values depended on the major quality of taste (e.g., bitter large, sour small).

Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

Science.gov (United States)

Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

2008-11-15

Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions.

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

Science.gov (United States)

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

2017-10-01

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

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.

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

International Nuclear Information System (INIS)

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

1997-01-01

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

Induction Heating System Applied to Injection Moulding of Micro and Nano Structures

DEFF Research Database (Denmark)

Menotti, Stefano

The present Ph.D. thesis contains a study concerning induction heating system applied to injection moulding of micro and nano structures. The overall process chain was considered and investigated during the project including part design, simulation, conventional and non-conventional tooling...... part. In fact one of the main problems in micro injection moulding is the premature freezing of the polymer flow inside the cavity and often is not possible to obtain a full replica of the nano/micro structures embed on the surfaces. Some other defects that can be avoided with the use of an additional...

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

International Nuclear Information System (INIS)

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

2001-01-01

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

Development of a UV-Cleavable Protecting Group for Hydroxylamines, Synthesis of a StructurallyWide Variety of Hydroxamic Acids, and Identification of Histone Deacetylase Inhibitors

DEFF Research Database (Denmark)

Mortensen, Kim Thollund

Photo-cleavable protecting groups are highly applicable for the synthesis of structural complex and sensitive compounds, including biological important molecules. Herein, we present the development of a novel O-hydroxylamine photo-cleavable protecting group, based on the methyl-6-nitroveratryl...... moiety. We demonstrate the application of the protected hydroxylamine derivative for the synthesis of N-alkylated hydroxamic acids. We have shown that the construct is stable toward a diverse set of reaction conditions, as well as orthogonal with conventional protection groups. The O......-protected hydroxylamine derivative was applied to synthesize a small collection of N-alkylated hydroxamic acids as inhibitors of the histone deacetylase enzymes, an important class of enzymes for the treatment of a range of diseases, most importantly cancer. During my external stay at Nanyang Technological University...

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.

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.

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

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.

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.

Monte Carlo Simulation of Ferroelectric Domain Structure and Applied Field Response in Two Dimensions

Energy Technology Data Exchange (ETDEWEB)

Potter, Jr., B.G.; Tikare, V.; Tuttle, B.A.

1999-06-30

A 2-D, lattice-Monte Carlo approach was developed to simulate ferroelectric domain structure. The model currently utilizes a Hamiltonian for the total energy based only upon electrostatic terms involving dipole-dipole interactions, local polarization gradients and the influence of applied electric fields. The impact of boundary conditions on the domain configurations obtained was also examined. In general, the model exhibits domain structure characteristics consistent with those observed in a tetragonally distorted ferroelectric. The model was also extended to enable the simulation of ferroelectric hysteresis behavior. Simulated hysteresis loops were found to be very similar in appearance to those observed experimentally in actual materials. This qualitative agreement between the simulated hysteresis loop characteristics and real ferroelectric behavior was also confirmed in simulations run over a range of simulation temperatures and applied field frequencies.

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

International Nuclear Information System (INIS)

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

2008-01-01

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

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

International Nuclear Information System (INIS)

Wang Shutao; Song Yanlin; Jiang Lei

2007-01-01

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

Electrochemical activity of iron in acid treated bentonite and influence of added nickel

Energy Technology Data Exchange (ETDEWEB)

Mudrinić, T., E-mail: tihana@nanosys.ihtm.bg.ac.rs [University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Center for Catalysis and Chemical Engineering, Njegoševa 12, 11000 Belgrade (Serbia); Mojović, Z.; Milutinović-Nikolić, A. [University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Center for Catalysis and Chemical Engineering, Njegoševa 12, 11000 Belgrade (Serbia); Mojović, M. [University of Belgrade, Faculty of Physical Chemistry, Studenski trg 12-16, 11000 Belgrade (Serbia); Žunić, M. [University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Center for Catalysis and Chemical Engineering, Njegoševa 12, 11000 Belgrade (Serbia); Vukelić, N. [University of Belgrade, Faculty of Physical Chemistry, Studenski trg 12-16, 11000 Belgrade (Serbia); Jovanović, D. [University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Center for Catalysis and Chemical Engineering, Njegoševa 12, 11000 Belgrade (Serbia)

2015-10-30

Highlights: • Mild acid treatment followed by incorporation of nickel was performed on bentonite. • Modified bentonites based electrodes were tested in H{sub 2}SO{sub 4} by cyclic voltammetry. • Acid treatment increased current response of electroactive iron within smectite. • Incorporation of Ni improved reversibility of Fe{sup 2+}/Fe{sup 3+} oxidation/reduction process. - Abstract: Bentonite originated from Mečji Do, Serbia, was submitted to acid treatment at 70 °C for 30 min, while only the concentration of applied HCl varied. The obtained acid treated samples were used to modify glassy carbon (GC) electrode. The effect of applied acid treatment on the electrochemical behavior of GC electrodes modified with these materials was investigated. Furthermore, the effect of the introduction of nickel into acid treated samples was studied. The incorporation of nickel into acid treated bentonite was achieved by either ion exchange or impregnation/decomposition method. The obtained samples were characterized using the following methods: inductively coupled plasma (ICP), X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy and electron spin resonance (ESR) spectroscopy. The electrochemical behavior of these samples was tested by cyclic voltammetry in 0.1 mol dm{sup −3} H{sub 2}SO{sub 4} solution. The ICP, FTIR and ESR results exhibited a slight decrease of iron content in the acid treated samples. XRD and FTIR results confirmed that the conditions applied for the acid treatment were mild enough for the smectite structure to be preserved. The electrocatalytic test showed that the current response of Fe{sup 2+}/Fe{sup 3+} oxidation/reduction process increased on the GC electrodes separately modified with each of the acid treated samples in comparison with current obtained on the GC electrode modified with untreated sample. These results indicated that applied acid treatment probably increased the accessibility of the electroactive iron within

Site-specific estimates of water yield applied in regional acid sensitivity surveys across western Canada

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Patrick D. SHAW

2010-08-01

Full Text Available Runoff or water yield is an important input to the Steady-State Water Chemistry (SSWC model for estimating critical loads of acidity. Herein, we present site-specific water yield estimates for a large number of lakes (779 across three provinces of western Canada (Manitoba, Saskatchewan, and British Columbia using an isotope mass balance (IMB approach. We explore the impact of applying site-specific hydrology as compared to use of regional runoff estimates derived from gridded datasets in assessing critical loads of acidity to these lakes. In general, the average water yield derived from IMB is similar to the long-term average runoff; however, IMB results suggest a much larger range in hydrological settings of the lakes, attributed to spatial heterogeneity in watershed characteristics and landcover. The comparison of critical loads estimates from the two methods suggests that use of average regional runoff data in the SSWC model may overestimate critical loads for the majority of lakes due to systematic skewness in the actual runoff distributions. Implications for use of site-specific hydrology in regional critical loads assessments across western Canada are discussed.

Tailoring the Synergistic Bronsted-Lewis acidic effects in Heteropolyacid catalysts: Applied in Esterification and Transesterification Reactions.

Science.gov (United States)

Tao, Meilin; Xue, Lifang; Sun, Zhong; Wang, Shengtian; Wang, Xiaohong; Shi, Junyou

2015-09-16

In order to investigate the influences of Lewis metals on acidic properties and catalytic activities, a series of Keggin heteropolyacid (HPA) catalysts, HnPW11MO39 (M = Ti(IV), Cu(II), Al(III), Sn(IV), Fe(III), Cr(III), Zr(IV) and Zn(II); for Ti and Zr, the number of oxygen is 40), were prepared and applied in the esterification and transesterification reactions. Only those cations with moderate Lewis acidity had a higher impact. Ti Substituted HPA, H5PW11TiO40, posse lower acid content compared with Ti(x)H(3-4x)PW12O40 (Ti partial exchanged protons in saturated H3PW12O40), which demonstrated that the Lewis metal as an addenda atom (H5PW11TiO40) was less efficient than those as counter cations (Ti(x)H(3-4x)PW12O40). On the other hand, the highest conversion reached 92.2% in transesterification and 97.4% in esterification. Meanwhile, a good result was achieved by H5PW11TiO40 in which the total selectivity of DAG and TGA was 96.7%. In addition, calcination treatment to H5PW11TiO40 make it insoluble in water which resulted in a heterogeneous catalyst feasible for reuse.

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

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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.

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

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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.

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

Science.gov (United States)

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

2017-12-11

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

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).

Structural evolution of amino acid crystals under stress from a non-empirical density functional

International Nuclear Information System (INIS)

Sabatini, Riccardo; Küçükbenli, Emine; De Gironcoli, Stefano; Kolb, Brian; Thonhauser, T

2012-01-01

Use of the non-local correlation functional vdW-DF (from ‘van der Waals density functional’; Dion M et al 2004 Phys. Rev. Lett. 92 246401) has become a popular approach for including van der Waals interactions within density functional theory. In this work, we extend the vdW-DF theory and derive the corresponding stress tensor in a fashion similar to the LDA and GGA approach, which allows for a straightforward implementation in any electronic structure code. We then apply our methodology to investigate the structural evolution of amino acid crystals of glycine and l-alanine under pressure up to 10 GPa - with and without van der Waals interactions - and find that for an accurate description of intermolecular interactions and phase transitions in these systems, the inclusion of van der Waals interactions is crucial. For glycine, calculations including the vdW-DF (vdW-DF-c09x) functional are found to systematically overestimate (underestimate) the crystal lattice parameters, yet the stability ordering of the different polymorphs is determined accurately, at variance with the GGA case. In the case of l-alanine, our vdW-DF results agree with recent experiments that question the phase transition reported for this crystal at 2.3 GPa, as the a and c cell parameters happen to become equal but no phase transition is observed.

Group I mGlu receptors potentiate synaptosomal [{sup 3}H]glutamate release independently of exogenously applied arachidonic acid

Energy Technology Data Exchange (ETDEWEB)

Reid, M.E.; Toms, N.J.; Bedingfield, J.S.; Roberts, P.J. [Department of Pharmacology, School of Medical Sciences, University of Bristol, University Walk, Bristol, BS8 1TD (United Kingdom)

1999-04-01

In the current study, we have characterized group I metabotropic glutamate (mGlu) receptor enhancement of 4-aminopyridine (4AP)-evoked [{sup 3}H]glutamate release from rat cerebrocortical synaptosomes. The broad spectrum mGlu receptor agonist (1S,3R)-1-aminocyclopentane-1,3-dicarboxylic acid ((1S,3R)-ACPD, 10 {mu}M) increased 4AP-evoked [{sup 3}H]glutamate release (143.32{+-}2.73% control) only in the presence of exogenously applied arachidonic acid; an effect reversed by the inclusion of bovine serum albumin (BSA, fatty acid free). In contrast, the selective group I mGlu receptor agonist (S)-3,5-dihydroxyphenylglycine (DHPG) potentiated (EC{sub 50}=1.60{+-}0.25 {mu}M; E{sub max}=147.61{+-}10.96% control) 4AP-evoked [{sup 3}H]glutamate release, in the absence of arachidonic acid. This potentiation could be abolished by either the selective mGlu{sub 1} receptor antagonist (R,S)-1-aminoindan-1,5-dicarboxylic acid (AIDA, 1 mM) or the selective PKC inhibitor (Ro 31-8220, 10 {mu}M) and was BSA-insensitive. The selective mGlu{sub 5} receptor agonist (R,S)-2-chloro-5-hydroxyphenylglycine (CHPG, 300{mu}M) was without effect. DHPG (100 {mu}M) also potentiated both 30 mM and 50 mM K{sup +}-evoked [{sup 3}H]glutamate release (121.60{+-}12.77% and 121.50{+-}4.45% control, respectively). DHPG (100 {mu}M) failed to influence both 4AP-stimulated {sup 45}Ca{sup 2+} influx and 50 mM K{sup +}-induced changes in synaptosomal membrane potential. Possible group I mGlu receptor suppression of tonic adenosine A{sub 1} receptor, group II/III mGlu receptors or GABA{sub B} receptor activity is unlikely since 4AP-evoked [{sup 3}H]glutamate release was insensitive to the selective inhibitory receptor antagonists 8-cyclopentyl-1,3-dimethylxanthine, (R,S)-{alpha}-cyclopropyl-4-phosphonophenylglycine or CGP55845A, respectively. These data suggest an 'mGlu{sub 1} receptor-like' receptor potentiates [{sup 3}H]glutamate release from cerebrocortical synaptosomes in the absence of

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2006-03-31

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

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, ...

In silico discovery of novel Retinoic Acid Receptor agonist structures

Directory of Open Access Journals (Sweden)

Samuels Herbert H

2001-06-01

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

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

Interpolation/penalization applied for strength design of 3D thermoelastic structures

DEFF Research Database (Denmark)

Pedersen, Pauli; Pedersen, Niels L.

2012-01-01

compliance. This is proved for thermoelastic structures by sensitivity analysis of compliance that facilitates localized determination of sensitivities, and the compliance is not identical to the total elastic energy (twice strain energy). An explicit formula for the difference is derived and numerically...... parameter interpolation in explicit form is preferred, and the influence of interpolation on compliance sensitivity analysis is included. For direct strength maximization the sensitivity analysis of local von Mises stresses is demanding. An applied recursive procedure to obtain uniform energy density...

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

Influence of exogenously applied abscisic acid on carotenoid content and water uptake in flowers of the tea plant (Camellia sinensis).

Science.gov (United States)

Baldermann, Susanne; Yang, Ziyin; Sakai, Miwa; Fleischmann, Peter; Morita, Akio; Todoroki, Yasushi; Watanabe, Naoharu

2013-05-01

Carotenoids are a major class of plant pigments and fulfill many functions in different organisms that either produce or consume them. Although the color of the stamina of tea (Camellia sinensis) flowers is clearly due to the presence of carotenoids, the carotenoid profile and content remain to be discovered. We investigated the carotenoid profile of tea flowers and determined changes in concentrations over the floral development. The flowers contained oxygenated xanthophylls such as neoxanthin, lutein and zeaxanthin, as well as the hydrocarbons β-carotene and α-carotene. Flowers of the tea plant contain to vegetables comparable amounts of carotenoids. The content of 9'-cis-epoxycarotenoids, which serve as abscisic acid precursors, as well as changes in concentration of abscisic acid were studied. The concentrations of carotenoids decreased whereas the abscisic acid content increased over the floral development. Exogenously applied S-abscisic acid affected water uptake, flower opening and carotenoid accumulation. In summary, this paper reports, for the first time, the carotenoid profile and content of tea flowers. The study revealed that carotenoids in tea flowers are an interesting target in respect of possible applications of tea flower extracts as well as biological functions of abscisic acid during floral development. © 2012 Society of Chemical Industry.

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.

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

International Nuclear Information System (INIS)

Ding Fei; Diao Jianxiong; Yang Xinling; Sun Ying

2011-01-01

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

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.

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Applied to Quantitative Proteomics of Bacillus subtilis

DEFF Research Database (Denmark)

Soufi, Boumediene; Kumar, C.; Gnad, F.

2010-01-01

We applied stable isotope labeling by amino acids in cell culture (SILAC) to large-scale quantitative proteomics analyses of the model bacterium Bacillus subtilis in two physiological conditions: growth on succinate and growth under phosphate starvation. Using a B. subtilis strain auxotrophic...... of the most comprehensive quantitative proteomics studies in bacteria, covering more than 75% of the B. subtilis genes expressed in the log phase of growth. Furthermore, we detect and quantify dynamics of 35 Ser/Thr/Tyr phosphorylation sites under growth on succinate, and 10 phosphorylation sites under...

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.

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

Science.gov (United States)

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

2017-03-01

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

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...

Physico-chemical analysis of tannery solid waste and structural characterization of its isolated humic acids after composting.

Science.gov (United States)

Amir, Soumia; Benlboukht, Fatima; Cancian, Nadia; Winterton, Peter; Hafidi, Mohamed

2008-12-30

In Marrakech, solid by-products from tanneries are highly polluting, generating large amounts of nitrogenous and organic matter. In the present study composting is tested as a cost-effective method for waste management to overcome many of the environmental hazards and produce a stable, rich material for soil fertilization. Two composting trials were conducted after neutralization by ammonia or lime. The aim of the neutralization was to avoid the antimicrobial effects of the acidity in the tannery waste, thus ensuring correct composting. Different techniques such as elemental analysis and 13C NMR spectroscopy were applied to analyse humic acids isolated from raw and composted materials, and to monitor the process of tannery waste composting, and the stability and maturity of the final product according to the means of neutralization. Comparison of data showed similar behaviour in both trials, but the composting process appeared to be more complete following neutralization with lime. The C, H and N content decreased, while the O increased. The FTIR and 13C NMR spectra show the decrease of aliphatic compounds demonstrated by the reduction of absorbance around 2922cm(-1) and of the resonance in the C-alkyl area around 0-55ppm. The humic acids newly formed during composting were richer in the O-N alkyl and oxidized aromatic structures that increased almost twofold on composting after neutralization with lime. The first principal component axis PC1 (54%) separated C-aliphatic, C-carboxylic and other less stable and less polycondensed compounds such as polyphenols from the more polycondensed O-N alkyl and oxidized C-aromatic compounds.

BATCH PROCESS INTEGRATION OF APPLYING TECHNOLOGY OF ACID CARMINIC PINCH

OpenAIRE

Erazo E., Raymundo; Cárdenas R., Jorge L.; Woolcott H., Juan C.

2014-01-01

This work was developed in order to implement the PINCH technology integration batch process for carminic acid. The method used consisted of the application of the concepts of bottle necks total process (OPB) together with part-time models (TAM) and time fractionated! (TSM). The drying operation is identified as the rate limiting step of the process identifying it as an OPB plant capacity. The extraction yield was 95% w / p carminic acid with an energy savings of approximately 60% of the...

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.

Structural and morphological changes in P3HT thin film transistors applying an electric field

Energy Technology Data Exchange (ETDEWEB)

Tiwari, Deepak Kumar; Grigorian, Souren; Pietsch, Ullrich [University of Siegen (Germany); Flesch, Heinz; Resel, Roland [University of Siegen (Germany); Graz University of Technology (Austria)

2010-07-01

We report on electric field dependent crystalline structure and morphological changes of drop casting and spin coated poly(3-hexylthiophene) (P3HT) thin films. In order to probe the morphological changes induced by an applied electric field the samples were covered with thin source/drain electrodes separated by a small channel of 2 mm width. A series of x-ray reflectivity, X-ray grazing incidence out-of-plane and in-plane scans have been performed as function of the applied electric voltage. The (100) peak shows a decrease in intensity with increase of the applied electric field. This might be caused by Joule heating and the creation of current induced defects in the P3HT film. On other hand the (020) peak intensity shows much stronger changes with applied field. Considering the *-* stacking direction the measured effect can be directly related to a change in the electric transport. The observed changes in structure are reversible and the current-voltage cycle can be repeated several times. For X-ray reflectivity major changes have been found close to critical angle of total external reflection indicating the film becomes less dense and increases in surface roughness with increase of the voltage. This change in surface behaviour could be confirmed by in-situ AFM measurements.

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

Systems and strippable coatings for decontaminating structures that include porous material

Science.gov (United States)

Fox, Robert V [Idaho Falls, ID; Avci, Recep [Bozeman, MT; Groenewold, Gary S [Idaho Falls, ID

2011-12-06

Methods of removing contaminant matter from porous materials include applying a polymer material to a contaminated surface, irradiating the contaminated surface to cause redistribution of contaminant matter, and removing at least a portion of the polymer material from the surface. Systems for decontaminating a contaminated structure comprising porous material include a radiation device configured to emit electromagnetic radiation toward a surface of a structure, and at least one spray device configured to apply a capture material onto the surface of the structure. Polymer materials that can be used in such methods and systems include polyphosphazine-based polymer materials having polyphosphazine backbone segments and side chain groups that include selected functional groups. The selected functional groups may include iminos, oximes, carboxylates, sulfonates, .beta.-diketones, phosphine sulfides, phosphates, phosphites, phosphonates, phosphinates, phosphine oxides, monothio phosphinic acids, and dithio phosphinic acids.

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

Science.gov (United States)

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

2010-08-01

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

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

Science.gov (United States)

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

2018-04-30

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

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

Science.gov (United States)

Teschke, Omar; Soares, David Mendez

2016-03-29

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

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

Science.gov (United States)

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

1981-08-04

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

Hydrolysis of dilute acid-pretreated cellulose under mild hydrothermal conditions.

Science.gov (United States)

Chimentão, R J; Lorente, E; Gispert-Guirado, F; Medina, F; López, F

2014-10-13

The hydrolysis of dilute acid-pretreated cellulose was investigated in a conventional oven and under microwave heating. Two acids--sulfuric and oxalic--were studied. For both hydrothermal conditions (oven and microwave) the resultant total organic carbon (TOC) values obtained by the hydrolysis of the cellulose pretreated with sulfuric acid were higher than those obtained by the hydrolysis of the cellulose pretreated with oxalic acid. However, the dicarboxylic acid exhibited higher hydrolytic efficiency towards glucose. The hydrolysis of cellulose was greatly promoted by microwave heating. The Rietveld method was applied to fit the X-ray patterns of the resultant cellulose after hydrolysis. Oxalic acid preferentially removed the amorphous region of the cellulose and left the crystalline region untouched. On the other hand, sulfuric acid treatment decreased the ordering of the cellulose by partially disrupting its crystalline structure. Copyright © 2014 Elsevier Ltd. All rights reserved.

Hydration of amino acids: FTIR spectra and molecular dynamics studies.

Science.gov (United States)

Panuszko, Aneta; Adamczak, Beata; Czub, Jacek; Gojło, Emilia; Stangret, Janusz

2015-11-01

The hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results, molecular dynamics simulations of amino acids were performed. The structural-energetic characteristic of these solute-affected water molecules shows that, on average, water affected by amino acids forms stronger and shorter H-bonds than those in pure water. Differences in the influence of amino acids on water structure have been noticed. The effect of the hydrophobic side chain of an amino acid on the solvent interactions seems to be enhanced because of the specific cooperative coupling of water strong H-bond chain, connecting the carboxyl and amino groups, with the clathrate-like H-bond network surrounding the hydrocarbon side chain. The parameter derived from the spectral data, which corresponds to the contributions of the population of weak hydrogen bonds of water molecules which have been substituted by the stronger ones in the hydration sphere of amino acids, correlated well with the amino acid hydrophobicity indexes.

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

Energy Technology Data Exchange (ETDEWEB)

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

2012-07-01

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

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

International Nuclear Information System (INIS)

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

2011-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2011-02-15

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

The Effect of Various Acids to the Gelation Process to the Silica Gel Characteristic Using Organic Silica

Science.gov (United States)

Rahman, NA; Widiyastuti, W.; Sigit, D.; Ajiza, M.; Sujana, W.

2018-01-01

Bagasse ash is solid waste of cane sugar industry which contain of silica more than 51%. Some previous study of silica gel from bagasse ash have been conducted often and been applied. This study concerns about the effect of various acid used in the process of gelation to the characteristic of silica gel produced. Then, this silica gel will be used as adsorbent. As that, the silica gel must fulfill the requirements of adsorbent, as have good pores characteristics, fit in mesoporous size so that adsorbent diffusion process is not disturbed. A fitted pores size of silica gel can be prepared by managing acid concentration used. The effect of acid, organic acid (tartaric acid) and inorganic acid (hydrochloric acid), is investigated in detail. The acid is added into sodium silicate solution in that the gel is formed, the pores structures can be investigated with BET, the crystal form is analyzed with XRD and the pore structure is analyzed visually with SEM. By managing the acid concentration added, it gets the effect of acid to the pore structure of silica gel. The bigger concentration is, the bigger the pore’s size of silica gel produced.

SGFM applied to the calculation of surface band structure of V

International Nuclear Information System (INIS)

Baquero, R.; Velasco, V.R.; Garcia Moliner, F.

1986-07-01

The surface Green function matching (SGFM) method has been developed recently to deal with a great variety of problems in a unified way. The method was first developed for continuum systems. The recent advances for discrete structures can deal with surfaces, interfaces, quantum wells, superlattices, intercalated layered compounds, and other systems. Several applications of this formalism are being carried out. In the present note we will describe how the formalism applies to the calculation of the electronic surface band structure of vanadium which is a quite interesting transition metal with very active magnetic properties at the surface, in particular at the (100) surface. It is straightforward, on the basis of the calculation presented here, to obtain the magnetic moment on the surface, for example, through the method followed by G. Allan or the surface paramagnon density which should be particularly enhanced at this surface as compared to the bulk

Origin and structures of groundwater humic substances from three Danish aquifers

DEFF Research Database (Denmark)

Grøn, C.; Wassenaar, L.; Krog, M.

1996-01-01

and halogens, hydrolyzable amino acids and carbohydrates, carbon isotopes) applied to aquatic humic and fulvic acids led to consistent structural interpretations for each of the three aquifers studied. For humic substances in two-aquifers, the analyses suggested source rocks in agreement with geological......Structural, chemical, and isotopic parameters were used to identify the origins of groundwater humic substances from three Danish aquifers. A variety of analytical techniques (visible light absorption, molecular weight distribution, C-13-NMR spectroscopy, elemental composition with major elements...

Applying a foil queue micro-electrode in micro-EDM to fabricate a 3D micro-structure

Science.gov (United States)

Xu, Bin; Guo, Kang; Wu, Xiao-yu; Lei, Jian-guo; Liang, Xiong; Guo, Deng-ji; Ma, Jiang; Cheng, Rong

2018-05-01

Applying a 3D micro-electrode in a micro electrical discharge machining (micro-EDM) can fabricate a 3D micro-structure with an up and down reciprocating method. However, this processing method has some shortcomings, such as a low success rate and a complex process for fabrication of 3D micro-electrodes. By focusing on these shortcomings, this paper proposed a novel 3D micro-EDM process based on the foil queue micro-electrode. Firstly, a 3D micro-electrode was discretized into several foil micro-electrodes and these foil micro-electrodes constituted a foil queue micro-electrode. Then, based on the planned process path, foil micro-electrodes were applied in micro-EDM sequentially and the micro-EDM results of each foil micro-electrode were able to superimpose the 3D micro-structure. However, the step effect will occur on the 3D micro-structure surface, which has an adverse effect on the 3D micro-structure. To tackle this problem, this paper proposes to reduce this adverse effect by rounded corner wear at the end of the foil micro-electrode and studies the impact of machining parameters on rounded corner wear and the step effect on the micro-structure surface. Finally, using a wire cutting voltage of 80 V, a current of 0.5 A and a pulse width modulation ratio of 1:4, the foil queue micro-electrode was fabricated by wire electrical discharge machining. Also, using a pulse width of 100 ns, a pulse interval of 200 ns, a voltage of 100 V and workpiece material of 304# stainless steel, the foil queue micro-electrode was applied in micro-EDM for processing of a 3D micro-structure with hemispherical features, which verified the feasibility of this process.

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

Science.gov (United States)

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

2016-09-01

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

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.

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...

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

Science.gov (United States)

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

2014-12-01

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

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.

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

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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.

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

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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.

Vectorial magnetometry with the magneto-optic Kerr effect applied to Co/Cu/Co trilayer structures

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Daboo, C.; Bland, J. A. C.; Hicken, R. J.; Ives, A. J. R.; Baird, M. J.; Walker, M. J.

1993-05-01

We describe an arrangement in which the magnetization components parallel and perpendicular to the applied field are both determined from longitudinal magneto-optic Kerr effect measurements. This arrangement differs from the usual procedures in that the same optical geometry is used but the magnet geometry altered. This leads to two magneto-optic signals which are directly comparable in magnitude thereby giving the in-plane magnetization vector directly. We show that it is of great value to study both in-plane magnetization vector components when studying coupled structures where significant anisotropies are also present. We discuss simulations which show that it is possible to accurately determine the coupling strength in such structures by examining the behavior of the component of magnetization perpendicular to the applied field in the vicinity of the hard in-plane anisotropy axis. We illustrate this technique by examining the magnetization and magnetic anisotropy behavior of ultrathin Co/Cu(111)/Co (dCu=20 Å and 27 Å) trilayer structures prepared by molecular beam epitaxy, in which coherent rotation of the magnetization vector is observed when the magnetic field B is applied along the hard in-plane anisotropy axis, with the magnitude of the magnetization vector constant and close to its bulk value. Results of micromagnetic calculations closely reproduce the observed parallel and perpendicular magnetization loops, and yield strong uniaxial magnetic anisotropies in both layers, while the interlayer coupling appears to be absent or negligible in comparison with the anisotropy strengths.

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

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Nalin CW Goonesekere

2009-06-01

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

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

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

2007-12-15

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

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.

Classroom Research: GC Studies of Linoleic and Linolenic Fatty Acids Found in French Fries

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Crowley, Janice P.; Deboise, Kristen L.; Marshall, Megan R.; Shaffer, Hannah M.; Zafar, Sara; Jones, Kevin A.; Palko, Nick R.; Mitsch, Stephen M.; Sutton, Lindsay A.; Chang, Margaret; Fromer, Ilana; Kraft, Jake; Meister, Jessica; Shah, Amar; Tan, Priscilla; Whitchurch, James

2002-07-01

A study of fatty-acid ratios in French fries has proved to be an excellent choice for an entry-level research class. This research develops reasoning skills and involves the subject of breast cancer, a major concern of American society. Analysis of tumor samples removed from women with breast cancer revealed high ratios of linoleic to linolenic acid, suggesting a link between the accelerated growth of breast tumors and the combination of these two fatty acids. When the ratio of linoleic to linolenic acid was approximately 9 to 1, accelerated growth was observed. Since these fatty acids are found in cooking oils, Wichita Collegiate students, under the guidance of their chemistry teacher, decided that an investigation of the ratios of these two fatty acids should be conducted. A research class was structured using a gas chromatograph for the analysis. Separation of linoleic from linolenic acid was successfully accomplished. The students experienced inductive experimental research chemistry as it applies to everyday life. The structure of this research class can serve as a model for high school and undergraduate college research curricula.

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

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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.

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

Science.gov (United States)

Gontrani, Lorenzo

2018-06-01

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

Demolition of RC structures by applying electric current through rebars

International Nuclear Information System (INIS)

Nakagawa, Wahei; Nishita, Itaru; Kasai, Yoshio.

1987-01-01

Recently, the dismantling works of reinforced concrete structures increased rapidly. On the other hand, in urban districts, the strict restriction of noise, vibration and dust is carried out, and the development of no vibration, no noise construction method is desired. The dismantling method by electrically heating reinforcing bars was developed for separating the surface layer of concrete radioactivated and contaminated in the dismantling works of nuclear power stations, but it can be applied also to the dismantling of general reinforced concrete structures. As the method of electrically heating reinforcing bars, there are direct electrifying method and induction heating method, and here, the direct electrifying method is discussed. When large current is passed directly through reinforcing bars in concrete as electric resistors, their temperature rises rapidly to about 450 deg C. As the result, the surrounding concrete cracks and loses the adhesion due to the dehydration. By striking lightly, the concrete separates, thus dismantling becomes easy. The preparation, electrode terminals, heating temperature, the cracking of concrete, the secondary breaking after heating, dust in dismantling and broken pieces, and the features and the fields of application of this method are reported. (Kako, I.)

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-12-01

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

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Regulation of maize kernel weight and carbohydrate metabolism by abscisic acid applied at the early and middle post-pollination stages in vitro.

Science.gov (United States)

Zhang, Li; Li, Xu-Hui; Gao, Zhen; Shen, Si; Liang, Xiao-Gui; Zhao, Xue; Lin, Shan; Zhou, Shun-Li

2017-09-01

Abscisic acid (ABA) accumulates in plants under drought stress, but views on the role of ABA in kernel formation and abortion are not unified. The response of the developing maize kernel to exogenous ABA was investigated by excising kernels from cob sections at four days after pollination and culturing in vitro with different concentrations of ABA (0, 5, 10, 100μM). When ABA was applied at the early post-pollination stage (EPPS), significant weight loss was observed at high ABA concentration (100μM), which could be attributed to jointly affected sink capacity and activity. Endosperm cells and starch granules were decreased significantly with high concentration, and ABA inhibited the activities of soluble acid invertase and acid cell wall invertase, together with earlier attainment of peak values. When ABA was applied at the middle post-pollination stage (MPPS), kernel weight was observably reduced with high concentration and mildly increased with low concentration, which was regulated due to sink activity. The inhibitory effect of high concentration and the mild stimulatory effect of low concentration on sucrose synthase and starch synthase activities were noted, but a peak level of ADP-glucose pyrophosphorylase (AGPase) was stimulated in all ABA treatments. Interestingly, AGPase peak values were advanced by low concentration and postponed by high concentration. In addition, compared with the control, the weight of low ABA concentration treatments were not statistically significant at the two stages, whereas weight loss from high concentration applied at EPPS was considerably obvious compared with that of the MPPS, but neither led to kernel abortion. The temporal- and dose-dependent impacts of ABA reveal a complex process of maize kernel growth and development. Copyright © 2017 Elsevier GmbH. All rights reserved.

Structural-functional model of medical students’ professional-applied physical training

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A.V. Petryshyn

2016-10-01

Full Text Available Purpose: to work out and experimentally prove model of professional-applied physical training of medical higher educational establishments’ students. Material: in the research 80 students participated. In questioning physical education instructors of medical higher education establishments (n=20 participated. Results: influence of students’ professionally important characteristics on general physical fitness indicators and functional state has been shown. Directions of students’ physical fitness parameters’ individual diagnostic and control over physical education effectiveness have been offered. Volumes of physical exercises in the structure of training have been found: special training (15-20% and competition exercises (20-30%. Conclusions: the need in raising the level of professionally important for students’ abilities has been noted: speed power, static power endurance, power endurance, coordination of arms’ movements, static balance.

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

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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.

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

Science.gov (United States)

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

2010-06-01

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

Content and structure of future teachers’ aesthetic perception of fine and decorative applied art creations

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Liudmyla Lisunova

2017-03-01

Full Text Available The content and structure of future teachers’ aesthetic perception of fine and decorativeapplied art creations in the system of professional training are delivered in this article. Thestructural components and stages (phases of aesthetic perception process are determined, therole of art as the most powerful source of reality in the process of future teachers’ aestheticperception of art are revealed.Key words: contents and structure of aesthetic perception, future teachers of art, fineand decorative applied art creations

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

International Nuclear Information System (INIS)

Atalay, Y.

2004-01-01

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

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

DEFF Research Database (Denmark)

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

2006-01-01

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

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

DEFF Research Database (Denmark)

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

1998-01-01

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

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

Superficial basal cell carcinoma treated with 70% trichloroacetic acid applied topically: a case study

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Chiriac A

2017-02-01

Full Text Available Anca Chiriac,1–3 Piotr Brzezinski,4 Cosmin Moldovan,5 Cristian Podoleanu,6 Marius Florin Coros,7 Simona Stolnicu8 1Department of Dermatology, Nicolina Medical Center, Iasi, 2Department of Dermatology, Apollonia University, Iasi, 3Department of Dermatology, P. Poni Research Institute, Romanian Academy Iasi, Romania; 4Department of Dermatology, 6th Military Support Unit, Utska, Poland; 5Department of Histology, 6Department of Cardiology, 7Department of Surgery, 8Department of Pathology, University of Medicine and Pharmacy of Targu‑Mures, Targu-Mures, Romania Background: Basal cell carcinoma (BCC is the most common form of skin cancer, affecting millions of people worldwide. The treatment concept for BCCs is the surgical one, but it is costly, as such, searching for alternative medical therapeutics is justified. Aim: To highlight the efficacy of high concentration (70% trichloroacetic acid (TCA as a choice therapy for low-risk BCC. Method and patient: Authors present, for the first time, the use of a high concentration TCA applied once a week for 2 consecutive weeks with a toothpick, on a patient with BCC on the right preauricular area. Results: On examination 4 weeks later, the lesion was not clinically and dermatoscopically evidenced. Conclusion: High concentration TCA could be an effective and safe, non-invasive choice of therapy for low-risk BCC, easy to perform, not expensive, with good cosmetic results, especially for patients who are not likely to undergo invasive or expensive treatments. Keywords: basal cell carcinoma, therapy, trichloroacetic acid, dermatology

Structural characterization of complex systems by applying a combination of scattering and spectroscopic methods

International Nuclear Information System (INIS)

Klose, G.

1999-01-01

Lyotropic mesophases possess lattice dimensions of the order of magnitude of the length of their molecules. Consequently, the first Bragg reflections of such systems appear at small scattering angles (small angle scattering). A combination of scattering and NMR methods was applied to study structural properties of POPC/C 12 E n mixtures. Generally, the ranges of existence of the liquid crystalline lamellar phase, the dimension of the unit-cell of the lamellae and important structural parameters of the lipid and surfactant molecules in the mixed bilayers were determined. With that the POPC/C 12 E 4 bilayer represents one of the best structurally characterized mixed model membranes. It is a good starting system for studying the interrelation with other e.g. dynamic or thermodynamic properties. (K.A.)

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.

FRACTAL ANALYSIS OF PHYSICAL ADSORPTION ON SURFACES OF ACID ACTIVATED BENTONITES FROM SERBIA

Directory of Open Access Journals (Sweden)

Ljiljana Rožić

2008-11-01

Full Text Available Solid surfaces are neither ideally regular, that is, morphological and energeticcally homogeneous, nor are they fully irregular or fractal. Instead, real solid surfaces exhibit a limited degree of organization quantified by the fractal dimension, D. Fractal analysis was applied to investigate the effect of concentrations of HCl solutions on the structural and textural properties of chemically activated bentonite from southern Serbia. Acid treatment of bentonites is applied in order to remove impurities and various exchangeable cations from bentonite clay. Important physical changes in acid-activated smectite are the increase of the specific surface area and of the average pore volume, depending on acid strength, time and temperature of a treatment. On the basis of the sorption-structure analysis, the fractal dimension of the bentonite surfaces was determined by Mahnke and Mögel method. The fractal dimension evaluated by this method was 2.11 for the AB3 and 1.94 for the AB4.5 sample. The estimation of the values of the fractal dimension of activated bentonites was performed in the region of small pores, 0.5 nm < rp < 2 nm.

The role of topically applied L-ascorbic acid in ex-vivo examination of burn-injured human skin

Science.gov (United States)

Pielesz, Anna; Biniaś, Dorota; Bobiński, Rafał; Sarna, Ewa; Paluch, Jadwiga; Waksmańska, Wioletta

2017-10-01

Wound treatment and healing is complex and is comprised of an elaborate set of processes including cellular, spectroscopic and biochemical ones as well as the ;reaction; of local tissue to thermal injury. Vitamin C as L-ascorbic acid (LA) prevents injurious effects of oxidants because it reduces reactive oxygen species to stable molecules, it becomes oxidized to the short-lived ascorbyl radical. As a result, antioxidant treatment may contribute to minimizing injury in burn patients. The aim of this study is to assess changes in molecular structure of collagen extracted from human epidermis burn wound scab during incubation of the epidermis in L-ascorbic acid solution. The study will be performed using FTIR and FT Raman spectroscopies. During this research it was observed that the intensity of Raman peaks increased where healing was being modified by LA. The intensity of the amide III band at 1247 cm- 1 relative to the intensity at 1326 cm- 1 was used to test tissue repair degree at the incision site. FTIR spectra were recorded from frozen specimens of serum modified by LA; an analysis of shifts in the amide I band position was conducted. The appearance of a new band for frozen samples modified by LA was observed around 1149-1220 cm- 1. The above conclusions confirmed the creation of hydrogen bonds between Nsbnd H stretch and Cdbnd O. Samples being incubated in solutions of L-ascorbic acid demonstrated the absence of electrophoretic bands of albumin. Alterations in the surface of the skin incubated in L-ascorbic acid were investigated with the use of Scanning Electron Microscopy (SEM). A decrease in external symptoms of burn injury was noted in the damaged epidermis incubated in L-ascorbic acid.

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

Science.gov (United States)

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

2016-07-21

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

Exogenously applied abscisic acid to Yan73 (V. vinifera) grapes enhances phenolic content and antioxidant capacity of its wine.

Science.gov (United States)

Xi, Zhu-Mei; Meng, Jiang-Fei; Huo, Shan-Shan; Luan, Li-Ying; Ma, Li-Na; Zhang, Zhen-Wen

2013-06-01

Yan73 is a 'teinturier' red wine variety cultivated in China and widely used in winemaking to strengthen red wine colour. The objective of this study was to evaluate the effect of exogenous abscisic acid (ABA) applied to the grapevine cluster on the antioxidant capacity and phenolic content of the wine made from Yan73. Two hundred mg/l ABA was applied on Yan73 grapevine cluster during veraison. As they mature, these ABA-treated and untreated grape berries were transformed into wines, respectively, and the phenolic content and antioxidant capacity of these wines were compared. The results showed that phenolic content (total phenolics, tannins, flavonoids and anthocyanins) and antioxidant capacity were higher in the wine produced with ABA-treated Yan73 grapes than those in the wine from untreated grapes. Compared to Cabernet Sauvignon wine, Yan73 wine had higher phenolic content and stronger antioxidant capacity. These strongly suggest that exogenously applied ABA to Yan73 grapes can enhance phenolic content and antioxidant capacity of its wine, and Yan73 wine has the higher utilization value and potential for development.

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

Science.gov (United States)

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

2017-08-01

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

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

International Nuclear Information System (INIS)

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

1996-01-01

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

Fatty acids are required for epidermal permeability barrier function.

Science.gov (United States)

Mao-Qiang, M; Elias, P M; Feingold, K R

1993-08-01

The permeability barrier is mediated by a mixture of ceramides, sterols, and free fatty acids arranged as extracellular lamellar bilayers in the stratum corneum. Whereas prior studies have shown that cholesterol and ceramides are required for normal barrier function, definitive evidence for the importance of nonessential fatty acids is not available. To determine whether epidermal fatty acid synthesis also is required for barrier homeostasis, we applied 5-(tetradecyloxy)-2-furancarboxylic acid (TOFA), an inhibitor of acetyl CoA carboxylase, after disruption of the barrier by acetone or tape stripping. TOFA inhibits epidermal fatty acid by approximately 50% and significantly delays barrier recovery. Moreover, coadministration of palmitate with TOFA normalizes barrier recovery, indicating that the delay is due to a deficiency in bulk fatty acids. Furthermore, TOFA treatment also delays the return of lipids to the stratum corneum and results in abnormalities in the structure of lamellar bodies, the organelle which delivers lipid to the stratum corneum. In addition, the organization of secreted lamellar body material into lamellar bilayers within the stratum corneum interstices is disrupted by TOFA treatment. Finally, these abnormalities in lamellar body and stratum corneum membrane structure are corrected by coapplication of palmitate with TOFA. These results demonstrate a requirement for bulk fatty acids in barrier homeostasis. Thus, inhibiting the epidermal synthesis of any of the three key lipids that form the extracellular, lipid-enriched membranes of the stratum corneum results in an impairment in barrier homeostasis.

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

Science.gov (United States)

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

2012-10-01

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

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

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Leonardus Vergütz

2015-12-01

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

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

Science.gov (United States)

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

2010-08-10

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

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...

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

Science.gov (United States)

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

2014-04-01

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

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)

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

Directory of Open Access Journals (Sweden)

Seunghee Cho

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

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.

Reduction reactions applied for synthesizing different nano-structured materials

Energy Technology Data Exchange (ETDEWEB)

Albuquerque Brocchi, Eduardo de; Correia de Siqueira, Rogério Navarro [Department of Materials Engineering, PUC-Rio, Rua Marquês de São Vicente, 225, Gávea, 22453-900 Rio de Janeiro, RJ (Brazil); Motta, Marcelo Senna [Basck Ltd. (United Kingdom); Moura, Francisco José, E-mail: moura@puc-rio.br [Department of Materials Engineering, PUC-Rio, Rua Marquês de São Vicente, 225, Gávea, 22453-900 Rio de Janeiro, RJ (Brazil); Solórzano-Naranjo, Ivan Guillermo [Department of Materials Engineering, PUC-Rio, Rua Marquês de São Vicente, 225, Gávea, 22453-900 Rio de Janeiro, RJ (Brazil)

2013-06-15

Different materials have been synthesized by alternative routes: nitrates thermal decomposition to prepare oxide or co-formed oxides and reduction by hydrogen or graphite to obtain mixed oxides, composites or alloys. These chemical-based synthesis routes are described and thermodynamics studies and kinetics data are presented to support its feasibility. In addition, selective reduction reactions have been applied to successfully produce metal/ceramic composites, and alloys. Structural characterization has been carried out by X-ray Diffraction and, more extensively, Transmission Electron Microscopy operating in conventional diffraction contrast (CTEM) and high-resolution mode (HRTEM), indicated the possibility of obtaining oxide and alloy crystals of sizes ranging between 20 and 40 nm. - Highlights: • The viability in obtaining Ni–Co, Cu–Al, Mn–Al co-formed nano oxides was evaluated. • Partial and complete H{sub 2} reduction were used to produce alloy, composite and Spinel. • XRD, TEM and HREM techniques were used to characterize the obtained nanostructures.

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-07-01

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

Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity.

Directory of Open Access Journals (Sweden)

Zhiqiang Yan

Full Text Available Protein-nucleic acid (protein-DNA and protein-RNA recognition is fundamental to the regulation of gene expression. Determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital to understanding the regulation function. Recently, quantitative computational approach has been becoming an alternative of experimental technique for predicting the structures and interactions of biomolecular recognition. However, the progress of protein-nucleic acid structure prediction, especially protein-RNA, is far behind that of the protein-ligand and protein-protein structure predictions due to the lack of reliable and accurate scoring function for quantifying the protein-nucleic acid interactions. In this work, we developed an accurate scoring function (named as SPA-PN, SPecificity and Affinity of the Protein-Nucleic acid interactions for protein-nucleic acid interactions by incorporating both the specificity and affinity into the optimization strategy. Specificity and affinity are two requirements of highly efficient and specific biomolecular recognition. Previous quantitative descriptions of the biomolecular interactions considered the affinity, but often ignored the specificity owing to the challenge of specificity quantification. We applied our concept of intrinsic specificity to connect the conventional specificity, which circumvents the challenge of specificity quantification. In addition to the affinity optimization, we incorporated the quantified intrinsic specificity into the optimization strategy of SPA-PN. The testing results and comparisons with other scoring functions validated that SPA-PN performs well on both the prediction of binding affinity and identification of native conformation. In terms of its performance, SPA-PN can be widely used to predict the protein-nucleic acid structures and quantify their interactions.

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

Science.gov (United States)

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

2016-03-01

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

Direct enantioselective conjugate addition of carboxylic acids with chiral lithium amides as traceless auxiliaries.

Science.gov (United States)

Lu, Ping; Jackson, Jeffrey J; Eickhoff, John A; Zakarian, Armen

2015-01-21

Michael addition is a premier synthetic method for carbon-carbon and carbon-heteroatom bond formation. Using chiral dilithium amides as traceless auxiliaries, we report the direct enantioselective Michael addition of carboxylic acids. A free carboxyl group in the product provides versatility for further functionalization, and the chiral reagent can be readily recovered by extraction with aqueous acid. The method has been applied in the enantioselective total synthesis of the purported structure of pulveraven B.

Design optimization applied in structural dynamics

NARCIS (Netherlands)

Akcay-Perdahcioglu, Didem; de Boer, Andries; van der Hoogt, Peter; Tiskarna, T

2007-01-01

This paper introduces the design optimization strategies, especially for structures which have dynamic constraints. Design optimization involves first the modeling and then the optimization of the problem. Utilizing the Finite Element (FE) model of a structure directly in an optimization process

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)

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

Science.gov (United States)

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

2018-04-03

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

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.

Monoclonal Antibodies Follow Distinct Aggregation Pathways During Production-Relevant Acidic Incubation and Neutralization

DEFF Research Database (Denmark)

Pedersen, Thomas Skamris; Tian, Xinsheng; Thorolfsson, Matthias

2016-01-01

and orthogonal analytical methods, including small-angle X-ray scattering and dynamic light scattering and supplemented the experimental data with crystal structure-based spatial aggregation propensity (SAP) calculations. RESULTS: We revealed distinct solution behaviors between the three mAb models: At acidic p......PURPOSE: Aggregation aspects of therapeutic monoclonal antibodies (mAbs) are of common concern to the pharmaceutical industry. Low pH treatment is applied during affinity purification and to inactivate endogenous retroviruses, directing interest to the mechanisms of acid-induced antibody...... distinguish between reversible and irreversible mAb aggregation pathways at early stages of acidic treatment....

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.

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

Science.gov (United States)

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

2016-05-10

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

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...

Observation of multipactor suppression in a dielectric-loaded accelerating structure using an applied axial magnetic field

International Nuclear Information System (INIS)

Jing, C.; Konecny, R.; Antipov, S.; Chang, C.; Gold, S. H.; Schoessow, P.; Kanareykin, A.; Gai, W.

2013-01-01

Efforts by a number of institutions to develop a Dielectric-Loaded Accelerating (DLA) structure capable of supporting high gradient acceleration when driven by an external radio frequency source have been ongoing over the past decade. Single surface resonant multipactor has been previously identified as one of the major limitations on the practical application of DLA structures in electron accelerators. In this paper, we report the results of an experiment that demonstrated suppression of multipactor growth in an X-band DLA structure through the use of an applied axial magnetic field. This represents an advance toward the practical use of DLA structures in many accelerator applications

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.

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

to ortho in homopyrimidine TINAs. Thus, for para-TINAs the bulge insertion of an intercalator led to high thermal stability of Hoogsteen-type parallel triplexes and duplexes, whereas Watson-Cricktype duplexes were destabilized. In the case of ortho-TINA, both Hoogsteen and Watson-Crick-type complexes were......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...

Ibotenic acid and thioibotenic acid

DEFF Research Database (Denmark)

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

2004-01-01

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

Encapsulating fly ash and acidic process waste water in brick structure

International Nuclear Information System (INIS)

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

2010-01-01

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

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.

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

Directory of Open Access Journals (Sweden)

Graham Smith

2016-03-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2008-04-15

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

The combined effects of urea application and simulated acid rain on soil acidification and microbial community structure.

Science.gov (United States)

Liu, Xingmei; Zhou, Jian; Li, Wanlu; Xu, Jianming; Brookes, Philip C

2014-05-01

Our aim was to test the effects of simulated acid rain (SAR) at different pHs, when applied to fertilized and unfertilized soils, on the leaching of soil cations (K, Ca, Mg, Na) and Al. Their effects on soil pH, exchangeable H(+) and Al(3+) and microbial community structure were also determined. A Paleudalfs soil was incubated for 30 days, with and without an initial application of urea (200 mg N kg(-1)soil) as nitrogen (N) fertilizer. The soil was held in columns and leached with SAR at three pH levels. Six treatments were tested: SAR of pH 2.5, 4.0 and 5.6 leaching on unfertilized soil (T1, T2 and T3), and on soils fertilized with urea (T4, T5 and T6). Increasing acid inputs proportionally increased cation leaching in both unfertilized and fertilized soils. Urea application increased the initial Ca and Mg leaching, but had no effect on the total concentrations of Ca, Mg and K leached. There was no significant difference for the amount of Na leached between the different treatments. The SAR pH and urea application had significant effects on soil pH, exchangeable H(+) and Al(3+). Urea application, SAR treated with various pH, and the interactions between them all had significant impacts on total phospholipid fatty acids (PLFAs). The highest concentration of total PLFAs occurred in fertilized soils with SAR pH5.6 and the lowest in soils leached with the lowest SAR pH. Soils pretreated with urea then leached with SARs of pH 4.0 and 5.6 had larger total PLFA concentrations than soil without urea. Bacterial, fungal, actinomycete, Gram-negative and Gram-positive bacterial PLFAs had generally similar trends to total PLFAs.

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

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

Science.gov (United States)

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

2010-01-01

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

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

Science.gov (United States)

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

2010-04-02

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

Natural terpene derivatives as new structural task-specific ionic liquids to enhance the enantiorecognition of acidic enantiomers on teicoplanin-based stationary phase by high-performance liquid chromatography.

Science.gov (United States)

Flieger, Jolanta; Feder-Kubis, Joanna; Tatarczak-Michalewska, Małgorzata; Płazińska, Anita; Madejska, Anna; Swatko-Ossor, Marta

2017-06-01

We present the specific cooperative effect of a semisynthetic glycopeptide antibiotic teicoplanin and chiral ionic liquids containing the (1R,2S,5R)-(-)-menthol moiety on the chiral recognition of enantiomers of mandelic acid, vanilmandelic acid, and phenyllactic acid. Experiments were performed chromatographically on an Astec Chirobiotic T chiral stationary phase applying the mobile phase with the addition of the chiral ionic liquids. The stereoselective binding of enantiomers to teicoplanin in presence of new chiral ionic liquids were evaluated applying thermodynamic measurements and the docking simulations. Both the experimental and theoretical methods revealed that the chiral recognition of enantiomers in the presence of new chiral ionic liquids was enthalpy driven. The changes of the teicoplanin conformation occurring upon binding of the chiral ionic liquids are responsible for the differences in the standard changes in Gibbs energy (ΔG 0 ) values obtained for complexes formed by the R and S enantiomers and teicoplanin. Docking simulations revealed the steric adjustment between the chiral ionic liquids cyclohexane ring (chair conformation) and the β-d-glucosamine ring of teicoplanin and additionally hydrophobic interactions between the decanoic aliphatic chain of teicoplanin and the alkyl group of the tested salts. The obtained terpene derivatives can be considered as "structural task-specific ionic liquids" responsible for enhancing the chiral resolution in synergistic systems with two chiral selectors. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Structure and Functioning of a Low-Budget Center for Applied Linguistics: The Brazilian Experience.

Science.gov (United States)

Gomes de Matos, Francisco

1980-01-01

Describes the structure and functioning of the "Centro de Linguistica Aplicada do Instituto de Idiomas Yazigi" of Sao Paulo and comments on its role in promoting applied linguistics studies in Latin America. Also outlines the Center's historical background and its educational services, particularly those related to the teaching of…

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-05-28

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

Influence of acidified acidity to uranium bioleaching

International Nuclear Information System (INIS)

Li Jiang; Liu Yajie; Zheng Zhihong; Yuan Baohua; Shen Chuan; Shi Weijun

2012-01-01

The relationship between the acidified acidity and the acid consumption and uranium leaching rate in the process of uranium bioleaching is investigated. Results indicate that higher uranium leaching rate is obtained when the relatively high acidity was applied at beginning. For different minerals, although the original acidity should be different, lower original acidity was not better for shortening leaching period and improving uranium leaching rate. It confirms 30-40 g/L sulfuric acid as the original acidity was more suitable and more than 30 g/ L should be applied if the mineral particle sizes were larger. (authors)

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.

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

NARCIS (Netherlands)

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

1988-01-01

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

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

International Nuclear Information System (INIS)

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

2007-01-01

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

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.

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

Science.gov (United States)

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

2015-09-01

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

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

International Nuclear Information System (INIS)

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

1977-01-01

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

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.

Direct Enantioselective Conjugate Addition of Carboxylic Acids with Chiral Lithium Amides as Traceless Auxiliaries

Science.gov (United States)

2016-01-01

Michael addition is a premier synthetic method for carbon–carbon and carbon–heteroatom bond formation. Using chiral dilithium amides as traceless auxiliaries, we report the direct enantioselective Michael addition of carboxylic acids. A free carboxyl group in the product provides versatility for further functionalization, and the chiral reagent can be readily recovered by extraction with aqueous acid. The method has been applied in the enantioselective total synthesis of the purported structure of pulveraven B. PMID:25562717

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.

Aminolysis of resin-bound N-nosylaziridine-2-carboxylic acids

DEFF Research Database (Denmark)

Olsen, Christian A; Christensen, Caspar; Nielsen, Birgitte

2006-01-01

[Structure: see text] Solid-phase synthesis is a rapidly developing area of organic chemistry, of particular importance for medicinal chemistry and chemical biology. Aziridines have previously only rarely been applied in solid-phase synthesis. In the present work, aminolysis of resin-bound, sprin......-loaded N-nitrobenzenesulfonyl-activated aziridine-2-carboxylic acids has been optimized and employed in the synthesis of a number of open-chain and heterocyclic scaffolds, including enantiopure products....

Speckle photography applied to measure deformations of very large structures

Science.gov (United States)

Conley, Edgar; Morgan, Chris K.

1995-04-01

Fundamental principles of mechanics have recently been brought to bear on problems concerning very large structures. Fields of study include tectonic plate motion, nuclear waste repository vault closure mechanisms, the flow of glacier and sea ice, and highway bridge damage assessment and residual life prediction. Quantitative observations, appropriate for formulating and verifying models, are still scarce however, so the need to adapt new methods of experimental mechanics is clear. Large dynamic systems often exist in environments subject to rapid change. Therefore, a simple field technique that incorporates short time scales and short gage lengths is required. Further, the measuring methods must yield displacements reliably, and under oft-times adverse field conditions. Fortunately, the advantages conferred by an experimental mechanics technique known as speckle photography nicely fulfill this rather stringent set of performance requirements. Speckle seemed to lend itself nicely to the application since it is robust and relatively inexpensive. Experiment requirements are minimal -- a camera, high resolution film, illumination, and an optically rough surface. Perhaps most important is speckle's distinct advantage over point-by-point methods: It maps the two dimensional displacement vectors of the whole field of interest. And finally, given the method's high spatial resolution, relatively short observation times are necessary. In this paper we discuss speckle, two variations of which were used to gage the deformation of a reinforced concrete bridge structure subjected to bending loads. The measurement technique proved to be easily applied, and yielded the location of the neutral axis self consistently. The research demonstrates the feasibility of using whole field techniques to detect and quantify surface strains of large structures under load.

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.

Towards control of aggregational behaviour of alpha-lactalbumin at acidic pH.

Science.gov (United States)

Pedersen, Jane B; Fojan, Peter; Sorensen, John; Petersen, Steffen B

2006-07-01

alpha-Lactalbumin (alpha-La) undergoes considerable structural changes upon loss of bound Ca2+ at acidic pH, leaving alpha-La in a molten globule structure. Using fluorescence the present work provides more insight into the structural transition of alpha-La at acidic pH leading to protein aggregation, most likely caused by a combination of hydrophobic and electrostatic interactions. The rate of aggregation is determined by the protein concentration and temperature applied. Availability of Ca2+ stabilises the protein, and thus prevent aggregation at pH values as low as pH 2.9. In contrast, presence of Cu2+ induces a destabilisation of the protein, which can be explained by a binding to the Zn2+ binding site in alpha-La, possibly resulting in structural alterations of the protein. In general, presence of anions destabilize alpha-La at pH values below pI, with SO4(2-) exhibiting the strongest effect on the protein stability, thus correlating well with the Hofmeister series. At more acidic pH values far from pI, alpha-La becomes more stable towards ion induced aggregation, since higher ion activity is required to efficiently screen the charges on the protein surface. The results presented in this paper provide detailed knowledge on the external parameters leading to aggregation of alpha-La at acidic pH, thus permitting rational design of the aggregation process.

Understanding longitudinal wood fiber ultra-structure for producing cellulose nanofibrils using disk milling with diluted acid prehydrolysis

Science.gov (United States)

Yanlin Qin; Xueqing Qiu; Junyong Zhu

2016-01-01

Here we used dilute oxalic acid to pretreat a kraft bleached Eucalyptus pulp (BEP) fibers to facilitate mechanical fibrillation in producing cellulose nanofibrils using disk milling with substantial mechanical energy savings. We successfully applied a reaction kinetics based combined hydrolysis factor (CHFx) as a severity factor to quantitatively...

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

Directory of Open Access Journals (Sweden)

Isabel Bento

2006-11-01

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

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.

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

Directory of Open Access Journals (Sweden)

Ning Zhang

2007-10-01

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

Discrimination symbol applying method for sintered nuclear fuel product

International Nuclear Information System (INIS)

Ishizaki, Jin

1998-01-01

The present invention provides a symbol applying method for applying discrimination information such as an enrichment degree on the end face of a sintered nuclear product. Namely, discrimination symbols of information of powders are applied by a sintering aid to the end face of a molded member formed by molding nuclear fuel powders under pressure. Then, the molded product is sintered. The sintering aid comprises aluminum oxide, a mixture of aluminum oxide and silicon dioxide, aluminum hydride or aluminum stearate alone or in admixture. As an applying means of the sintering aid, discrimination symbols of information of powders are drawn by an isostearic acid on the end face of the molded product, and the sintering aid is sprayed thereto, or the sintering aid is applied directly, or the sintering aid is suspended in isostearic acid, and the suspension is applied with a brush. As a result, visible discrimination information can be applied to the sintered member easily. (N.H.)

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

Science.gov (United States)

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

2012-01-01

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

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

KAUST Repository

Shkurenko, Aleksander

2018-02-19

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

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

Science.gov (United States)

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

2018-01-01

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

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

Science.gov (United States)

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

2015-06-01

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

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

International Nuclear Information System (INIS)

Ilyasoglu, H.

2017-01-01

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

Characterization of applied fields for ion mobility in traveling wave based structures for lossless ion manipulations (SLIM)

Energy Technology Data Exchange (ETDEWEB)

Hamid, Ahmed M.; Prabhakaran Nair Syamala Amma, Aneesh; Garimella, Venkata BS; Ibrahim, Yehia M.; Smith, Richard D.

2018-03-21

Ion mobility (IM) is rapidly gaining attention for the analysis of biomolecules due to the ability to distinguish the shapes of ions. However, conventional constant electric field drift tube IM has limited resolving power, constrained by practical limitations on the path length and maximum applied voltage. The implementation of traveling waves (TW) in IM removes the latter limitation, allowing higher resolution to be achieved using extended path lengths. These can be readily obtainable in structures for lossless ion manipulations (SLIM), which are fabricated from electric fields that are generated by appropriate potentials applied to arrays of electrodes patterned on two parallel surfaces. In this work we have investigated the relationship between the various SLIM variables, such as electrode dimensions, inter-surface gap, and the TW applied voltages, that directly impact the fields experienced by ions. Ion simulation and theoretical calculations have been utilized to understand the dependence of SLIM geometry and effective electric field. The variables explored impact both ion confinement and the observed IM resolution in Structures for Lossless Ion Manipulations (SLIM) modules.

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...

Acid dip for dosemeter

International Nuclear Information System (INIS)

Stewart, J.C.; McWhan, A.F.

1982-01-01

Background signal in a PTFE based dosemeter caused by impurities in the PTFE and in the active component such as lithium fluoride is substantially reduced by treating the dosemeter with acid. The optimum treatment involves use of hydrofluoric acid at room temperature for approximately one minute, followed by thorough washing with methanol, and finally drying. This treatment is best applied after the original manufacture of the dosemeters. It may also be applied to existing dosemeters after they have been in use for some time. The treatment produces a permanent effect in reducing both the light induced signal and the non-light induced signal. The process may be applied to all types of dosemeter manufactured from PTFE or other plastics or resins which are able to resist brief exposure to acid. The treatment works particularly well with dosemeters based on PTFE and lithium fluoride. It is also applicable to dosemeters based on calcium sulphate, lithium borate and magnesium borate. Acids which may be used include hydrofluoric, hydrochloric, nitric, phosphoric and sulphuric. (author)

Exploring causal networks of bovine milk fatty acids in a multivariate mixed model context

DEFF Research Database (Denmark)

Bouwman, Aniek C; Valente, Bruno D; Janss, Luc L G

2014-01-01

Knowledge regarding causal relationships among traits is important to understand complex biological systems. Structural equation models (SEM) can be used to quantify the causal relations between traits, which allow prediction of outcomes to interventions applied to such a network. Such models...... are fitted conditionally on a causal structure among traits, represented by a directed acyclic graph and an Inductive Causation (IC) algorithm can be used to search for causal structures. The aim of this study was to explore the space of causal structures involving bovine milk fatty acids and to select...

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

Science.gov (United States)

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

2013-02-01

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

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

Amino acid properties conserved in molecular evolution.

Directory of Open Access Journals (Sweden)

Witold R Rudnicki

Full Text Available That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts - one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications.

Recent Advances in Fluorescent Arylboronic Acids for Glucose Sensing

Directory of Open Access Journals (Sweden)

Jon Stefan Hansen

2013-12-01

Full Text Available Continuous glucose monitoring (CGM is crucial in order to avoid complications caused by change in blood glucose for patients suffering from diabetes mellitus. The long-term consequences of high blood glucose levels include damage to the heart, eyes, kidneys, nerves and other organs, among others, caused by malign glycation of vital protein structures. Fluorescent monitors based on arylboronic acids are promising candidates for optical CGM, since arylboronic acids are capable of forming arylboronate esters with 1,2-cis-diols or 1,3-diols fast and reversibly, even in aqueous solution. These properties enable arylboronic acid dyes to provide immediate information of glucose concentrations. Thus, the replacement of the commonly applied semi-invasive and non-invasive techniques relying on glucose binding proteins, such as concanavalin A, or enzymes, such as glucose oxidase, glucose dehydrogenase and hexokinases/glucokinases, might be possible. The recent progress in the development of fluorescent arylboronic acid dyes will be emphasized in this review.

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

Science.gov (United States)

Goonesekere, Nalin Cw

2009-01-01

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

Molecular interaction of pinic acid with sulfuric acid

DEFF Research Database (Denmark)

Elm, Jonas; Kurtén, Theo; Bilde, Merete

2014-01-01

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

Sequential injection redox or acid-base titration for determination of ascorbic acid or acetic acid.

Science.gov (United States)

Lenghor, Narong; Jakmunee, Jaroon; Vilen, Michael; Sara, Rolf; Christian, Gary D; Grudpan, Kate

2002-12-06

Two sequential injection titration systems with spectrophotometric detection have been developed. The first system for determination of ascorbic acid was based on redox reaction between ascorbic acid and permanganate in an acidic medium and lead to a decrease in color intensity of permanganate, monitored at 525 nm. A linear dependence of peak area obtained with ascorbic acid concentration up to 1200 mg l(-1) was achieved. The relative standard deviation for 11 replicate determinations of 400 mg l(-1) ascorbic acid was 2.9%. The second system, for acetic acid determination, was based on acid-base titration of acetic acid with sodium hydroxide using phenolphthalein as an indicator. The decrease in color intensity of the indicator was proportional to the acid content. A linear calibration graph in the range of 2-8% w v(-1) of acetic acid with a relative standard deviation of 4.8% (5.0% w v(-1) acetic acid, n=11) was obtained. Sample throughputs of 60 h(-1) were achieved for both systems. The systems were successfully applied for the assays of ascorbic acid in vitamin C tablets and acetic acid content in vinegars, respectively.

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

Science.gov (United States)

Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

2014-09-18

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

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...

Graphitic carbon nitride nanosheets doped graphene oxide for electrochemical simultaneous determination of ascorbic acid, dopamine and uric acid

International Nuclear Information System (INIS)

Zhang, Hanqiang; Huang, Qitong; Huang, Yihong; Li, Feiming; Zhang, Wuxiang; Wei, Chan; Chen, Jianhua; Dai, Pingwang; Huang, Lizhang; Huang, Zhouyi; Kang, Lianping; Hu, Shirong; Hao, Aiyou

2014-01-01

Graphical abstract: Schematic drawing of electrochemical oxidize AA, DA and UA on graphitic carbon nitride nanosheets-graphene oxide composite modified electrode. - Highlights: • Synthesize g-C 3 N 4 , GO and CNNS-GO composite. • CNNS-GO composite was the first time for simultaneous determination of AA, DA and UA. • CNNS-GO/GCE displays fantastic selectivity and sensitivity for AA, DA and UA. • CNNS-GO/GCE was applied to detect real sample with satisfactory results. - Abstract: Graphitic carbon nitride nanosheets with a graphite-like structure have strong covalent bonds between carbon and nitride atoms, and nitrogen atoms in the carbon architecture can accelerate the electron transfer and enhance electrical properties effectually. The graphitic carbon nitride nanosheets-graphene oxide composite was synthesized. And the electrochemical performance of the composite was investigated by cyclic voltammetry and differential pulse voltammetry ulteriorly. Due to the synergistic effects of layer-by-layer structures by π-π stacking or charge-transfer interactions, graphitic carbon nitride nanosheets-graphene oxide composite can improved conductivity, electro-catalytic and selective oxidation performance. The proposed graphitic carbon nitride nanosheets-graphene oxide composite modified electrode was employed for simultaneous determination of ascorbic acid, dopamine and uric acid in their mixture solution, it exhibited distinguished sensitivity, wide linear range and low detection limit. Moreover, the modified electrode was applied to detect urine and dopamine injection sample, and then the samples were spiked with certain concentration of three substances with satisfactory recovery results

Methodology for modeling the disinfection efficiency of fresh-cut leafy vegetables wash water applied on peracetic acid combined with lactic acid.

Science.gov (United States)

Van Haute, S; López-Gálvez, F; Gómez-López, V M; Eriksson, Markus; Devlieghere, F; Allende, Ana; Sampers, I

2015-09-02

A methodology to i) assess the feasibility of water disinfection in fresh-cut leafy greens wash water and ii) to compare the disinfectant efficiency of water disinfectants was defined and applied for a combination of peracetic acid (PAA) and lactic acid (LA) and comparison with free chlorine was made. Standardized process water, a watery suspension of iceberg lettuce, was used for the experiments. First, the combination of PAA+LA was evaluated for water recycling. In this case disinfectant was added to standardized process water inoculated with Escherichia coli (E. coli) O157 (6logCFU/mL). Regression models were constructed based on the batch inactivation data and validated in industrial process water obtained from fresh-cut leafy green processing plants. The UV254(F) was the best indicator for PAA decay and as such for the E. coli O157 inactivation with PAA+LA. The disinfection efficiency of PAA+LA increased with decreasing pH. Furthermore, PAA+LA efficacy was assessed as a process water disinfectant to be used within the washing tank, using a dynamic washing process with continuous influx of E. coli O157 and organic matter in the washing tank. The process water contamination in the dynamic process was adequately estimated by the developed model that assumed that knowledge of the disinfectant residual was sufficient to estimate the microbial contamination, regardless the physicochemical load. Based on the obtained results, PAA+LA seems to be better suited than chlorine for disinfecting process wash water with a high organic load but a higher disinfectant residual is necessary due to the slower E. coli O157 inactivation kinetics when compared to chlorine. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Science.gov (United States)

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

2011-10-11

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

Locked nucleic acid

DEFF Research Database (Denmark)

Jepsen, Jan Stenvang; Sørensen, Mads D; Wengel, Jesper

2004-01-01

Locked nucleic acid (LNA) is a class of nucleic acid analogs possessing very high affinity and excellent specificity toward complementary DNA and RNA, and LNA oligonucleotides have been applied as antisense molecules both in vitro and in vivo. In this review, we briefly describe the basic...

Prediction of molecular crystal structures

International Nuclear Information System (INIS)

Beyer, Theresa

2001-01-01

The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol -1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

Prediction of molecular crystal structures

Energy Technology Data Exchange (ETDEWEB)

Beyer, Theresa

2001-07-01

The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

Labeling of eukaryotic messenger RNA 5' terminus with phosphorus -32: use of tobacco acid pyrophosphatase for removal of cap structures

International Nuclear Information System (INIS)

Lockard, R.E.; Rieser, L.; Vournakis, J.N.

1981-01-01

In recent years, there has been a growing appreciation of the potential applications of 5'- 32 P-end-labeled mRNA, not only for screening recombinant clones and mapping gene structure, but also for revealing possible nucleotide sequence and structural signals within mRNA molecules themselves, which may be important for eukaryotic mRNA processing and turnover and for controlling differential rates of translational initiation. Three major problems, however, have retarded progress in this area, lack of methods for efficient and reproducible removal of m7G5ppp5'-cap structures, which maintain the integrity of an RNA molecule; inability to generate a sufficient amount of labeled mRNA, owing to the limited availability of most pure mRNA species; and the frequent problem of RNA degradation during in vitro end-labeling owing to RNAse contamination. The procedures presented here permit one to decap and label minute quantities of mRNA, effectively. Tobacco acid pyrophosphatase is relatively efficient in removing cap structures from even nanogram quantities of available mRNA, and enough radioactivity can be easily generated from minute amounts ofintact mRNA with very high-specific-activity [gamma- 32 P]ATP and the inhibition of ribonuclease contamination with diethylpyrocarbonate. These procedures can be modified and applied to almost any other type of RNA molecule as well. In Section III of this volume, we explore in detail how effectively 5'-end-labeled mRNA can be used not only for nucleotide sequence analysis, but also for mapping mRNA secondary structure

Evolution of the magnetic structure of TbRu{sub 2}Al{sub 10} in applied field

Energy Technology Data Exchange (ETDEWEB)

White, R., E-mail: Reyner.White@student.adfa.edu.au [School of Physical, Environmental and Mathematical Sciences, The University of New South Wales, Canberra, ACT, 2600 (Australia); Hutchison, W.D. [School of Physical, Environmental and Mathematical Sciences, The University of New South Wales, Canberra, ACT, 2600 (Australia); Mizushima, T. [Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555 (Japan); Studer, A.J. [Bragg Institute, Australian Nuclear Science and Technology Organisation, Kirrawee DC, NSW, 2232 (Australia)

2016-09-15

TbRu{sub 2}Al{sub 10} is found to undergo two magnetic phase transitions as a function of temperature and three as a function of applied field at low temperature. The Tb{sup 3+} magnetic moments order antiferromagnetically along the c-axis at 15.0(3) K, with an incommensurate sinusoidally modulated structure with a propagation vector of k = (0, 0.759(1), 0). At 6.5(3) K the structure switches to square wave order. Analysis of single crystal TbRu{sub 2}Al{sub 10} has revealed that this square wave structure is altered to a ‘pulse wave’ on application of a 1.30 T magnetic field along the c-axis, with two in fifty of the magnetic moments across the structure changing direction to be aligned parallel with the direction of the field. At 1.85 T a further three moments flip, leading to a duty cycle of 60% and resulting in a total change of one in ten moments from the starting square wave structure. - Highlights: • The magnetic and physical properties of the intermetallic TbRu{sub 2}Al{sub 10} were examined. • TbRu{sub 2}Al{sub 10} was found to order antiferromagnetically at 15.0(3) K. • Neutron powder diffraction revealed sinusoidal magnetic ordering below 15 K. • Single crystal neutron diffraction revealed square wave magnetic order at 2 K. • An applied magnetic field along the c-axis forces the moments into pulse wave order.

Investigating Move Structure of English Applied Linguistics Research Article Discussions Published in International and Thai Journals

Science.gov (United States)

Amnuai, Wirada; Wannaruk, Anchalee

2013-01-01

This study investigates the rhetorical move structure of English applied linguistic research article Discussions published in Thai and international journals. Two corpora comprising of 30 Thai Discussions and 30 international Discussions were analyzed using Yang & Allison's (2003) move model. Based on the analysis, both similarities and…

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

Science.gov (United States)

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

1998-10-01

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

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

Science.gov (United States)

Kinjo, Akira R; Nakamura, Haruki

2013-01-01

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

Vibrational spectroscopy and principal component analysis for conformational study of virus nucleic acids

Science.gov (United States)

Dovbeshko, G. I.; Repnytska, O. P.; Pererva, T.; Miruta, A.; Kosenkov, D.

2004-07-01

Conformation analysis of mutated DNA-bacteriophages (PLys-23, P23-2, P47- the numbers have been assigned by T. Pererva) induced by MS2 virus incorporated in Ecoli AB 259 Hfr 3000 has been done. Surface enhanced infrared absorption (SEIRA) spectroscopy and principal component analysis has been applied for solving this problem. The nucleic acids isolated from the mutated phages had a form of double stranded DNA with different modifications. The nucleic acid from phage P47 was undergone the structural rearrangement in the most degree. The shape and position ofthe fine structure of the Phosphate asymmetrical band at 1071cm-1 as well as the stretching OH vibration at 3370-3390 cm-1 has indicated to the appearance ofadditional OH-groups. The Z-form feature has been found in the base vibration region (1694 cm-1) and the sugar region (932 cm-1). A supposition about modification of structure of DNA by Z-fragments for P47 phage has been proposed. The P23-2 and PLys-23 phages have showed the numerous minor structural changes also. On the basis of SEIRA spectra we have determined the characteristic parameters of the marker bands of nucleic acid used for construction of principal components. Contribution of different spectral parameters of nucleic acids to principal components has been estimated.

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-09-01

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

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Monitoring of monooctanoyl phosphatidylcholine synthesis by enzymatic acidolysis between soybean phosphatidylcholine and caprylic acid by thin-layer chromatography with a flame ionization detector

DEFF Research Database (Denmark)

Vikbjerg, Anders Falk; Mu, Huiling; Xu, Xuebing

2005-01-01

Thin-layer chromatography with flame ionization detector (TLC-FID) method was used for monitoring the production of structured phospholipids (ML-type: L-long chain fatty acids; M-medium chain fatty acids) by enzyme-catalyzed acidolysis between soybean phosphatidylcholine (PC) and caprylic acid....... It was found that the structured PC fractionated into 2-3 distinct bands on both plate thin layer chromatography (TLC) and Chromarod TLC. These 3 bands represented PC of LL-type, ML-type and MM-type, respectively. The TLC-FID method was applied in the present study to examine the influence of enzyme dosage...

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

CSIR Research Space (South Africa)

Neppalli, R

2014-01-01

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

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

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

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

Science.gov (United States)

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

2017-01-01

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

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.

Wafer Cakes of Improved Amino Acid Structure

Directory of Open Access Journals (Sweden)

Roksolana Boidunyk

2017-11-01

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

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

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Bo Xu

2012-06-01

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

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.

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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

Science.gov (United States)

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

2014-08-01

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

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...

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

Directory of Open Access Journals (Sweden)

I. JURANIC

2000-11-01

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

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.

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

Energy Technology Data Exchange (ETDEWEB)

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

2012-01-15

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2011-01-01

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