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Sample records for pdb carbohydrate residue

  1. pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files.

    PubMed

    Lütteke, Thomas; von der Lieth, Claus-W

    2004-06-04

    Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of glycans is a prerequisite for a complete understanding of their biological functions. The largest source of biomolecular 3D structures is the Protein Data Bank. However, about 30% of all 1663 PDB entries (version September 2003) containing carbohydrates comprise errors in glycan description. Unfortunately, no software is currently available which aligns the 3D information with the reported assignments. It is the aim of this work to fill this gap. The pdb-care program http://www.glycosciences.de/tools/pdb-care/ is able to identify and assign carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported. Additionally, the reliability of reported and calculated connectivities for molecules listed within the HETATOM records is checked and unusual values are reported. Frequent use of pdb-care will help to improve the quality of carbohydrate data contained in the PDB. Automatic assignment of carbohydrate structures contained in PDB entries will enable the cross-linking of glycobiology resources with genomic and proteomic data collections.

  2. pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files

    PubMed Central

    Lütteke, Thomas; von der Lieth, Claus-W

    2004-01-01

    Background Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of glycans is a prerequisite for a complete understanding of their biological functions. The largest source of biomolecular 3D structures is the Protein Data Bank. However, about 30% of all 1663 PDB entries (version September 2003) containing carbohydrates comprise errors in glycan description. Unfortunately, no software is currently available which aligns the 3D information with the reported assignments. It is the aim of this work to fill this gap. Results The pdb-care program is able to identify and assign carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported. Additionally, the reliability of reported and calculated connectivities for molecules listed within the HETATOM records is checked and unusual values are reported. Conclusion Frequent use of pdb-care will help to improve the quality of carbohydrate data contained in the PDB. Automatic assignment of carbohydrate structures contained in PDB entries will enable the cross-linking of glycobiology resources with genomic and proteomic data collections. PMID:15180909

  3. Permethylation Linkage Analysis Techniques for Residual Carbohydrates

    USDA-ARS?s Scientific Manuscript database

    Permethylation analysis is the classic approach to establishing the position of glycosidic linkages between sugar residues. Typically, the carbohydrate is derivatized to form acid-stable methyl ethers, hydrolyzed, peracetylated, and analyzed by gas chromatography-mass spectrometry (GC-MS). The pos...

  4. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.

    PubMed

    Jo, Sunhwan; Cheng, Xi; Islam, Shahidul M; Huang, Lei; Rui, Huan; Zhu, Allen; Lee, Hui Sun; Qi, Yifei; Han, Wei; Vanommeslaeghe, Kenno; MacKerell, Alexander D; Roux, Benoît; Im, Wonpil

    2014-01-01

    CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since it is originally developed in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations including free energy calculation and large-scale coarse-grained representation. Here, we describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field generation, incorporation of methanethiosulfonate spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids. These new features are expected to be useful in advanced biomolecular modeling and simulation of proteins. © 2014 Elsevier Inc. All rights reserved.

  5. CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Non-standard Residues

    PubMed Central

    Jo, Sunhwan; Cheng, Xi; Islam, Shahidul M.; Huang, Lei; Rui, Huan; Zhu, Allen; Lee, Hui Sun; Qi, Yifei; Han, Wei; Vanommeslaeghe, Kenno; MacKerell, Alexander D.; Roux, Benoît; Im, Wonpil

    2016-01-01

    CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations including free energy calculation and large-scale coarse-grained representation. Here, we describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field generation, incorporation of methanethiosulfonate (MTS) spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids. These new features are expected to be useful in advanced biomolecular modeling and simulation of proteins. PMID:25443960

  6. Incorporation of Carbohydrate Residues into Peroxidase Isoenzymes in Horseradish Roots

    PubMed Central

    Lew, Jow Y.; Shannon, Leland M.

    1973-01-01

    Sliced root tissue of the horseradish plant (Armoracia rusticana), when incubated with mannose-U-14C, incorporated radioactivity into peroxidase isoenzymes. Over 90% of the radioactivity in the highly purified peroxidase isoenzymes was present in the neutral sugar residues of the molecule, i.e. fucose, arabinose, xylose, mannose. When the root slices were incubated simultaneously with leucine-4,5-3H and mannose-U-14C, cycloheximide strongly inhibited leucine incorporation into the peptide portion of peroxidase isoenzymes but had little effect on the incorporation of 14C into the neutral sugars. These results indicated that synthesis of the peptide portion of peroxidase was completed before the monosaccharide residues were attached to the molecule. This temporal relationship between the synthesis of protein and the attachment of carbohydrate residues in the plant glycoprotein, horseradish peroxidase, appears to be similar to that reported for glycoprotein biosynthesis in many mammalian systems. PMID:16658584

  7. Review: Use of residual dipolar couplings to determine the structure of carbohydrates.

    PubMed

    Canales, A; Jiménez-Barbero, J; Martín-Pastor, M

    2012-12-01

    Solution nuclear magnetic resonance spectroscopy is especially useful in the carbohydrate field. The measurement of residual dipolar couplings provides long-range structural information, a valuable complement for the structural study of carbohydrates either in its free form or in the bound state to proteins. They permit to deduce the geometry and the flexibility of the glycosidic linkages, which have a major influence on the conformation of carbohydrates and their overall shape. This article reviews the current application of the residual dipolar couplings methodology to carbohydrates.

  8. Residual carbohydrates from in vitro digested processed rapeseed ( Brassica napus ) meal.

    PubMed

    Pustjens, Annemieke M; de Vries, Sonja; Gerrits, Walter J J; Kabel, Mirjam A; Schols, Henk A; Gruppen, Harry

    2012-08-29

    Rapeseed meal (RSM) was subjected to different physical or chemical pretreatments to decrease residual, hard to degrade carbohydrates and to improve fermentability of RSM polysaccharides. Next, these pretreated samples were in vitro digested and fermented, with or without the addition of commercial pectinolytic enzymes. Remaining carbohydrates were quantified, and two physical characteristics were analyzed: (1) water-binding capacity (WBC) of the insoluble residue and (2) viscosity of the soluble fraction. Mild acid pretreatment in combination with commercial pectinolytic enzyme mixtures showed best digestion of RSM carbohydrates; only 32% of the total carbohydrate content remained. For most pretreatments, addition of commercial pectinolytic enzymes had the strongest effect on lowering the WBC of the in vitro incubated RSM. In the cases that less carbohydrate remained after in vitro digestion, the WBC of the residue decreased, and less gas seems to be produced during fermentation.

  9. Carbohydrates

    MedlinePlus

    ... glossary girlshealth.gov home http://www.girlshealth.gov/ Home Nutrition Nutrition basics Carbohydrates Carbohydrates Carbohydrates (say: kar-boh-HEYE-drayts) are the body's main source of energy. They are sometimes called "carbs" for short. If ...

  10. Characterization of protein and carbohydrate mid-IR spectral features in crop residues

    NASA Astrophysics Data System (ADS)

    Xin, Hangshu; Zhang, Yonggen; Wang, Mingjun; Li, Zhongyu; Wang, Zhibo; Yu, Peiqiang

    2014-08-01

    To the best of our knowledge, a few studies have been conducted on inherent structure spectral traits related to biopolymers of crop residues. The objective of this study was to characterize protein and carbohydrate structure spectral features of three field crop residues (rice straw, wheat straw and millet straw) in comparison with two crop vines (peanut vine and pea vine) by using Fourier transform infrared spectroscopy (FTIR) technique with attenuated total reflectance (ATR). Also, multivariate analyses were performed on spectral data sets within the regions mainly related to protein and carbohydrate in this study. The results showed that spectral differences existed in mid-IR peak intensities that are mainly related to protein and carbohydrate among these crop residue samples. With regard to protein spectral profile, peanut vine showed the greatest mid-IR band intensities that are related to protein amide and protein secondary structures, followed by pea vine and the rest three field crop straws. The crop vines had 48-134% higher spectral band intensity than the grain straws in spectral features associated with protein. Similar trends were also found in the bands that are mainly related to structural carbohydrates (such as cellulosic compounds). However, the field crop residues had higher peak intensity in total carbohydrates region than the crop vines. Furthermore, spectral ratios varied among the residue samples, indicating that these five crop residues had different internal structural conformation. However, multivariate spectral analyses showed that structural similarities still exhibited among crop residues in the regions associated with protein biopolymers and carbohydrate. Further study is needed to find out whether there is any relationship between spectroscopic information and nutrition supply in various kinds of crop residue when fed to animals.

  11. Carbohydrates

    MedlinePlus

    Carbohydrates are one of the main types of nutrients. They are the most important source of energy for your body. Your digestive system changes carbohydrates into glucose (blood sugar). Your body uses this ...

  12. Some characteristics of the residue obtained after pronase treatment of sheep erythrocyte membranes. II. Carbohydrate patterns.

    PubMed

    Marinari, U M; Averame, M M; Casu, A; Nanni, G

    1977-01-01

    The composition of single carbohydrate classes of intact and pronase treated sheep erythrocyte membranes has been studied. In comparison with the data obtained from untreated stromata after proteolytic digestion the amount of each class of sugars is decreased. A high disappearance of sialic acids and hexosamines can be observed. Nevertheless if the total sugar content is referred to the residual protein content (16% of the native proteins, an enrichment in carbohydrates, specially neutral hexoses, can be observed. The results indicate that most of the carbohydrate fractions solubilized by pronase treatment are sialic acids and hexosamines. Different molar ratios obtained for the single carbohydrate classes in comparison with NANA before and after pronase treatment suggest a microheterogeneity of the glycoprotein structure of sheep erythrocyte membranes. By the use of several analytical methods the residue obtained after pronase treatment shows two major fractions containing proteins, lipids and carbohydrates. The data are discussed in view of the possible arrangement of lipo-glycoproteins in sheep erythrocyte membrane.

  13. Carbohydrates.

    PubMed

    Cocinero, Emilio J; Çarçabal, Pierre

    2015-01-01

    Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).

  14. Application of sedimentary carbohydrate residues in a study of organic facies and natural gas occurrences

    NASA Astrophysics Data System (ADS)

    Swain, F. M.

    Recent aquatic environments and resulting organic facies can be characterized by types and amounts of carbohydrate residues. Characteristics are based on source organisms, degree and type of degradation, and reactions with associated compounds in the mineral-kerogen-humus complex. Selected modern environments are typified by the following presently known carbohydrate suites: (1) deep sea, mid-Pacific, mid-Atlantic Oceans—glucose, galactose, furfurals, low total carbohydrates (TC); (2) deep gulf, Gulf of California—glu, gal, xylose, mannose, furfurals, moderate to high TC; (3) continental shelf, eastern North America—glu, xyl, gal, furfurals, high TC; (5) oligotrophic lake, Minnesota—furfurals, low TC; (6) eutrophic lake, Minnesota—glu, xyl, arabinose, gal, rhamnose, man, ribose, furfurals, glucuronic acid, high TC; (7) bog, Minnesota—glu, ara, xyl, gal, man, rib, very high TC. Polysaccharides are rare to absent in modern deep sea deposits but have been found in Lower Quaternary and younger deep gulf sediments. Cellulose, alpha- and beta-amylose and laminaran are common in shallow marine and lacustrine sediments. Methane, derived from both terrestrial and aquatic higher plant residues is high in yield in freshwater marshes and bogs and in eutrophic lake sediments, moderate in salt-water marshes and estuaries and relatively low in offshore marine sediments. Nitrogen and carbon dioxide are the commonest non-hydrocarbon gases. In many samples studied, xylans appear to predominate over other plant polysaccharide as methane sources. Carbohydrate residues in ancient rocks, based on examples from North America, show a tentative, but as yet poorly investigated, relationship to environmental organic facies and should prove to be useful in natural gas exploration.

  15. Effect of the secondary structure of carbohydrate residues of alpha 1-acid glycoprotein (orosomucoid) on the local dynamics of Trp residues.

    PubMed

    Albani, Jihad René

    2004-01-01

    We studied in this work the relation between the secondary structure of the carbohydrate residues of alpha1-acid glycoprotein and the local motions of Trp residues of the protein. We measured for this purpose the fluorescence emission intensity and anisotropy of the Trp residues between -46 and +30 degrees of the sialylated and asialylated protein. Our results indicate that, in both forms, the global profile of the emission intensity with temperature shows that Trp residues display static and collisional interaction with the neighboring amino acids. However, the profile of the asialylated form is more structured than that observed for the sialylated protein. The Y-plot analysis of the emission-anisotropy results indicated that the frictional resistance to rotation of the surface Trp residue is less important in the sialylated protein than in the asialylated form. This result is in good agreement with the fact that, in the asialylated conformation, the carbohydrate residues are closer to the protein surface than in the sialylated form, thereby increasing the contact of the surface Trp residue with the neighboring amino acids. Also, the interaction between the carbohydrate residues and the surface Trp residue contributes to the modification of the frictional resistance to rotation of the fluorophore.

  16. Selenium Protects Retinal Cells from Cisplatin-Induced Alterations in Carbohydrate Residues

    PubMed Central

    Akşit, Dilek; Yazıcı, Alper; Akşit, Hasan; Sarı, Esin S.; Yay, Arzu; Yıldız, Onur; Kılıç, Adil; Ermiş, Sıtkı S.; Seyrek, Kamil

    2016-01-01

    Background: Investigate alterations in the expression and localization of carbohydrate units in rat retinal cells exposed to cisplatin toxicity. Aims: The aim of the study was to evaluate putative protective effects of selenium on retinal cells subjected to cisplatin. Study Design: Animal experiment. Methods: Eighteen healthy Wistar rats were divided into three equal groups: 1. Control, 2. Cisplatin and 3. Cisplatin+selenium groups. After anesthesia, the right eye of each rat was enucleated. Results: Histochemically, retinal cells of control groups reacted with α-2,3-bound sialic acid-specific Maackia amurensis lectin (MAA) strongly, while cisplatin reduced the staining intensity for MAA. However, selenium administration alleviated the reducing effect of cisplatin on the binding sites for MAA in retinal cells. The staining intensity for N-acetylgalactosamine (GalNAc residues) specific Griffonia simplicifolia-1 (GSL–1) was relatively slight in control animals and cisplatin reduced this slight staining for GSL-1 further. Selenium administration mitigated the reducing effect of cisplatin on the binding sites for GSL-1. A diffuse staining for N-acetylglucosamine (GlcNAc) specific wheat germ agglutinin (WGA) was observed throughout the retina of the control animals. In particular, cells localized in the inner plexiform and photoreceptor layers are reacted strongly with WGA. Compared to the control animals, binding sites for WGA in the retina of rats given cisplatin were remarkably decreased. However, the retinal cells of rats given selenium reacted strongly with WGA. Conclusion: Cisplatin reduces α-2,3-bound sialic acid, GlcNAc and GalNAc residues in certain retinal cells. However, selenium alleviates the reducing effect of cisplatin on carbohydrate residues in retinal cells. PMID:27606141

  17. Relation between the secondary structure of carbohydrate residues of alpha1-acid glycoprotein (orosomucoid) and the fluorescence of the protein.

    PubMed

    Albani, Jihad R

    2003-05-01

    We studied in this work the relation that exists between the secondary structure of the glycans of alpha(1)-acid glycoprotein and the fluorescence of the Trp residues of the protein. We calculated for that the efficiency of quenching and the radiative and non-radiative constants. Our results indicate that the glycans display a spatial structure that is modified upon asialylation. The asialylated conformation is closer to the protein matrix than the sialylated form, inducing by that a decrease in the fluorescence parameters of the Trp residues. In fact, the mean quantum yield of Trp residues in sialylated and asialylated alpha(1)-acid glycoprotein are 0.0645 and 0.0385, respectively. Analysis of the fluorescence emission of alpha(1)-acid glycoprotein as the result of two contributions (surface and hydrophobic domains) indicates that quantum yields of both classes of Trp residues are lower when the protein is in the asialylated form. Also, the mean fluorescence lifetime of Trp residues decreases from 2.285 ns in the sialylated protein to 1.948 ns in the asialylated one. The radiative rate constant k(r) of the Trp residues in the sialylated alpha(1)-acid glycoprotein is higher than that in the asialylated protein. Thus, the carbohydrate residues are closer to the Trp residues in the absence of sialic acid. The modification of the spatial conformation of the glycans upon asialylation is confirmed by the decrease of the fluorescence lifetimes of Calcofluor, a fluorophore that binds to the carbohydrate residues. Finally, thermal intensity quenching of Calcofluor bound to alpha(1)-acid glycoprotein shows that the carbohydrate residues have slower residual motions in the absence of sialic acid residues.

  18. Creative PDB`s (parts databases)

    SciTech Connect

    Cote, T.J.

    1998-12-31

    PDB component property entries and creative picklists can make the schematic entry process and downstream tools such as BOM generation more useful. This presentation will show how creative PDB`s can enhance the design process. Examples of PDB entries developed at Los Alamos National Laboratory will be discussed.

  19. Interaction between carbohydrate residues of alpha1-acid glycoprotein (orosomucoid) and saturating concentrations of Calcofluor White. A fluorescence study.

    PubMed

    Albani, J R; Sillen, A; Plancke, Y D; Coddeville, B; Engelborghs, Y

    2000-07-24

    Calcofluor White is a fluorescent probe that interacts with polysaccharides and is commonly used in clinical studies. Interaction between Calcofluor White and carbohydrate residues of alpha1-acid glycoprotein (orosomucoid) was previously followed by fluorescence titration of the Trp residues of the protein. A stoichiometry of one Calcofluor for one protein has been found [J.R. Albani and Y.D. Plancke, Carbohydr. Res., 318 (1999) 193-200]. Alpha1-acid glycoprotein contains 40% carbohydrate by weight and has up to 16 sialic acid residues. Since binding of Calcofluor to alpha1-acid glycoprotein occurs mainly on the carbohydrate residues, we studied in the present work the interaction between Calcofluor and the protein by following the fluorescence change of the fluorophore. In order to establish the role of the sialic acid residues in the interaction, the experiments were performed with the sialylated and asialylated protein. Interaction of Calcofluor with sialylated alpha1-acid glycoprotein induces a red shift of the emission maximum of the fluorophore from 438 to 450 nm at saturation (one Calcofluor for one sialic acid) and an increase in the fluorescence intensity. At saturation the fluorescence intensity increase levels off. Binding of Calcofluor to asialylated acid glycoprotein does not change the position of the emission maximum of the fluorophore and induces a decrease in its fluorescence intensity. Saturation occurs when 10 molecules of Calcofluor are bound to 1 mol of alpha1-acid glycoprotein. Since the protein contains five heteropolysaccharide groups, we have 2 mol of Calcofluor for each group. Addition of free sialic acid to Calcofluor induces a continuous decrease in the fluorescence intensity of the fluorophore but does not change the position of the emission maximum. Our results confirm the presence of a defined spatial conformation of the sialic acid residues, a conformation that disappears when they are free in solution. Dynamics studies on Calcofluor

  20. PDB-Metrics: a web tool for exploring the PDB contents.

    PubMed

    Fileto, Renato; Kuser, Paula R; Yamagishi, Michel E B; Ribeiro, André A; Quinalia, Thiago G; Franco, Eduardo H; Mancini, Adauto L; Higa, Roberto H; Oliveira, Stanley R M; Santos, Edgard H; Vieira, Fabio D; Mazoni, Ivan; Cruz, Sergio A B; Neshich, Goran

    2006-06-30

    PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein sequence, structure and function. It summarizes the characteristics of the collection of protein structure descriptions deposited in the Protein Data Bank (PDB) and provides a Web interface to search and browse the PDB, using a variety of alternative criteria. PDB-Metrics is a powerful tool for bioinformaticians to examine the data span in the PDB from several perspectives. Although other Web sites offer some similar resources to explore the PDB contents, PDB-Metrics is among those with the most complete set of such facilities, integrated into a single Web site. This program has been developed using SQLite, a C library that provides all the query facilities of a database management system.

  1. Bioethanol production from carbohydrate-enriched residual biomass obtained after lipid extraction of Chlorella sp. KR-1.

    PubMed

    Lee, Ok Kyung; Oh, You-Kwan; Lee, Eun Yeol

    2015-11-01

    The residual biomass of Chlorella sp. KR-1 obtained after lipid extraction was used for saccharification and bioethanol production. The carbohydrate was saccharified using simple enzymatic and chemical methods using Pectinex at pH 5.5 and 45°C and 0.3N HCl at 121°C for 15min with 76.9% and 98.2% yield, respectively, without any pretreatment. The residual biomass contained 49.7% carbohydrate consisting of 82.4% fermentable sugar and 17.6% non-fermentable sugar, which is valuable for bioethanol fermentation. Approximately 98.2% of the total carbohydrate was converted into monosaccharide (fermentable+non-fermentable sugar) using dilute acid saccharification. The fermentable sugar was subsequently fermented to bioethanol through separate hydrolysis and fermentation with a fermentation yield of 79.3%. Overall, 0.4g ethanol/g fermentable sugar and 0.16g ethanol/g residual biomass were produced. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Facilitating the enzymatic saccharification of pulped bamboo residues by degrading the remained xylan and lignin-carbohydrates complexes.

    PubMed

    Huang, Caoxing; He, Juan; Li, Xin; Min, Douyong; Yong, Qiang

    2015-09-01

    Kraft pulping was performed on bamboo residues and its impact on the chemical compositions and the enzymatic digestibility of the samples were investigated. To improve the digestibility of sample by degrading the xylan and lignin-carbohydrates complexes (LCCs), xylanase and α-L-arabinofuranosidase (AF) were supplemented with cellulase. The results showed more carbohydrates were remained in the samples pulped with low effective alkali (EA) charge, compared to conventional kraft pulping. When 120 IU/g xylanase and 15 IU/g AF were supplemented with 20 FPU/g cellulase, the xylan degradation yield of the sample pulped with 12% EA charge increased from 68.20% to 88.35%, resulting in an increased enzymatic saccharification efficiency from 58.98% to 83.23%. The amount of LCCs in this sample decreased from 8.63/100C9 to 2.99/100C9 after saccharification with these enzymes. The results indicated that degrading the remained xylan and LCCs in the pulp could improve its enzymatic digestibility.

  3. Application of information theory to a three-body coarse-grained representation of proteins in the PDB: insights into the structural and evolutionary roles of residues in protein structure.

    PubMed

    Thompson, Jared J; Tabatabaei Ghomi, Hamed; Lill, Markus A

    2014-12-01

    Knowledge-based methods for analyzing protein structures, such as statistical potentials, primarily consider the distances between pairs of bodies (atoms or groups of atoms). Considerations of several bodies simultaneously are generally used to characterize bonded structural elements or those in close contact with each other, but historically do not consider atoms that are not in direct contact with each other. In this report, we introduce an information-theoretic method for detecting and quantifying distance-dependent through-space multibody relationships between the sidechains of three residues. The technique introduced is capable of producing convergent and consistent results when applied to a sufficiently large database of randomly chosen, experimentally solved protein structures. The results of our study can be shown to reproduce established physico-chemical properties of residues as well as more recently discovered properties and interactions. These results offer insight into the numerous roles that residues play in protein structure, as well as relationships between residue function, protein structure, and evolution. The techniques and insights presented in this work should be useful in the future development of novel knowledge-based tools for the evaluation of protein structure. © 2014 Wiley Periodicals, Inc.

  4. Ionic liquid crystals as alignment medium to measure residual dipolar couplings for carbohydrates.

    PubMed

    Dama, Murali; Berger, Stefan

    2013-08-09

    Ionic liquids consisting of N-dodecyl-N-methyl pyrrolidinium bromide [C12MPB] in a mixture with D2O, decanol, and DMSO were for the first time found to give anisotropic molecular alignment in magnetic fields and are useful to measure residual dipolar couplings (RDCs) from polar analytes, for example, glucose. The system shows less quadrupolar splitting of the deuterated solvent signal compared with other liquid crystal systems and hence less undesired line broadening.

  5. Effect of binding of Calcofluor White on the carbohydrate residues of alpha1-acid glycoprotein (orosomucoid) on the structure and dynamics of the protein moiety. A fluorescence study.

    PubMed

    Albani, J R

    2001-08-23

    Calcofluor White is a fluorescent probe that interacts with polysaccharides and is commonly used in clinical studies. Interaction between Calcofluor White and carbohydrate residues of alpha1-acid glycoprotein (orosomucoid) was previously studied at low and high concentrations of Calcofluor compared to that of the protein. alpha1-Acid glycoprotein contains 40% carbohydrate by weight and has up to 16 sialic acid residues. At equimolar concentrations of Calcofluor and alpha1-acid glycoprotein, the fluorophore displays free motions [Albani, J. R.; Sillen, A.; Coddeville, B.; Plancke, Y. D.; Engelborghs, Y. Carbohydr. Res. 1999, 322, 87-94], while at high concentration of Calcofluor, its surrounding microenvironment is rigid, inducing the rigidity of the fluorophore itself [Albani, J. R.; Sillen, A.; Plancke, Y. D.; Coddeville, B.; Engelborghs, Y. Carbohydr. Res. 2000, 327, 333-340]. In the present work, red-edge excitation spectra and steady-state anisotropy studies performed on Trp residues in the presence of Calcofluor, showed that the apparent dynamics of Trp residues are not modified. However, deconvoluting the emission spectra with two different methods into different components, reveals that the structure of the protein matrix has been disrupted in the presence of high Calcofluor concentrations.

  6. Analysis and validation of carbohydrate three-dimensional structures

    SciTech Connect

    Lütteke, Thomas

    2009-02-01

    The article summarizes the information that is gained from and the errors that are found in carbohydrate structures in the Protein Data Bank. Validation tools that can locate these errors are described. Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein–carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein–carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures.

  7. Novel temperature-responsive polymer brushes with carbohydrate residues facilitate selective adhesion and collection of hepatocytes

    PubMed Central

    Idota, Naokazu; Ebara, Mitsuhiro; Kotsuchibashi, Yohei; Narain, Ravin; Aoyagi, Takao

    2012-01-01

    Temperature-responsive glycopolymer brushes were designed to investigate the effects of grafting architectures of the copolymers on the selective adhesion and collection of hypatocytes. Homo, random and block sequences of N-isopropylacrylamide and 2-lactobionamidoethyl methacrylate were grafted on glass substrates via surface-initiated atom transfer radical polymerization. The galactose/lactose-specific lectin RCA120 and HepG2 cells were used to test for specific recognition of the polymer brushes containing galactose residues over the lower critical solution temperatures (LCSTs). RCA120 showed a specific binding to the brush surfaces at 37 °C. These brush surfaces also facilitated the adhesion of HepG2 cells at 37 °C under nonserum conditions, whereas no adhesion was observed for NIH-3T3 fibroblasts. When the temperature was decreased to 25 °C, almost all the HepG2 cells detached from the block copolymer brush, whereas the random copolymer brush did not release the cells. The difference in releasing kinetics of cells from the surfaces with different grafting architectures can be explained by the correlated effects of significant changes in LCST, mobility, hydrophilicity and mechanical properties of the grafted polymer chains. These findings are important for designing ‘on–off’ cell capture/release substrates for various biomedical applications such as selective cell separation. PMID:27877533

  8. Novel temperature-responsive polymer brushes with carbohydrate residues facilitate selective adhesion and collection of hepatocytes

    NASA Astrophysics Data System (ADS)

    Idota, Naokazu; Ebara, Mitsuhiro; Kotsuchibashi, Yohei; Narain, Ravin; Aoyagi, Takao

    2012-12-01

    Temperature-responsive glycopolymer brushes were designed to investigate the effects of grafting architectures of the copolymers on the selective adhesion and collection of hypatocytes. Homo, random and block sequences of N-isopropylacrylamide and 2-lactobionamidoethyl methacrylate were grafted on glass substrates via surface-initiated atom transfer radical polymerization. The galactose/lactose-specific lectin RCA120 and HepG2 cells were used to test for specific recognition of the polymer brushes containing galactose residues over the lower critical solution temperatures (LCSTs). RCA120 showed a specific binding to the brush surfaces at 37 °C. These brush surfaces also facilitated the adhesion of HepG2 cells at 37 °C under nonserum conditions, whereas no adhesion was observed for NIH-3T3 fibroblasts. When the temperature was decreased to 25 °C, almost all the HepG2 cells detached from the block copolymer brush, whereas the random copolymer brush did not release the cells. The difference in releasing kinetics of cells from the surfaces with different grafting architectures can be explained by the correlated effects of significant changes in LCST, mobility, hydrophilicity and mechanical properties of the grafted polymer chains. These findings are important for designing ‘on-off’ cell capture/release substrates for various biomedical applications such as selective cell separation.

  9. Modifications of carbohydrate residues in the sheep oviductal ampulla after superovulation.

    PubMed

    Desantis, S; Accogli, G; Silvestre, F; Binetti, F; Caira, M; Lacalandra, G M

    2015-04-01

    Epithelium of oviductal ampulla was studied in normal and in superovulated sheep using morphologic analysis and lectin glycohistochemistry. The lining epithelium consisted of two types of cells, ciliated and nonciliated cells. Unlike superovulated samples, the nonciliated cells from control ewes showed apical protrusions indicating an apocrine secretory activity. The ciliated cells showed lectin-binding sites mainly at the level of the cilia which bound all the used lectins except Peanut agglutinin, suggesting the lack of glycans terminating with Galβ1,3GalNAc. In superovulated specimens, the ciliated cells with high mannosylated glycans Concanavalin A (Con A) and GlcNAc and GalNac termini Griffonia simplicifolia agglutinin II (GSA II) and Dolicurus biflorus agglutinin (DBA) decreased. The luminal surface of nonciliated cells showed all investigated sugar residues in controls, whereas it was lacking in high mannosylated (Con A) and terminal GalNAcα1,3(LFucα1,2)Galβ1,3/4GlcNAcβ1 sequence (DBA) in superovulated ewes. Apical protrusions from control ampullae nonciliated cells showed glycans containing mannose, GlcNac, GalNAc, galactose, and α2,3-linked sialic acid (Con A, KOH-sialidase- Wheat germ agglutnin [WGA], GSA II, SBA, Griffonia simplicifolia agglutinin-isolectin B4 [GSA I-B4], Maackia amurensis agglutinin II [MAL II]). The supranuclear cytoplasm of nonciliated cells expressed terminal GlcNAc (GSA II) in all specimens, also O-linked glycans (mucin-type glycans) with GalNAc and sialic acid termini (Helix pomatia agglutinin [HPA] and MAL II) in control animals, and also N-linked glycans with fucose, galactose, lactosamine, and α2,3-linked sialic acid termini (Ulex europaeus agglutinin I [UEA I], GSA I-B4, Ricinus communis agglutinin120 [RCA120], and Sambucus nigra agglutinin [SNA] ) in superovulated ewes. These results report for the first time that the superovulation treatment affects the secretory activity and the glycan pattern of the epithelium lining

  10. Dynamics of carbohydrate residues of alpha 1-acid glycoprotein (orosomucoid) followed by red-edge excitation spectra and emission anisotropy studies of Calcofluor White.

    PubMed

    Albani, J R; Sillen, A; Coddeville, B; Plancke, Y D; Engelborghs, Y

    1999-11-23

    Dynamics studies on Calcofluor White bound to the carbohydrate residues of sialylated and asialylated alpha 1-acid glycoprotein (orosomucoid) have been performed. The interaction between the fluorophore and the protein was found to occur preferentially with the glycan residues with a dependence on their spatial conformation. In the presence of sialylated alpha 1-acid glycoprotein, excitation at the red edge of the absorption spectrum of calcofluor does not lead to a shift in the fluorescence emission maximum (440 nm) of the fluorophore. Thus, the emission of calcofluor occurs from a relaxed state. This is confirmed by anisotropy studies as a function of temperature (Perrin plot). In the presence of asialylated alpha 1-acid glycoprotein, red-edge excitation spectra show an important shift (8 nm) of the fluorescence emission maximum of the probe. This reveals that emission of calcofluor occurs before relaxation of the surrounding carbohydrate residues occurs. Emission from a non-relaxed state means that Calcofluor molecules are bound tightly to the carbohydrate residues, a result confirmed by anisotropy studies.

  11. PDB file parser and structure class implemented in Python.

    PubMed

    Hamelryck, Thomas; Manderick, Bernard

    2003-11-22

    The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

  12. Increase in the carbohydrate content of the microalgae Spirulina in culture by nutrient starvation and the addition of residues of whey protein concentrate.

    PubMed

    Vieira Salla, Ana Cláudia; Margarites, Ana Cláudia; Seibel, Fábio Ivan; Holz, Luiz Carlos; Brião, Vandré Barbosa; Bertolin, Telma Elita; Colla, Luciane Maria; Costa, Jorge Alberto Vieira

    2016-06-01

    Non-renewable sources that will end with time are the largest part of world energy consumption, which emphasizes the necessity to develop renewable sources of energy. This necessity has created opportunities for the use of microalgae as a biofuel. The use of microalgae as a feedstock source for bioethanol production requires high yields of both biomass and carbohydrates. With mixotrophic cultures, wastewater can be used to culture algae. The aim of the study was to increase the carbohydrate content in the microalgae Spirulina with the additions of residues from the ultra and nanofiltration of whey protein. The nutrient deficit in the Zarrouk medium diluted to 20% and the addition of 2.5% of both residue types led to high carbohydrate productivity (60 mg L(-1) d(-1)). With these culture conditions, the increase in carbohydrate production in Spirulina indicated that the conditions were appropriate for use with microalgae as a feedstock in the production of bioethanol. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Studying and Polishing the PDB's Macromolecules

    PubMed Central

    Richardson, Jane S.; Richardson, David C.

    2012-01-01

    Macromolecular crystal structures are among the best of scientific data, providing detailed insight into these complex and biologically important molecules with a relatively low level of error and subjectivity. However, there are two notable problems with getting the most information from them. The first is that the models are not perfect: there is still opportunity for improving them, and users need to evaluate whether the local reliability in a structure is up to answering their question of interest. The second is that protein and nucleic acid molecules are highly complex and individual, inherently handed and 3-dimensional, and the cooperative and subtle interactions that govern their detailed structure and function are not intuitively evident. Thus there is a real need for graphical representations and descriptive classifications that enable molecular 3D literacy. We have spent our career working to understand these elegant molecules ourselves, and building tools to help us and others determine and understand them better. The Protein Data Bank (PDB) has of course been vital and central to this undertaking. Here we combine some history of our involvement as depositors, illustrators, evaluators, and end-users of PDB structures with commentary on how best to study and draw scientific inferences from them. PMID:23023928

  14. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

    PubMed

    Burley, Stephen K; Berman, Helen M; Kleywegt, Gerard J; Markley, John L; Nakamura, Haruki; Velankar, Sameer

    2017-01-01

    The Protein Data Bank (PDB)--the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes--was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.

  15. Analysis and validation of carbohydrate three-dimensional structures

    PubMed Central

    Lütteke, Thomas

    2009-01-01

    Knowledge of the three-dimensional structures of the carbo­hydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein–carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein–carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures. PMID:19171971

  16. Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket

    PubMed Central

    Dingjan, Tamir; Imberty, Anne; Pérez, Serge; Yuriev, Elizabeth; Ramsland, Paul A.

    2017-01-01

    Burkholderia ambifaria is an opportunistic respiratory pathogen belonging to the Burkholderia cepacia complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the B. ambifaria genome, BambL, is able to adhere to lung tissue, and may play a role in respiratory infection. X-ray crystallography has revealed the bound complex structures for four fucosylated human blood group epitopes (blood group B, H type 1, H type 2, and Lex determinants). The present study employed computational approaches, including docking and molecular dynamics (MD), to extend the structural analysis of BambL-oligosaccharide complexes to include four additional blood group saccharides (A, Lea, Leb, and Ley) and a library of blood-group-related carbohydrates. Carbohydrate recognition is dominated by interactions with fucose via a hydrogen-bonding network involving Arg15, Glu26, Ala38, and Trp79 and a stacking interaction with Trp74. Additional hydrogen bonds to non-fucose residues are formed with Asp30, Tyr35, Thr36, and Trp74. BambL recognition is dominated by interactions with fucose, but also features interactions with other parts of the ligands that may modulate specificity or affinity. The detailed computational characterization of the BambL carbohydrate-binding site provides guidelines for the future design of lectin inhibitors. PMID:28680402

  17. Mutational Insights into the Roles of Amino Acid Residues in Ligand Binding for Two Closely Related Family 16 Carbohydrate Binding Modules

    SciTech Connect

    Su, Xiaoyun; Agarwal, Vinayak; Dodd, Dylan; Bae, Brian; Mackie, Roderick I.; Nair, Satish K.; Cann, Isaac K.O.

    2010-11-22

    Carbohydrate binding modules (CBMs) are specialized proteins that bind to polysaccharides and oligosaccharides. Caldanaerobius polysaccharolyticus Man5ACBM16-1/CBM16-2 bind to glucose-, mannose-, and glucose/mannose-configured substrates. The crystal structures of the two proteins represent the only examples in CBM family 16, and studies that evaluate the roles of amino acid residues in ligand binding in this family are lacking. In this study, we probed the roles of amino acids (selected based on CBM16-1/ligand co-crystal structures) on substrate binding. Two tryptophan (Trp-20 and Trp-125) and two glutamine (Gln-81 and Gln-93) residues are shown to be critical in ligand binding. Additionally, several polar residues that flank the critical residues also contribute to ligand binding. The CBM16-1 Q121E mutation increased affinity for all substrates tested, whereas the Q21G and N97R mutants exhibited decreased substrate affinity. We solved CBM/substrate co-crystal structures to elucidate the molecular basis of the increased substrate binding by CBM16-1 Q121E. The Gln-121, Gln-21, and Asn-97 residues can be manipulated to fine-tune ligand binding by the Man5A CBMs. Surprisingly, none of the eight residues investigated was absolutely conserved in CBM family 16. Thus, the critical residues in the Man5A CBMs are either not essential for substrate binding in the other members of this family or the two CBMs are evolutionarily distinct from the members available in the current protein database. Man5A is dependent on its CBMs for robust activity, and insights from this study should serve to enhance our understanding of the interdependence of its catalytic and substrate binding modules.

  18. Residual gastric volume evaluation with ultrasonography after ingestion of carbohydrate- or carbohydrate plus glutamine-enriched beverages: a randomized, crossover clinical trial with healthy volunteers.

    PubMed

    Gomes, Paulo Cesar; Caporossi, Cervantes; Aguilar-Nascimento, Jose Eduardo; Silva, Ageo Mario Candido da; Araujo, Viviane Maeve Tavares de

    2017-01-01

    - Abbreviation of preoperative fasting to 2 hours with maltodextrin (CHO)-enriched beverage is a safe procedure and may enhance postoperative recovery. Addition of glutamine (GLN) to CHO beverages may include potential benefits to the metabolism. However, by adding a nitrogenous source to CHO beverages, gastric emptying may be delayed and increase the risk of bronchoaspiration during anesthesia. - In this study of safety, we aimed at investigating the residual gastric volume (RGV) 2 hours after the intake of either CHO beverage alone or CHO beverage combined with GLN. - We performed a randomized, crossover clinical trial. We assessed RGV by means of abdominal ultrasonography (US) in 20 healthy volunteers (10 males and 10 females) after an overnight fast of 8 hours. Then, they were randomized to receive 600 mL (400 mL immediately after US followed by another 200 mL 2 hours afterwards) of either CHO (12.5% maltodextrin) or CHO-GLN (12.5% maltodextrin plus 15 g GLN). Two sequential US evaluations were done at 120 and 180 minutes after ingestion of the second dose. The interval of time between ingestion of the two types of beverages was 2 weeks. - The mean (SD) RGV observed after 8 hours fasting (13.56±13.25 mL) did not statistically differ (P>0.05) from the RGV observed after ingesting CHO beverage at both 120 (16.32±11.78 mL) and 180 minutes (14.60±10.39 mL). The RGV obtained at 120 (15.63±18.83 mL) and 180 (13.65±10.27 mL) minutes after CHO-GLN beverage also was not significantly different from the fasting condition. - The RGV at 120 and 180 minutes after ingestion of CHO beverage combined with GLN is similar to that observed after an overnight fast.

  19. Synergy of Lewis and Brønsted acids on catalytic hydrothermal decomposition of carbohydrates and corncob acid hydrolysis residues to 5-hydroxymethylfurfural

    PubMed Central

    Wang, Chao; Zhang, Liming; Zhou, Tian; Chen, Jiachuan; Xu, Feng

    2017-01-01

    5-hydroxymethylfurfural (HMF) is an important platform molecule in the synthesis of various chemicals and materials. Herein, we reported a simple and effective dehydration of glucose-based carbohydrates to HMF in a biphasic system containing cyclopentyl methyl ether as the organic phase and AlCl3 with minute amounts of HCl as co-catalysts. The results showed that the mixed catalysts had a positive synergistic catalytic effect on glucose conversion to HMF compared with single AlCl3 or HCl catalyst. For glucose, the highest HMF yield of 54.5% was achieved at 175 °C for 20 min. More importantly, the optimal catalytic system was so efficient that it achieved one of the highest reported yields of HMF (30.5%) directly from corncob acid hydrolysis residues. Thus, the catalytic system can become a promising route for effective utilization of biomass in future biorefineries. PMID:28084456

  20. Synergy of Lewis and Brønsted acids on catalytic hydrothermal decomposition of carbohydrates and corncob acid hydrolysis residues to 5-hydroxymethylfurfural.

    PubMed

    Wang, Chao; Zhang, Liming; Zhou, Tian; Chen, Jiachuan; Xu, Feng

    2017-01-13

    5-hydroxymethylfurfural (HMF) is an important platform molecule in the synthesis of various chemicals and materials. Herein, we reported a simple and effective dehydration of glucose-based carbohydrates to HMF in a biphasic system containing cyclopentyl methyl ether as the organic phase and AlCl3 with minute amounts of HCl as co-catalysts. The results showed that the mixed catalysts had a positive synergistic catalytic effect on glucose conversion to HMF compared with single AlCl3 or HCl catalyst. For glucose, the highest HMF yield of 54.5% was achieved at 175 °C for 20 min. More importantly, the optimal catalytic system was so efficient that it achieved one of the highest reported yields of HMF (30.5%) directly from corncob acid hydrolysis residues. Thus, the catalytic system can become a promising route for effective utilization of biomass in future biorefineries.

  1. Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling

    PubMed Central

    Jo, Sunhwan; Lee, Hui Sun; Skolnick, Jeffrey; Im, Wonpil

    2013-01-01

    Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures. PMID:23516343

  2. Understanding Carbohydrates

    MedlinePlus

    ... Size: A A A Listen En Español Understanding Carbohydrates How much and what type of carbohydrate foods ... glucose levels in your target range. Explore: Understanding Carbohydrates Glycemic Index and Diabetes Learn about the glycemic ...

  3. Ultrasensitive Capillary Electrophoretic Analysis of Potentially Immunogenic Carbohydrate Residues in Biologics: Galactose-α-1,3-Galactose Containing Oligosaccharides

    PubMed Central

    Szabo, Zoltan; Guttman, Andras; Bones, Jonathan; Shand, Randi L.; Meh, David; Karger, Barry L.

    2012-01-01

    With the recent growth of the global monoclonal antibody market, ultrasensitive techniques are required for rapid analysis of possible immunogenic residues, such as galactose-α-1,3-galactose (α-1,3-Gal) on therapeutic proteins expressed in murine or CHO cell lines. We report a capillary electrophoretic approach in conjunction with exoglycosidase digestion for structural elucidation of N-linked IgG glycans containing the above immunogenic epitope. The method uses commercially available reagents and instrumentation, thus making the described methodology readily available for implementation and validation within the biotechnology industry. The method was first evaluated using polyclonal mouse IgG N-glycans which are known to contain α-1,3-Gal containing epitopes. High reproducibility in migration time enabled determination of GU values for five α-1,3-Gal containing structures. The method was successfully applied to the analysis of a NCI reference standard monoclonal antibody and two development phase monoclonal antibodies. The limit of detection and limit of quantitation were 1 and 2 µg of intact protein IgG starting material, respectively, further indicating the high sensitivity of the described method. PMID:22571495

  4. Carbohydrate binding properties of banana (Musa acuminata) lectin I. Novel recognition of internal alpha1,3-linked glucosyl residues.

    PubMed

    Mo, H; Winter, H C; Van Damme, E J; Peumans, W J; Misaki, A; Goldstein, I J

    2001-05-01

    Examination of lectins of banana (Musa acuminata) and the closely related plantain (Musa spp.) by the techniques of quantitative precipitation, hapten inhibition of precipitation, and isothermal titration calorimetry showed that they are mannose/glucose binding proteins with a preference for the alpha-anomeric form of these sugars. Both generate precipitin curves with branched chain alpha-mannans (yeast mannans) and alpha-glucans (glycogens, dextrans, and starches), but not with linear alpha-glucans containing only alpha1,4- and alpha1,6-glucosidic bonds (isolichenan and pullulan). The novel observation was made that banana and plantain lectins recognize internal alpha1,3-linked glucosyl residues, which occur in the linear polysaccharides elsinan and nigeran. Concanavalin A and lectins from pea and lentil, also mannose/glucose binding lectins, did not precipitate with any of these linear alpha-glucans. This is, the authors believe, the first report of the recognition of internal alpha1,3-glucosidic bonds by a plant lectin. It is possible that these lectins are present in the pulp of their respective fruit, complexed with starch.

  5. Crystal structure of an enzymatically inactive trans-sialidase-like lectin from Trypanosoma cruzi: the carbohydrate binding mechanism involves residual sialidase activity.

    PubMed

    Oppezzo, Pablo; Obal, Gonzalo; Baraibar, Martín A; Pritsch, Otto; Alzari, Pedro M; Buschiazzo, Alejandro

    2011-09-01

    Trans-sialidases are surface-located proteins in Trypanosoma cruzi that participate in key parasite-host interactions and parasite virulence. These proteins are encoded by a large multigenic family, with tandem-repeated and individual genes dispersed throughout the genome. While a large number of genes encode for catalytically active enzyme isoforms, many others display mutations that involve catalytic residues. The latter ultimately code for catalytically inactive proteins with very high similarity to their active paralogs. These inactive members have been shown to be lectins, able to bind sialic acid and galactose in vitro, although their cellular functions are yet to be fully established. We now report structural and biochemical evidence extending the current molecular understanding of these lectins. We have solved the crystal structure of one such catalytically inactive trans-sialidase-like protein, after soaking with a specific carbohydrate ligand, sialyl-α2,3-lactose. Instead of the expected trisaccharide, the binding pocket was observed occupied by α-lactose, strongly suggesting that the protein retains residual hydrolytic activity. This hypothesis was validated by enzyme kinetics assays, in comparison to fully active wild-type trans-sialidase. Surface plasmon resonance also confirmed that these trans-sialidase-like lectins are not only able to bind small oligosaccharides, but also sialylated glycoproteins, which is relevant in the physiologic scenario of parasite infection. Inactive trans-sialidase proteins appear thus to be β-methyl-galactosyl-specific lectins, evolved within an exo-sialidase scaffold, thus explaining why their lectin activity is triggered by the presence of terminal sialic acid.

  6. Using ATR-FT/IR to detect carbohydrate-related molecular structure features of carinata meal and their in situ residues of ruminal fermentation in comparison with canola meal

    NASA Astrophysics Data System (ADS)

    Xin, Hangshu; Yu, Peiqiang

    2013-10-01

    .05) during 48 h ruminal degradation in both carinata meal and canola meal. Although carinata meal differed from canola meal in some carbohydrate spectral parameters, multivariate results from agglomerative hierarchical cluster analysis and principal component analysis showed that both original and in situ residues of two meals were not fully distinguished from each other within carbohydrate spectral regions. It was concluded that carbohydrate structural conformation could be detected in carinata meal by using ATR-FT/IR techniques and further study is needed to explore more information on molecular spectral features of other functional group such as protein structure profile and their association with potential nutrient supply and availability of carinata meal in animals.

  7. Using ATR-FT/IR to detect carbohydrate-related molecular structure features of carinata meal and their in situ residues of ruminal fermentation in comparison with canola meal.

    PubMed

    Xin, Hangshu; Yu, Peiqiang

    2013-10-01

    decreased (P<0.05) during 48 h ruminal degradation in both carinata meal and canola meal. Although carinata meal differed from canola meal in some carbohydrate spectral parameters, multivariate results from agglomerative hierarchical cluster analysis and principal component analysis showed that both original and in situ residues of two meals were not fully distinguished from each other within carbohydrate spectral regions. It was concluded that carbohydrate structural conformation could be detected in carinata meal by using ATR-FT/IR techniques and further study is needed to explore more information on molecular spectral features of other functional group such as protein structure profile and their association with potential nutrient supply and availability of carinata meal in animals.

  8. PDB explorer -- a web based algorithm for protein annotation viewer and 3D visualization.

    PubMed

    Nayarisseri, Anuraj; Shardiwal, Rakesh Kumar; Yadav, Mukesh; Kanungo, Neha; Singh, Pooja; Shah, Pratik; Ahmed, Sheaza

    2014-12-01

    The PDB file format, is a text format characterizing the three dimensional structures of macro molecules available in the Protein Data Bank (PDB). Determined protein structure are found in coalition with other molecules or ions such as nucleic acids, water, ions, Drug molecules and so on, which therefore can be described in the PDB format and have been deposited in PDB database. PDB is a machine generated file, it's not human readable format, to read this file we need any computational tool to understand it. The objective of our present study is to develop a free online software for retrieval, visualization and reading of annotation of a protein 3D structure which is available in PDB database. Main aim is to create PDB file in human readable format, i.e., the information in PDB file is converted in readable sentences. It displays all possible information from a PDB file including 3D structure of that file. Programming languages and scripting languages like Perl, CSS, Javascript, Ajax, and HTML have been used for the development of PDB Explorer. The PDB Explorer directly parses the PDB file, calling methods for parsed element secondary structure element, atoms, coordinates etc. PDB Explorer is freely available at http://www.pdbexplorer.eminentbio.com/home with no requirement of log-in.

  9. Carbohydrate markers of organism purity and growth environment

    SciTech Connect

    Wunschel, David S.; Fox, Alvin

    2012-01-01

    Recent experience with Bacillus spore characterization has demonstrated that carbohydrate content can provide potentially vital bioforensic information. Like other metabolites, the carbohydrate profiles of samples reflect variations in cellular structures as well as presence of residual carbohydrates from the medium found as trace components. The presence and characteristics of residual carbohydrates, such as agar, represent strong indicators of culturing method. The methods to detect residual carbohydrates can be extended to other compounds used in processing and preservation of microbes in a dry form.

  10. Carbohydrate-Aromatic Interactions in Proteins.

    PubMed

    Hudson, Kieran L; Bartlett, Gail J; Diehl, Roger C; Agirre, Jon; Gallagher, Timothy; Kiessling, Laura L; Woolfson, Derek N

    2015-12-09

    Protein-carbohydrate interactions play pivotal roles in health and disease. However, defining and manipulating these interactions has been hindered by an incomplete understanding of the underlying fundamental forces. To elucidate common and discriminating features in carbohydrate recognition, we have analyzed quantitatively X-ray crystal structures of proteins with noncovalently bound carbohydrates. Within the carbohydrate-binding pockets, aliphatic hydrophobic residues are disfavored, whereas aromatic side chains are enriched. The greatest preference is for tryptophan with an increased prevalence of 9-fold. Variations in the spatial orientation of amino acids around different monosaccharides indicate specific carbohydrate C-H bonds interact preferentially with aromatic residues. These preferences are consistent with the electronic properties of both the carbohydrate C-H bonds and the aromatic residues. Those carbohydrates that present patches of electropositive saccharide C-H bonds engage more often in CH-π interactions involving electron-rich aromatic partners. These electronic effects are also manifested when carbohydrate-aromatic interactions are monitored in solution: NMR analysis indicates that indole favorably binds to electron-poor C-H bonds of model carbohydrates, and a clear linear free energy relationships with substituted indoles supports the importance of complementary electronic effects in driving protein-carbohydrate interactions. Together, our data indicate that electrostatic and electronic complementarity between carbohydrates and aromatic residues play key roles in driving protein-carbohydrate complexation. Moreover, these weak noncovalent interactions influence which saccharide residues bind to proteins, and how they are positioned within carbohydrate-binding sites.

  11. Recommendations of the wwPDB NMR Validation Task Force

    PubMed Central

    Montelione, Gaetano T.; Nilges, Michael; Bax, Ad; Güntert, Peter; Herrmann, Torsten; Richardson, Jane S.; Schwieters, Charles; Vranken, Wim F.; Vuister, Geerten W.; Wishart, David S.; Berman, Helen M.; Kleywegt, Gerard J.; Markley, John L.

    2013-01-01

    As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D structures, chemical shifts, and other NMR data are broadly impacting biology, chemistry, and medicine. Structure model assessment is a critical area of NMR methods development, and is an essential component of the process of making these structures accessible and useful to the wider scientific community. For these reasons, the Worldwide Protein Data Bank (wwPDB) has convened an NMR Validation Task Force (NMR-VTF) to work with the wwPDB partners in developing metrics and policies for biomolecular NMR data harvesting, structure representation, and structure quality assessment. This paper summarizes the recommendations of the NMR-VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure quality assessment. PMID:24010715

  12. g2pDB: A Database Mapping Protein Post-Translational Modifications to Genomic Coordinates.

    PubMed

    Keegan, Sarah; Cortens, John P; Beavis, Ronald C; Fenyö, David

    2016-03-04

    Large scale proteomics have made it possible to broadly screen samples for the presence of many types of post-translational modifications, such as phosphorylation, acetylation, and ubiquitination. This type of data has allowed the localization of these modifications to either a specific site on a proteolytically generated peptide or to within a small domain on the peptide. The resulting modification acceptor sites can then be mapped onto the appropriate protein sequences and the information archived. This paper describes the usage of a very large archive of experimental observations of human post-translational modifications to create a map of the most reproducible modification observations onto the complete set of human protein sequences. This set of modification acceptor sites was then directly translated into the genomic coordinates for the codons for the residues at those sites. We constructed the database g2pDB using this protein-to-codon site mapping information. The information in g2pDB has been made available through a RESTful-style API, allowing researchers to determine which specific protein modifications would be perturbed by a set of observed nucleotide variants determined by high throughput DNA or RNA sequencing.

  13. Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree.

    PubMed

    DeForte, Shelly; Uversky, Vladimir N

    2016-03-01

    Missing regions in X-ray crystal structures in the Protein Data Bank (PDB) have played a foundational role in the study of intrinsically disordered protein regions (IDPRs), especially in the development of in silico predictors of intrinsic disorder. However, a missing region is only a weak indication of intrinsic disorder, and this uncertainty is compounded by the presence of ambiguous regions, where more than one structure of the same protein sequence "disagrees" in terms of the presence or absence of missing residues. The question is this: are these ambiguous regions intrinsically disordered, or are they the result of static disorder that arises from experimental conditions, ensembles of structures, or domain wobbling? A novel way of looking at ambiguous regions in terms of the pattern between multiple PDB structures has been demonstrated. It was found that the propensity for intrinsic disorder increases as the level of ambiguity decreases. However, it is also shown that ambiguity is more likely to occur as the protein region is placed within different environmental conditions, and even the most ambiguous regions as a set display compositional bias that suggests flexibility. The results suggested that ambiguity is a natural result for many IDPRs crystallized under different conditions and that static disorder and wobbling domains are relatively rare. Instead, it is more likely that ambiguity arises because many of these regions were conditionally or partially disordered.

  14. Vivaldi: Visualization and validation of biomacromolecular NMR structures from the PDB

    PubMed Central

    Hendrickx, Pieter M S; Gutmanas, Aleksandras; Kleywegt, Gerard J

    2013-01-01

    We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases. Vivaldi was designed for both expert NMR spectroscopists and casual non-expert users who wish to obtain a better grasp of the information content and quality of NMR structures in the public archive. © Proteins 2013. © 2012 Wiley Periodicals, Inc. PMID:23180575

  15. PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory.

    PubMed

    Niknam, Niloofar; Khakzad, Hamed; Arab, Seyed Shahriar; Naderi-Manesh, Hossein

    2016-05-01

    The integrative and cooperative nature of protein structure involves the assessment of topological and global features of constituent parts. Network concept takes complete advantage of both of these properties in the analysis concomitantly. High compatibility to structural concepts or physicochemical properties in addition to exploiting a remarkable simplification in the system has made network an ideal tool to explore biological systems. There are numerous examples in which different protein structural and functional characteristics have been clarified by the network approach. Here, we present an interactive and user-friendly Matlab-based toolbox, PDB2Graph, devoted to protein structure network construction, visualization, and analysis. Moreover, PDB2Graph is an appropriate tool for identifying critical nodes involved in protein structural robustness and function based on centrality indices. It maps critical amino acids in protein networks and can greatly aid structural biologists in selecting proper amino acid candidates for manipulating protein structures in a more reasonable and rational manner. To introduce the capability and efficiency of PDB2Graph in detail, the structural modification of Calmodulin through allosteric binding of Ca(2+) is considered. In addition, a mutational analysis for three well-identified model proteins including Phage T4 lysozyme, Barnase and Ribonuclease HI, was performed to inspect the influence of mutating important central residues on protein activity.

  16. Carbohydrate Analysis

    NASA Astrophysics Data System (ADS)

    Bemiller, James N.

    Carbohydrates are important in foods as a major source of energy, to impart crucial textural properties, and as dietary fiber which influences physiological processes. Digestible carbohydrates, which are converted into monosaccharides, which are absorbed, provide metabolic energy. Worldwide, carbohydrates account for more than 70% of the caloric value of the human diet. It is recommended that all persons should limit calories from fat (the other significant source) to not more than 30% and that most of the carbohydrate calories should come from starch. Nondigestible polysaccharides (all those other than starch) comprise the major portion of dietary fiber (Sect. 10.5). Carbohydrates also contribute other attributes, including bulk, body, viscosity, stability to emulsions and foams, water-holding capacity, freeze-thaw stability, browning, flavors, aromas, and a range of desirable textures (from crispness to smooth, soft gels). They also provide satiety. Basic carbohydrate structures, chemistry, and terminology can be found in references (1, 2).

  17. Carbohydrate bioavailability.

    PubMed

    Englyst, Klaus N; Englyst, Hans N

    2005-07-01

    There is consensus that carbohydrate foods, in the form of fruit, vegetables and whole-grain products, are beneficial to health. However, there are strong indications that highly processed, fibre-depleted, and consequently rapidly digestible, energy-dense carbohydrate food products can lead to over-consumption and obesity-related diseases. Greater attention needs to be given to carbohydrate bioavailability, which is determined by the chemical identity and physical form of food. The objective of the present concept article is to provide a rational basis for the nutritional characterisation of dietary carbohydrates. Based on the properties of carbohydrate foods identified to be of specific relevance to health, we propose a classification and measurement scheme that divides dietary carbohydrates into glycaemic carbohydrates (digested and absorbed in the small intestine) and non-glycaemic carbohydrates (enter the large intestine). The glycaemic carbohydrates are characterised by sugar type, and by the likely rate of digestion described by in vitro measurements for rapidly available glucose and slowly available glucose. The main type of non-glycaemic carbohydrates is the plant cell-wall NSP, which is a marker of the natural fibre-rich diet recognised as beneficial to health. Other non-glycaemic carbohydrates include resistant starch and the resistant short-chain carbohydrates (non-digestible oligosaccharides), which should be measured and researched in their own right. The proposed classification and measurement scheme is complementary to the dietary fibre and glycaemic index concepts in the promotion of healthy diets with low energy density required for combating obesity-related diseases.

  18. Selective production of hemicellulose-derived carbohydrates from wheat straw using dilute HCl or FeCl3 solutions under mild conditions. X-ray and thermo-gravimetric analysis of the solid residues.

    PubMed

    Marcotullio, G; Krisanti, E; Giuntoli, J; de Jong, W

    2011-05-01

    The present work explores the combined production of hemicellulose-derived carbohydrates and an upgraded solid residue from wheat straw using a dilute-acid pretreatment at mild temperature. Dilute aqueous HCl solutions were studied at temperatures of 100 and 120°C, and they were compared to dilute FeCl(3) under the same conditions. Comparable yields of soluble sugars and acetic acid were obtained, affording an almost complete removal of pentoses when using 200 mM aqueous solutions at 120°C. The solid residues of pretreatment were characterized showing a preserved crystallinity of the cellulose, and a almost complete removal of ash forming matter other than Si. Results showed upgraded characteristic of the residues for thermal conversion applications compared to the untreated wheat straw.

  19. Reading PDB: perception of molecules from 3D atomic coordinates.

    PubMed

    Urbaczek, Sascha; Kolodzik, Adrian; Groth, Inken; Heuser, Stefan; Rarey, Matthias

    2013-01-28

    The analysis of small molecule crystal structures is a common way to gather valuable information for drug development. The necessary structural data is usually provided in specific file formats containing only element identities and three-dimensional atomic coordinates as reliable chemical information. Consequently, the automated perception of molecular structures from atomic coordinates has become a standard task in cheminformatics. The molecules generated by such methods must be both chemically valid and reasonable to provide a reliable basis for subsequent calculations. This can be a difficult task since the provided coordinates may deviate from ideal molecular geometries due to experimental uncertainties or low resolution. Additionally, the quality of the input data often differs significantly thus making it difficult to distinguish between actual structural features and mere geometric distortions. We present a method for the generation of molecular structures from atomic coordinates based on the recently published NAOMI model. By making use of this consistent chemical description, our method is able to generate reliable results even with input data of low quality. Molecules from 363 Protein Data Bank (PDB) entries could be perceived with a success rate of 98%, a result which could not be achieved with previously described methods. The robustness of our approach has been assessed by processing all small molecules from the PDB and comparing them to reference structures. The complete data set can be processed in less than 3 min, thus showing that our approach is suitable for large scale applications.

  20. Residue-centric modeling and design of saccharide and glycoconjugate structures.

    PubMed

    Labonte, Jason W; Adolf-Bryfogle, Jared; Schief, William R; Gray, Jeffrey J

    2017-02-15

    The RosettaCarbohydrate framework is a new tool for modeling a wide variety of saccharide and glycoconjugate structures. This report describes the development of the framework and highlights its applications. The framework integrates with established protocols within the Rosetta modeling and design suite, and it handles the vast complexity and variety of carbohydrate molecules, including branching and sugar modifications. To address challenges of sampling and scoring, RosettaCarbohydrate can sample glycosidic bonds, side-chain conformations, and ring forms, and it utilizes a glycan-specific term within its scoring function. Rosetta can work with standard PDB, GLYCAM, and GlycoWorkbench (.gws) file formats. Saccharide residue-specific chemical information is stored internally, permitting glycoengineering and design. Carbohydrate-specific applications described herein include virtual glycosylation, loop-modeling of carbohydrates, and docking of glyco-ligands to antibodies. Benchmarking data are presented and compared to other studies, demonstrating Rosetta's ability to predict glyco-ligand binding. The framework expands the tools available to glycoscientists and engineers. © 2016 Wiley Periodicals, Inc.

  1. Carbohydrate Loading.

    ERIC Educational Resources Information Center

    Csernus, Marilyn

    Carbohydrate loading is a frequently used technique to improve performance by altering an athlete's diet. The objective is to increase glycogen stored in muscles for use in prolonged strenuous exercise. For two to three days, the athlete consumes a diet that is low in carbohydrates and high in fat and protein while continuing to exercise and…

  2. Carbohydrate Loading.

    ERIC Educational Resources Information Center

    Csernus, Marilyn

    Carbohydrate loading is a frequently used technique to improve performance by altering an athlete's diet. The objective is to increase glycogen stored in muscles for use in prolonged strenuous exercise. For two to three days, the athlete consumes a diet that is low in carbohydrates and high in fat and protein while continuing to exercise and…

  3. Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

    PubMed Central

    Schroeder, Michael

    2013-01-01

    Drug repositioning applies established drugs to new disease indications with increasing success. A pre-requisite for drug repurposing is drug promiscuity (polypharmacology) – a drug’s ability to bind to several targets. There is a long standing debate on the reasons for drug promiscuity. Based on large compound screens, hydrophobicity and molecular weight have been suggested as key reasons. However, the results are sometimes contradictory and leave space for further analysis. Protein structures offer a structural dimension to explain promiscuity: Can a drug bind multiple targets because the drug is flexible or because the targets are structurally similar or even share similar binding sites? We present a systematic study of drug promiscuity based on structural data of PDB target proteins with a set of 164 promiscuous drugs. We show that there is no correlation between the degree of promiscuity and ligand properties such as hydrophobicity or molecular weight but a weak correlation to conformational flexibility. However, we do find a correlation between promiscuity and structural similarity as well as binding site similarity of protein targets. In particular, 71% of the drugs have at least two targets with similar binding sites. In order to overcome issues in detection of remotely similar binding sites, we employed a score for binding site similarity: LigandRMSD measures the similarity of the aligned ligands and uncovers remote local similarities in proteins. It can be applied to arbitrary structural binding site alignments. Three representative examples, namely the anti-cancer drug methotrexate, the natural product quercetin and the anti-diabetic drug acarbose are discussed in detail. Our findings suggest that global structural and binding site similarity play a more important role to explain the observed drug promiscuity in the PDB than physicochemical drug properties like hydrophobicity or molecular weight. Additionally, we find ligand flexibility to have a

  4. Counting carbohydrates

    MedlinePlus

    ... There are 3 major types of carbohydrates: Sugars Starches Fiber Sugars are found naturally in some foods ... syrups, such as those added to canned fruit Starches are found naturally in foods. Your body breaks ...

  5. PDB_REDO: constructive validation, more than just looking for errors.

    PubMed

    Joosten, Robbie P; Joosten, Krista; Murshudov, Garib N; Perrakis, Anastassis

    2012-04-01

    Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R(free) and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise `static' structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets.

  6. PDB_REDO: constructive validation, more than just looking for errors

    PubMed Central

    Joosten, Robbie P.; Joosten, Krista; Murshudov, Garib N.; Perrakis, Anastassis

    2012-01-01

    Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R free and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise ‘static’ structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets. PMID:22505269

  7. PDB ligand conformational energies calculated quantum-mechanically.

    PubMed

    Sitzmann, Markus; Weidlich, Iwona E; Filippov, Igor V; Liao, Chenzhong; Peach, Megan L; Ihlenfeldt, Wolf-Dietrich; Karki, Rajeshri G; Borodina, Yulia V; Cachau, Raul E; Nicklaus, Marc C

    2012-03-26

    We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient

  8. Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive.

    PubMed

    Shao, Chenghua; Yang, Huanwang; Westbrook, John D; Young, Jasmine Y; Zardecki, Christine; Burley, Stephen K

    2017-03-07

    Following deployment of an augmented validation system by the Worldwide Protein Data Bank (wwPDB) partnership, the quality of crystal structures entering the PDB has improved. Of significance are improvements in quality measures now prominently displayed in the wwPDB validation report. Comparisons of PDB depositions made before and after introduction of the new reporting system show improvements in quality measures relating to pairwise atom-atom clashes, side-chain torsion angle rotamers, and local agreement between the atomic coordinate structure model and experimental electron density data. These improvements are largely independent of resolution limit and sample molecular weight. No significant improvement in the quality of associated ligands was observed. Principal component analysis revealed that structure quality could be summarized with three measures (Rfree, real-space R factor Z score, and a combined molecular geometry quality metric), which can in turn be reduced to a single overall quality metric readily interpretable by all PDB archive users.

  9. hpvPDB: An Online Proteome Reserve for Human Papillomavirus

    PubMed Central

    Jena, Lingaraja; Daf, Sangeeta; Mohod, Kanchan; Goyal, Peyush; Varma, Ashok K.

    2013-01-01

    Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB) domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design. PMID:24465243

  10. Defining and searching for structural motifs using DeepView/Swiss-PdbViewer

    PubMed Central

    2012-01-01

    Background Today, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. Recognition of structural motifs, by comparison, is less well developed and much less frequently used, possibly due to a lack of easily accessible and easy to use software. Results In this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structural motifs may be defined and searched for in large protein structure databases, and we show that common structural motifs involved in stabilizing protein folds are present in evolutionarily and structurally unrelated proteins, also in deeply buried locations which are not obviously related to protein function. Conclusions The possibility to define custom motifs and search for their occurrence in other proteins permits the identification of recurrent arrangements of residues that could have structural implications. The possibility to do so without having to maintain a complex software/hardware installation on site brings this technology to experts and non-experts alike. PMID:22823337

  11. Healthy carbohydrates

    USDA-ARS?s Scientific Manuscript database

    Functional foods include dietary fiber consisting of health-promoting carbohydrates. We have produced novel prebiotics from orange peel and observed that they extend the shelf life of probiotic bacteria in synbiotics. Some pectic-oligosaccharides and xyloglucan-oligosaccharides also have anti-adhesi...

  12. Learning about Carbohydrates

    MedlinePlus

    ... What Happens in the Operating Room? Learning About Carbohydrates KidsHealth > For Kids > Learning About Carbohydrates A A ... of energy for the body. Two Types of Carbohydrates There are two major types of carbohydrates (or ...

  13. Learning about Carbohydrates

    MedlinePlus

    ... Real Lifesaver Kids Talk About: Coaches Learning About Carbohydrates KidsHealth > For Kids > Learning About Carbohydrates Print A ... source of energy for the body. What Are Carbohydrates? There are two major types of carbohydrates (or ...

  14. PDB4DNA: Implementation of DNA geometry from the Protein Data Bank (PDB) description for Geant4-DNA Monte-Carlo simulations

    NASA Astrophysics Data System (ADS)

    Delage, E.; Pham, Q. T.; Karamitros, M.; Payno, H.; Stepan, V.; Incerti, S.; Maigne, L.; Perrot, Y.

    2015-07-01

    This paper describes PDB4DNA, a new Geant4 user application, based on an independent, cross-platform, free and open source C++ library, so-called PDBlib, which enables use of atomic level description of DNA molecule in Geant4 Monte Carlo particle transport simulations. For the evaluation of direct damage induced on the DNA molecule by ionizing particles, the application makes use of an algorithm able to determine the closest atom in the DNA molecule to energy depositions. Both the PDB4DNA application and the PDBlib library are available as free and open source under the Geant4 license.

  15. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

    PubMed

    Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M; Berrisford, John M; Conroy, Matthew J; Dana, Jose M; Gore, Swanand P; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M S; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A; Mukhopadhyay, Abhik; Oldfield, Thomas J; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, Robert A; Wainwright, Michael E; Deshpande, Mandar S; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R; Clark, Alice R; Smart, Oliver S; Korir, Paul K; Kleywegt, Gerard J

    2016-01-04

    The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

    PubMed Central

    Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M.; Berrisford, John M.; Conroy, Matthew J.; Dana, Jose M.; Gore, Swanand P.; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M. S.; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A.; Mukhopadhyay, Abhik; Oldfield, Thomas J.; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, Robert A.; Wainwright, Michael E.; Deshpande, Mandar S.; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R.; Clark, Alice R.; Smart, Oliver S.; Korir, Paul K.; Kleywegt, Gerard J.

    2016-01-01

    The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the ‘best structures’ for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data. PMID:26476444

  17. Biological Macromolecular Structures Data from the RCSB Protein Data Bank (RCSB PDB)

    DOE Data Explorer

    The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium that works to improve understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. The RCSB PDB is one of three sites serving as deposition, data processing, and distribution sites of the Protein Data Bank Archive. Each site provides its own view of the primary data, thus providing a variety of tools and resources for the global community. RCSB is also the official keeper for the PDB archive, with sole access authority to the PDB archive directory structure and contents. The RCSB PDB Information Portal for Biological Macromolecular Structures offers online tools for search and retrieval, for visualizing structures, for depositing, validating, or downloading data, news and highlights, a discussion forum, and links to other areas of related research. The PDB archive is a repository of atomic coordinates and other information describing proteins and other important biological macromolecules. Structural biologists use methods such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy to determine the location of each atom relative to each other in the molecule. They then deposit this information, which is then annotated and publicly released into the archive by the wwPDB. Results can be viewed as 3-D images or models.

  18. Pre-calculated protein structure alignments at the RCSB PDB website

    PubMed Central

    Prlić, Andreas; Bliven, Spencer; Rose, Peter W.; Bluhm, Wolfgang F.; Bizon, Chris; Godzik, Adam; Bourne, Philip E.

    2010-01-01

    Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user. Availability and Implementation: A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org Contact: andreas@sdsc.edu; pbourne@ucsd.edu PMID:20937596

  19. Carbohydrate Counting and Diabetes

    MedlinePlus

    ... targets, you will need to balance your carbohydrate intake with physical activity and diabetes medicines or insulin shots. How much carbohydrate do I need each day? The daily amount of carbohydrate, protein, and fat for people with diabetes has not ...

  20. All about Carbohydrate Counting

    MedlinePlus

    Toolkit No. 14 All About Carbohydrate Counting What is carbohydrate counting? Carbohydrate counting is a way to plan your meals. It can help ... Diabetes Association, Inc. 2/14 Toolkit No. 14: All About Carbohydrate Counting continued The chart at the ...

  1. Carbohydrate and dietary fiber

    USDA-ARS?s Scientific Manuscript database

    Carbohydrate provides 50 to 60% of the calories consumed by the average American. Although relatively little carbohydrate is needed in the diet, carbohydrate spares protein and fat being metabolized for calories. The principal dietary carbohydrates are sugars and starches. Sugars (simple carbohydrat...

  2. MetalPDB: a database of metal sites in biological macromolecular structures.

    PubMed

    Andreini, Claudia; Cavallaro, Gabriele; Lorenzini, Serena; Rosato, Antonio

    2013-01-01

    We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal-macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner.

  3. MetalPDB: a database of metal sites in biological macromolecular structures

    PubMed Central

    Andreini, Claudia; Cavallaro, Gabriele; Lorenzini, Serena; Rosato, Antonio

    2013-01-01

    We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal–macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner. PMID:23155064

  4. Web servers and services for electrostatics calculations with APBS and PDB2PQR

    SciTech Connect

    Unni, Samir; Huang, Yong; Hanson, Robert M.; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred; Nielsen, Jens E.; Baker, Nathan A.

    2011-04-02

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/.

  5. Web servers and services for electrostatics calculations with APBS and PDB2PQR

    PubMed Central

    Unni, Samir; Huang, Yong; Hanson, Robert; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W.; Nielsen, Jens E.; Baker, Nathan A.

    2011-01-01

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. PMID:21425296

  6. Web servers and services for electrostatics calculations with APBS and PDB2PQR.

    PubMed

    Unni, Samir; Huang, Yong; Hanson, Robert M; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W; Nielsen, Jens E; Baker, Nathan A

    2011-05-01

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization of electrostatic potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. Copyright © 2011 Wiley Periodicals, Inc.

  7. Comparison of temporal trends in VOCs as measured with PDB samplers and low-flow sampling methods

    USGS Publications Warehouse

    Harte, P.T.

    2002-01-01

    Analysis of temporal trends in tetrachloroethylene (PCE) concentration determined by two sample techniques showed that passive diffusion bag (pdb) samplers adequately sample the large variation in PCE concentrations at the site. The slopes of the temporal trends in concentrations were comparable between the two techniques, and the pdb sample concentration generally reflected the instantaneous concentration sampled by the low-flow technique. Thus, the pdb samplers provided an appropriate sampling technique for PCE at these wells. One or two wells did not make the case for widespread application of pdb samples at all sites. However, application of pdb samples in some circumstances was appropriate for evaluating temporal and spatial variations in VOC concentrations, thus, should be considered as a useful tool in hydrogeology.

  8. Chemical doping and high-pressure studies of layered β -PdB i2 single crystals

    NASA Astrophysics Data System (ADS)

    Zhao, Kui; Lv, Bing; Xue, Yu-Yi; Zhu, Xi-Yu; Deng, L. Z.; Wu, Zheng; Chu, C. W.

    2015-11-01

    We have systematically grown large single crystals of the layered compounds β -PdB i2 , and both the hole-doped PdB i2 -xP bx and the electron-doped N axPdB i2 , and studied their magnetic and transport properties. Hall effect measurements on PdB i2 , PdB i1.8P b0.2 , and N a0.057PdB i2 show that the charge transport is dominated by electrons in all of the samples. The electron concentration is substantially reduced upon Pb doping in PdB i2 -xP bx and increased upon Na intercalation in N axPdB i2 , indicating effective hole doping by Pb and electron doping by Na. We observed a monotonic decrease of the superconducting transition temperature (Tc) from 5.4 K in undoped PdB i2 to less than 2 K for x >0.35 in hole-doped PdB i2 -xP bx . Meanwhile, a rapid decrease of Tc with Na intercalation is also observed in the electron-doped N axPdB i2 , which is in disagreement with the theoretical expectation. In addition, both the magnetoresistance and Hall resistance further reveal evidence for a possible spin excitation associated with Fermi surface reconstruction at ˜50 K in the Na-intercalated PdB i2 sample. The complete phase diagram is thus established from hole doping to electron doping. Meanwhile, a high-pressure study of the undoped PdB i2 shows that the Tc is linearly suppressed under pressure with a d Tc/d P coefficient of -0.28 K/GPa.

  9. Definition of immunogenic carbohydrate epitopes.

    PubMed

    Paschinger, Katharina; Fabini, Gustáv; Schuster, David; Rendić, Dubravko; Wilson, Iain B H

    2005-01-01

    Carbohydrates are known as sources of immunological cross-reactivity of allergenic significance. In celery and in cypress pollen, the major allergens Api g 5 and Cup a 1 are recognised by antisera raised against anti-horseradish peroxidase and by patients' IgE which apparently bind carbohydrate epitopes; mass spectrometric analysis of the tryptic peptides and of their N-glycans showed the presence of oligosaccharides carrying both xylose and core alpha1,3-fucose residues. Core alpha1,3-fucose residues are also a feature of invertebrates: genetic and biochemical studies on the fruitfly Drosophila melanogaster, the parasitic trematode Schistosoma mansoni and the nematode worm Caenorhabditis elegans indicate that these organisms possess core alpha1,3-fucosyltransferases. Various experiments have shown that fucosyltransferases from both fly and worm are responsible in vivo and in vitro for the synthesis of N-glycans which cross-react with anti-horseradish peroxidase; thus, we can consider these enzymes as useful tools in generating standard compounds for testing cross-reactive carbohydrate epitopes of allergenic interest.

  10. Protein segment finder: an online search engine for segment motifs in the PDB.

    PubMed

    Samson, Abraham O; Levitt, Michael

    2009-01-01

    Finding related conformations in the Protein Data Bank (PDB) is essential in many areas of bioscience. To assist this task, we designed a search engine that uses a compact database to quickly identify protein segments obeying a set of primary, secondary and tertiary structure constraints. The database contains information such as amino acid sequence, secondary structure, disulfide bonds, hydrogen bonds and atoms in contact as calculated from all protein structures in the PDB. The search engine parses the database and returns hits that match the queried parameters. The conformation search engine, which is notable for its high speed and interactive feedback, is expected to assist scientists in discovering conformation homologs and predicting protein structure. The engine is publicly available at http://ari.stanford.edu/psf and it will also be used in-house in an automatic mode aimed at discovering new protein motifs.

  11. Carbohydrates and Diabetes

    MedlinePlus

    ... Right Sport for You Healthy School Lunch Planner Carbohydrates and Diabetes KidsHealth > For Teens > Carbohydrates and Diabetes ... Los carbohidratos y la diabetes Carbs and Blood Sugar Keeping your blood sugar levels on track means ...

  12. Sequence-similar, structure-dissimilar protein pairs in the PDB

    PubMed Central

    Kosloff, Mickey; Kolodny, Rachel

    2008-01-01

    It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which “redundant” structures have been removed, based on a sequence-based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence-similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence-based structural superpositions and geometry-based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence-based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry-based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence-based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry-based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information

  13. Implementation of Smooth Continuous Camera Trajectories for Viewing PDB and VRML Objects

    NASA Astrophysics Data System (ADS)

    Pahor, Milan

    2005-05-01

    A parametrically defined camera trajectory enabling the accurate and systematic scanning of the entire surface of virtual (Protein Data Bank (PDB)) proteins is developed and implemented. The smooth continuous path guarantees that each local region of the protein is inspected from a variety of directions in a controlled and uniform manner. Manipulation of several parameters governs the density, character and duration of the scan. Applications to the analysis of other real and virtual objects are also considered.

  14. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

    PubMed

    Adams, Paul D; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A; Berman, Helen M; Bhat, Talapady N; Blaney, Jeff M; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K; Case, David A; Clark, Kirk L; Darden, Tom; Emsley, Paul; Feher, Victoria A; Feng, Zukang; Groom, Colin R; Harris, Seth F; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E; Markley, John L; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T; Padyana, Anil K; Peishoff, Catherine E; Pieniazek, Susan; Read, Randy J; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna C; Warren, Gregory L; Westbrook, John D; Williams, Pamela; Yang, Huanwang; Young, Jasmine

    2016-04-05

    Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Capillary electrophoresis of carbohydrates.

    PubMed

    Oefner, P J; Chiesa, C

    1994-08-01

    Capillary electrophoresis has emerged as a highly promising technique for the analysis of mono- and oligosaccharides. The approaches developed for overcoming the lack of chromophoric and fluorophoric functions in most carbohydrates involve the use of indirect photometric detection, amperometry, mass spectrometry, and precolumn derivatization with various tags. The merits and drawbacks of the derivatizing agents, including 2-aminopyridine, 4-amino-benzoic acid and its analogues, which for the first time permitted the reproducible determination of aldoses, uronic acids and even ketoses in the low femtomole range by means of readily available UV detection, and other agents such as 8-aminonaphthalene-1,3,6-trisulphonic acid, 1-phenyl-3-methyl-5-pyrazolone and 3-(4-carboxybenzoyl)-2-quinoline-carboxaldehyde, are discussed in detail. Means to secure electromigration of the usually neutral carbohydrates are: (i) ionization of hydroxyl groups at high pH; (ii) complexation of vicinal or alternate hydroxyl groups with borate or other charged compounds such as alkaline earth metal ions; (iii) derivatization with a reagent possessing ionizable functions; and (iv) partitioning into a pseudostationary phase such as sodium dodecyl sulphate micelles. Each alternative has its own analytical rewards, and combinations of the above mechanisms allow the two-dimensional and perhaps even three-dimensional mapping of oligosaccharides. Pyridylaminated oligosaccharides, for instance, have been separated both according to size by exploiting differences in the charge-to-mass ratio, with the charge being identical for each oligomer under acidic conditions due to protonation of the imino group incorporated by precolumn derivatization, as well as on the basis of structural differences, as a consequence of differences in the ease of borate complexation of the peripheral monosaccharide residues. It is also shown that the 4-aminobenzonitrile derivatives of mono- and disaccharides can be separated

  16. PhyreStorm: A Web Server for Fast Structural Searches Against the PDB.

    PubMed

    Mezulis, Stefans; Sternberg, Michael J E; Kelley, Lawrence A

    2016-02-22

    The identification of structurally similar proteins can provide a range of biological insights, and accordingly, the alignment of a query protein to a database of experimentally determined protein structures is a technique commonly used in the fields of structural and evolutionary biology. The PhyreStorm Web server has been designed to provide comprehensive, up-to-date and rapid structural comparisons against the Protein Data Bank (PDB) combined with a rich and intuitive user interface. It is intended that this facility will enable biologists inexpert in bioinformatics access to a powerful tool for exploring protein structure relationships beyond what can be achieved by sequence analysis alone. By partitioning the PDB into similar structures, PhyreStorm is able to quickly discard the majority of structures that cannot possibly align well to a query protein, reducing the number of alignments required by an order of magnitude. PhyreStorm is capable of finding 93±2% of all highly similar (TM-score>0.7) structures in the PDB for each query structure, usually in less than 60s. PhyreStorm is available at http://www.sbg.bio.ic.ac.uk/phyrestorm/. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  17. Carbohydrates for fermentation.

    PubMed

    Peters, Dietmar

    2006-01-01

    Biomass accumulated by the photosynthetic fixation of carbon dioxide is the only renewable carbon source, and hence, the only renewable raw material for the chemical industry. Carbohydrates are the main constituents of biomass and occur as cell wall and storage carbohydrates, transportation carbohydrates and glycoconjugates. Cellulose, hemicelluloses and starch in particular as well as pectin, inulin and saccharose to a smaller extent are the most abundant carbohydrates. Glucose is the most important monosaccharide and monomer of polysaccharides in natural carbohydrates. Thus, it is the most abundant organic compound on earth. Production of pulp from wood cellulose, applications of starch for paper making as well as uses of glucose and saccharose for fermentation are the most important chemical and technical uses of carbohydrates. Carbohydrates used as fermentation feedstock are essential for the chemical industry. Their importance is steadily growing due to the increasing implementation of biotechnological processes.

  18. Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences.

    PubMed

    Dutta, Shuchismita; Zardecki, Christine; Goodsell, David S; Berman, Helen M

    2010-10-01

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education worldwide by providing an essential resource of information on biomolecular structures. In addition to serving as a deposition, data-processing and distribution center for PDB data, the RCSB PDB offers resources and online materials that different audiences can use to customize their structural biology instruction. These include resources for general audiences that present macromolecular structure in the context of a biological theme, method-based materials for researchers who take a more traditional approach to the presentation of structural science, and materials that mix theme-based and method-based approaches for educators and students. Through these efforts the RCSB PDB aims to enable optimal use of structural data by researchers, educators and students designing and understanding experiments in biology, chemistry and medicine, and by general users making informed decisions about their life and health.

  19. PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

    PubMed

    Lee, Jonas; Kim, Sung Hou

    2009-04-01

    The Protein Data Bank file format is the format most widely used by protein crystallographers and biologists to disseminate and manipulate protein structures. Despite this, there are few user-friendly software packages available to efficiently edit and extract raw information from PDB files. This limitation often leads to many protein crystallographers wasting significant time manually editing PDB files. PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is a stand-alone application written in Java which frees users from the hassles associated with platform/operating system-dependent installation and usage. PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/.

  20. Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria.

    PubMed Central

    Postma, P W; Lengeler, J W; Jacobson, G R

    1993-01-01

    Numerous gram-negative and gram-positive bacteria take up carbohydrates through the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS). This system transports and phosphorylates carbohydrates at the expense of PEP and is the subject of this review. The PTS consists of two general proteins, enzyme I and HPr, and a number of carbohydrate-specific enzymes, the enzymes II. PTS proteins are phosphoproteins in which the phospho group is attached to either a histidine residue or, in a number of cases, a cysteine residue. After phosphorylation of enzyme I by PEP, the phospho group is transferred to HPr. The enzymes II are required for the transport of the carbohydrates across the membrane and the transfer of the phospho group from phospho-HPr to the carbohydrates. Biochemical, structural, and molecular genetic studies have shown that the various enzymes II have the same basic structure. Each enzyme II consists of domains for specific functions, e.g., binding of the carbohydrate or phosphorylation. Each enzyme II complex can consist of one to four different polypeptides. The enzymes II can be placed into at least four classes on the basis of sequence similarity. The genetics of the PTS is complex, and the expression of PTS proteins is intricately regulated because of the central roles of these proteins in nutrient acquisition. In addition to classical induction-repression mechanisms involving repressor and activator proteins, other types of regulation, such as antitermination, have been observed in some PTSs. Apart from their role in carbohydrate transport, PTS proteins are involved in chemotaxis toward PTS carbohydrates. Furthermore, the IIAGlc protein, part of the glucose-specific PTS, is a central regulatory protein which in its nonphosphorylated form can bind to and inhibit several non-PTS uptake systems and thus prevent entry of inducers. In its phosphorylated form, P-IIAGlc is involved in the activation of adenylate cyclase and thus in the

  1. RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.

    PubMed

    Quinn, Gregory B; Bi, Chunxiao; Christie, Cole H; Pang, Kyle; Prlić, Andreas; Nakane, Takanori; Zardecki, Christine; Voigt, Maria; Berman, Helen M; Bourne, Philip E; Rose, Peter W

    2015-01-01

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB's integrated MyPDB service. RCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org). © The Author 2014. Published by Oxford University Press.

  2. Carbohydrates in Supramolecular Chemistry.

    PubMed

    Delbianco, Martina; Bharate, Priya; Varela-Aramburu, Silvia; Seeberger, Peter H

    2016-02-24

    Carbohydrates are involved in a variety of biological processes. The ability of sugars to form a large number of hydrogen bonds has made them important components for supramolecular chemistry. We discuss recent advances in the use of carbohydrates in supramolecular chemistry and reveal that carbohydrates are useful building blocks for the stabilization of complex architectures. Systems are presented according to the scaffold that supports the glyco-conjugate: organic macrocycles, dendrimers, nanomaterials, and polymers are considered. Glyco-conjugates can form host-guest complexes, and can self-assemble by using carbohydrate-carbohydrate interactions and other weak interactions such as π-π interactions. Finally, complex supramolecular architectures based on carbohydrate-protein interactions are discussed.

  3. Solvent interactions determine carbohydrate conformation

    PubMed Central

    Kirschner, Karl N.; Woods, Robert J.

    2001-01-01

    The relationship between the three-dimensional structures of oligosaccharides and polysaccharides and their biological properties has been the focus of many recent studies. The overall conformation of an oligosaccharide depends primarily on the orientation of the torsion angles (φ, ψ, and ω) between glycosyl residues. Numerous experimental studies have shown that in glucopyranosides the ω-torsion angle (O6-C6-C5-O5) displays a preference for gauche orientations, in disagreement with predictions based on gas-phase quantum mechanics calculations. In contrast, the ω-angle in galactopyranosides displays a high proportion of the anti-orientation. For oligosaccharides containing glycosidic linkages at the 6-position (1→6 linked), variations in rotamer population have a direct effect on the oligosaccharides' structure and function, and yet the physical origin of these conformational preferences remains unclear. Although it is generally recognized that the gauche effect in carbohydrates is a solvent-dependent phenomenon, the mechanism through which solvent induces the gauche preference is not understood. In the present work, quantum mechanics and solvated molecular dynamics calculations were performed on two representative carbohydrates, methyl α-d-glucopyranoside and methyl α-d-galactopyranoside. We show that correct reproduction of the experimental rotamer distributions about the ω-angles is obtained only after explicit water is included in the molecular dynamics simulations. The primary role of the water appears to be to disrupt the hydrogen bonding within the carbohydrate, thereby allowing the rotamer populations to be determined by internal electronic and steric repulsions between the oxygen atoms. The results reported here provide a quantitative explanation of the conformational behavior of (1→6)-linked carbohydrates. PMID:11526221

  4. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB-REDO strategies

    SciTech Connect

    Rimsa, Vadim; Eadsforth, Thomas C.; Joosten, Robbie P.; Hunter, William N.

    2014-02-01

    The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase. A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB-REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn{sup 2+}-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn{sup 2+}, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate.

  5. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies

    PubMed Central

    Rimsa, Vadim; Eadsforth, Thomas C.; Joosten, Robbie P.; Hunter, William N.

    2014-01-01

    A potential cytosolic metallocarboxypeptidase from Burk­holderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB_REDO were coupled with model–map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn2+-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn2+, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1′ recognition subsite that suggests specificity towards an acidic substrate. PMID:24531462

  6. PDB-wide collection of binding data: current status of the PDBbind database.

    PubMed

    Liu, Zhihai; Li, Yan; Han, Li; Li, Jie; Liu, Jie; Zhao, Zhixiong; Nie, Wei; Liu, Yuchen; Wang, Renxiao

    2015-02-01

    Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank (PDB). It thus provides the linkage between structural information and energetic properties of biomolecular complexes, which is especially desirable for computational studies or statistical analyses. Since its first public release in 2004, the PDBbind database has been updated on an annual basis. The latest release (version 2013) provides experimental binding affinity data for 10,776 biomolecular complexes in PDB, including 8302 protein-ligand complexes and 2474 other types of complexes. In this article, we will describe the current methods used for compiling PDBbind and the updated status of this database. We will also review some typical applications of PDBbind published in the scientific literature. All contents of this database are freely accessible at the PDBbind-CN Web server at http://www.pdbbind-cn.org/. wangrx@mail.sioc.ac.cn. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Parasite Carbohydrate Vaccines

    PubMed Central

    Jaurigue, Jonnel A.; Seeberger, Peter H.

    2017-01-01

    Vaccination is an efficient means of combating infectious disease burden globally. However, routine vaccines for the world's major human parasitic diseases do not yet exist. Vaccines based on carbohydrate antigens are a viable option for parasite vaccine development, given the proven success of carbohydrate vaccines to combat bacterial infections. We will review the key components of carbohydrate vaccines that have remained largely consistent since their inception, and the success of bacterial carbohydrate vaccines. We will then explore the latest developments for both traditional and non-traditional carbohydrate vaccine approaches for three of the world's major protozoan parasitic diseases—malaria, toxoplasmosis, and leishmaniasis. The traditional prophylactic carbohydrate vaccine strategy is being explored for malaria. However, given that parasite disease biology is complex and often arises from host immune responses to parasite antigens, carbohydrate vaccines against deleterious immune responses in host-parasite interactions are also being explored. In particular, the highly abundant glycosylphosphatidylinositol molecules specific for Plasmodium, Toxoplasma, and Leishmania spp. are considered exploitable antigens for this non-traditional vaccine approach. Discussion will revolve around the application of these protozoan carbohydrate antigens for vaccines currently in preclinical development. PMID:28660174

  8. Radioiodinated branched carbohydrates

    DOEpatents

    Goodman, Mark M.; Knapp, Jr., Furn F.

    1989-01-01

    A radioiodinated branched carbohydrate for tissue imaging. Iodine-123 is stabilized in the compound by attaching it to a vinyl functional group that is on the carbohydrate. The compound exhibits good uptake and retention and is promising in the development of radiopharmaceuticals for brain, heart and tumor imaging.

  9. Locked-ring C-Glycoside sugars. New carbohydrate products from plant cell walls.

    USDA-ARS?s Scientific Manuscript database

    Residual products from the fermentation of biomass for fuel ethanol production typically consist of complex carbohydrates, plus other products such as lignin. The analysis of these carbohydrate residues will be important for maximizing the fermentation process for optimal ethanol production. Techn...

  10. Pharmacophore searching: A potential solution for correcting unknown ligands (UNK) labelling errors in Protein Data Bank (PDB'S).

    PubMed

    Ibrahim, Musadiq; Lapthorn, Adrian Jonathan; Ibrahim, Mohammad

    2017-08-01

    The Protein Data Bank (PDB) is the single most important repository of structural data for proteins and other biologically relevant molecules. Therefore, it is critically important to keep the PDB data, error-free as much as possible. In this study, we have critically examined PDB structures of 292 protein molecules which have been deposited in the repository along with potentially incorrect ligands labelled as Unknown ligands (UNK). Pharmacophores were generated for all the protein structures by using Discovery Studio Visualizer (DSV) and Accelrys, Catalyst(®). The generated pharmacophores were subjected to the database search containing the reported ligand. Ligands obtained through Pharmacophore searching were then checked for fitting the observed electron density map by using Coot(®). The predicted ligands obtained via Pharmacophore searching fitted well with the observed electron density map, in comparison to the ligands reported in the PDB's. Based on our study we have learned that till may 2016, among 292 submitted structures in the PDB, at least 20 structures have ligands with a clear electron density but have been incorrectly labelled as unknown ligands (UNK). We have demonstrated that Pharmacophore searching and Coot(®) can provide potential help to find suitable known ligands for these protein structures, the former for ligand search and the latter for electron density analysis. The use of these two techniques can facilitate the quick and reliable labelling of ligands where the electron density map serves as a reference. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Carbohydrates as allergens.

    PubMed

    Commins, Scott P

    2015-01-01

    Complex carbohydrates are effective inducers of Th2 responses, and carbohydrate antigens can stimulate the production of glycan-specific antibodies. In instances where the antigen exposure occurs through the skin, the resulting antibody production can contain IgE class antibody. The glycan-stimulated IgE may be non-specific but may also be antigen specific. This review focuses on the production of cross-reactive carbohydrate determinants, the recently identified IgE antibody response to a mammalian oligosaccharide epitope, galactose-alpha-1,3-galactose (alpha-gal), as well as discusses practical implications of carbohydrates in allergy. In addition, the biological effects of carbohydrate antigens are reviewed in setting of receptors and host recognition.

  12. Carbohydrates and Diabetes (For Parents)

    MedlinePlus

    ... Habits for TV, Video Games, and the Internet Carbohydrates and Diabetes KidsHealth > For Parents > Carbohydrates and Diabetes ... many kids with diabetes take to stay healthy. Carbohydrates and Blood Sugar The two main forms of ...

  13. Computerized molecular modeling of carbohydrates

    USDA-ARS?s Scientific Manuscript database

    Computerized molecular modleing continues to increase in capability and applicability to carbohydrates. This chapter covers nomenclature and conformational aspects of carbohydrates, perhaps of greater use to carbohydrate-inexperienced computational chemists. Its comments on various methods and studi...

  14. O-glycosylation effects on family 1 carbohydrate-binding module solution structures.

    PubMed

    Happs, Renee M; Guan, Xiaoyang; Resch, Michael G; Davis, Mark F; Beckham, Gregg T; Tan, Zhongping; Crowley, Michael F

    2015-11-01

    Family 1 carbohydrate-binding modules (CBMs) are ubiquitous components of multimodular fungal enzymes that degrade plant cell wall polysaccharides and bind specifically to cellulose. Native glycosylation of family 1 CBMs has been shown to substantially impact multiple physical properties, including thermal and proteolytic stability and cellulose binding affinity. To gain molecular insights into the changes in CBM properties upon glycosylation, solution structures of two glycoforms of a Trichoderma reesei family 1 CBM were studied by NMR spectroscopy: a glycosylated family 1 CBM with a mannose group attached to both Thr1 and Ser3 and a second family 1 CBM with single mannose groups attached to Thr1, Ser3 and Ser14. The structures clearly reveal that monosaccharides at both Ser3 and Ser14 on family 1 CBMs present additional cellulose binding platforms, similar to well-characterized aromatic residues at the binding interface, which align to the cellulose surface. These results are in agreement with previous experimental work demonstrating that glycans at Ser3 and Ser14 impart significant improvements in binding affinity. Additionally, detailed analysis of the NMR structures and molecular simulations indicates that the protein backbone of the CBM is not significantly altered by attachment of monosaccharides, and that the mannose attached to Ser14 may be more flexible than the mannose at Ser3. Overall, the present study reveals how family 1 CBM structures are affected by covalent attachment of monosaccharides, which are likely important post-translational modifications of these common subdomains of fungal plant cell wall degrading enzymes. Structural data have been deposited in the RCSB Protein Data Bank (PDB codes: 2MWJ and 2MWK) and the BioMagRes Bank (BMRB codes: 25331 and 25332) for CBM_M2 and CBM_M3, respectively. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

  15. RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank

    SciTech Connect

    Quinn, Gregory B.; Bi, Chunxiao; Christie, Cole H.; Pang, Kyle; Prlic, Andreas; Nakane, Takanori; Zardecki, Christine; Voigt, Maria; Berman, Helen M.; Bourne, Philip E.; Rose, Peter W.

    2014-09-02

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Lastly, using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB's integrated MyPDB service.

  16. RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank

    DOE PAGES

    Quinn, Gregory B.; Bi, Chunxiao; Christie, Cole H.; ...

    2014-09-02

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Lastly, using the app, users from the general public to expert researchers can quickly search and visualize biomolecules,more » and add personal annotations via the RCSB PDB's integrated MyPDB service.« less

  17. RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank

    PubMed Central

    Quinn, Gregory B.; Bi, Chunxiao; Christie, Cole H.; Pang, Kyle; Prlić, Andreas; Nakane, Takanori; Zardecki, Christine; Voigt, Maria; Berman, Helen M.; Rose, Peter W.

    2015-01-01

    Summary: The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Using the app, users from the general public to expert researchers can quickly search and visualize biomolecules, and add personal annotations via the RCSB PDB’s integrated MyPDB service. Availability and implementation: RCSB PDB Mobile is freely available from the Apple App Store and Google Play (http://www.rcsb.org). Contact: pwrose@ucsd.edu PMID:25183487

  18. Gold glyconanoparticles for mimics and measurement of metal ion-mediated carbohydrate-carbohydrate interactions.

    PubMed

    Reynolds, Angela J; Haines, Alan H; Russell, David A

    2006-01-31

    To mimic and measure calcium ion-mediated carbohydrate-carbohydrate interactions, four lactose derivatives have been synthesized for assembly on gold nanoparticles. The series of lactose derivatives varied by the length of the thiolated ethylene glycol anchor chain [O(CH2CH2O)(m)CH2CH2SH; where m = 0, 1, 2, and 3] used to self-assemble the carbohydrates to the preformed gold nanoparticles of ca. 16 nm diameter. Upon addition of calcium ions to the lactose-stabilized nanoparticles, rapid carbohydrate-carbohydrate interactions were visualized and subsequently measured using UV-visible spectrometry and transmission electron microscopy (TEM). The nanoparticle aggregates formed via metal-mediated carbohydrate-carbohydrate interactions could be readily redispersed through the addition of EDTA. Multiple reaggregation and redispersion cycles were achieved, confirming that the aggregation process was due to metal ion-mediated carbohydrate interactions rather than calcium chelation by residual citrate ions on the particle surface. The essential involvement of the lactose moiety in Ca2+ complexation was shown by control measurements on related D-glucose-derivatized nanoparticles, where a significantly reduced aggregation response was obtained only at high ion concentrations. Other group 2 metal ions with radii larger than that of calcium, viz., barium and strontium, were also shown to mediate the aggregation of the lactose-stabilized nanoparticles. The induced aggregation of the lactose nanoparticles was determined to be quantitatively dependent upon the calcium ion concentration. Furthermore, the analytical sensitivity of the calcium-induced aggregation and the linear dynamic range were dependent on the length of the ethylene glycol anchor chain. The shortest ethylene glycol chain (m = 0) gave the most sensitive response with the optimum limit of detection (0.8 mM Ca2+), whereas the longest ethylene glycol chain (m = 3) provides a measurement of calcium ion concentration

  19. Psychobiological effects of carbohydrates.

    PubMed

    Spring, B; Chiodo, J; Harden, M; Bourgeois, M J; Mason, J D; Lutherer, L

    1989-05-01

    The authors studied whether the fatiguing effects of eating lunch are greater for carbohydrate-rich meals than for other meals, and related the time course of behavioral change to plasma glucose, insulin, and amino acids. On different occasions, in counterbalanced order, normal women (N = 7) fasted overnight, ate a standard breakfast, and at lunch either continued to fast or ate a high-carbohydrate, low-protein meal; a hedonically similar meal containing both carbohydrate and protein; or a high-protein, low-carbohydrate meal. Meals were isocaloric and equated for fat content. Only the carbohydrate meal significantly increased fatigue, which could not be attributed to hypoglycemia because plasma glucose remained elevated. Fatigue began approximately, when the carbohydrate meal elevated the plasma tryptophan ratio but ended even though the ratio remained elevated. Fatigue after a high-carbohydrate lunch could not be explained by reactive hypoglycemia or sweet taste, and could partially be explained by the hypothesis that fatigue parallels an elevation of the tryptophan ratio.

  20. Carbohydrate counting of food.

    PubMed

    Hegar, Karin; Heiber, Stefanie; Brändle, Michael; Christ, Emanuel; Keller, Ulrich

    2011-07-07

    Carbohydrate counting is a principal strategy in nutritional management of type 1 diabetes. The Nutri-Learn buffet (NLB) is a new computer-based tool for patient instruction in carbohydrate counting. It is based on food dummies made of plastic equipped with a microchip containing relevant food content data. The tool enables the dietician to assess the patient's food counting abilities and the patient to learn in a hands-on interactive manner to estimate food contents such as carbohydrate content. Multicentre randomised controlled trial in 134 patients with type 1 diabetes comparing the use of the Nutri-Learn buffet in determining and improving ability to estimate the carbohydrate content of food with the use of conventional counselling tools (i.e. pictures and tables). The NLB group showed significantly better carbohydrate estimation values than the control group. In particular, there was a significant improvement in estimation of starches, fruits and sweets. The NLB was preferred by patients and dieticians in that rating of carbohydrate was closer to reality than the use of conventional tools, and since the tool has a play element, is interactive and adjustable, and can be used with only minimal knowledge of a specific language. Adjustment of preprandial insulin doses to the amounts of dietary carbohydrates ingested during the subsequent meal resulted in improved metabolic control in previous studies. The present study demonstrated that the new tool (Nutri-Learn buffet) improved teaching and learning of carbohydrate counting. In addition, it allowed an objective assessment of the carbohydrate counting skills of patients by the dietician. The findings therefore suggest that the tool is helpful in nutritional counselling of patients with diabetes mellitus.

  1. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

    PubMed

    Sali, Andrej; Berman, Helen M; Schwede, Torsten; Trewhella, Jill; Kleywegt, Gerard; Burley, Stephen K; Markley, John; Nakamura, Haruki; Adams, Paul; Bonvin, Alexandre M J J; Chiu, Wah; Peraro, Matteo Dal; Di Maio, Frank; Ferrin, Thomas E; Grünewald, Kay; Gutmanas, Aleksandras; Henderson, Richard; Hummer, Gerhard; Iwasaki, Kenji; Johnson, Graham; Lawson, Catherine L; Meiler, Jens; Marti-Renom, Marc A; Montelione, Gaetano T; Nilges, Michael; Nussinov, Ruth; Patwardhan, Ardan; Rappsilber, Juri; Read, Randy J; Saibil, Helen; Schröder, Gunnar F; Schwieters, Charles D; Seidel, Claus A M; Svergun, Dmitri; Topf, Maya; Ulrich, Eldon L; Velankar, Sameer; Westbrook, John D

    2015-07-07

    Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, on October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models?

  2. Carbohydrates: functionality in foods.

    PubMed

    Chinachoti, P

    1995-04-01

    Many functional requirements are met by the use of simple and complex carbohydrates in food. Carbohydrates offer a wide range of rheological and other properties, including solubility, cryoprotection, sweetening effect, hygroscopicity, crystallization inhibition, flavor encapsulation, and coating ability. These properties are based on chemical structure and interactions with other molecules through hydrogen bonding, ionic effect, and the formation of complexes with lipids and proteins. The ability to understand these properties directly affects the development of food products and processes. Thus, the functionality of carbohydrates in foods integrates precise knowledge of chemical structure and behavior with practical applications in the development and preparation of foods.

  3. Carbohydrates and Depression.

    ERIC Educational Resources Information Center

    Wurtman, Richard J.; Wurtman, Judith J.

    1989-01-01

    Describes the symptoms, such as appetite change and mood fluctuation, basic mechanisms, and some treatments of Seasonal Affective Disorder (SAD), Carbohydrate-Craving Obesity (CCO) and Premenstrual Syndrome (PMS). Provides several tables and diagrams, and three reading references. (YP)

  4. Disorders of Carbohydrate Metabolism

    MedlinePlus

    ... containing foods are long chains of simple sugar molecules. These longer molecules must also be broken down by the body. ... of carbohydrates. Glycogen is made of many glucose molecules linked together. The sugar glucose is the body’s ...

  5. Carbohydrate Dehydration Demonstrations.

    ERIC Educational Resources Information Center

    Dolson, David A.; And Others

    1995-01-01

    Discusses the impact of various factors on the "charring reaction" of a carbohydrate with concentrated sulfuric acid including the type of sugar, the degree of fineness of the sugar crystals, and the amount of water added. (JRH)

  6. Carbohydrate Metabolism Disorders

    MedlinePlus

    Metabolism is the process your body uses to make energy from the food you eat. Food is ... disorder, something goes wrong with this process. Carbohydrate metabolism disorders are a group of metabolic disorders. Normally ...

  7. Carbohydrates and Depression.

    ERIC Educational Resources Information Center

    Wurtman, Richard J.; Wurtman, Judith J.

    1989-01-01

    Describes the symptoms, such as appetite change and mood fluctuation, basic mechanisms, and some treatments of Seasonal Affective Disorder (SAD), Carbohydrate-Craving Obesity (CCO) and Premenstrual Syndrome (PMS). Provides several tables and diagrams, and three reading references. (YP)

  8. Carbohydrate Dehydration Demonstrations.

    ERIC Educational Resources Information Center

    Dolson, David A.; And Others

    1995-01-01

    Discusses the impact of various factors on the "charring reaction" of a carbohydrate with concentrated sulfuric acid including the type of sugar, the degree of fineness of the sugar crystals, and the amount of water added. (JRH)

  9. Carbohydrate intake and obesity.

    PubMed

    van Dam, R M; Seidell, J C

    2007-12-01

    The prevalence of obesity has increased rapidly worldwide and the importance of considering the role of diet in the prevention and treatment of obesity is widely acknowledged. This paper reviews data on the effects of dietary carbohydrates on body fatness. Does the composition of the diet as related to carbohydrates affect the likelihood of passive over-consumption and long-term weight change? In addition, methodological limitations of both observational and experimental studies of dietary composition and body weight are discussed. Carbohydrates are among the macronutrients that provide energy and can thus contribute to excess energy intake and subsequent weight gain. There is no clear evidence that altering the proportion of total carbohydrate in the diet is an important determinant of energy intake. However, there is evidence that sugar-sweetened beverages do not induce satiety to the same extent as solid forms of carbohydrate, and that increases in sugar-sweetened soft drink consumption are associated with weight gain. Findings from studies on the effect of the dietary glycemic index on body weight have not been consistent. Dietary fiber is associated with a lesser degree of weight gain in observational studies. Although it is difficult to establish with certainty that fiber rather than other dietary attributes are responsible, whole-grain cereals, vegetables, legumes and fruits seem to be the most appropriate sources of dietary carbohydrate.

  10. Digestion and Absorption of Carbohydrates

    USDA-ARS?s Scientific Manuscript database

    Carbohydrates are the major dietary sources of energy for humans. While most dietary carbohydrates are derived from multiple botanical sources, lactose and trehalose are the only animal-derived carbohydrates. Digestion of starch, the carbohydrate most abundantly consumed by humans, depends on the c...

  11. The prediction of the degree of exposure to solvent of amino acid residues via genetic programming

    SciTech Connect

    Handley, S.

    1994-12-31

    In this paper I evolve programs that predict the degree of exposure to solvent (the buriedness) of amino acid residues given only the primary structure. I use genetic programming to evolve programs that take as input the primary structure and that output the buriedness of each residue. I trained these programs on a set of 82 proteins from the Brookhaven Protein Data Bank (PDB) and cross-validated them on a separate testing set of 40 proteins, also from the PDB. The best program evolved had a correlation of 0.434 between the predicted and observed buriednesses on the testing set.

  12. Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE

    PubMed Central

    Névéol, Aurélie; Wilbur, W. John; Lu, Zhiyong

    2012-01-01

    High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/ PMID:22685160

  13. Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.

    PubMed

    Névéol, Aurélie; Wilbur, W John; Lu, Zhiyong

    2012-01-01

    High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/

  14. Diarrhea caused by carbohydrate malabsorption.

    PubMed

    Hammer, Heinz F; Hammer, Johann

    2012-09-01

    This article will focus on the role of the colon in the pathogenesis of diarrhea in carbohydrate malabsorption or physiologically incomplete absorption of carbohydrates, and on the most common manifestation of carbohydrate malabsorption, lactose malabsorption. In addition, incomplete fructose absorption, the role of carbohydrate malabsorption in other malabsorptive diseases, and congenital defects that lead to malabsorption will be covered. The article concludes with a section on diagnostic tools to evaluate carbohydrate malabsorption. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. Carbohydrate and exercise performance: the role of multiple transportable carbohydrates.

    PubMed

    Jeukendrup, Asker E

    2010-07-01

    Carbohydrate feeding has been shown to be ergogenic, but recently substantial advances have been made in optimizing the guidelines for carbohydrate intake during prolonged exercise. It was found that limitations to carbohydrate oxidation were in the absorptive process most likely because of a saturation of carbohydrate transporters. By using a combination of carbohydrates that use different intestinal transporters for absorption it was shown that carbohydrate delivery and oxidation could be increased. Studies demonstrated increases in exogenous carbohydrate oxidation rates of up to 65% of glucose: fructose compared with glucose only. Exogenous carbohydrate oxidation rates reach values of 1.75 g/min whereas previously it was thought that 1 g/min was the absolute maximum. The increased carbohydrate oxidation with multiple transportable carbohydrates was accompanied by increased fluid delivery and improved oxidation efficiency, and thus the likelihood of gastrointestinal distress may be diminished. Studies also demonstrated reduced fatigue and improved exercise performance with multiple transportable carbohydrates compared with a single carbohydrate. Multiple transportable carbohydrates, ingested at high rates, can be beneficial during endurance sports in which the duration of exercise is 3 h or more.

  16. Survey of phosphorylation near drug binding sites in the Protein Data Bank (PDB) and their effects

    PubMed Central

    Smith, Kyle P.; Gifford, Kathleen M.; Waitzman, Joshua S.; Rice, Sarah E.

    2014-01-01

    While it is currently estimated that 40–50% of eukaryotic proteins are phosphorylated, little is known about the frequency and local effects of phosphorylation near pharmaceutical inhibitor binding sites. In this study, we investigated how frequently phosphorylation may affect the binding of drug inhibitors to target proteins. We examined the 453 non-redundant structures of soluble mammalian drug target proteins bound to inhibitors currently available in the Protein Data Bank (PDB). We cross-referenced these structures with phosphorylation data available from the PhosphoSitePlus database. 322/453 (71%) of drug targets have evidence of phosphorylation that has been validated by multiple methods or labs. For 132/453 (29%) of those, the phosphorylation site is within 12Å of the small molecule-binding site, where it would likely alter small molecule binding affinity. We propose a framework for distinguishing between drug-phosphorylation site interactions that are likely to alter the efficacy of drugs vs. those that are not. In addition we highlight examples of well-established drug targets, such as estrogen receptor alpha, for which phosphorylation may affect drug affinity and clinical efficacy. Our data suggest that phosphorylation may affect drug binding and efficacy for a significant fraction of drug target proteins. PMID:24833420

  17. A guest molecule-host cavity fitting algorithm to mine PDB for small molecule targets.

    PubMed

    Byrem, William C; Armstead, Stephen C; Kobayashi, Shunji; Eckenhoff, Roderic G; Eckmann, David M

    2006-08-01

    Inhaled anesthetic molecule occupancy of a protein internal cavity depends in part on the volumes of the guest molecule and the host site. Current algorithms to determine volume and surface area of cavities in proteins whose structures have been determined and cataloged make no allowance for shape or small degrees of shape adjustment to accommodate a guest. We developed an algorithm to determine spheroid dimensions matching cavity volume and surface area and applied it to screen the cavities of 6,658 nonredundant structures stored in the Protein Data Bank (PDB) for potential targets of halothane (2-bromo-2-chloro-1,1,1-trifluoroethane). Our algorithm determined sizes of prolate and oblate spheroids matching dimensions of each cavity found. If those spheroids could accommodate halothane (radius 2.91 A) as a guest, we determined the packing coefficient. 394,766 total cavities were identified. Of 58,681 cavities satisfying the fit criteria for halothane, 11,902 cavities had packing coefficients in the range of 0.46-0.64. This represents 20.3% of cavities large enough to hold halothane, 3.0% of all cavities processed, and found in 2,432 protein structures. Our algorithm incorporates shape dependence to screen guest-host relationships for potential small molecule occupancy of protein cavities. Proteins with large numbers of such cavities are more likely to be functionally altered by halothane.

  18. Carbohydrates in therapeutics.

    PubMed

    Kilcoyne, Michelle; Joshi, Lokesh

    2007-07-01

    Awareness of the importance of carbohydrates in living systems and medicine is growing due to the increasing understanding of their biological and pharmacological relevance. Carbohydrates are ubiquitous and perform a wide array of biological roles. Carbohydrate-based or -modified therapeutics are used extensively in cardiovascular and hematological treatments ranging from inflammatory diseases and anti-thrombotic treatments to wound healing. Heparin is a well-known and widely used example of a carbohydrate-based drug but will not be discussed as it has been extensively reviewed. We will detail carbohydrate-based and -modified therapeutics, both those that are currently marketed or in various stages of clinical trials and those that are potential therapeutics based on promising preclinical investigations. Carbohydrate-based therapeutics include polysaccharide and oligosaccharide anti-inflammatory, anti-coagulant and anti-thrombotic agents from natural and synthetic sources, some as an alternative to heparin and others which were designed based on known structure-functional relationships. Some of these compounds have multiple biological effects, showing anti-adhesive, anti-HIV and anti-arthrithic activities. Small molecules, derivatives or mimetics of complement inhibitors, are detailed for use in limiting ischemia/ reperfusion injuries. Monosaccharides, both natural and synthetic, have been investigated for their in vivo anti-inflammatory and cardioprotective properties. Modification by glycosylation of natural products, or glycosylation-mimicking modification, has a significant effect on the parent molecule including increased plasma half-life and refining or increasing desired functions. It is hoped that this review will highlight the vast therapeutic potential of these natural bioactive molecules.

  19. Organocatalytic synthesis of carbohydrates.

    PubMed

    Mlynarski, Jacek; Gut, Bartosz

    2012-01-21

    The key role of carbohydrates in biological processes and their visible existence in our everyday life have stimulated the interest of leading research groups on the smart and simple synthesis of common and rare sugar molecules. Now, more than 120 years after Fischer's first synthesis of (D)-glucose (1890), we are witnessing important development in this field of total synthesis. Using modern methods of direct activation of carbonyl compounds chemists can prepare sugars in an elegant and efficient way similar to that of Nature. This tutorial review presents recent impressive progress in the area of de novo synthesis of carbohydrates by using organocatalytic direct aldol reaction as a key step.

  20. Carbohydrates, pollinators, and cycads.

    PubMed

    Marler, Thomas E; Lindström, Anders J

    2015-01-01

    Cycad biology, ecology, and horticulture decisions are not supported by adequate research, and experiments in cycad physiology in particular have been deficient. Our recent report on free sugar content in a range of cycad taxa and tissues sets the stage for developing continued carbohydrate research. Growth and development of cycad pollen, mediation of the herbivory traits of specialist pollinators, and support of expensive strobilus behavioral traits are areas of cycad pollination biology that would benefit from a greater understanding of the role of carbohydrate relations.

  1. Carbohydrates, pollinators, and cycads

    PubMed Central

    Marler, Thomas E; Lindström, Anders J

    2015-01-01

    Cycad biology, ecology, and horticulture decisions are not supported by adequate research, and experiments in cycad physiology in particular have been deficient. Our recent report on free sugar content in a range of cycad taxa and tissues sets the stage for developing continued carbohydrate research. Growth and development of cycad pollen, mediation of the herbivory traits of specialist pollinators, and support of expensive strobilus behavioral traits are areas of cycad pollination biology that would benefit from a greater understanding of the role of carbohydrate relations. PMID:26479502

  2. Understanding carbohydrate-carbohydrate interactions by means of glyconanotechnology.

    PubMed

    de la Fuente, Jesus M; Penadés, Soledad

    2004-01-01

    Carbohydrate-carbohydrate interaction is a reliable and versatile mechanism for cell adhesion and recognition. Glycosphingolipid (GSL) clusters at the cell membrane are mainly involved in this interaction. To investigate carbohydrate-carbohydrate interaction an integrated strategy (Glyconanotechnology) was developed. This strategy includes polyvalent tools (gold glyconanoparticles) mimicking GSL clustering at the cell membrane as well as analytical techniques such as AFM, TEM, and SPR to evaluate the interactions. The results obtained by means of this strategy and current status are presented.

  3. Carbohydrates, Sugar, and Your Child

    MedlinePlus

    ... Part of a Healthy Diet? en español Los carbohidratos, el azúcar y su hijo What Are Carbohydrates? ... a person's risk of developing health problems like diabetes. Some carbohydrate-dense foods are healthier than others. ...

  4. Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d

    PubMed Central

    2010-01-01

    Background Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB) for coplanar aromatic motifs similar to those found in known glycan-binding proteins. Results The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO) enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192) in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. Conclusions Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure. PMID:20678238

  5. Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

    PubMed

    Lagerstedt, Ingvar; Moore, William J; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R; Kleywegt, Gerard J

    2013-11-01

    The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed.

  6. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

    SciTech Connect

    Adams, Paul  D.; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A.; Berman, Helen  M.; Bhat, Talapady  N.; Blaney, Jeff  M.; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen  K.; Case, David  A.; Clark, Kirk  L.; Darden, Tom; Emsley, Paul; Feher, Victoria  A.; Feng, Zukang; Groom, Colin  R.; Harris, Seth  F.; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard  J.; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan  E.; Markley, John  L.; Miller, Matthew; Minor, Wladek; Montelione, Gaetano  T.; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert  T.; Padyana, Anil  K.; Peishoff, Catherine E.; Pieniazek, Susan; Read, Randy  J.; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas  C.; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna  C.; Warren, Gregory  L.; Westbrook, John  D.; Williams, Pamela; Yang, Huanwang; Young, Jasmine

    2016-04-05

    Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ~75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery/design, and the goodness-of-fit of ligand models to electron density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide Protein Data Bank/Cambridge Crystallographic Data Centre/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the Protein Data Bank? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.

  7. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

    DOE PAGES

    Adams, Paul  D.; Aertgeerts, Kathleen; Bauer, Cary; ...

    2016-04-05

    Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ~75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery/design, and the goodness-of-fit of ligand models to electron density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide Protein Data Bank/Cambridge Crystallographicmore » Data Centre/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the Protein Data Bank? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.« less

  8. Outcome of the first wwPDB/CCDC/D3R Ligand Validation Workshop

    PubMed Central

    Adams, Paul D.; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A.; Berman, Helen M.; Bhat, Talapady N.; Blaney, Jeff; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K.; Case, David A.; Clark, Kirk L.; Darden, Tom; Emsley, Paul; Feher, Victoria A.; Feng, Zukang; Groom, Colin R.; Harris, Seth F.; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J.; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E.; Markley, John L.; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T.; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T.; Padyana, Anil K.; Peishoff, Catherine E.; Pieniazek, Susan; Read, Randy J.; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C.; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna; Warren, Gregory L.; Westbrook, John D.; Williams, Pamela; Yang, Huanwang; Young, Jasmine

    2016-01-01

    Summary Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ~75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery/design, and the goodness-of-fit of ligand models to electron density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide Protein Data Bank/Cambridge Crystallographic Data Centre/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the Protein Data Bank? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. PMID:27050687

  9. Carbohydrates for training and competition.

    PubMed

    Burke, Louise M; Hawley, John A; Wong, Stephen H S; Jeukendrup, Asker E

    2011-01-01

    An athlete's carbohydrate intake can be judged by whether total daily intake and the timing of consumption in relation to exercise maintain adequate carbohydrate substrate for the muscle and central nervous system ("high carbohydrate availability") or whether carbohydrate fuel sources are limiting for the daily exercise programme ("low carbohydrate availability"). Carbohydrate availability is increased by consuming carbohydrate in the hours or days prior to the session, intake during exercise, and refuelling during recovery between sessions. This is important for the competition setting or for high-intensity training where optimal performance is desired. Carbohydrate intake during exercise should be scaled according to the characteristics of the event. During sustained high-intensity sports lasting ~1 h, small amounts of carbohydrate, including even mouth-rinsing, enhance performance via central nervous system effects. While 30-60 g · h(-1) is an appropriate target for sports of longer duration, events >2.5 h may benefit from higher intakes of up to 90 g · h(-1). Products containing special blends of different carbohydrates may maximize absorption of carbohydrate at such high rates. In real life, athletes undertake training sessions with varying carbohydrate availability. Whether implementing additional "train-low" strategies to increase the training adaptation leads to enhanced performance in well-trained individuals is unclear.

  10. Analysis of residue conformations in peptides in Cambridge structural database and protein-peptide structural complexes.

    PubMed

    Raghavender, Upadhyayula Surya

    2017-03-01

    A comprehensive statistical analysis of the geometric parameters of peptide chains in a reduced dataset of protein-peptide complexes in Protein Data Bank (PDB) is presented. The angular variables describing the backbone conformations of amino acid residues in peptide chains shed insights into the conformational preferences of peptide residues interacting with protein partners. Nonparametric statistical approaches are employed to evaluate the interrelationships and associations in structural variables. Grouping of residues based on their structure into chemical classes reveals characteristic trends in parameter relationships. A comparison of canonical amino acid residues in free peptide structures in Cambridge structural database (CSD) with identical residues in PDB complexes, suggests that the information can be integrated from both the structural repositories enabling efficient and accurate modeling of biologically active peptides. © 2016 John Wiley & Sons A/S.

  11. Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

    PubMed Central

    Joosten, Robbie P.; Womack, Thomas; Vriend, Gert; Bricogne, Gérard

    2009-01-01

    The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Auto­mated gradient refinement is an effective method to achieve this goal, but real-space intervention is most often required in order to adequately address problems detected by structure-validation software. In order to improve the existing protocol, automated re-refinement was combined with structure validation and difference-density peak analysis to produce a catalogue of problems in PDB entries that are amenable to automatic correction. It is shown that re-refinement can be effective in producing improvements, which are often associated with the systematic use of the TLS parameterization of B factors, even for relatively new and high-resolution PDB entries, while the accompanying manual or semi-manual map analysis and fitting steps show good prospects for eventual automation. It is proposed that the potential for simultaneous improvements in methods and in re-refinement results be further encouraged by broadening the scope of depositions to include refinement metadata and ultimately primary rather than reduced X-ray data. PMID:19171973

  12. Carbohydrate and carbohydrate + protein for cycling time-trial performance.

    PubMed

    Osterberg, Kristin L; Zachwieja, Jeffrey J; Smith, Johneric W

    2008-02-01

    Carbohydrate intake during endurance exercise delays the onset of fatigue and improves performance. Two recent cycling studies have reported increased time to exhaustion when protein is ingested together with carbohydrate. The purpose of the present study was to test the hypothesis that ingestion of a carbohydrate + protein beverage will lead to significant improvements in cycling time-trial performance relative to placebo and carbohydrate alone. Thirteen cyclists completed 120 min of constant-load ergometer cycling. Thereafter, participants performed a time-trial in which they completed a set amount of work (7 kJ kg(-1)) as quickly as possible. Participants completed four experimental trials, the first for familiarization and then three randomized, double-blind treatments consisting of a placebo, carbohydrate, and carbohydrate + protein. Participants received 250 ml of beverage every 15 min during the constant-load ride. Time-trial performance for carbohydrate (37.1 min, s = 3.8) was significantly (P < 0.05) faster than placebo (39.7 min, s = 4.6). Time-trial performance for carbohydrate + protein (38.8 min, s = 5.5) was not significantly different from either placebo or carbohydrate. Ingestion of a carbohydrate beverage during two hours of constant-load cycling significantly enhanced subsequent time-trial performance compared with placebo. The carbohydrate + protein beverage provided no additional performance benefit.

  13. Proteins of unknown function in the Protein Data Bank (PDB): an inventory of true uncharacterized proteins and computational tools for their analysis.

    PubMed

    Nadzirin, Nurul; Firdaus-Raih, Mohd

    2012-10-08

    Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB). Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files) that were categorized under "unknown function" are true examples of proteins of unknown function at this point in time. The remainder 1465 entries also annotated as such appear to be able to have their annotations re-assessed, based on the availability of direct functional characterization experiments for the protein itself, or for homologous sequences or structures thus enabling computational function inference.

  14. Vapor-phase diethyl oxalate pretreatment of wood chips. Part 2, Release of hemicellulosic carbohydrates

    Treesearch

    William Kenealy; Eric Horn; Mark Davis; Ross Swaney; Carl Houtman

    2007-01-01

    Wood chips of pine, spruce, aspen, and maple were treated at 135–1408C with diethyl oxalate (DEO) and analyzed for extractable and residual carbohydrates. Under these conditions, DEO hydrolyzes to ethanol and oxalic acid (OA). The amount and identity of carbohydrates released from the chips were species-dependent. For all wood species, increasing the amount of chemical...

  15. Carbohydrates as Fat Replacers.

    PubMed

    Peng, Xingyun; Yao, Yuan

    2017-02-28

    The overconsumption of dietary fat contributes to various chronic diseases, which encourages attempts to develop and consume low-fat foods. Simple fat reduction causes quality losses that impede the acceptance of foods. Fat replacers are utilized to minimize the quality deterioration after fat reduction or removal to achieve low-calorie, low-fat claims. In this review, the forms of fats and their functions in contributing to food textural and sensory qualities are discussed in various food systems. The connections between fat reduction and quality loss are described in order to clarify the rationales of fat replacement. Carbohydrate fat replacers usually have low calorie density and provide gelling, thickening, stabilizing, and other texture-modifying properties. In this review, carbohydrates, including starches, maltodextrins, polydextrose, gums, and fibers, are discussed with regard to their interactions with other components in foods as well as their performances as fat replacers in various systems.

  16. Carbohydrate force fields

    PubMed Central

    Foley, B. Lachele; Tessier, Matthew B.; Woods, Robert J.

    2014-01-01

    Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion. PMID:25530813

  17. Modeling protein recognition of carbohydrates.

    PubMed

    Laederach, Alain; Reilly, Peter J

    2005-09-01

    We have a limited understanding of the details of molecular recognition of carbohydrates by proteins, which is critical to a multitude of biological processes. Furthermore, carbohydrate-modifying proteins such as glycosyl hydrolases and phosphorylases are of growing importance as potential drug targets. Interactions between proteins and carbohydrates have complex thermodynamics, and in general the specific positioning of only a few hydroxyl groups determines their binding affinities. A thorough understanding of both carbohydrate and protein structures is thus essential to predict these interactions. An atomic-level view of carbohydrate recognition through structures of carbohydrate-active enzymes complexed with transition-state inhibitors reveals some of the distinctive molecular features unique to protein-carbohydrate complexes. However, the inherent flexibility of carbohydrates and their often water-mediated hydrogen bonding to proteins makes simulation of their complexes difficult. Nonetheless, recent developments such as the parameterization of specific force fields and docking scoring functions have greatly improved our ability to predict protein-carbohydrate interactions. We review protein-carbohydrate complexes having defined molecular requirements for specific carbohydrate recognition by proteins, providing an overview of the different computational techniques available to model them. Copyright 2005 Wiley-Liss, Inc.

  18. Carbohydrate post-glycosylational modifications

    PubMed Central

    Yu, Hai; Chen, Xi

    2008-01-01

    Carbohydrate modification is a common phenomenon in nature. Many carbohydrate modifications such as some epimerization, O-acetylation, O-sulfation, O-methylation, N-deacetylation, and N-sulfation, take place after the formation of oligosaccharide or polysaccharide backbones. These modifications can be categorized as carbohydrate post-glycosylational modifications (PGMs). Carbohydrate PGMs further extend the complexity of the structures and the synthesis of carbohydrates and glycoconjugates. They also increase the capacity of the biological information that can be controlled by finely tuning the structures of carbohydrates. Developing efficient methods to obtain structurally defined naturally occurring oligosaccharides, polysaccharides, and glycoconjugates with carbohydrate PGMs is essential for understanding the biological significance of carbohydrate PGMs. Combine with high-throughput screening methods, synthetic carbohydrates with PGMs are invaluable probes in structure-activity relationship studies. We illustrate here several classes of carbohydrates with PGMs and their applications. Recent progress in chemical, enzymatic, and chemoenzymatic syntheses of these carbohydrates and their derivatives are also presented. PMID:17340000

  19. Carbohydrates in xenotransplantation.

    PubMed

    Ezzelarab, Mohamed; Ayares, David; Cooper, David K C

    2005-08-01

    The success of allotransplantation has led to an increasing shortage of human organs from deceased donors. This crisis could be resolved by the use of organs from an anatomically suitable animal, such as the pig. The pig and human have, however, been evolving differently for approximately 80 million years, and numerous immunological and physiological barriers have developed that need to be overcome. Differences in carbohydrate epitopes on pig and human cells have been found to play a major role in some of the immunological barriers that have been identified to date. The rejection caused by the presence of galactose-alpha1,3-galactose (Gal) on the pig vascular endothelium and of natural anti-Gal antibodies in humans has recently been prevented by the breeding of pigs that do not express Gal, achieved by knocking out the gene for the enzyme alpha1,3-galactosyltransferase, which was made possible by the introduction of nuclear transfer/embryo transfer techniques. N-glycolylneuraminic acid (the so-called Hanganutziu-Deicher antigen) has been identified as another carbohydrate antigen present in pigs that may need to be deleted if xenotransplantation is to be successful, although some doubt remains regarding its importance. There remain other antipig antibodies against hitherto unidentified antigenic targets that may well be involved in graft destruction; their possible carbohydrate target epitopes are discussed.

  20. Heat capacity changes in carbohydrates and protein-carbohydrate complexes.

    PubMed

    Chavelas, Eneas A; García-Hernández, Enrique

    2009-05-13

    Carbohydrates are crucial for living cells, playing myriads of functional roles that range from being structural or energy-storage devices to molecular labels that, through non-covalent interaction with proteins, impart exquisite selectivity in processes such as molecular trafficking and cellular recognition. The molecular bases that govern the recognition between carbohydrates and proteins have not been fully understood yet. In the present study, we have obtained a surface-area-based model for the formation heat capacity of protein-carbohydrate complexes, which includes separate terms for the contributions of the two molecular types. The carbohydrate model, which was calibrated using carbohydrate dissolution data, indicates that the heat capacity contribution of a given group surface depends on its position in the saccharide molecule, a picture that is consistent with previous experimental and theoretical studies showing that the high abundance of hydroxy groups in carbohydrates yields particular solvation properties. This model was used to estimate the carbohydrate's contribution in the formation of a protein-carbohydrate complex, which in turn was used to obtain the heat capacity change associated with the protein's binding site. The model is able to account for protein-carbohydrate complexes that cannot be explained using a previous model that only considered the overall contribution of polar and apolar groups, while allowing a more detailed dissection of the elementary contributions that give rise to the formation heat capacity effects of these adducts.

  1. Noncaloric Benefits of Carbohydrates.

    PubMed

    Reddy, B Ravinder

    2015-01-01

    Noncaloric benefits of carbohydrates are due to the presence of dietary fibers, which are a heterogeneous group of natural food sources and form an important component of a healthy diet. They differ in physiochemical properties such as solubility, fermentability and viscosity. They have a wide range of physiological effects resulting in gastrointestinal and systemic benefits. These include appetite, satiety, bowel transit time and function, production of short-chain fatty acids and certain vitamins, and effects on gut microbiota, immunity and inflammation, as well as mineral absorption. They also help to control the glycemic status and serum lipid levels, resulting in reduced incidence rates of atherosclerosis, hypertension, stroke and cardiovascular diseases.

  2. GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project.

    PubMed

    Jeong, Seul-Ki; Hancock, William S; Paik, Young-Ki

    2015-09-04

    Since the launch of the Chromosome-centric Human Proteome Project (C-HPP) in 2012, the number of "missing" proteins has fallen to 2932, down from ∼5932 since the number was first counted in 2011. We compared the characteristics of missing proteins with those of already annotated proteins with respect to transcriptional expression pattern and the time periods in which newly identified proteins were annotated. We learned that missing proteins commonly exhibit lower levels of transcriptional expression and less tissue-specific expression compared with already annotated proteins. This makes it more difficult to identify missing proteins as time goes on. One of the C-HPP goals is to identify alternative spliced product of proteins (ASPs), which are usually difficult to find by shot-gun proteomic methods due to their sequence similarities with the representative proteins. To resolve this problem, it may be necessary to use a targeted proteomics approach (e.g., selected and multiple reaction monitoring [S/MRM] assays) and an innovative bioinformatics platform that enables the selection of target peptides for rarely expressed missing proteins or ASPs. Given that the success of efforts to identify missing proteins may rely on more informative public databases, it was necessary to upgrade the available integrative databases. To this end, we attempted to improve the features and utility of GenomewidePDB by integrating transcriptomic information (e.g., alternatively spliced transcripts), annotated peptide information, and an advanced search interface that can find proteins of interest when applying a targeted proteomics strategy. This upgraded version of the database, GenomewidePDB 2.0, may not only expedite identification of the remaining missing proteins but also enhance the exchange of information among the proteome community. GenomewidePDB 2.0 is available publicly at http://genomewidepdb.proteomix.org/.

  3. Being a binding site: characterizing residue composition of binding sites on proteins.

    PubMed

    Iván, Gábor; Szabadka, Zoltán; Grolmusz, Vince

    2007-12-30

    The Protein Data Bank contains the description of more than 45,000 three-dimensional protein and nucleic-acid structures today. Started to exist as the computer-readable depository of crystallographic data complementing printed articles, the proper interpretation of the content of the individual files in the PDB still frequently needs the detailed information found in the citing publication. This fact implies that the fully automatic processing of the whole PDB is a very hard task. We first cleaned and re-structured the PDB data, then analyzed the residue composition of the binding sites in the whole PDB for frequency and for hidden association rules. Main results of the paper: (i) the cleaning and repairing algorithm (ii) redundancy elimination from the data (iii) application of association rule mining to the cleaned non-redundant data set. We have found numerous significant relations of the residue-composition of the ligand binding sites on protein surfaces, summarized in two figures. One of the classical data-mining methods for exploring implication-rules, the association-rule mining, is capable to find previously unknown residue-set preferences of bind ligands on protein surfaces. Since protein-ligand binding is a key step in enzymatic mechanisms and in drug discovery, these uncovered preferences in the study of more than 19,500 binding sites may help in identifying new binding protein-ligand pairs.

  4. Clustered Carbohydrates in Synthetic Vaccines†

    PubMed Central

    Peri, Francesco

    2013-01-01

    Are there general rules to achieve efficient immunization against carbohydrate antigens? Thanks to technological advances in glycobiology and glycochemistry we entered in a new era in which the rational design of carbohydrate vaccines has become an achievable goal. Aim of this Tutorial Review is to present the most recent achievements in the field of semi and fully synthetic carbohydrate vaccines against viruses, bacteria and cancer. It is also pointed out that the understanding of the chemical and biochemical processes related to immunization allows the modern chemist to rationally design carbohydrate vaccines with improved efficiency. PMID:23250562

  5. Issues in Nutrition: Carbohydrates.

    PubMed

    Thompson, Margaret E; Noel, Mary Barth

    2017-01-01

    Carbohydrates include sugars, starches, and dietary fibers. Resistant starches resemble fiber in their behavior in the intestinal tract, and may have positive effects on blood glucose levels and the gut microbiome. Fibers are classified as soluble and insoluble, but most fiber-containing foods contain a mixture of soluble and insoluble fiber. Soluble fiber has been shown to lower low-density lipoprotein cholesterol levels. Many artificial sweeteners and other sugar substitutes are available. Most natural sources of sweeteners also are energy sources. Many artificial sweeteners contain no kilocalories in the amounts typically used. Sugar alcohols may have a laxative effect when consumed in large amounts. Glycemic index and glycemic load are measurements that help quantify serum glucose response after ingestion of particular foods. These measurements may be affected by the combination of foods consumed in a given meal, and the glycemic index may vary among individuals eating the same meal. Eating foods with a low glycemic index may help prevent development of type 2 diabetes. There is no definitive evidence to recommend low-carbohydrate diets over low-fat diets for long-term weight loss; they are equally effective. Written permission from the American Academy of Family Physicians is required for reproduction of this material in whole or in part in any form or medium.

  6. Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins.

    PubMed

    Jo, Sunhwan; Song, Kevin C; Desaire, Heather; MacKerell, Alexander D; Im, Wonpil

    2011-11-15

    Understanding how glycosylation affects protein structure, dynamics, and function is an emerging and challenging problem in biology. As a first step toward glycan modeling in the context of structural glycobiology, we have developed Glycan Reader and integrated it into the CHARMM-GUI, http://www.charmm-gui.org/input/glycan. Glycan Reader greatly simplifies the reading of PDB structure files containing glycans through (i) detection of carbohydrate molecules, (ii) automatic annotation of carbohydrates based on their three-dimensional structures, (iii) recognition of glycosidic linkages between carbohydrates as well as N-/O-glycosidic linkages to proteins, and (iv) generation of inputs for the biomolecular simulation program CHARMM with the proper glycosidic linkage setup. In addition, Glycan Reader is linked to other functional modules in CHARMM-GUI, allowing users to easily generate carbohydrate or glycoprotein molecular simulation systems in solution or membrane environments and visualize the electrostatic potential on glycoprotein surfaces. These tools are useful for studying the impact of glycosylation on protein structure and dynamics. Copyright © 2011 Wiley Periodicals, Inc.

  7. Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins

    PubMed Central

    Jo, Sunhwan; Song, Kevin C.; Desaire, Heather; MacKerell, Alexander D.; Im, Wonpil

    2011-01-01

    Understanding how glycosylation affects protein structure, dynamics, and function is an emerging and challenging problem in biology. As a first step toward glycan modeling in the context of structural glycobiology, we have developed Glycan Reader and integrated it into the CHARMM-GUI, http://www.charmm-gui.org/input/glycan. Glycan Reader greatly simplifies the reading of PDB structure files containing glycans through (i) detection of carbohydrate molecules, (ii) automatic annotation of carbohydrates based on their three-dimensional structures, (iii) recognition of glycosidic linkages between carbohydrates as well as N-/O-glycosidic linkages to proteins, and (iv) generation of inputs for the biomolecular simulation program CHARMM with the proper glycosidic linkage setup. In addition, Glycan Reader is linked to other functional modules in CHARMM-GUI, allowing users to easily generate carbohydrate or glycoprotein molecular simulation systems in solution or membrane environments and visualize the electrostatic potential on glycoprotein surfaces. These tools are useful for studying the impact of glycosylation on protein structure and dynamics. PMID:21815173

  8. Impact of Dietary Carbohydrate and Protein Levels on Carbohydrate Metabolism

    ERIC Educational Resources Information Center

    Lasker, Denise Ann

    2009-01-01

    The goal of this dissertation was to investigate the impact of changing dietary carbohydrate (CARB) intakes within recommended dietary guidelines on metabolic outcomes specifically associated with glycemic regulations and carbohydrate metabolism. This research utilized both human and animal studies to examine changes in metabolism across a wide…

  9. Impact of Dietary Carbohydrate and Protein Levels on Carbohydrate Metabolism

    ERIC Educational Resources Information Center

    Lasker, Denise Ann

    2009-01-01

    The goal of this dissertation was to investigate the impact of changing dietary carbohydrate (CARB) intakes within recommended dietary guidelines on metabolic outcomes specifically associated with glycemic regulations and carbohydrate metabolism. This research utilized both human and animal studies to examine changes in metabolism across a wide…

  10. Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation*

    PubMed Central

    Payne, Christina M.; Bomble, Yannick J.; Taylor, Courtney B.; McCabe, Clare; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.

    2011-01-01

    Proteins employ aromatic residues for carbohydrate binding in a wide range of biological functions. Glycoside hydrolases, which are ubiquitous in nature, typically exhibit tunnels, clefts, or pockets lined with aromatic residues for processing carbohydrates. Mutation of these aromatic residues often results in significant activity differences on insoluble and soluble substrates. However, the thermodynamic basis and molecular level role of these aromatic residues remain unknown. Here, we calculate the relative ligand binding free energy by mutating tryptophans in the Trichoderma reesei family 6 cellulase (Cel6A) to alanine. Removal of aromatic residues near the catalytic site has little impact on the ligand binding free energy, suggesting that aromatic residues immediately upstream of the active site are not directly involved in binding, but play a role in the glucopyranose ring distortion necessary for catalysis. Removal of aromatic residues at the entrance and exit of the Cel6A tunnel, however, dramatically impacts the binding affinity, suggesting that these residues play a role in chain acquisition and product stabilization, respectively. The roles suggested from differences in binding affinity are confirmed by molecular dynamics and normal mode analysis. Surprisingly, our results illustrate that aromatic-carbohydrate interactions vary dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, these results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for biomass utilization. Generally, these results suggest that nature employs aromatic-carbohydrate interactions with a wide range of binding affinities for diverse functions. PMID:21965672

  11. JET2 Viewer: a database of predicted multiple, possibly overlapping, protein–protein interaction sites for PDB structures

    PubMed Central

    Ripoche, Hugues; Laine, Elodie; Ceres, Nicoletta; Carbone, Alessandra

    2017-01-01

    The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET2 at large-scale on more than 20 000 chains. JET2 strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET2 analyses. Predictions were evaluated on more than 15 000 experimentally characterized protein interfaces. This is, to our knowledge, the largest evaluation of a protein binding site prediction method. The overall performance of JET2 on all interfaces are: Sen = 52.52, PPV = 51.24, Spe = 80.05, Acc = 75.89. The data can be used to foster new strategies for protein–protein interactions modulation and interaction surface redesign. PMID:27899675

  12. An impression of coffee carbohydrates.

    PubMed

    Arya, Meenakshi; Rao, L Jagan Mohan

    2007-01-01

    Coffee is one of the most popular beverages in the world. It is consumed for its refreshing and stimulating properties. Carbohydrates are the major constituents of coffee beans and serve various functions like binding of aroma, stabilization of foam, formation of sedimentation, and increased viscosity of the extract. The principal low molecular weight carbohydrate is sucrose and no evidence of other simple oligosaccharides has been found. Polysaccharide fraction from green coffee is dominated by arabinogalactan, galactomannan, and cellulose. The polysaccharide content is reduced during roasting due to degradation to low molecular weight carbohydrates (viz., mono and oligosaccharide) and become more extractable. Various methods that can be employed to extract the carbohydrate from roasted coffee are sequential extraction, acid hydroloysis, hot water extraction, enzymatic extraction etc. Carbohydrates from coffee can be quantitatively determined by liquid chromatography, high performance anion exchange chromatography, size exclusion chromatography, and high performance liquid chromatography. Besides improving the organoleptic quality of the coffee beverage, carbohydrates also possess various biological activities such as lowering colon cancer risk. Besides their sheer mass, a variety of evidences testify to the important contribution that the polysaccharide content makes to the character of the final brew. Although a number of chemical and enzymatic methods have been devised to isolate and quantify the carbohydrates of R&G coffee, till date hot water extraction is the only method which can be accepted as a most feasible process and hence, there is wide scope of further research for the efficient and economically viable technology for extraction of carbohydrates from coffee.

  13. Stereochemical Control in Carbohydrate Chemistry

    ERIC Educational Resources Information Center

    Batchelor, Rhys; Northcote, Peter T.; Harvey, Joanne E.; Dangerfield, Emma M.; Stocker, Bridget L.

    2008-01-01

    Carbohydrates, in the form of glycoconjugates, have recently been shown to control a wide range of cellular processes. Accordingly, students interested in the study of organic chemistry and biomedical sciences should be exposed to carbohydrate chemistry. To this end, we have developed a sequence of experiments that leads the student from the…

  14. Stereochemical Control in Carbohydrate Chemistry

    ERIC Educational Resources Information Center

    Batchelor, Rhys; Northcote, Peter T.; Harvey, Joanne E.; Dangerfield, Emma M.; Stocker, Bridget L.

    2008-01-01

    Carbohydrates, in the form of glycoconjugates, have recently been shown to control a wide range of cellular processes. Accordingly, students interested in the study of organic chemistry and biomedical sciences should be exposed to carbohydrate chemistry. To this end, we have developed a sequence of experiments that leads the student from the…

  15. METHODOLOGICAL CHALLENGES IN CARBOHYDRATE ANALYSIS

    USDA-ARS?s Scientific Manuscript database

    Carbohydrates can provide up to 80% of the dry matter in animal diets, yet their specific evaluation for research and diet formulation is only now becoming a focus in the animal sciences. Partitioning of dietary carbohydrates for nutritional purposes should reflect differences in digestion and ferm...

  16. The new carbohydrate intake recommendations.

    PubMed

    Jeukendrup, Asker

    2013-01-01

    Carbohydrate intake during prolonged exercise has been shown to increase endurance capacity and improve performance. Until recently, the advice was to ingest 30-60 g of carbohydrate per hour. The upper limit was based on studies that demonstrated that intakes greater than 60-70 g/h would not result in greater exogenous carbohydrate oxidation rates. The lower limit was an estimated guess of the minimum amount of carbohydrate required for ergogenic effects. In addition, the advice was independent of the type, the duration or the intensity of the activity as well as the level of athlete. Since 2004, significant advances in the understanding of the effects of carbohydrate intake during exercise have made it possible to be much more prescriptive and individual with the advice. Studies revealed that oxidation rates can reach much higher values (up to 105 g/h) when multiple transportable carbohydrates are ingested (i.e. glucose:fructose). It has also been observed that carbohydrate ingested during shorter higher intensity exercise (1 h, 80%VO2max) can improve performance, although mechanisms are distinctly different. These findings resulted in new recommendations that are dependent on the duration and intensity of exercise and not only specify the quantity of carbohydrate to be ingested but also the type. Copyright © 2013 Nestec Ltd., Vevey/S. Karger AG, Basel.

  17. Synthesis of carbohydrate-based surfactants

    SciTech Connect

    Pemberton, Jeanne E.; Polt, Robin L.; Maier, Raina M.

    2016-11-22

    The present invention provides carbohydrate-based surfactants and methods for producing the same. Methods for producing carbohydrate-based surfactants include using a glycosylation promoter to link a carbohydrate or its derivative to a hydrophobic compound.

  18. Abuse potential of carbohydrates for overweight carbohydrate cravers

    PubMed Central

    Spring, Bonnie; Schneider, Kristin; Smith, Malaina; Kendzor, Darla; Appelhans, Bradley; Hedeker, Donald; Pagoto, Sherry

    2010-01-01

    Rationale The long-rejected construct of food addiction is undergoing re-examination. Objectives . To evaluate whether a novel carbohydrate food shows abuse potential for rigorously defined carbohydrate cravers, as evidenced by selective self-administration and mood enhancement during double-blind discrimination testing. Methods Discrete trials choice testing was performed with 61 overweight (BMI m=27.64, SD=2.59) women (ages 18–45; 19.70% African American) whose diet records showed >4 weekly afternoon/evening emotional eating episodes confined to snacks with carbohydrate:protein ≥ 6:1. After being induced into a sad mood, participants were exposed, double-blind and in counterbalanced order, to taste-matched carbohydrate and protein beverages. They were asked to choose and self-administer the drink that made them feel better. Results Women overwhelmingly chose the carbohydrate beverage, even though blinded. Mixed-effects regression modeling, controlling for beverage order, revealed greater liking and greater reduction in dysphoria following the carbohydrate beverage compared to the protein beverage, but no differential effect on vigor. Conclusion For women who crave them, carbohydrates appear to display abuse potential, plausibly contributing to overconsumption and overweight. PMID:18273603

  19. An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II) from Penicillium purpurogenum

    NASA Astrophysics Data System (ADS)

    Colombres, Marcela; Garate, José A.; Lagos, Carlos F.; Araya-Secchi, Raúl; Norambuena, Patricia; Quiroz, Soledad; Larrondo, Luis; Pérez-Acle, Tomas; Eyzaguirre, Jaime

    2008-01-01

    The soft-rot fungus Penicillium purpurogenum secretes to the culture medium a variety of enzymes related to xylan biodegradation, among them three acetyl xylan esterases (AXE I, II and III). AXE II has 207 amino acids; it belongs to family 5 of the carbohydrate esterases and its structure has been determined by X-ray crystallography at 0.9 Å resolution (PDB 1G66). The enzyme possesses the α/β hydrolase fold and the catalytic triad typical of serine esterases (Ser90, His187 and Asp175). AXE II can hydrolyze esters of a large variety of alcohols, but it is restricted to short chain fatty acids. An analysis of its three-dimensional structure shows that a loop that covers the active site may be responsible for this strict specificity. Cutinase, an enzyme that hydrolyzes esters of long chain fatty acids and shows a structure similar to AXE II, lacks this loop. In order to generate an AXE II with this broader specificity, the preparation of a mutant lacking residues involving this loop (Gly104 to Ala114) was proposed. A set of molecular simulation experiments based on a comparative model of the mutant enzyme predicted a stable structure. Using site-directed mutagenesis, the loop's residues have been eliminated from the AXE II cDNA. The mutant protein has been expressed in Aspergillus nidulans A722 and Pichia pastoris, and it is active towards a range of fatty acid esters of up to at least 14 carbons. The availability of an esterase with broader specificity may have biotechnological applications for the synthesis of sugar esters.

  20. Decarbonylation and dehydrogenation of carbohydrates

    DOEpatents

    Andrews, Mark A.; Klaeren, Stephen A.

    1991-01-01

    Carbohydrates, especially aldose or ketose sugars, including those whose carbonyl group is masked by hemi-acetal or hemi-ketal formation, are decarbonylated by heating the feed carbohydrate together with a transition metal complex in a suitable solvent. Also, primary alcohols, including sugar alditols are simultaneously dehydrogenated and decarbonylated by heating a mixture of rhodium and ruthenium complexes and the alcohol and optionally a hydrogen acceptor in an acceptable solvent. Such defarbonylation and/or dehydrogenation of sugars provides a convenient procedure for the synthesis of certain carbohydrates and may provide a means for the conversion of biomass into useful products.

  1. Monitoring lectin interactions with carbohydrates.

    PubMed

    de Bentzmann, Sophie; Varrot, Annabelle; Imberty, Anne

    2014-01-01

    Protein-carbohydrate interactions are often involved in the first step of infection and Pseudomonas aeruginosa produces several proteins that are able to bind specifically to glycan epitopes present on host epithelia. The experimental approaches for studying protein-carbohydrate interaction have been inspired, with some adaptations, from those commonly used for protein-protein or protein-ligand interactions. A range of methods are described herein for detecting lectin activity, screening for monosaccharide or oligosaccharide specificity, determining the affinity of binding together with thermodynamics and kinetics parameters, and producing crystal of lectin-carbohydrate complexes for further structural studies.

  2. FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately.

    PubMed

    Budowski-Tal, Inbal; Nov, Yuval; Kolodny, Rachel

    2010-02-23

    Fast identification of protein structures that are similar to a specified query structure in the entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We present FragBag: An ultrafast and accurate method for comparing protein structures. We describe a protein structure by the collection of its overlapping short contiguous backbone segments, and discretize this set using a library of fragments. Then, we succinctly represent the protein as a "bags-of-fragments"-a vector that counts the number of occurrences of each fragment-and measure the similarity between two structures by the similarity between their vectors. Our representation has two additional benefits: (i) it can be used to construct an inverted index, for implementing a fast structural search engine of the entire PDB, and (ii) one can specify a structure as a collection of substructures, without combining them into a single structure; this is valuable for structure prediction, when there are reliable predictions only of parts of the protein. We use receiver operating characteristic curve analysis to quantify the success of FragBag in identifying neighbor candidate sets in a dataset of over 2,900 structures. The gold standard is the set of neighbors found by six state of the art structural aligners. Our best FragBag library finds more accurate candidate sets than the three other filter methods: The SGM, PRIDE, and a method by Zotenko et al. More interestingly, FragBag performs on a par with the computationally expensive, yet highly trusted structural aligners STRUCTAL and CE.

  3. Carbohydrates and Diabetes (For Parents)

    MedlinePlus

    ... two main forms of carbohydrates are sugars and starches. Types of sugars include fructose (sugar found in ... sugar found in milk and yogurt). Types of starches include vegetables like potatoes, corn, and peas; grains, ...

  4. Carbohydrate composition of candy bars.

    PubMed

    Hurst, W J; Martin, R A; Zoumas, B L

    1983-07-01

    The data in Table 1 show a wide variation among products and when added to other available data provide a more complete picture of the carbohydrate composition of candy bars. Interestingly, the sucrose content of the bars in Table 1 ranges from a low of 19.12% to a high of 56.06%. Extensive use of corn syrup is clearly evident in ingrediated bar types (categories e and f). Although the higher saccharides of corn syrup were not quantitated, we think that this article adds to the knowledge of the carbohydrate composition of the best-selling candy bars, since previously only a carbohydrate by difference value was available. This report provides the health professional with an update on carbohydrate composition of a large number of candy bars.

  5. Protecting Groups in Carbohydrate Chemistry

    NASA Astrophysics Data System (ADS)

    Pétursson, Sigthór

    1997-11-01

    The most important protecting groups in carbohydrate chemistry are reviewed. The paper is aimed at those beginning to specialize in synthetic carbohydrate chemistry and at teachers with other specialties who wish to go beyond the content of general organic chemistry textbooks. Acetals and ketals are of fundamental importance in carbohydrate chemistry and their chemistry is presented first. In contrast to the base stability of the acetals, are the base labile esters. The complimentary use of these two protecting methods is illustrated. Methyl and benzyl ethers have a long history both in synthetic carbohydrate chemistry and in the structural studies of polysaccharides. In synthetic work benzyl ethers are the most useful. Silyl ethers are also well established in carbohydrate chemistry and the use of these protecting methods is illustrated. Phase transfer reactions and the use of cyclic stannylene derivatives to enhance the regioselectivity in the introduction of protecting groups, especially ethers, is discussed as well as some results optained with stannous chloride catalyzed reactions of diaryldiphenylmethanes with vicinal diols which gave unexpected results. The paper ends with illustrative examples of the use of protecting groups in modern synthetic carbohydrate chemistry, namely the synthesis of nitrogen containing compounds belonging to an important class of polyhydroxylated cyclic amines. Compounds of this class are potent inhibitors of glycosidase enzymes.

  6. Carbohydrate digestibility and metabolic effects.

    PubMed

    Wong, Julia M W; Jenkins, David J A

    2007-11-01

    There is a history of interest in the metabolic effects of alterations in small intestinal digestion and colonic fermentation of carbohydrate. It is believed that the rate of digestion of carbohydrate determines the place and form in which carbohydrate is absorbed. Slowly absorbed or lente carbohydrate sources may reduce postprandial glucose surges and the need for insulin with important implications for lowering coronary heart disease risk and reducing diabetes incidence. Carbohydrates that are not digested in the small intestine will enter the colon, and those that are fermentable will be salvaged as short-chain fatty acids in the colon and at the same time may stimulate colonic microflora, such as bifidobacteria. This process may have metabolic effects in the gut and throughout the host, possibly related to short-chain fatty acid products, although these effects are less well documented. One important aspect of colonic fermentation is the stimulation of certain populations of the colonic microflora, which may assist in the biotransformation of bioactive food components including the cleaving of plant phenolics from their glycone to produce the more rapidly absorbed aglycone. However, human studies have been limited. Therefore, further studies are required to explore these important aspects of metabolism related to the rate of carbohydrate absorption and fermentation and their implications in health and disease.

  7. A Systematic Analysis of the Structures of Heterologously Expressed Proteins and Those from Their Native Hosts in the RCSB PDB Archive

    PubMed Central

    Zhou, Ren-Bin; Lu, Hui-Meng; Liu, Jie; Shi, Jian-Yu; Zhu, Jing; Lu, Qin-Qin; Yin, Da-Chuan

    2016-01-01

    Recombinant expression of proteins has become an indispensable tool in modern day research. The large yields of recombinantly expressed proteins accelerate the structural and functional characterization of proteins. Nevertheless, there are literature reported that the recombinant proteins show some differences in structure and function as compared with the native ones. Now there have been more than 100,000 structures (from both recombinant and native sources) publicly available in the Protein Data Bank (PDB) archive, which makes it possible to investigate if there exist any proteins in the RCSB PDB archive that have identical sequence but have some difference in structures. In this paper, we present the results of a systematic comparative study of the 3D structures of identical naturally purified versus recombinantly expressed proteins. The structural data and sequence information of the proteins were mined from the RCSB PDB archive. The combinatorial extension (CE), FATCAT-flexible and TM-Align methods were employed to align the protein structures. The root-mean-square distance (RMSD), TM-score, P-value, Z-score, secondary structural elements and hydrogen bonds were used to assess the structure similarity. A thorough analysis of the PDB archive generated five-hundred-seventeen pairs of native and recombinant proteins that have identical sequence. There were no pairs of proteins that had the same sequence and significantly different structural fold, which support the hypothesis that expression in a heterologous host usually could fold correctly into their native forms. PMID:27517583

  8. Biologically-Inspired Peptide Reagents for Enhancing IMS-MS Analysis of Carbohydrates

    NASA Astrophysics Data System (ADS)

    Bohrer, Brian C.; Clemmer, David E.

    2011-09-01

    The binding properties of a peptidoglycan recognition protein are translated via combinatorial chemistry into short peptides. Non-adjacent histidine, tyrosine, and arginine residues in the protein's binding cleft that associate specifically with the glycan moiety of a peptidoglycan substrate are incorporated into linear sequences creating a library of 27 candidate tripeptide reagents (three possible residues permutated across three positions). Upon electrospraying the peptide library and carbohydrate mixtures, some noncovalent complexes are observed. The binding efficiencies of the peptides vary according to their amino acid composition as well as the disaccharide linkage and carbohydrate ring-type. In addition to providing a charge-carrier for the carbohydrate, peptide reagents can also be used to differentiate carbohydrate isomers by ion mobility spectrometry. The utility of these peptide reagents as a means of enhancing ion mobility analysis of carbohydrates is illustrated by examining four glucose-containing disaccharide isomers, including a pair that is not resolved by ion mobility alone. The specificity and stoichiometry of the peptide-carbohydrate complexes are also investigated. Trihistidine demonstrates both suitable binding efficiency and successful resolution of disaccharides isomers, suggesting it may be a useful reagent in IMS analyses of carbohydrates.

  9. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

    SciTech Connect

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-10-01

    Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

  10. Foreword: Carbohydrate Research: a half century of carbohydrate science.

    PubMed

    Horton, Derek

    2015-02-11

    The article traces the history of the journal Carbohydrate Research from its debut in 1964 and its subsequent evolution to the present day, viewed from the perspective of one of the founding editors who served as a receiving editor until 2005. The concept of an international journal focused on the broad aspects of carbohydrate science found ready acceptance in the research community, and its volumes now serve as a unified archive of a significant proportion of published research data on all molecular aspects of carbohydrates. Changes in the editor line-up over the years are noted, along with the transition to electronic publishing, and the role of key people in the Elsevier Company toward the success of the journal. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data.

    PubMed

    Terwilliger, Thomas C; Bricogne, Gerard

    2014-10-01

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

  12. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

    SciTech Connect

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-09-30

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

  13. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

    DOE PAGES

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-09-30

    Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when itmore » was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.« less

  14. Carbohydrate chemistry in drug discovery.

    PubMed

    Galan, M Carmen; Benito-Alifonso, David; Watt, Gregory M

    2011-05-21

    The multitude of roles that carbohydrates and their glyco-conjugates play in biological processes has stimulated great interest in determining the nature of their interactions in both normal and diseased states. Manipulating such interactions will provide leads for drug discovery. Of the major classes of biomolecule, carbohydrates are the most structurally diverse. This hetereogeneity makes isolation of pure samples, and in sufficient amounts, from biological sources extremely difficult. Chemical synthesis offers the advantage of producing pure and structurally defined oligosaccharides for biological investigations. Although the complex nature of carbohydrates means that this is challenging, recent advances in the field have facilitated access to these molecules. The synthesis and isolation of oligosaccharides combined with progress in glycoarray technology have aided the identification of new carbohydrate-binding drug targets. This review aims to provide an overview of the latest advancements in carbohydrate chemistry and the role of these complex molecules in drug discovery, focusing particularly on synthetic methodologies, glycosaminoglycans, glycoprotein synthesis and vaccine development over the last few years.

  15. Aminooxylated Carbohydrates: Synthesis and Applications.

    PubMed

    Pifferi, Carlo; Daskhan, Gour Chand; Fiore, Michele; Shiao, Tze Chieh; Roy, René; Renaudet, Olivier

    2017-08-09

    Among other classes of biomolecules, carbohydrates and glycoconjugates are widely involved in numerous biological functions. In addition to addressing the related synthetic challenges, glycochemists have invested intense efforts in providing access to structures that can be used to study, activate, or inhibit these biological processes. Over the past few decades, aminooxylated carbohydrates have been found to be key building blocks for achieving these goals. This review provides the first in-depth overview covering several aspects related to the syntheses and applications of aminooxylated carbohydrates. After a brief introduction to oxime bonds and their relative stabilities compared to related C═N functions, synthetic aspects of oxime ligation and methodologies for introducing the aminooxy functionality onto both glycofuranosyls and glycopyranosyls are described. The subsequent section focuses on biological applications involving aminooxylated carbohydrates as components for the construcion of diverse architectures. Mimetics of natural structures represent useful tools for better understanding the features that drive carbohydrate-receptor interaction, their biological output and they also represent interesting structures with improved stability and tunable properties. In the next section, multivalent structures such as glycoclusters and glycodendrimers obtained through oxime ligation are described in terms of synthetic design and their biological applications such as immunomodulators. The second-to-last section discusses miscellaneous applications of oxime-based glycoconjugates, such as enantioselective catalysis and glycosylated oligonucleotides, and conclusions and perspectives are provided in the last section.

  16. Cancer Vaccines and Carbohydrate Epitopes

    PubMed Central

    Heimburg-Molinaro, Jamie; Lum, Michelle; Vijay, Geraldine; Jain, Miten; Almogren, Adel; Rittenhouse-Olson, Kate

    2011-01-01

    Tumor-associated carbohydrate antigens (TACA) result from the aberrant glycosylation that is seen with transformation to a tumor cell. The carbohydrate antigens that have been found to be tumor-associated include the mucin related Tn, Sialyl Tn, and Thomsen-Friedenreich antigens, the blood group Lewis related LewisY, Sialyl LewisX and Sialyl LewisA, and LewisX, (also known as stage-specific embryonic antigen-1, SSEA-1), the glycosphingolipids Globo H and stage-specific embryonic antigen-3 (SSEA-3), the sialic acid containing glycosphingolipids, the gangliosides GD2, GD3, GM2, fucosyl GM1, and Neu5GcGM3, and polysialic acid. Recent developments have furthered our understanding of the T-independent type II response that is seen in response to carbohydrate antigens. The selection of a vaccine target antigen is based on not only the presence of the antigen in a variety of tumor tissues but also on the role this antigen plays in tumor growth and metastasis. These roles for TACAs are being elucidated. Newly acquired knowledge in understanding the T-independent immune response and in understanding the key roles that carbohydrates play in metastasis are being applied in attempts to develop an effective vaccine response to TACAs. The role of each of the above mentioned carbohydrate antigens in cancer growth and metastasis and vaccine attempts using these antigens will be described. PMID:21964054

  17. CHARACTERIZATION OF THE CARBOHYDRATE COMPONENTS OF Taenia solium ONCOSPHERE PROTEINS AND THEIR ROLE IN THE ANTIGENICITY

    PubMed Central

    Arana, Yanina; Verastegui, Manuela; Tuero, Iskra; Grandjean, Louis; Garcia, Hector H.; Gilman, Robert H.

    2015-01-01

    This study examines the carbohydrate composition of Taenia solium whole oncosphere antigens (WOAs), in order to improve the understanding of the antigenicity of the T. solium. Better knowledge of oncosphere antigens is crucial to accurately diagnose previous exposure to T. solium eggs and thus predict the development of neurocysticercosis. A set of seven lectins conjugates with wide carbohydrate specificity were used on parasite fixations and somatic extracts. Lectin fluorescence revealed that D-mannose, D-glucose, D-galactose and N-acetyl-D-galactosamine residues were the most abundant constituents of carbohydrate chains on the surface of T. solium oncosphere. Lectin blotting showed that post-translational modification with N-glycosylation was abundant while little evidence of O-linked carbohydrates was observed. Chemical oxidation and enzymatic deglycosylation in situ were performed to investigate the immunoreactivity of the carbohydrate moieties. Linearizing or removing the carbohydrate moieties from the protein backbones did not diminish the immunoreactivity of these antigens, suggesting that a substantial part of the host immune response against T. solium oncosphere is directed against the peptide epitopes on the parasite antigens. Finally, using carbohydrate probes, we demonstrated for the first time that the presence of several lectins on the surface of the oncosphere was specific to carbohydrates found in intestinal mucus, suggesting a possible role in initial attachment of the parasite to host cells. PMID:23982308

  18. Characterization of the carbohydrate components of Taenia solium oncosphere proteins and their role in the antigenicity.

    PubMed

    Arana, Yanina; Verastegui, Manuela; Tuero, Iskra; Grandjean, Louis; Garcia, Hector H; Gilman, Robert H

    2013-10-01

    This study examines the carbohydrate composition of Taenia solium whole oncosphere antigens (WOAs), in order to improve the understanding of the antigenicity of the T. solium. Better knowledge of oncosphere antigens is crucial to accurately diagnose previous exposure to T. solium eggs and thus predict the development of neurocysticercosis. A set of seven lectins conjugates with wide carbohydrate specificity were used on parasite fixations and somatic extracts. Lectin fluorescence revealed that D-mannose, D-glucose, D-galactose and N-acetyl-D-galactosamine residues were the most abundant constituents of carbohydrate chains on the surface of T. solium oncosphere. Lectin blotting showed that posttranslational modification with N-glycosylation was abundant while little evidence of O-linked carbohydrates was observed. Chemical oxidation and enzymatic deglycosylation in situ were performed to investigate the immunoreactivity of the carbohydrate moieties. Linearizing or removing the carbohydrate moieties from the protein backbones did not diminish the immunoreactivity of these antigens, suggesting that a substantial part of the host immune response against T. solium oncosphere is directed against the peptide epitopes on the parasite antigens. Finally, using carbohydrate probes, we demonstrated for the first time that the presence of several lectins on the surface of the oncosphere was specific to carbohydrates found in intestinal mucus, suggesting a possible role in initial attachment of the parasite to host cells.

  19. Challenges with nonfiber carbohydrate methods.

    PubMed

    Hall, M B

    2003-12-01

    Nonfiber carbohydrates (NFC) encompass a compositionally and nutritionally diverse group exclusive of those carbohydrates found in NDF. Their content in feeds has often been described as a single value estimated by difference as 100% of dry matter minus the percentages of CP, NDF (adjusted for CP in NDF), ether extract, and ash. A calculated value was used because of difficulties with assays for individual NFC, but it does not differentiate among nutritionally distinct NFC. Errors in NFC estimation can arise from not accounting for CP in NDF and when multipliers other than 6.25 are appropriate to estimate CP. Analyses that begin to distinguish among NFC are those for starch, soluble fiber (non-NDF, nonstarch polysaccharides), and low molecular weight carbohydrates (mono- and oligosaccharides). Many starch analyses quantify alpha-glucans through specific hydrolysis of alpha-(1 --> 4) and alpha-(1 --> 6) linkages in the glucan, and measurement of released glucose. Incomplete gelatinization and hydrolysis will lead to underestimation of starch content. Starch values are inflated by enzyme preparations that hydrolyze carbohydrates other than alpha-glucan, measurement of all released monosaccharides without specificity for glucose, and failure to exclude free glucose present in the unhydrolyzed sample. Soluble fiber analyses err in a fashion similar to NFC if estimation of CP requires multipliers other than 6.25, or if contaminants such as CP and starch have not been properly accounted. Depolymerization and incomplete precipitation can also decrease soluble fiber estimates. The low molecular weight carbohydrates have been defined as carbohydrates soluble in 78 to 80% ethanol, which separates them from polysaccharides. They can be measured in extracts using broad-spectrum colorimetric assays (phenol-sulfuric acid assay or reducing sugar analysis of acid hydrolyzed samples) or chromatographic methods. Limitations of the colorimetric assays include lack of differentiation

  20. New carbohydrate-based materials

    SciTech Connect

    Callstrom, M.R.

    1992-07-01

    We have prepared a series of new carbohydrate-based materials based on the use of carbohydrates as a template for the introduction of functionality to polymeric materials with complete regio- and stereochemical control. The synthesis of these new materials by the use of chemical and enzymatic methods allows for the rational design of new materials based on the properties of the monomeric subunit. These materials have potential applications that range from their use in enhanced oil recovery to biodegradable plastics to biological applications including targeted drug delivery and enzyme stabilization.

  1. NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB

    PubMed Central

    Doreleijers, Jurgen F.; Vranken, Wim F.; Schulte, Christopher; Markley, John L.; Ulrich, Eldon L.; Vriend, Gert; Vuister, Geerten W.

    2012-01-01

    For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists are available, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. The accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculation using the available experimental data and present-day software. Such efforts, however, generally fail on half of all NMR ensembles due to the syntactic and semantic heterogeneity of the underlying data and the wide variety of formats used for their deposition. We have combined the remediated restraint information from our NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank and the Common Interface for NMR structure Generation (CING) structure validation reports into the weekly updated NRG-CING database (http://nmr.cmbi.ru.nl/NRG-CING). Eleven programs have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available experimental NMR data. The longitudinal validation of these data in a publicly available relational database yields a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The remediated NMR experimental data sets and validation reports are freely available online. PMID:22139937

  2. PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

    PubMed

    Azuara, Cyril; Lindahl, Erik; Koehl, Patrice; Orland, Henri; Delarue, Marc

    2006-07-01

    We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.

  3. Stepwise extraction of proteins and carbohydrates from soybean seed.

    PubMed

    Kasai, Naoya; Ikehara, Hiroko

    2005-05-18

    The stepwise hot water extraction of soybeans, which were extractions in a series of procedures of whole soybean seeds, dehulled and sliced ones, and pressed ones carried out by autoclaving, was investigated to study the localization in the seed and their characteristics. The characteristics of each extraction were studied by HPLC, SDS-PAGE, components analysis, microscopic observation, and effect for some enzymes. Carbohydrates were easier to extract than protein. In the extractions, the ratio of uronic acid per total sugar was constantly about 0.3. A comparison of these extracts, soybean milk, extraction from defatted soybean meal, and soybean milk residues was also carried out, and the characteristics and the localization were investigated. Mid-sized proteins in soybean milk were easy to extract. However, hardly any high molecular weight proteins or high molecular weight carbohydrates were extracted. The proteins and carbohydrates were considered to be localized in the middle lamella and in the protein and/or oil bodies of the cell, and the proteins and carbohydrates were gradually extracted through seed and cell breaking. Gelation was observed only in the boiled extracts from whole seeds. Pepsin and trypsin digests of the high molecular weight protein had inhibitory activity against the angiotensin I converting enzyme.

  4. Residual Cap

    NASA Image and Video Library

    2006-05-10

    This MOC image shows a summertime view of the south polar residual cap of Mars. In this image, mesas composed largely of solid carbon dioxide are separated from one another by irregularly-shaped depressions

  5. Low-digestible carbohydrates in practice.

    PubMed

    Grabitske, Hollie A; Slavin, Joanne L

    2008-10-01

    Low-digestible carbohydrates are carbohydrates that are incompletely or not absorbed in the small intestine but are at least partly fermented by bacteria in the large intestine. Fiber, resistant starch, and sugar alcohols are types of low-digestible carbohydrates. Given potential health benefits (including a reduced caloric content, reduced or no effect on blood glucose levels, non-cariogenic effect), the prevalence of low-digestible carbohydrates in processed foods is increasing. Low-digestible carbohydrate fermentation in the gut causes gastrointestinal effects, especially at higher intakes. We review the wide range of low-digestible carbohydrates in food products, offer advice on identifying low-digestible carbohydrates in foods and beverages, and make suggestions for intakes of low-digestible carbohydrates.

  6. Carbohydrates - Multiple Languages: MedlinePlus

    MedlinePlus

    ... Supplements Videos & Tools You Are Here: Home → Multiple Languages → All Health Topics → Carbohydrates URL of this page: https://medlineplus.gov/languages/carbohydrates.html Other topics A-Z A B ...

  7. AMPK beta subunits display isoform specific affinities for carbohydrates.

    PubMed

    Koay, Ann; Woodcroft, Ben; Petrie, Emma J; Yue, Helen; Emanuelle, Shane; Bieri, Michael; Bailey, Michael F; Hargreaves, Mark; Park, Jong-Tae; Park, Kwan-Hwa; Ralph, Stuart; Neumann, Dietbert; Stapleton, David; Gooley, Paul R

    2010-08-04

    AMP-activated protein kinase (AMPK) is a heterotrimer of catalytic (alpha) and regulatory (beta and gamma) subunits with at least two isoforms for each subunit. AMPK beta1 is widely expressed whilst AMPK beta2 is highly expressed in muscle and both beta isoforms contain a mid-molecule carbohydrate-binding module (beta-CBM). Here we show that beta2-CBM has evolved to contain a Thr insertion and increased affinity for glycogen mimetics with a preference for oligosaccharides containing a single alpha-1,6 branched residue. Deletion of Thr-101 reduces affinity for single alpha-1,6 branched oligosaccharides by 3-fold, while insertion of this residue into the equivalent position in the beta1-CBM sequence increases affinity by 3-fold, confirming the functional importance of this residue. Copyright (c) 2010. Published by Elsevier B.V.

  8. Biophysical characterization of laforin-carbohydrate interaction.

    PubMed

    Dias, David M; Furtado, Joana; Wasielewski, Emeric; Cruz, Rui; Costello, Bernard; Cole, Lindsay; Faria, Tiago Q; Baaske, Philipp; Brito, Rui M M; Ciulli, Alessio; Simões, Isaura; Macedo-Ribeiro, Sandra; Faro, Carlos; Geraldes, Carlos F G C; Castanheira, Pedro

    2016-02-01

    Laforin is a human dual-specificity phosphatase (DSP) involved in glycogen metabolism regulation containing a carbohydrate-binding module (CBM). Mutations in the gene coding for laforin are responsible for the development of Lafora disease, a progressive fatal myoclonus epilepsy with early onset, characterized by the intracellular deposition of abnormally branched, hyperphosphorylated insoluble glycogen-like polymers, called Lafora bodies. Despite the known importance of the CBM domain of laforin in the regulation of glycogen metabolism, the molecular mechanism of laforin-glycogen interaction is still poorly understood. Recently, the structure of laforin with bound maltohexaose was determined and despite the importance of such breakthrough, some molecular interaction details remained missing. We herein report a thorough biophysical characterization of laforin-carbohydrate interaction using soluble glycans. We demonstrated an increased preference of laforin for the interaction with glycans with higher order of polymerization and confirmed the importance of tryptophan residues for glycan interaction. Moreover, and in line with what has been described for other CBMs and lectins, our results confirmed that laforin-glycan interactions occur with a favourable enthalpic contribution counter-balanced by an unfavourable entropic contribution. The analysis of laforin-glycan interaction through the glycan side by saturation transfer difference (STD)-NMR has shown that the CBM-binding site can accommodate between 5 and 6 sugar units, which is in line with the recently obtained crystal structure of laforin. Overall, the work in the present study complements the structural characterization of laforin and sheds light on the molecular mechanism of laforin-glycan interaction, which is a pivotal requisite to understand the physiological and pathological roles of laforin. © 2016 Authors; published by Portland Press Limited.

  9. Carbohydrate markers of pancreatic cancer.

    PubMed

    Szajda, Sławomir Dariusz; Waszkiewicz, Napoleon; Chojnowska, Sylwia; Zwierz, Krzysztof

    2011-01-01

    Pancreatic cancer is the fourth most common cause of death from cancer in the world and the sixth in Europe. Pancreatic cancer is more frequent in males than females. Worldwide, following diagnosis of pancreatic cancer, <2% of patients survive for 5 years, 8% survive for 2 years and <50% survive for only approx. 3 months. The biggest risk factor in pancreatic cancer is age, with a peak of morbidity at 65 years. Difficulty in the diagnosis of pancreatic cancer causes a delay in its detection. It is one of the most difficult cancers to diagnose and therefore to treat successfully. Additional detection of carbohydrate markers may offer a better diagnosis of pancreatic cancer. Carbohydrate markers of cancer may be produced by the cancer itself or by the body in response to cancer, whose presence in body fluids suggests the presence and growth of the cancer. The most widely used, and best-recognized, carbohydrate marker of pancreatic cancer is CA 19-9 [CA (carbohydrate antigen) 19-9]. However, the relatively non-specific nature of CA 19-9 limits its routine use in the early diagnosis of pancreatic cancer, but it may be useful in monitoring treatment of pancreatic cancer (e.g. the effectiveness of chemotherapy), as a complement to other diagnostic methods. Some other carbohydrate markers of pancreatic cancer may be considered, such as CEA (carcinoembryonic antigen), CA 50 and CA 242, and the mucins MUC1, MUC2 and MUC5AC, but enzymes involved in the processing of glycoconjugates could also be involved. Our preliminary research shows that the activity of lysosomal exoglycosidases, including HEX (N-acetyl-β-D-hexosaminidase), GAL (β-D-galactosidase), FUC (α-L-fucosidase) and MAN (α-D-mannosidase), in serum and urine may be used in the diagnosis of pancreatic cancer.

  10. Carbohydrate-based immune adjuvants

    PubMed Central

    Petrovsky, Nikolai; Cooper, Peter D

    2011-01-01

    The role for adjuvants in human vaccines has been a matter of vigorous scientific debate, with the field hindered by the fact that for over 80 years, aluminum salts were the only adjuvants approved for human use. To this day, alum-based adjuvants, alone or combined with additional immune activators, remain the only adjuvants approved for use in the USA. This situation has not been helped by the fact that the mechanism of action of most adjuvants has been poorly understood. A relative lack of resources and funding for adjuvant development has only helped to maintain alum’s relative monopoly. To seriously challenge alum’s supremacy a new adjuvant has many major hurdles to overcome, not least being alum’s simplicity, tolerability, safety record and minimal cost. Carbohydrate structures play critical roles in immune system function and carbohydrates also have the virtue of a strong safety and tolerability record. A number of carbohydrate compounds from plant, bacterial, yeast and synthetic sources have emerged as promising vaccine adjuvant candidates. Carbohydrates are readily biodegradable and therefore unlikely to cause problems of long-term tissue deposits seen with alum adjuvants. Above all, the Holy Grail of human adjuvant development is to identify a compound that combines potent vaccine enhancement with maximum tolerability and safety. This has proved to be a tough challenge for many adjuvant contenders. Nevertheless, carbohydrate-based compounds have many favorable properties that could place them in a unique position to challenge alum’s monopoly over human vaccine usage. PMID:21506649

  11. Carbohydrates as enantioinduction components in stereoselective catalysis

    PubMed Central

    Henderson, Alexander S.

    2016-01-01

    Carbohydrate derivatives are readily available chiral molecules, yet they are infrequently employed as enantioinduction components in stereoselective catalysis. In this review, synthetic approaches to carbohydrate-based ligands and catalysts are outlined, along with example applications in enantioselective catalysis. A wide range of carbohydrate-based functionality is covered, and key trends and future opportunities are identified. PMID:27064817

  12. The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens

    PubMed Central

    Chakraborty, Sandeep; Phu, My; de Morais, Tâmara Prado; Nascimento, Rafael; Goulart, Luiz Ricardo; Rao, Basuthkar J.; Asgeirsson, Bjarni; Dandekar, Abhaya M.

    2015-01-01

    The therapeutic potential of α-helical anti-microbial peptides (AH-AMP) to combat pathogens is fast gaining prominence. Based on recently published open access software for characterizing α-helical peptides (PAGAL), we elucidate a search methodology (SCALPEL) that leverages the massive structural data pre-existing in the PDB database to obtain AH-AMPs belonging to the host proteome. We provide in vitro validation of SCALPEL on plant pathogens ( Xylella fastidiosa, Xanthomonas arboricola and Liberibacter crescens) by identifying AH-AMPs that mirror the function and properties of cecropin B, a well-studied AH-AMP. The identified peptides include a linear AH-AMP present within the existing structure of phosphoenolpyruvate carboxylase (PPC20), and an AH-AMP mimicing the properties of the two α-helices of cecropin B from chitinase (CHITI25). The minimum inhibitory concentration of these peptides are comparable to that of cecropin B, while anionic peptides used as control failed to show any inhibitory effect on these pathogens. Substitute therapies in place of conventional chemotherapies using membrane permeabilizing peptides like these might also prove effective to target cancer cells. The use of native structures from the same organism could possibly ensure that administration of such peptides will be better tolerated and not elicit an adverse immune response. We suggest a similar approach to target Ebola epitopes, enumerated using PAGAL recently, by selecting suitable peptides from the human proteome, especially in wake of recent reports of cationic amphiphiles inhibiting virus entry and infection. PMID:26629331

  13. Ectoine and 5-hydroxyectoine accumulation in the halophile Virgibacillus halodenitrificans PDB-F2 in response to salt stress.

    PubMed

    Tao, Ping; Li, Hui; Yu, Yunjiang; Gu, Jidong; Liu, Yongdi

    2016-08-01

    The moderately halophilic bacterium Virgibacillus halodenitrificans PDB-F2 copes with salinity by synthesizing or taking up compatible solutes. The main compatible solutes in this strain were ectoine and hydroxyectoine, as determined by (1)H nuclear magnetic resonance spectroscopy ((1)H-NMR). A high-performance liquid chromatography (HPLC) analysis showed that ectoine was the major solute that was synthesized in response to elevated salinity, while hydroxyectoine was a minor solute. However, the hydroxyectoine/ectoine ratio increased from 0.04 at 3 % NaCl to 0.45 at 15 % NaCl in the late exponential growth phase. A cluster of ectoine biosynthesis genes was identified, including three genes in the order of ectA, ectB, and ectC. The hydroxyectoine biosynthesis gene ectD was not part of the ectABC gene cluster. Reverse transcription-quantitative polymerase chain reactions (RT-qPCR) showed that the expression of the ect genes was salinity dependent. The expression of ectABC reached a maximum at 12 % NaCl, while ectD expression increased up to 15 % NaCl. Ectoine and hydroxyectoine production was growth phase dependent. The hydroxyectoine/ectoine ratio increased from 0.018 in the early exponential phase to 0.11 in the stationary phase at 5 % NaCl. Hydroxyectoine biosynthesis started much later than ectoine biosynthesis after osmotic shock, and the temporal expression of the ect genes differed under these conditions, with the ectABC genes being expressed first, followed by ectD gene. Increased culture salinity triggered ectoine or hydroxyectoine uptake when they were added to the medium. Hydroxyectoine was accumulated preferentially when both ectoine and hydroxyectoine were provided exogenously.

  14. Overall carbohydrate-binding properties of Castanea crenata agglutinin (CCA).

    PubMed

    Nomura, Keiichi; Takahashi, Nobuyuki; Hirose, Masaaki; Nakamura, Sachiko; Yagi, Fumio

    2005-09-05

    The carbohydrate-binding properties of Castanea crenata agglutinin (CCA) were investigated by an enzyme-linked lectin absorbent assay. The binding ability of each carbohydrate was compared using IC(50) values. CCA exhibited mannose/glucose specificity, as observed with many mannose-binding jacalin-related lectins. For oligosaccharides containing glucose, it has been shown that the degree of polymerization and the linkage mode of glucose residues have no effect on CCA-carbohydrate interaction; thus, only the non-reducing end glucose unit in glucooligosaccharides may be involved in the interaction with CCA. Among mannooligosaccharides, CCA strongly recognized alpha-(1-->3)-D-Man-[alpha-D-Man-(1-->6)]-D-Man, which is a core in N-linked carbohydrate chains. By considering the results with glycoproteins, it is likely that CCA binds preferentially to mono- or non-sialylated biantennary carbohydrate chains. We also obtained K(d) values by analysis of the dependency of the IC(50) on CCA concentration, based on the hypothesis that CCA has a single binding site or two equivalent binding sites. The estimated K(d) values for mannose, glucose and alpha-(1-->3)-D-Man-[alpha-D-Man-(1-->6)]-D-Man were 2.39, 7.19 and 0.483 mM, respectively. The relative binding abilities showed good agreement with the relative inhibition intensities. Isothermal calorimetric titration was carried out to directly estimate the dissociation constants of CCA for mannose and for alpha-D-Man-(1-->3)-D-Man. The values were 2.34 mM for mannose and 0.507 mM alpha-D-Man-(1-->3)-D-Man. These results suggest that the relative inhibition intensity represents the ratio of K(d) values and that CCA has a single or two equivalent binding sites.

  15. Streptococcus oralis Neuraminidase Modulates Adherence to Multiple Carbohydrates on Platelets.

    PubMed

    Singh, Anirudh K; Woodiga, Shireen A; Grau, Margaret A; King, Samantha J

    2017-03-01

    Adherence to host surfaces is often mediated by bacterial binding to surface carbohydrates. Although it is widely appreciated that some bacterial species express glycosidases, previous studies have not considered whether bacteria bind to multiple carbohydrates within host glycans as they are modified by bacterial glycosidases. Streptococcus oralis is a leading cause of subacute infective endocarditis. Binding to platelets is a critical step in disease; however, the mechanisms utilized by S. oralis remain largely undefined. Studies revealed that S. oralis, like Streptococcus gordonii and Streptococcus sanguinis, binds platelets via terminal sialic acid. However, unlike those organisms, S. oralis produces a neuraminidase, NanA, which cleaves terminal sialic acid. Further studies revealed that following NanA-dependent removal of terminal sialic acid, S. oralis bound exposed β-1,4-linked galactose. Adherence to both these carbohydrates required Fap1, the S. oralis member of the serine-rich repeat protein (SRRP) family of adhesins. Mutation of a conserved residue required for sialic acid binding by other SRRPs significantly reduced platelet binding, supporting the hypothesis that Fap1 binds this carbohydrate. The mechanism by which Fap1 contributes to β-1,4-linked galactose binding remains to be defined; however, binding may occur via additional domains of unknown function within the nonrepeat region, one of which shares some similarity with a carbohydrate binding module. This study is the first demonstration that an SRRP is required to bind β-1,4-linked galactose and the first time that one of these adhesins has been shown to be required for binding of multiple glycan receptors. Copyright © 2017 American Society for Microbiology.

  16. Streptococcus oralis Neuraminidase Modulates Adherence to Multiple Carbohydrates on Platelets

    PubMed Central

    Singh, Anirudh K.; Woodiga, Shireen A.; Grau, Margaret A.

    2016-01-01

    ABSTRACT Adherence to host surfaces is often mediated by bacterial binding to surface carbohydrates. Although it is widely appreciated that some bacterial species express glycosidases, previous studies have not considered whether bacteria bind to multiple carbohydrates within host glycans as they are modified by bacterial glycosidases. Streptococcus oralis is a leading cause of subacute infective endocarditis. Binding to platelets is a critical step in disease; however, the mechanisms utilized by S. oralis remain largely undefined. Studies revealed that S. oralis, like Streptococcus gordonii and Streptococcus sanguinis, binds platelets via terminal sialic acid. However, unlike those organisms, S. oralis produces a neuraminidase, NanA, which cleaves terminal sialic acid. Further studies revealed that following NanA-dependent removal of terminal sialic acid, S. oralis bound exposed β-1,4-linked galactose. Adherence to both these carbohydrates required Fap1, the S. oralis member of the serine-rich repeat protein (SRRP) family of adhesins. Mutation of a conserved residue required for sialic acid binding by other SRRPs significantly reduced platelet binding, supporting the hypothesis that Fap1 binds this carbohydrate. The mechanism by which Fap1 contributes to β-1,4-linked galactose binding remains to be defined; however, binding may occur via additional domains of unknown function within the nonrepeat region, one of which shares some similarity with a carbohydrate binding module. This study is the first demonstration that an SRRP is required to bind β-1,4-linked galactose and the first time that one of these adhesins has been shown to be required for binding of multiple glycan receptors. PMID:27993975

  17. A development of chimeric VEGFR2 TK inhibitor based on two ligand conformers from PDB: 1Y6A complex--medicinal chemistry consequences of a TKs analysis.

    PubMed

    Lintnerová, Lucia; García-Caballero, Melissa; Gregáň, Fridrich; Melicherčík, Milan; Quesada, Ana R; Dobiaš, Juraj; Lác, Ján; Sališová, Marta; Boháč, Andrej

    2014-01-24

    VEGFR2 is an important mediator of angiogenesis and influences fate of some cancer stem cells. Here we analysed all 34 structures of VEGFR2 TK available from PDB database. From them a complex PDB: 1Y6A has an exceptional AAZ ligand bound to TK in form of two conformers (U- and S-shaped). This observation inspired us to develop three chimeric bispyridyl VEGFR2 inhibitors by combining structural features of both AAZ conformers and/or their relative ligand AAX (PDB: 1Y6B). Our most interesting inhibitor 22SYM has an enzymatic VEGFR2 TK activity (IC50: 15.1 nM) comparable or better to the active compounds from clinical drugs Nexavar and Sutent. 22SYM inhibits growth, migration and tube formation of endothelial cells (EC) and selectively induces EC apoptosis. 22SYM also inhibits in vivo angiogenesis in Zebrafish embryo assay. Additionally to the above results, we proved here that tyrosine kinases in an inactive form possessing Type I inhibitors can adopt both a closed or an opened conformation of kinase A-loop independently on their DFG-out arrangement. We proposed here that an activity of certain Type I inhibitors (e.g. 22SYM-like) in complex with DFG-out TK can be negatively influenced by collisions with a dynamically moving TK A-loop.

  18. Disorders of carbohydrate digestion and absorption.

    PubMed

    Heitlinger, L A; Lebenthal, E

    1988-04-01

    The carbohydrate malabsorptive syndromes are frequently seen by pediatricians. The congenital deficiency states are quite rare, but adult type hypolactasia and lactose intolerance following rotavirus infection are recognized with increasing frequency by primary care physicians. Therapy for these disorders involves identification of the offending carbohydrate, removal of the carbohydrate from the diet, and exclusion of other entities that may result in carbohydrate malabsorption but not respond to its removal from the diet. Prognosis for both the primary and secondary carbohydrate malabsorption syndromes is excellent. Compliance with diets for those pediatric patients who will require lifelong therapy remains problematic.

  19. Hydrothermal carbonization of agricultural residues.

    PubMed

    Oliveira, Ivo; Blöhse, Dennis; Ramke, Hans-Günter

    2013-08-01

    The work presented in this article addresses the application of hydrothermal carbonization (HTC) to produce a solid fuel named HTC-Biochar, whose characteristics are comparable to brown coal. Several batch HTC experiments were performed using agricultural residues (AR) as substrates, commonly treated in farm-based biogas plants in Germany. Different AR were used in different combinations with other biomass residues. The biogas potential from the resulting process water was also determined. The combination of different AR lead to the production of different qualities of HTC-Biochars as well as different mass and energy yields. Using more lignocellulosic residues lead to higher mass and energy yields for the HTC-Biochar produced. Whilst residues rich in carbohydrates of lower molecular weight such as corn silage and dough residues lead to the production of a HTC-Biochar of better quality and more similar to brown coal. Process water achieved a maximum of 16.3 L CH4/kg FM (fresh matter).

  20. Stacking Interactions between Carbohydrate and Protein Quantified by Combination of Theoretical and Experimental Methods

    PubMed Central

    Nečasová, Ivona; Mishra, Sushil Kumar; Komárek, Jan; Koča, Jaroslav

    2012-01-01

    Carbohydrate – receptor interactions are an integral part of biological events. They play an important role in many cellular processes, such as cell-cell adhesion, cell differentiation and in-cell signaling. Carbohydrates can interact with a receptor by using several types of intermolecular interactions. One of the most important is the interaction of a carbohydrate's apolar part with aromatic amino acid residues, known as dispersion interaction or CH/π interaction. In the study presented here, we attempted for the first time to quantify how the CH/π interaction contributes to a more general carbohydrate - protein interaction. We used a combined experimental approach, creating single and double point mutants with high level computational methods, and applied both to Ralstonia solanacearum (RSL) lectin complexes with α-l-Me-fucoside. Experimentally measured binding affinities were compared with computed carbohydrate-aromatic amino acid residue interaction energies. Experimental binding affinities for the RSL wild type, phenylalanine and alanine mutants were −8.5, −7.1 and −4.1 kcal.mol−1, respectively. These affinities agree with the computed dispersion interaction energy between carbohydrate and aromatic amino acid residues for RSL wild type and phenylalanine, with values −8.8, −7.9 kcal.mol−1, excluding the alanine mutant where the interaction energy was −0.9 kcal.mol−1. Molecular dynamics simulations show that discrepancy can be caused by creation of a new hydrogen bond between the α-l-Me-fucoside and RSL. Observed results suggest that in this and similar cases the carbohydrate-receptor interaction can be driven mainly by a dispersion interaction. PMID:23056230

  1. Carbohydrates in peptide and protein design.

    PubMed

    Jensen, Knud J; Brask, Jesper

    2005-01-01

    Monosaccharides and amino acids are fundamental building blocks in the assembly of nature's polymers. They have different structural aspects and, to a significant extent, different functional groups. Oligomerization gives rise to oligosaccharides and peptides, respectively. While carbohydrates and peptides can be found conjoined in nature, e.g., in glycopeptides, the aim of this review is the radical redesign of peptide structures using carbohydrates, particularly monosaccharides and cyclic oligosaccharides, to produce novel peptides, peptidomimetics, and abiotic proteins. These hybrid molecules, chimeras, have properties arising largely from the combination of structural characteristics of carbohydrates with the functional group diversity of peptides. This field includes de novo designed synthetic glycopeptides, sugar (carbohydrate) amino acids, carbohydrate scaffolds for nonpeptidal peptidomimetics of cyclic peptides, cyclodextrin functionalized peptides, and carboproteins, i.e., carbohydrate-based proteinmimetics. These successful applications demonstrate the general utility of carbohydrates in peptide and protein architecture.

  2. RABBIT ANTIBODIES TO STREPTOCOCCAL CARBOHYDRATES

    PubMed Central

    Braun, Dietmar G.; Eichmann, Klaus; Krause, Richard M.

    1969-01-01

    In a search for possible genetic factors which may influence the immune response to the streptococcal carbohydrates, over 100 rabbits have been immunized with streptococcal vaccines, and representative examples of high and low response pairs mated. The concentration of precipitins to the group—specific carbohydrates has been measured in the antisera following primary intravenous immunization with heat-killed streptococcal vaccines, Group A, Group A-variant, and Group C. For the majority of rabbits, the concentration of precipitins varied between 1 and 10 mg/ml of antiserum; while in the minority, it was between 11 and 32 mg/ml. The offspring of rabbits with high antibody levels had a significantly higher concentration of antibody than was seen in the offspring of rabbits of low response parents. Such data suggest that the magnitude of the immune response to these carbohydrate antigens is under some form of genetic control. Not uncommonly in rabbits with hyper-γ-globulinemia following primary immunization, the group-specific precipitins are the predominant component of the γ-globulin. An unusual feature of such components is that they are electrophoretically monodisperse, and possess individual antigenic specificity. In this respect they resemble the myeloma proteins. When a response of this sort is not seen after primary immunization, it may occur after secondary immunization. Therefore, prior exposure to the same or closely related antigen may also have an influence on the occurrence of high concentrations of such uniform antibodies. PMID:5766948

  3. Carbohydrate Nanoparticles for Brain Delivery.

    PubMed

    Lalatsa, A; Barbu, E

    2016-01-01

    Many brain tumors and neurological diseases can greatly benefit from the use of emerging nanotechnologies based on targeted nanomedicines that are able to noninvasively transport highly potent and specific pharmaceuticals across the blood-brain barrier. Carbohydrates have received considerable interest as materials for drug carriers due to their natural origin and inherent biodegradability and biocompatibility, as well as due to their hydrophilic character and ease of chemical modification combined with low cost and the possibility for large-scale manufacturing. This chapter provides an overview of the latest research involving the use of carbohydrate-based nanoparticles for drug delivery to the central nervous system. After reviewing the challenges posed by delivering drugs into the brain, the current state-of-the-art approaches for delivery of actives across the blood-brain barrier, including invasive and noninvasive strategies, are presented. A particular focus has been placed on chitosan polymers as they are among the most promising carbohydrate nanocarriers for the preparation and testing of chitosan-based nanomedicines that led, in preclinical proof-of-concept studies, to enhanced brain drug levels and increased pharmacodynamics responses after intravenous, nasal, and oral administration. While chitosan nanoparticles are to date among the most studied and most promising carriers, approaches based on other polysaccharides such as dextran, pullulan, and cellulose warrant further research in the attempt to advance the existing technologies for overcoming the blood-brain barrier. © 2016 Elsevier Inc. All rights reserved.

  4. Preliminary results of sugar maple carbohydrate and growth response under vacuum and gravity sap extraction

    Treesearch

    Mark L. Isselhardt; Timothy D. Perkins; Abby K. van den Berg; Paul G. Schaberg

    2016-01-01

    Recent technological advancements have increased the amount of sugar-enriched sap that can be extracted from sugar maple (Acer saccharum). This pilot study quantified overall sugar removal and the impacts of vacuum (60 cm Hg) and gravity sap extraction on residual nonstructural carbohydrate (NSC) concentrations and on stem and twig growth. Vacuum...

  5. Electrocatalysis in proteins, nucleic acids and carbohydrates.

    PubMed

    Paleček, Emil; Bartošík, Martin; Ostatná, Veronika; Trefulka, Mojmír

    2012-02-01

    The ability of proteins to catalyze hydrogen evolution has been known for more than 80 years, but the poorly developed d.c. polarographic "pre-sodium wave" was of little analytical use. Recently, we have shown that by using constant current chronopotentiometric stripping analysis, proteins produce a well-developed peak H at hanging mercury drop and solid amalgam electrodes. Peak H sensitively reflects changes in protein structures due to protein denaturation, single amino acid exchange, etc. at the picomole level. Unmodified DNA and RNA do not yield such a peak, but they produce electrocatalytic voltammetric signals after modification with osmium tetroxide complexes with nitrogen ligands [Os(VIII)L], binding covalently to pyrimidine bases in nucleic acids. Recently, it has been shown that six-valent [Os(VI)L] complexes bind to 1,2-diols in polysaccharides and oligosaccharides, producing voltammetric responses similar to those of DNA-Os(VIII)L adducts. Electrocatalytic peaks produced by Os-modified nucleic acids, proteins (reaction with tryptophan residues) and carbohydrates are due to the catalytic hydrogen evolution, allowing determination of oligomers at the picomolar level.

  6. Peptide mimotopes of Mycobacterium tuberculosis carbohydrate immunodeterminants

    PubMed Central

    2004-01-01

    Cell-surface saccharides of Mycobacterium tuberculosis appear to be crucial factors in tuberculosis pathogenicity and could be useful antigens in tuberculosis immunodiagnosis. In the present study, we report the successful antigenic and immunogenic mimicry of mannose-containing cell-wall compounds of M. tuberculosis by dodecamer peptides identified by phage-display technology. Using a rabbit antiserum raised against M. tuberculosis cell-surface saccharides as a target for biopanning, peptides with three different consensus sequences were identified. Phage-displayed and chemically synthesized peptides bound to the anticarbohydrate antiserum. Rabbit antibodies elicited against the peptide QEPLMGTVPIRAGGGS recognize the mannosylated M. tuberculosis cell-wall antigens arabinomannan and lipoarabinomannan, and the glycosylated recombinant protein alanine/proline-rich antigen. Furthermore, antibodies were also able to react with mannan from Saccharomyces cerevisiae, but not with phosphatidylinositol dimannosides or arabinogalactan from mycobacteria. These results suggest that the immunogenic peptide mimics oligomannosidic epitopes. Interestingly, this report provides evidence that, in contrast with previously known carbohydrate mimotopes, no aromatic residues are necessary in a peptide sequence for mimicking unusual glycoconjugates synthesized by mycobacteria. The possible usefulness of the identified peptide mimotopes as surrogate reagents for immunodiagnosis and for the study of functional roles of the native non-peptide epitopes is discussed. PMID:15560754

  7. Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms.

    PubMed

    Tsai, Keng-Chang; Jian, Jhih-Wei; Yang, Ei-Wen; Hsu, Po-Chiang; Peng, Hung-Pin; Chen, Ching-Tai; Chen, Jun-Bo; Chang, Jeng-Yih; Hsu, Wen-Lian; Yang, An-Suei

    2012-01-01

    Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins; information on key carbohydrate-binding residues could suggest site-directed mutagenesis experiments, design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novel encoding scheme of the three-dimensional probability density maps describing the distributions of 36 non-covalent interacting atom types around protein surfaces. One machine learning model was trained for each of the 30 protein atom types. The machine learning algorithms predicted tentative carbohydrate binding sites on query proteins by recognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures. The prediction results for all protein atom types were integrated into surface patches as tentative carbohydrate binding sites based on normalized prediction confidence level. The prediction capabilities of the predictors were benchmarked by a 10-fold cross validation on 497 non-redundant proteins with known carbohydrate binding sites. The predictors were further tested on an independent test set with 108 proteins. The residue-based Matthews correlation coefficient (MCC) for the independent test was 0.45, with prediction precision and sensitivity (or recall) of 0.45 and 0.49 respectively. In addition, 111 unbound carbohydrate-binding protein structures for which the structures were determined in the absence of the carbohydrate ligands were predicted with the trained predictors. The overall

  8. Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms

    PubMed Central

    Tsai, Keng-Chang; Jian, Jhih-Wei; Yang, Ei-Wen; Hsu, Po-Chiang; Peng, Hung-Pin; Chen, Ching-Tai; Chen, Jun-Bo; Chang, Jeng-Yih; Hsu, Wen-Lian; Yang, An-Suei

    2012-01-01

    Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins; information on key carbohydrate-binding residues could suggest site-directed mutagenesis experiments, design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novel encoding scheme of the three-dimensional probability density maps describing the distributions of 36 non-covalent interacting atom types around protein surfaces. One machine learning model was trained for each of the 30 protein atom types. The machine learning algorithms predicted tentative carbohydrate binding sites on query proteins by recognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures. The prediction results for all protein atom types were integrated into surface patches as tentative carbohydrate binding sites based on normalized prediction confidence level. The prediction capabilities of the predictors were benchmarked by a 10-fold cross validation on 497 non-redundant proteins with known carbohydrate binding sites. The predictors were further tested on an independent test set with 108 proteins. The residue-based Matthews correlation coefficient (MCC) for the independent test was 0.45, with prediction precision and sensitivity (or recall) of 0.45 and 0.49 respectively. In addition, 111 unbound carbohydrate-binding protein structures for which the structures were determined in the absence of the carbohydrate ligands were predicted with the trained predictors. The overall

  9. A systematic study of chemogenomics of carbohydrates.

    PubMed

    Gu, Jiangyong; Luo, Fang; Chen, Lirong; Yuan, Gu; Xu, Xiaojie

    2014-03-04

    Chemogenomics focuses on the interactions between biologically active molecules and protein targets for drug discovery. Carbohydrates are the most abundant compounds in natural products. Compared with other drugs, the carbohydrate drugs show weaker side effects. Searching for multi-target carbohydrate drugs can be regarded as a solution to improve therapeutic efficacy and safety. In this work, we collected 60 344 carbohydrates from the Universal Natural Products Database (UNPD) and explored the chemical space of carbohydrates by principal component analysis. We found that there is a large quantity of potential lead compounds among carbohydrates. Then we explored the potential of carbohydrates in drug discovery by using a network-based multi-target computational approach. All carbohydrates were docked to 2389 target proteins. The most potential carbohydrates for drug discovery and their indications were predicted based on a docking score-weighted prediction model. We also explored the interactions between carbohydrates and target proteins to find the pathological networks, potential drug candidates and new indications.

  10. Structural consequences of chromophore formation and exploration of conserved lid residues amongst naturally occurring fluorescent proteins

    NASA Astrophysics Data System (ADS)

    Zimmer, Matthew H.; Li, Binsen; Shahid, Ramza; Peshkepija, Paola; Zimmer, Marc

    2014-01-01

    Computational methods were used to generate the lowest energy conformations of the immature precyclized forms of the 28 naturally occurring GFP-like proteins deposited in the pdb. In all 28 GFP-like proteins, the beta-barrel contracts upon chromophore formation and becomes more rigid. Our prior analysis of over 260 distinct naturally occurring GFP-like proteins revealed that most of the conserved residues are located in the top and bottom of the barrel in the turns between the β-sheets (Ong et al. 2011) [1]. Structural analyses, molecular dynamics simulations and the Anisotropic Network Model were used to explore the role of these conserved lid residues as possible folding nuclei. Our results are internally consistent and show that the conserved residues in the top and bottom lids undergo relatively less translational movement than other lid residues, and a number of these residues may play an important role as hinges or folding nuclei in the fluorescent proteins.

  11. Carbohydrates

    MedlinePlus

    ... peas, and garbanzo beans Starchy vegetables, such as potatoes, corn, green peas, and parsnips Whole grains, such ... your daily fruit servings from whole fruits. Limit sweets, sugar-sweetened beverages, and alcohol. Limit added sugars ...

  12. Carbohydrates

    MedlinePlus

    ... found in certain vegetables, such as potatoes, beans, peas, and corn. They are also found in breads, ... Foods high in fiber include fruits, vegetables, beans, peas, nuts, seeds, and whole-grain foods (such as ...

  13. Reuteran and levan as carbohydrate sinks in transgenic sugarcane.

    PubMed

    Bauer, Rolene; Basson, Carin E; Bekker, Jan; Eduardo, Iban; Rohwer, Johann M; Uys, Lafras; van Wyk, Johannes H; Kossmann, Jens

    2012-12-01

    The present study reports the effect of high molecular weight bacterial fructan (levan) and glucan (reuteran) on growth and carbohydrate partitioning in transgenic sugarcane plants. These biopolymers are products of bacterial glycosyltransferases, enzymes that catalyze the polymerization of glucose or fructose residues from sucrose. Constructs, targeted to different subcellular compartments (cell wall and cytosol) and driven by the Cauliflower mosaic virus-35S: maize-ubiquitin promoter, were introduced into sugarcane by biolistic transformation. Polysaccharide accumulation severely affected growth of callus suspension cultures. Regeneration of embryonic callus tissue into plants proved problematic for cell wall-targeted lines. When targeted to the cytosol, only plants with relative low levels of biopolymer accumulation survived. In internodal stalk tissue that accumulate reuteran (max 0.03 mg/g FW), sucrose content (ca 60 mg/g FW) was not affected, while starch content (<0.4 mg/g FW) was increased up to four times. Total carbohydrate content was not significantly altered. On the other hand, starch and sucrose levels were significantly reduced in plants accumulating levan (max 0.01 mg/g FW). Heterologous expression resulted in a reduction in total carbohydrate assimilation rather than a simple diversion by competition for substrate.

  14. Surface characterization of carbohydrate microarrays.

    PubMed

    Scurr, David J; Horlacher, Tim; Oberli, Matthias A; Werz, Daniel B; Kroeck, Lenz; Bufali, Simone; Seeberger, Peter H; Shard, Alexander G; Alexander, Morgan R

    2010-11-16

    Carbohydrate microarrays are essential tools to determine the biological function of glycans. Here, we analyze a glycan array by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to gain a better understanding of the physicochemical properties of the individual spots and to improve carbohydrate microarray quality. The carbohydrate microarray is prepared by piezo printing of thiol-terminated sugars onto a maleimide functionalized glass slide. The hyperspectral ToF-SIMS imaging data are analyzed by multivariate curve resolution (MCR) to discern secondary ions from regions of the array containing saccharide, linker, salts from the printing buffer, and the background linker chemistry. Analysis of secondary ions from the linker common to all of the sugar molecules employed reveals a relatively uniform distribution of the sugars within the spots formed from solutions with saccharide concentration of 0.4 mM and less, whereas a doughnut shape is often formed at higher-concentration solutions. A detailed analysis of individual spots reveals that in the larger spots the phosphate buffered saline (PBS) salts are heterogeneously distributed, apparently resulting in saccharide concentrated at the rim of the spots. A model of spot formation from the evaporating sessile drop is proposed to explain these observations. Saccharide spot diameters increase with saccharide concentration due to a reduction in surface tension of the saccharide solution compared to PBS. The multivariate analytical partial least squares (PLS) technique identifies ions from the sugars that in the complex ToF-SIMS spectra correlate with the binding of galectin proteins.

  15. [Carbohydrates synthesized by the spirulines].

    PubMed

    Quillet, M

    1975-01-01

    Carbohydrates roughly constitute 15 p. 100 of the dry matter of Sirulina. They are extracted after complete delipidation, by successive exhaustions: first with ethanol of decreasing title, then with cold water slightly acidified by chlorhydric acid in order to drain out the calcium of the phytate; then by neutral boiling water; at last by alkaline or acidic warm solutions. After neutralization, suitable defecation and concentration, carbohydrates are either purified by a slow cristalization or hydrolyzed and analysed by usual techniques of chromatography on paper or on column of borated resins. Glucose, levulose, sucrose, glycerol and several polyols are so detected. They are in small amounts and of little nutritional interest. There is no trehalose. The carbohydrate storage products are mainly a glucosan and a rhamnosan, both containing glucosamine. There is about 2 p. 100 of the glucosan and 10 p. 100 of the rhamnosan, the composition of which are, in molar ratio: (see text). More or less phosphated cyclitols constitute, together with a small amount of glycogen, the rest of the metabolisable part. The cell-walls which could not be perfectly purified were degraded either by HC1 or by enzymes (pronase, neuraminidase). So have been found glucosamine and muramic acid, associated with peptides rich in glycine, serine, alanine, glutamic acid. These results joined to the presence, formerly signaled, of a rhamnosan, reveal a relationship between Spirulina and some Gram(+) bacteria. It is a fact that the celle-walls of Spirulina actually, though weakly, take the Gram coloration. To conclude, Spirulina presents some alimental interest.

  16. Benefits and hazards of dietary carbohydrate.

    PubMed

    Connor, William E; Duell, P Barton; Connor, Sonja L

    2005-11-01

    Since the dawn of civilization, carbohydrate has comprised the largest source of energy in the diet for most populations. The source of the carbohydrate has been from plants in the form of complex carbohydrate high in fiber. Only in affluent cultures has sugar contributed so much of the total energy. When carbohydrate is consumed as a major component of a plant-based diet, a high-carbohydrate, low-fat diet is associated with low plasma levels of total and low-density lipoprotein cholesterol, less coronary heart disease, less diabetes, and less obesity. Very low-carbohydrate (ketogenic) diets may provide short-term solutions but do not lead to a long-term solution for most people.

  17. Applications of synthetic carbohydrates to chemical biology.

    PubMed

    Lepenies, Bernd; Yin, Jian; Seeberger, Peter H

    2010-06-01

    Access to synthetic carbohydrates is an urgent need for the development of carbohydrate-based drugs, vaccines, adjuvants as well as novel drug delivery systems. Besides traditional synthesis in solution, synthetic carbohydrates have been generated by chemoenzymatic methods as well as automated solid-phase synthesis. Synthetic oligosaccharides have proven to be useful for identifying ligands of carbohydrate-binding proteins such as C-type lectins and siglecs using glycan arrays. Furthermore, glyconanoparticles and glycodendrimers have been used for specific targeting of lectins of the immune system such as selectins, DC-SIGN, and CD22. This review focuses on how diverse carbohydrate structures can be synthetically derived and highlights the benefit of synthetic carbohydrates for glycobiology.

  18. New fabrication and applications of carbohydrate arrays.

    PubMed

    Huang, Gangliang; Chen, Xin; Xiao, Feng

    2014-01-01

    Carbohydrate arrays are used as high-throughput screening platforms to study the carbohydrate-mediated recognition events for glycobiology. The polysaccharide arrays are easy to fabricate by non-covalently or covalently immobilizing polysaccharides onto array surfaces because polysaccharides have hydrophobic interactions. Oligosaccharides must be derived and covalently or non-covalently immobilized onto array surfaces to fabricate oligosaccharide arrays because they have hydrophilic interactions. At the moment, carbohydrate arrays are mainly used to study the carbohydrate-protein interactions and carbohydrate-binding lectins or antibodies, which are possible to be applied to clinics and diagnoses. This review mainly summed up the new fabrication strategies of carbohydrate arrays and their applications in recent four years.

  19. Dietary Plans for Carbohydrate Loading

    DTIC Science & Technology

    1989-11-01

    NUTS - CASHEWS -OIL ROASTED 6.00 TBSPS 48.8 GMS Nutrient Values Kcalories 4071 Kcal Carbohydrate 574.3 Gm Protein 168.1 Gm Fat 125.4 Gm Protein: 16...ENR 2.00 ITEMS 28.00 Gm (5%) ORANGE JUICE-CAN 1.00 CUP 24.50 Gm (4%) SOUP-VEGETABLE-CAN-LOW SOD 1.50 CUPS 21.60 Gm (4%) NUTS - CASHEWS -OIL ROASTED 6.00...LOW SOD 8 POUNDS 4 KILOS Beverages FRUIT PUNCH DRINK-CAN 5 POUNDS 2 KILOS (3 QUARTS) Nuts & Seeds NUTS - CASHEWS -OIL ROASTED 1 POUND 488 GRAMS Fats & Oils

  20. ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.

    PubMed

    Sehnal, David; Svobodová Vařeková, Radka; Pravda, Lukáš; Ionescu, Crina-Maria; Geidl, Stanislav; Horský, Vladimír; Jaiswal, Deepti; Wimmerová, Michaela; Koča, Jaroslav

    2015-01-01

    Following the discovery of serious errors in the structure of biomacromolecules, structure validation has become a key topic of research, especially for ligands and non-standard residues. ValidatorDB (freely available at http://ncbr.muni.cz/ValidatorDB) offers a new step in this direction, in the form of a database of validation results for all ligands and non-standard residues from the Protein Data Bank (all molecules with seven or more heavy atoms). Model molecules from the wwPDB Chemical Component Dictionary are used as reference during validation. ValidatorDB covers the main aspects of validation of annotation, and additionally introduces several useful validation analyses. The most significant is the classification of chirality errors, allowing the user to distinguish between serious issues and minor inconsistencies. Other such analyses are able to report, for example, completely erroneous ligands, alternate conformations or complete identity with the model molecules. All results are systematically classified into categories, and statistical evaluations are performed. In addition to detailed validation reports for each molecule, ValidatorDB provides summaries of the validation results for the entire PDB, for sets of molecules sharing the same annotation (three-letter code) or the same PDB entry, and for user-defined selections of annotations or PDB entries. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Regioselective azidotrimethylsilylation of carbohydrates and applications thereof.

    PubMed

    L, Mallikharjuna Rao; Yousuf, Syed Khalid; Mukherjee, Debaraj; Taneja, Subhash Chandra

    2012-12-07

    Azidotrimethylsilylation of carbohydrates (monosaccharides and disaccharides) has been achieved in high yields under Mitsunobu conditions. The azidation of carbohydrates is effected at 0 °C essentially only at the primary alcoholic position in mono, di- and triols in protected/unprotected glycosides, whereas the remaining secondary hydroxyl groups got silylated. Surprisingly, no azidation of the secondary hydroxyls was observed in all the carbohydrate substrates. Applications of the methodology for the synthesis of amino sugars, triazoles and azasugars are reported.

  2. Digestion of carbohydrates in the pig.

    PubMed

    Drochner, W

    1993-01-01

    A review of carbohydrate digestion in the pig is given. The cascade of digestion in the mouth, stomach, small and large intestine is described. Principles of enzymatic and fermentative digestion according to new results with fistulated animals are discussed. The efficacy and quality of fermentation in the large intestine depending on level and quality of carbohydrates in the diet are demonstrated. Some aspects of energetical efficacy of hindgut digestion are discussed. Dietetic effects of carbohydrates are described.

  3. LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria.

    PubMed

    González-Díaz, Humberto; Munteanu, Cristian R; Postelnicu, Lucian; Prado-Prado, Francisco; Gestal, Marcos; Pazos, Alejandro

    2012-03-01

    Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense.

  4. Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii

    DOE PAGES

    Zurawski, Jeffrey V.; Khatibi, Piyum A.; Akinosho, Hannah O.; ...

    2017-06-16

    Improving access to the carbohydrate content of lignocellulose is key to reducing recalcitrance for microbial deconstruction and conversion to fuels and chemicals. Caldicellulosiruptor bescii completely solubilizes naked microcrystalline cellulose, yet this transformation is impeded within the context of the plant cell wall by a network of lignin and hemicellulose. Here, the bioavailability of carbohydrates toC. bescii at 70°C was examined for reduced lignin transgenic switchgrass lines COMT3(+) and MYB Trans, their corresponding parental lines (cultivar Alamo) COMT3(–) and MYB wild type (WT), and the natural variant cultivar Cave-in-Rock (CR). Transgenic modification improved carbohydrate solubilization by C. bescii to 15%more » (2.3-fold) for MYB and to 36% (1.5-fold) for COMT, comparable to the levels achieved for the natural variant, CR (36%). Carbohydrate solubilization was nearly doubled after two consecutive microbial fermentations compared to one microbial step, but it never exceeded 50% overall. Hydrothermal treatment (180°C) prior to microbial steps improved solubilization 3.7-fold for the most recalcitrant line (MYB WT) and increased carbohydrate recovery to nearly 50% for the least recalcitrant lines [COMT3(+) and CR]. Alternating microbial and hydrothermal steps (T→M→T→M) further increased bioavailability, achieving carbohydrate solubilization ranging from 50% for MYB WT to above 70% for COMT3(+) and CR. Incomplete carbohydrate solubilization suggests that cellulose in the highly lignified residue was inaccessible; indeed, residue from the T→M→T→M treatment was primarily glucan and inert materials (lignin and ash). While C. bescii could significantly solubilize the transgenic switchgrass lines and natural variant tested here, additional or alternative strategies (physical, chemical, enzymatic, and/or genetic) are needed to eliminate recalcitrance.« less

  5. Ligand-mediated dimerization of a carbohydrate-binding molecule reveals a novel mechanism for protein-carbohydrate recognition.

    PubMed

    Flint, James; Nurizzo, Didier; Harding, Stephen E; Longman, Emma; Davies, Gideon J; Gilbert, Harry J; Bolam, David N

    2004-03-19

    The structural and thermodynamic basis for carbohydrate-protein recognition is of considerable importance. NCP-1, which is a component of the Piromyces equi cellulase/hemicellulase complex, presents a provocative model for analyzing how structural and mutational changes can influence the ligand specificity of carbohydrate-binding proteins. NCP-1 contains two "family 29" carbohydrate-binding modules designated CBM29-1 and CBM29-2, respectively, that display unusually broad specificity; the proteins interact weakly with xylan, exhibit moderate affinity for cellulose and mannan, and bind tightly to the beta-1,4-linked glucose-mannose heteropolymer glucomannan. The crystal structure of CBM29-2 in complex with cellohexaose and mannohexaose identified key residues involved in ligand recognition. By exploiting this structural information and the broad specificity of CBM29-2, we have used this protein as a template to explore the evolutionary mechanisms that can lead to significant changes in ligand specificity. Here, we report the properties of the E78R mutant of CBM29-2, which displays ligand specificity that is different from that of wild-type CBM29-2; the protein retains significant affinity for cellulose but does not bind to mannan or glucomannan. Significantly, E78R exhibits a stoichiometry of 0.5 when binding to cellohexaose, and both calorimetry and ultracentrifugation show that the mutant protein displays ligand-mediated dimerization in solution. The three-dimensional structure of E78R in complex with cellohexaose reveals the intriguing molecular basis for this "dimeric" binding mode that involves the lamination of the oligosaccharide between two CBM molecules. The 2-fold screw axis of the ligand is mirrored in the orientation of the two protein domains with adjacent sugar rings stacking against the equivalent aromatic residues in the binding site of each protein molecule of the molecular sandwich. The sandwiching of an oligosaccharide chain between two protein

  6. Advances in Food Composition Tables of Japan--Amino Acid, Fatty Acid and Available Carbohydrate Tables.

    PubMed

    Yasui, Takeshi

    2015-01-01

    The new revised version of the Standard Tables of Food Composition in Japan (STFCJ 2015) will be published in 2015. The aim of the present paper is to share information on issues we have encountered during the revision. New analytical data on amino acid composition will be provided for approximately 230 foods, fatty acid composition for approximately 140 foods, and available carbohydrate (starch, glucose, fructose, sucrose, maltose, and lactose) composition for approximately 340 foods. These data will be published separately as three supplements to the STFCJ 2015: amino acid tables, fatty acid tables, and available carbohydrate tables. Available carbohydrate tables will also provide polyol (sorbitol and mannitol) and organic acid (acetic acid, lactic acid, citric acid, etc.) data. In the supplements, amino acid content will be adjusted for protein content calculated as reference nitrogen multiplied by a nitrogen to protein conversion factor, and fatty acid content adjusted for extractable lipid content, as in previous revisions. Available carbohydrate content, however, will be adjusted for water content. Values of protein content calculated as the sum of amino acid residues , lipid content expressed as triacylglycerol equivalents of fatty acids , and available carbohydrate content will appear in the main tables of the STFCJ 2015. Protein, fat and available carbohydrate contents were significantly decreased when the preferred analytical methods of FAO were applied instead of the acceptable methods. Online publication of Japanese and English versions of these tables, reference materials, and a retrievable food composition database is planned.

  7. Dietary Carbohydrate, Glycemic Index, Glycemic Load, and Breast Cancer Risk Among Mexican Women.

    PubMed

    Amadou, Amina; Degoul, Julie; Hainaut, Pierre; Chajes, Veronique; Biessy, Carine; Torres Mejia, Gabriela; Huybrechts, Inge; Moreno Macia, Hortensia; Ortega, Caro; Angeles-Llerenas, Anjélica; Romieu, Isabelle

    2015-11-01

    Very few studies have focused on the relationship among dietary carbohydrates, glycemic index (GI), glycemic load (GL), and breast cancer risk in Latin American women. Our objective was to assess the associations among dietary carbohydrate, GI, GL, and risk of breast cancer, and to further investigate these associations by levels of overweight/obesity and physical activity. We used data from a Mexican population-based case-control study. We recruited a 1,000 women with incident breast cancer and 1,074 matched control women ages 35 to 69 years between 2004 and 2007. We used conditional logistic regression models and energy-adjusted carbohydrates, GI, and GL using the residual method. Total carbohydrate intake was associated with an increased risk of breast cancer among premenopausal women. The odds ratio in the highest versus the lowest quartile was 1.3 (95% confidence interval = 1.0, 1.7; P trend = 0.03). In stratified analyses by body mass index (BMI), the positive association between carbohydrate and risk of premenopausal breast cancer was only observed among overweight women. The odds ratio comparing the top with the bottom quartile was 1.9 (95% confidence interval = 1.2, 3.0; P trend = 0.01) among women with BMI ≥ 25 kg/m. No association was observed among women with BMI < 25 kg/m. Our findings suggest that high carbohydrate diets are associated with an increased risk of breast cancer among premenopausal Mexican women.

  8. Regioselective monodeprotection of peracetylated carbohydrates.

    PubMed

    Filice, Marco; Guisan, Jose M; Terreni, Marco; Palomo, Jose M

    2012-10-01

    This protocol describes the regioselective deprotection of single hydroxyls in peracetylated monosaccharides and disaccharides by enzymatic or chemoenzymatic strategies. The introduction of a one-pot enzymatic step by using immobilized biocatalysts obviates the requirement to carry out tedious workups and time-consuming purifications. By using this straightforward protocol, different per-O-acetylated glycopyranosides (mono- or disaccharides, 1-substituted or glycals) can be transformed into a whole set of differentially monodeprotected 1-alcohols, 3-alcohols, 4-alcohols and 6-alcohols in high yields. These tailor-made glycosyl acceptors can then be used for stereoselective glycosylation for oligosaccharide and glycoderivative synthesis. They have been successfully used as building blocks to synthesize tailor-made di- and trisaccharides involved in the structure of lacto-N-neo-tetraose and precursors of the tumor-associated carbohydrate antigen T and the antitumoral drug peracetylated β-naphtyl-lactosamine. We are able to prepare a purified monoprotected carbohydrate in between 1 and 4 d. With this protocol, the small library of monodeprotected products can be synthesized in 1-2 weeks.

  9. Off-line elimination of carbohydrates for amino acid analysis of samples with high carbohydrate content by ion-exchange chromatography.

    PubMed

    Ding, Yongsheng; Yu, Hong; Mou, Shifen

    2003-05-16

    This paper introduces a new off-line sample preparation that eliminates carbohydrates from amino acid samples containing a high carbohydrate content before analysis by anion-exchange chromatography and integrated pulsed amperometric detection. First, the sample is introduced into a cation-exchange column in the hydrogen form. Carbohydrates are removed completely using 0.02% formic acid as a transfer fluid, while only amino acids are retained. Amino acids are then extracted from the cation-exchange resin by 10 ml of 1 M ammonia. The ammonia collected is evaporated to dryness and the residue redissolved in water containing 20 mg/l NaN3 for injection. All amino acids are recovered following the carbohydrate removal step. The average recovery is 97.2%. The relative standard deviation for seven replicates is less than 5.2%. The usefulness of the method is illustrated with chromatograms of ratafia samples obtained before and after the off-line removal of carbohydrates.

  10. Carbohydrates and fat for training and recovery.

    PubMed

    Burke, Louise M; Kiens, Bente; Ivy, John L

    2004-01-01

    An important goal of the athlete's everyday diet is to provide the muscle with substrates to fuel the training programme that will achieve optimal adaptation for performance enhancements. In reviewing the scientific literature on post-exercise glycogen storage since 1991, the following guidelines for the training diet are proposed. Athletes should aim to achieve carbohydrate intakes to meet the fuel requirements of their training programme and to optimize restoration of muscle glycogen stores between workouts. General recommendations can be provided, preferably in terms of grams of carbohydrate per kilogram of the athlete's body mass, but should be fine-tuned with individual consideration of total energy needs, specific training needs and feedback from training performance. It is valuable to choose nutrient-rich carbohydrate foods and to add other foods to recovery meals and snacks to provide a good source of protein and other nutrients. These nutrients may assist in other recovery processes and, in the case of protein, may promote additional glycogen recovery when carbohydrate intake is suboptimal or when frequent snacking is not possible. When the period between exercise sessions is < 8 h, the athlete should begin carbohydrate intake as soon as practical after the first workout to maximize the effective recovery time between sessions. There may be some advantages in meeting carbohydrate intake targets as a series of snacks during the early recovery phase, but during longer recovery periods (24 h) the athlete should organize the pattern and timing of carbohydrate-rich meals and snacks according to what is practical and comfortable for their individual situation. Carbohydrate-rich foods with a moderate to high glycaemic index provide a readily available source of carbohydrate for muscle glycogen synthesis, and should be the major carbohydrate choices in recovery meals. Although there is new interest in the recovery of intramuscular triglyceride stores between

  11. RESIDUAL RISK ASSESSMENTS - RESIDUAL RISK ...

    EPA Pesticide Factsheets

    This source category previously subjected to a technology-based standard will be examined to determine if health or ecological risks are significant enough to warrant further regulation for Coke Ovens. These assesments utilize existing models and data bases to examine the multi-media and multi-pollutant impacts of air toxics emissions on human health and the environment. Details on the assessment process and methodologies can be found in EPA's Residual Risk Report to Congress issued in March of 1999 (see web site). To assess the health risks imposed by air toxics emissions from Coke Ovens to determine if control technology standards previously established are adequately protecting public health.

  12. C-type lectin-like carbohydrate recognition of the hemolytic lectin CEL-III containing ricin-type -trefoil folds.

    PubMed

    Hatakeyama, Tomomitsu; Unno, Hideaki; Kouzuma, Yoshiaki; Uchida, Tatsuya; Eto, Seiichiro; Hidemura, Haruki; Kato, Norihisa; Yonekura, Masami; Kusunoki, Masami

    2007-12-28

    CEL-III is a Ca(2+)-dependent hemolytic lectin, isolated from the marine invertebrate Cucumaria echinata. The three-dimensional structure of CEL-III/GalNAc and CEL-III/methyl alpha-galactoside complexes was solved by x-ray crystallographic analysis. In these complexes, five carbohydrate molecules were found to be bound to two carbohydrate-binding domains (domains 1 and 2) located in the N-terminal 2/3 portion of the polypeptide and that contained beta-trefoil folds similar to ricin B-chain. The 3-OH and 4-OH of bound carbohydrate molecules were coordinated with Ca(2+) located at the subdomains 1alpha, 1gamma, 2alpha, 2beta, and 2gamma, simultaneously forming hydrogen bond networks with nearby amino acid side chains, which is similar to carbohydrate binding in C-type lectins. The binding of carbohydrates was further stabilized by aromatic amino acid residues, such as tyrosine and tryptophan, through a stacking interaction with the hydrophobic face of carbohydrates. The importance of amino acid residues in the carbohydrate-binding sites was confirmed by the mutational analyses. The orientation of bound GalNAc and methyl alpha-galactoside was similar to the galactose moiety of lactose bound to the carbohydrate-binding site of the ricin B-chain, although the ricin B-chain does not require Ca(2+) ions for carbohydrate binding. The binding of the carbohydrates induced local structural changes in carbohydrate-binding sites in subdomains 2alpha and 2beta. Binding of GalNAc also induced a slight change in the main chain structure of domain 3, which could be related to the conformational change upon binding of specific carbohydrates to induce oligomerization of the protein.

  13. Biochemical suitability of crop residues for cellulosic ethanol: disincentives to nitrogen fertilization in corn agriculture.

    PubMed

    Gallagher, Morgan E; Hockaday, William C; Masiello, Caroline A; Snapp, Sieglinde; McSwiney, Claire P; Baldock, Jeffrey A

    2011-03-01

    Concerns about energy security and climate change have increased biofuel demand, particularly ethanol produced from cellulosic feedstocks (e.g., food crop residues). A central challenge to cropping for cellulosic ethanol is the potential environmental damage from increased fertilizer use. Previous analyses have assumed that cropping for carbohydrate in residue will require the same amount of fertilizer as cropping for grain. Using (13)C nuclear magnetic resonance, we show that increases in biomass in response to fertilization are not uniform across biochemical classes (carbohydrate, protein, lipid, lignin) or tissues (leaf and stem, grain, reproductive support). Although corn grain responds vigorously and nonlinearly, corn residue shows only modest increases in carbohydrate yields in response to high levels of fertilization (25% increase with 202 kg N ha(-1)). Lignin yields in the residue increased almost twice as much as carbohydrate yields in response to nitrogen, implying that residue feedstock quality declines as more fertilizer is applied. Fertilization also increases the decomposability of corn residue, implying that soil carbon sequestration becomes less efficient with increased fertilizer. Our results suggest that even when corn is grown for grain, benefits of fertilization decline rapidly after the ecosystem's N demands are met. Heavy application of fertilizer yields minimal grain benefits and almost no benefits in residue carbohydrates, while degrading the cellulosic ethanol feedstock quality and soil carbon sequestration capacity.

  14. Residual Cap

    NASA Technical Reports Server (NTRS)

    2006-01-01

    10 May 2006 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a summertime view of the south polar residual cap of Mars. In this image, mesas composed largely of solid carbon dioxide are separated from one another by irregularly-shaped depressions. The variation in brightness across this scene is a function of several factors including, but not limited to, varying proportions of dust and solid carbon dioxide, undulating topography, and differences in the roughness of the slopes versus the flat surfaces.

    Location near: 86.7oS, 343.3oW Image width: 3 km (1.9 mi) Illumination from: upper left Season: Southern Summer

  15. Determining a carbohydrate profile for Hansenula polymorpha

    NASA Technical Reports Server (NTRS)

    Petersen, G. R.

    1985-01-01

    The determination of the levels of carbohydrates in the yeast Hansenula polymorpha required the development of new analytical procedures. Existing fractionation and analytical methods were adapted to deal with the problems involved with the lysis of whole cells. Using these new procedures, the complete carbohydrate profiles of H. polymorpha and selected mutant strains were determined and shown to correlate favourably with previously published results.

  16. Determining a carbohydrate profile for Hansenula polymorpha

    NASA Technical Reports Server (NTRS)

    Petersen, G. R.

    1985-01-01

    The determination of the levels of carbohydrates in the yeast Hansenula polymorpha required the development of new analytical procedures. Existing fractionation and analytical methods were adapted to deal with the problems involved with the lysis of whole cells. Using these new procedures, the complete carbohydrate profiles of H. polymorpha and selected mutant strains were determined and shown to correlate favourably with previously published results.

  17. Vacuum ultraviolet photoionization of carbohydrates and nucleotides

    SciTech Connect

    Shin, Joong-Won; Bernstein, Elliot R.

    2014-01-28

    Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5{sup ′}-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C–C and C–O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.

  18. Carbohydrates from Detarium microcarpum bark extract.

    PubMed

    Abreu, Pedro; Relva, Angela

    2002-10-08

    The bark extract of the medicinal plant Detarium microcarpum was analysed for its carbohydrate content by GLC-CIMS. Preparative HPLC of the benzoylated carbohydrate fraction led to the isolation of L-quino-1,5-lactone, D-(-)-bornesitol, D-pinitol, myo-inositol, sucrose, D-glucose, and D-fructose benzoates, which were characterised by NMR spectroscopy experiments.

  19. Mastering ectomycorrhizal symbiosis: the impact of carbohydrates.

    PubMed

    Nehls, Uwe

    2008-01-01

    Mycorrhiza formation is the consequence of a mutualistic interaction between certain soil fungi and plant roots that helps to overcome nutritional limitations faced by the respective partners. In symbiosis, fungi contribute to tree nutrition by means of mineral weathering and mobilization of nutrients from organic matter, and obtain plant-derived carbohydrates as a response. Support with easily degradable carbohydrates seems to be the driving force for fungi to undergo this type of interaction. As a consequence, the fungal hexose uptake capacity is strongly increased in Hartig net hyphae of the model fungi Amanita muscaria and Laccaria bicolor. Next to fast carbohydrate uptake and metabolism, storage carbohydrates are of special interest. In functional A. muscaria ectomycorrhizas, expression and activity of proteins involved in trehalose biosynthesis is mainly localized in hyphae of the Hartig net, indicating an important function of trehalose in generation of a strong carbon sink by fungal hyphae. In symbiosis, fungal partners receive up to approximately 19 times more carbohydrates from their hosts than normal leakage of the root system would cause, resulting in a strong carbohydrate demand of infected roots and, as a consequence, a more efficient plant photosynthesis. To avoid fungal parasitism, the plant seems to have developed mechanisms to control carbohydrate drain towards the fungal partner and link it to the fungus-derived mineral nutrition. In this contribution, current knowledge on fungal strategies to obtain carbohydrates from its host and plant strategies to enable, but also to control and restrict (under certain conditions), carbon transfer are summarized.

  20. Carbohydrates as synthetic tools in organic chemistry.

    PubMed

    Boysen, Mike M K

    2007-01-01

    While amino acids, terpenes and alkaloids have found broad application as tools in stereoselective organic synthesis, carbohydrates have only lately been recognised as versatile starting materials for chiral auxiliaries, reagents, ligands and organocatalysts. The structural diversity of carbohydrates and the high density of functional groups offer a wide variety of opportunities for derivatization and tailoring of synthetic tools to a specific problem.

  1. Wood adhesives containing proteins and carbohydrates

    USDA-ARS?s Scientific Manuscript database

    In recent years there has been resurgent interest in using biopolymers as sustainable and environmentally friendly ingredients in wood adhesive formulations. Among them, proteins and carbohydrates are the most commonly used. In this chapter, an overview is given of protein-based and carbohydrate-...

  2. Determining a carbohydrate profile for Hansenula polymorpha.

    PubMed

    Petersen, G R

    1985-07-01

    The determination of the levels of carbohydrates in the yeast Hansenula polymorpha required the development of new analytical procedures. Existing fractionation and analytical methods were adapted to deal with the problems involved with the lysis of whole cells. Using these new procedures, the complete carbohydrates profiles of H. polymorpha and selected mutant strains were determined and shown to correlate favourably with previously published results.

  3. Vacuum ultraviolet photoionization of carbohydrates and nucleotides

    NASA Astrophysics Data System (ADS)

    Shin, Joong-Won; Bernstein, Elliot R.

    2014-01-01

    Carbohydrates (2-deoxyribose, ribose, and xylose) and nucleotides (adenosine-, cytidine-, guanosine-, and uridine-5'-monophosphate) are generated in the gas phase, and ionized with vacuum ultraviolet photons (VUV, 118.2 nm). The observed time of flight mass spectra of the carbohydrate fragmentation are similar to those observed [J.-W. Shin, F. Dong, M. Grisham, J. J. Rocca, and E. R. Bernstein, Chem. Phys. Lett. 506, 161 (2011)] for 46.9 nm photon ionization, but with more intensity in higher mass fragment ions. The tendency of carbohydrate ions to fragment extensively following ionization seemingly suggests that nucleic acids might undergo radiation damage as a result of carbohydrate, rather than nucleobase fragmentation. VUV photoionization of nucleotides (monophosphate-carbohydrate-nucleobase), however, shows that the carbohydrate-nucleobase bond is the primary fragmentation site for these species. Density functional theory (DFT) calculations indicate that the removed carbohydrate electrons by the 118.2 nm photons are associated with endocyclic C-C and C-O ring centered orbitals: loss of electron density in the ring bonds of the nascent ion can thus account for the observed fragmentation patterns following carbohydrate ionization. DFT calculations also indicate that electrons removed from nucleotides under these same conditions are associated with orbitals involved with the nucleobase-saccharide linkage electron density. The calculations give a general mechanism and explanation of the experimental results.

  4. One strike against low-carbohydrate diets

    USDA-ARS?s Scientific Manuscript database

    There is intense controversy over whether low-carbohydrate or low-fat diets are more efficacious for weight management. Using precise methodology, Hall et al. (2015) demonstrated that a low-carbohydrate diet promoted greater fat oxidation than an isocaloric low-fat diet but, in contrast to popular s...

  5. Industrial applications of marine carbohydrates.

    PubMed

    Sudha, Prasad N; Aisverya, S; Nithya, R; Vijayalakshmi, K

    2014-01-01

    Biomaterials have been used increasingly in various fields, such as drug delivery, imaging, and tissue engineering. The main reason justifying the widespread use of biomaterials relies on its valuable and low-cost source of new drugs. Current research goals are focused on identifying more potent and specific compounds with antitumor, immunomodulatory, antihyperlipidemic, anticoagulant, and antiviral activities. The increasing knowledge of structural analysis and chemical modifications enables the use of these marine carbohydrates in a newer way for the human welfare. This chapter focuses on the recent developments related to industrial and biomedical applications using chitin, chitosan, alginate, agar, and carrageenan derivatives and reports the main advances published over the last 10-15 years.

  6. The importance of dietary carbohydrates.

    PubMed

    Sánchez-Castillo, Claudia P; Hudson, Geoffrey J; Englyst, Hans N; Dewey, Peter; James, W Philip T

    2002-12-01

    Forty years ago carbohydrates (CHO) were regarded as a simple energy source whereas they are now recognized as important food components. The human diet contains a wide range of CHO, the vast majority of which are of plant origin. Modern techniques based on chemical classification of dietary CHO replaced the traditional "by difference" measurement. They provide a logical basis for grouping into categories of specific nutritional importance. The physiological effects of dietary CHO are highly dependent on the rate and extent of digestion and absorption in the small intestine and fermentation in the large intestine, interactions which promote human health. Current knowledge of the fate of dietary CHO means that the potentially undesirable properties of many modern foods could be altered by using processing techniques that yield foods with more intact plant cell wall structures. Such products would more closely resemble the foods in the pre-agriculture diet with respect to the rate of digestion and absorption of CHO in the small intestine. The potentially detrimental physiological consequences of eating sugars and starch that are rapidly digested and absorbed in the small intestine suggest that, as fibre, the form, as well as the amount of starch should be considered. Increasing consumer awareness of the relationship between diet and health has led to demands for more widespread nutrition labelling. The entry "carbohydrate" is required in most countries, and the value is usually obtained "by difference" and used in the calculation of energy content. However, the value provides no nutritional information per se. Food labels should provide values that aid consumers in selecting a healthy diet.

  7. High dietary carbohydrate and pancreatic lesion.

    PubMed

    Novelli, E L; Rodrigues, N L; França, E L; Gebra, L M; Ribas, B O

    1993-01-01

    The ability of high dietary carbohydrate to induce acute pancreatitis was investigated in groups of 16, 21-day and 15-month old rats fed different carbohydrate diets for 30 days. Significantly increased levels of serum amylase (2-fold), phospholipids (50%), phosphorus (2-fold), and lipoperoxides (8-fold) were observed in 15-month old rats fed a high-carbohydrate diet, compared to rats fed a diet with normal carbohydrate levels, indicating peroxidation of membrane lipids which caused final cell death and pancreatic lesion. Serum Cu-Zn superoxide dismutase activity was not altered. Daily administration of bovine Cu-Zn superoxide dismutase conjugated with polyethylene glycol prevented the serum level alterations and pancreatic lesions, indicating that the superoxide radical has a role in dietary carbohydrate-induced acute pancreatitis. No biochemical changes were observed in rats in which treatment was initiated on the 21st day of life indicating that this is an age-related lesion.

  8. Pneumococcal carbohydrate transport: food for thought.

    PubMed

    Buckwalter, Carolyn M; King, Samantha J

    2012-11-01

    Streptococcus pneumoniae relies exclusively on carbohydrates as a carbon source and devotes 30% of all transport mechanisms to carbohydrate import. Pneumococci utilize at least 32 carbohydrates in vitro. However, some proposed substrates are not human-derived, so it is unclear where they are encountered in the host niche, and other substrates remain unidentified. The majority of transporter loci are conserved, arguing against redundancy and instead for distinct roles during pathogenesis. Despite this, expression and regulation of carbohydrate transporters in vivo remain ill defined. Recent work has also demonstrated that multiple ABC transporters share an ATPase; whether this evolved for genome minimization or for transporter regulation remains unknown. Continued efforts to understand carbohydrate import may reveal novel vaccine and therapeutic targets and increase our understanding of pneumococcal pathogenesis. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Pneumococcal carbohydrate transport: food for thought

    PubMed Central

    Buckwalter, Carolyn M.; King, Samantha J.

    2012-01-01

    Streptococcus pneumoniae relies exclusively on carbohydrates as a carbon source and devotes 30% of all transport mechanisms to carbohydrate import. Pneumococci utilize at least 32 carbohydrates in vitro; yet, some proposed substrates are not human-derived making it unclear where they are encountered in the host niche while other substrates remain unidentified. The majority of transporter loci are conserved, arguing against redundancy and instead for distinct roles during pathogenesis. Despite this, expression and regulation of carbohydrate transporters in vivo remains ill-defined. Recent work has also demonstrated multiple ABC transporters share an ATPase; whether this evolved for genome minimization or for transporter regulation remains unknown. Continued efforts to understand carbohydrate import may reveal novel vaccine and therapeutic targets and increase understanding of pneumococcal pathogenesis. PMID:22959614

  10. Detailed insights from microarray and crystallographic studies into carbohydrate recognition by microneme protein 1 (MIC1) of Toxoplasma gondii

    PubMed Central

    Garnett, James A; Liu, Yan; Leon, Ester; Allman, Sarah A; Friedrich, Nikolas; Saouros, Savvas; Curry, Stephen; Soldati-Favre, Dominique; Davis, Benjamin G; Feizi, Ten; Matthews, Stephen

    2009-01-01

    The intracellular protozoan Toxoplasma gondii is among the most widespread parasites. The broad host cell range of the parasite can be explained by carbohydrate microarray screening analyses that have demonstrated the ability of the T. gondii adhesive protein, TgMIC1, to bind to a wide spectrum of sialyl oligosaccharide ligands. Here, we investigate by further microarray analyses in a dose-response format the differential binding of TgMIC1 to 2-3- and 2-6-linked sialyl carbohydrates. Interestingly, two novel synthetic fluorinated analogs of 3′SiaLacNAc1–4 and 3′SiaLacNAc1–3 were identified as highly potent ligands. To understand the structural basis of the carbohydrate binding specificity of TgMIC1, we have determined the crystal structures of TgMIC1 micronemal adhesive repeat (MAR)-region (TgMIC1-MARR) in complex with five sialyl-N-acetyllactosamine analogs. These crystal structures have revealed a specific, water-mediated hydrogen bond network that accounts for the preferential binding of TgMIC1-MARR to arrayed 2-3-linked sialyl oligosaccharides and the high potency of the fluorinated analogs. Furthermore, we provide strong evidence for the first observation of a C—F···H—O hydrogen bond within a lectin-carbohydrate complex. Finally, detailed comparison with other oligosaccharide-protein complexes in the Protein Data Bank (PDB) reveals a new family of sialic-acid binding sites from lectins in parasites, bacteria, and viruses. PMID:19593815

  11. Low-carbohydrate diets: an update on current research.

    PubMed

    Wylie-Rosett, Judith; Davis, Nichola J

    2009-10-01

    The diabetes and obesity epidemics have stimulated research to assess the benefits and potential risks of low-carbohydrate diets. Carbohydrate comprises less than 45% of calories in carbohydrate-restricted diets, but very low carbohydrate ketogenic diets may restrict carbohydrate to 20 g initially with variability in the carbohydrate level subsequently. Some research suggests that low-carbohydrate diets may achieve better early weight loss than comparison diets higher in carbohydrate. Studies of up to 1 year suggest that weight loss on low-carbohydrate diet is comparable with fat-restricted diets with higher carbohydrate content. Limited research has been conducted to evaluate low-carbohydrate diets in managing type 2 diabetes. Although science continues to advance in this field, current research suggests that low-carbohydrate diets can be a viable option for achieving weight loss and may have beneficial effects on glycemic control, triglyceride levels, and high-density lipoprotein cholesterol levels in some patients.

  12. Isolation of carbohydrate-metabolizing, extremely halophilic bacteria.

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Hochstein, L. I.

    1972-01-01

    Four previously unrecognized strains of extremely halophilic bacteria that utilize carbohydrates have been isolated. Gas production proved an unreliable index of carbohydrate metabolism; therefore, carbohydrate utilization was measured by determining acid formation and sugar disappearance during growth. By these procedures, carbohydrate utilization was readily detected. The results suggest that carbohydrate dissimilation by extremely halophilic bacteria may be more common than previously thought and that the apparent rarity of carbohydrate-metabolizing halophiles may be an artifact of the isolation procedures used.

  13. Carbohydrate Moieties and Cytoenzymatic Characterization of Hemocytes in Whiteleg Shrimp Litopenaeus vannamei

    PubMed Central

    Velázquez, Edwin; Rodríguez-Jaramillo, Carmen; Ascencio, Felipe

    2016-01-01

    Hemocytes represent one of the most important defense mechanisms against foreign material in Crustacea and are also involved in a variety of other physiological responses. Fluorescent lectin-binding assays and cytochemical reactions were used to identify specificity and distribution of carbohydrate moieties and presence of several hydrolytic enzymes, in hemocytes of whiteleg shrimp Litopenaeus vannamei. Two general classes of circulating hemocytes (granular and agranular) exist in L. vannamei, which express carbohydrates residues for FITC-conjugated lectins WGA, LEA, and PNA; UEA and Con-A were not observed. Enzymatic studies indicated that acid phosphatase, nonspecific esterase, and specific esterases were present; alkaline phosphatase was not observed. The enzymes and carbohydrates are useful tools in hemocyte classification and cellular defense mechanism studies. PMID:27833641

  14. Association between dietary carbohydrates and body weight.

    PubMed

    Ma, Yunsheng; Olendzki, Barbara; Chiriboga, David; Hebert, James R; Li, Youfu; Li, Wenjun; Campbell, MaryJane; Gendreau, Katherine; Ockene, Ira S

    2005-02-15

    The role of dietary carbohydrates in weight loss has received considerable attention in light of the current obesity epidemic. The authors investigated the association of body mass index (weight (kg)/height (m)(2)) with dietary intake of carbohydrates and with measures of the induced glycemic response, using data from an observational study of 572 healthy adults in central Massachusetts. Anthropometric measurements, 7-day dietary recalls, and physical activity recalls were collected quarterly from each subject throughout a 1-year study period. Data were collected between 1994 and 1998. Longitudinal analyses were conducted, and results were adjusted for other factors related to body habitus. Average body mass index was 27.4 kg/m(2) (standard deviation, 5.5), while the average percentage of calories from carbohydrates was 44.9 (standard deviation, 9.6). Mean daily dietary glycemic index was 81.7 (standard deviation, 5.5), and glycemic load was 197.8 (standard deviation, 105.2). Body mass index was found to be positively associated with glycemic index, a measure of the glycemic response associated with ingesting different types of carbohydrates, but not with daily carbohydrate intake, percentage of calories from carbohydrates, or glycemic load. Results suggest that the type of carbohydrate may be related to body weight. However, further research is required to elucidate this association and its implications for weight management.

  15. Carbohydrate Polymers for Nonviral Nucleic Acid Delivery

    PubMed Central

    Sizovs, Antons; McLendon, Patrick M.; Srinivasachari, Sathya

    2014-01-01

    Carbohydrates have been investigated and developed as delivery vehicles for shuttling nucleic acids into cells. In this review, we present the state of the art in carbohydrate-based polymeric vehicles for nucleic acid delivery, with the focus on the recent successes in preclinical models, both in vitro and in vivo. Polymeric scaffolds based on the natural polysaccharides chitosan, hyaluronan, pullulan, dextran, and schizophyllan each have unique properties and potential for modification, and these results are discussed with the focus on facile synthetic routes and favorable performance in biological systems. Many of these carbohydrates have been used to develop alternative types of biomaterials for nucleic acid delivery to typical polyplexes, and these novel materials are discussed. Also presented are polymeric vehicles that incorporate copolymerized carbohydrates into polymer backbones based on polyethylenimine and polylysine and their effect on transfection and biocompatibility. Unique scaffolds, such as clusters and polymers based on cyclodextrin (CD), are also discussed, with the focus on recent successes in vivo and in the clinic. These results are presented with the emphasis on the role of carbohydrate and charge on transfection. Use of carbohydrates as molecular recognition ligands for cell-type specific delivery is also briefly reviewed. We contend that carbohydrates have contributed significantly to progress in the field of non-viral DNA delivery, and these new discoveries are impactful for developing new vehicles and materials for treatment of human disease. PMID:21504102

  16. Safety of low-carbohydrate diets.

    PubMed

    Crowe, T C

    2005-08-01

    Low-carbohydrate diets have re-emerged into the public spotlight and are enjoying a high degree of popularity as people search for a solution to the population's ever-expanding waistline. The current evidence though indicates that low-carbohydrate diets present no significant advantage over more traditional energy-restricted diets on long-term weight loss and maintenance. Furthermore, a higher rate of adverse side-effects can be attributed to low-carbohydrate dieting approaches. Short-term efficacy of low-carbohydrate diets has been demonstrated for some lipid parameters of cardiovascular risk and measures of glucose control and insulin sensitivity, but no studies have ascertained if these effects represent a change in primary outcome measures. Low-carbohydrate diets are likely effective and not harmful in the short term and may have therapeutic benefits for weight-related chronic diseases although weight loss on such a program should be undertaken under medical supervision. While new commercial incarnations of the low-carbohydrate diet are now addressing overall dietary adequacy by encouraging plenty of high-fibre vegetables, fruit, low-glycaemic-index carbohydrates and healthier fat sources, this is not the message that reaches the entire public nor is it the type of diet adopted by many people outside of the world of a well-designed clinical trial. Health effects of long-term ad hoc restriction of inherently beneficial food groups without a concomitant reduction in body weight remains unanswered.

  17. Nutritional characterization and measurement of dietary carbohydrates.

    PubMed

    Englyst, K N; Liu, S; Englyst, H N

    2007-12-01

    Dietary carbohydrate characterization should reflect relevant nutritional and functional attributes, and be measured as chemically identified components. A nutritional classification based on these principles is presented, with a main grouping into 'available carbohydrates', which are digested and absorbed in the small intestine providing carbohydrates for metabolism, and 'resistant carbohydrates', which resist digestion in the small intestine or are poorly absorbed/metabolized. For the available carbohydrates, the chemical division into the starch and total sugars categories does not adequately reflect the physiological or nutritional attributes of foods. Characterizing carbohydrate release from starchy foods provides insight into some of the inherent mechanisms responsible for the varied metabolic effects. Also, a pragmatic approach to product signposting consistent with guidelines to limit free (or added) sugars is proposed. The most prominent of the resistant carbohydrates are the non-starch polysaccharides (NSP) from plant cell walls, which are characteristic of the largely unrefined plant foods that provide the evidence base for the definition and measurement of dietary fibre as 'intrinsic plant cell-wall polysaccharides' as proposed in conjunction with this paper and endorsed by the scientific update. Indigestibility in the small intestine was not considered to be an adequate basis for the definition of dietary fibre, as there is insufficient evidence to establish public health policy by this approach and concerns have been raised about potential detrimental effects of high intakes of rapidly fermentable resistant carbohydrates. Functional ingredients such as resistant starch and resistant oligosaccharides should therefore be researched and managed separately from dietary fibre, using specific health or function claims where appropriate. This structured approach to the characterization of nutritionally relevant features of dietary carbohydrates provides the

  18. Complex carbohydrates: the science and the label.

    PubMed

    1995-07-01

    This conference resulted in a foundation upon which consensus will be built in the future. Further, it provided a forum for the articulation of the critical need for carbohydrates in human nutrition. We have come a long way in the past 25 years in the food and nutrition sciences and this conference well illustrated that point. At the White House Conference on Nutrition in 1969, macronutrients were never even mentioned as being necessary to nutrition; only micronutrients were emphasized. In 1977 the term complex carbohydrate was used without definition in the Dietary Goals for the United States. This conference encapsulated the tremendous strides that have been made concerning the chemical, nutritional, biologic, and physiologic importance of carbohydrates in health and disease. It is fascinating to review the recommendations concerning complex carbohydrate from 1977 on. Recommendations were made by the Senate Select Committee in 1977; the Dietary Guidelines of 1980, 1985, and 1990; the Surgeon General's report of 1979 and 1988; the 10th edition of Recommended Dietary Allowances; the 1989 National Academy of Sciences Diet and Health: Implications for Reducing Chronic Disease Risk; the 1991 FDA proposal for labeling; and the 1992 Food Guide Pyramid. Indeed, as Dr. Joanne Slavin pointed out, "there is a wide range of consensus that increased complex carbohydrate is consistent with good health," and certainly as Dr. Gary Henderson said, "the term complex carbohydrate has equity with consumers." With this level of apparent clarity it is difficult at first to identify a problem for the food label. After all, if consumer health would benefit, why not simply do it? However, a problem does exist in that carbohydrates may be classified chemically in groups that are difficult to analyze and to define as to their physiologic function in the body. Indeed, complex carbohydrates defined by chain length may have molecular structures less complex than those of smaller units and may

  19. Carbohydrate functionalized carbon nanotubes and their applications.

    PubMed

    Gorityala, Bala Kishan; Ma, Jimei; Wang, Xin; Chen, Peng; Liu, Xue-Wei

    2010-08-01

    Carbon nanotubes (CNTs) have attracted tremendous attention in biomedical applications due to their molecular size and unique properties. This tutorial review summarizes the strategies to functionalize CNTs with bioactive carbohydrates, which improve their solubility, biocompatibility and biofunctionalities while preserving their desired properties. In addition, studies on the usage of carbohydrate functionalized CNTs to detect bacteria, to bind to specific lectins, to deliver glycomimetic drug molecules into cells and to probe cellular activities as biosensors are reviewed. Improvement in biocompatibility and introduction of bio-functionalities by integration of carbohydrate with CNTs are paving the way to glyconanotechnology and may provide new tools for glycobiological studies.

  20. Utilization of carbohydrates by radiation processing

    NASA Astrophysics Data System (ADS)

    Kume, T.; Nagasawa, N.; Yoshii, F.

    2002-03-01

    Upgrading and utilization of carbohydrates such as chitosan, sodium alginate, carrageenan, cellulose, pectin have been investigated for recycling these bio-resources and reducing the environmental pollution. These carbohydrates were easily degraded by irradiation and various kinds of biological activities such as anti-microbial activity, promotion of plant growth, suppression of heavy metal stress, phytoalexins induction, etc. were induced. On the other hand, some carbohydrate derivatives, carboxymethylcellulose and carboxymethylstarch, could be crosslinked under certain radiation condition and produce the biodegradable hydrogel for medical and agricultural use.

  1. Rapid Analysis of Listeria monocytogenes Cell Wall Teichoic Acid Carbohydrates by ESI-MS/MS

    PubMed Central

    Eugster, Marcel R.; Loessner, Martin J.

    2011-01-01

    We report the application of electrospray ionization (ESI) mass spectrometry for compositional characterization of wall teichoic acids (WTA), a major component of Gram-positive bacterial cell walls. Tandem mass spectrometry (ESI-MS/MS) of purified and chemically hydrolyzed monomeric WTA components provided sufficient information to identify WTA monomers and their specific carbohydrate constituents. A lithium matrix was used for ionization of uncharged WTA monomers, and successfully applied to analyze the WTA molecules of four Listeria strains differing in carbohydrate substitution on a conserved polyribitol-phosphate backbone structure. Carbohydrate residues such as N-acetylglucosamine or rhamnose linked to the WTA could directly be identified by ESI-MS/MS, circumventing the need for quantitative analysis by gas chromatography. The presence of a terminal N-acetylglucosamine residue tethered to the ribitol was confirmed using fluorescently labeled wheat-germ agglutinin. In conclusion, the mass spectrometry method described here will greatly facilitate compositional analysis and characterization of teichoic acids and similar macromolecules from diverse bacterial species, and represents a significant advance in the identification of serovar-specific carbohydrates and sugar molecules on bacteria. PMID:21738682

  2. Rapid analysis of Listeria monocytogenes cell wall teichoic acid carbohydrates by ESI-MS/MS.

    PubMed

    Eugster, Marcel R; Loessner, Martin J

    2011-01-01

    We report the application of electrospray ionization (ESI) mass spectrometry for compositional characterization of wall teichoic acids (WTA), a major component of gram-positive bacterial cell walls. Tandem mass spectrometry (ESI-MS/MS) of purified and chemically hydrolyzed monomeric WTA components provided sufficient information to identify WTA monomers and their specific carbohydrate constituents. A lithium matrix was used for ionization of uncharged WTA monomers, and successfully applied to analyze the WTA molecules of four Listeria strains differing in carbohydrate substitution on a conserved polyribitol-phosphate backbone structure. Carbohydrate residues such as N-acetylglucosamine or rhamnose linked to the WTA could directly be identified by ESI-MS/MS, circumventing the need for quantitative analysis by gas chromatography. The presence of a terminal N-acetylglucosamine residue tethered to the ribitol was confirmed using fluorescently labeled wheat-germ agglutinin. In conclusion, the mass spectrometry method described here will greatly facilitate compositional analysis and characterization of teichoic acids and similar macromolecules from diverse bacterial species, and represents a significant advance in the identification of serovar-specific carbohydrates and sugar molecules on bacteria.

  3. Cell-Wall Carbohydrates of the Endosperm of the Seed of Gleditsia triacanthos.

    PubMed

    Manzi, A E; Ancibor, E; Cerezo, A S

    1990-04-01

    The endosperm of the seed of Gleditsia triacanthos L. contains 18.55% of its dry weight as nonreserve, cell-wall carbohydrates. Of this carbohydrate material, comprising mainly mannose, galactose, and glucose, 76.1% was of low-molecular weight or highly hydrophilic. Mannose, galactose, and glucose were also the major sugar components of the polysaccharides extracted with alkali (23.1% of the cell-wall), while the same sugars, with minor amounts of arabinose, form the residues. Methylation analysis of the polysaccharides and the borate-sodium hydroxide residue indicate that the cell walls are built up on a network of galactomannans, with high Man/Gal ratios, reinforced with minor amounts of cellulose.

  4. Cell-Wall Carbohydrates of the Endosperm of the Seed of Gleditsia triacanthos1

    PubMed Central

    Manzi, Adriana E.; Ancibor, Elena; Cerezo, Alberto S.

    1990-01-01

    The endosperm of the seed of Gleditsia triacanthos L. contains 18.55% of its dry weight as nonreserve, cell-wall carbohydrates. Of this carbohydrate material, comprising mainly mannose, galactose, and glucose, 76.1% was of low-molecular weight or highly hydrophilic. Mannose, galactose, and glucose were also the major sugar components of the polysaccharides extracted with alkali (23.1% of the cell-wall), while the same sugars, with minor amounts of arabinose, form the residues. Methylation analysis of the polysaccharides and the borate-sodium hydroxide residue indicate that the cell walls are built up on a network of galactomannans, with high Man/Gal ratios, reinforced with minor amounts of cellulose. Images Figure 2 Figure 2 PMID:16667408

  5. Carbohydrate protease conjugates: Stabilized proteases for peptide synthesis

    SciTech Connect

    Wartchow, C.A.; Wang, Peng; Bednarski, M.D.; Callstrom, M.R. |

    1995-12-31

    The synthesis of oligopeptides using stable carbohydrate protease conjugates (CPCs) was examined in acetonitrile solvent systems. CPC[{alpha}-chymotrypsin] was used for the preparation of peptides containing histidine, phenylalanine, tryptophan in the P{sub 1} position in 60-93% yield. The CPC[{alpha}-chymotrypsin]-catalyzed synthesis of octamer Z-Gly-Gly-Phe-Gly-Gly-Phe-Gly-Gly-OEt from Z-Gly-Gly-Phe-Gly-Gly-Phe-OMe was achieved in 71% yield demonstrating that synthesis peptides containing both hydrophylic and hydrophobic amino acids. The P{sub 2} specificity of papain for aromatic residues was utilized for the 2 + 3 coupling of Z-Tyr-Gly-OMe to H{sub 2}N-Gly-Phe-Leu-OH to generate the leucine enkephalin derivative in 79% yield. Although papain is nonspecific for the hydrolysis of N-benzyloxycarbonyl amino acid methyl esters in aqueous solution, the rates of synthesis for these derivitives with nucleophile leucine tert-butyl ester differed by nearly 2 orders of magnitude. CPC[thermolysin] was used to prepare the aspartame precursor Z-Asp-Phe-OMe in 90% yield. The increased stability of CPCs prepared from periodate-modified poly(2-methacryl- amido-2-deoxy-D-glucose), poly(2-methacrylamido-2-deoxy-D-galactose), and poly(5-methacryl-amido-5-deoxy-D-ribose), carbohydrate materials designed to increase the aldehyde concentration in aqueous solution, suggests that the stability of CPCs is directly related to the aldehyde concentration of the carbohydrate material. Periodate oxidation of poly(2-methacrylamido-2-deoxy-D-glucose) followed by covalent attachment to {alpha}-chymotrypsin gave a CPC with catalytic activity in potassium phosphate buffer at 90{degrees}C for 2 h. 1 fig., 1 tab., 40 refs.

  6. Workshop to establish databases of carbohydrate spectra

    SciTech Connect

    1995-12-31

    The workshop was organized to formulate guidelines for establishing spectral databases of complex carbohydrates. The databases will enable the scientific community to avoid the great waste of research effort and funds that frequently occurs when carbohydrate chemists are forced to duplicate the structural characterization of previously characterized complex carbohydrates. Chemists waste their effort on repetitive characterizations because in the absence of spectral databases they are unaware they are analyzing a known molecule until they have completely determined its structure. Chemists will be able to avoid much of this wasted effort when the collections of mass and of nuclear magnetic resonance (NMR) spectra initiated at the workshop are subsequently developed into searchable databases. Then scientists only need query the databases with the spectrum or with information defining the spectrum of an unidentified carbohydrate to find out if it has been previously characterized.

  7. Characterizing the glycocalyx of poultry spermatozoa; semen cryopreservation methods alter the carbohydrate component of rooster sperm membrane glycoconjugates

    USDA-ARS?s Scientific Manuscript database

    The carbohydrate-rich zone on the sperm surface is essential for inmunoprotection in the female tract and early gamete interactions. We recently have shown the glycocalyx of chicken sperm to be extensively sialylated and contain residues of mannose, glucose, galactose, fucose, N-acetyl-galactosamine...

  8. Partition coefficients of organic contaminants with carbohydrates.

    PubMed

    Hung, Hsu-Wen; Lin, Tsair-Fuh; Chiou, Cary T

    2010-07-15

    In view of the current lack of reliable partition coefficients for organic compounds with carbohydrates (K(ch)), carefully measured values with cellulose and starch, the two major forms of carbohydrates, are provided for a wide range of compounds: short-chain chlorinated hydrocarbons, halogenated benzenes, alkyl benzenes, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls, and organochlorine pesticides. To ensure the accuracy of the K(ch) data, solute concentrations in both water and carbohydrate phases are measured by direct solvent extraction of the samples. For a given compound, the observed partition coefficient with cellulose (K(cl)) is virtually the same as that with starch (K(st)). This finding expedites the evaluation of organic contamination with different forms of carbohydrates. The presently determined K(ch) values of 13 PAHs are substantially lower (by 3-66 times) than the literature data; the latter are suspect as they were obtained with (i) presumably impure carbohydrate samples or (ii) indirectly measured equilibrium solute concentrations in carbohydrate and water phases. Although the K(ch) values are generally considerably lower than the respective K(ow) (octanol-water) or K(lipid) (lipid-water), accurate K(ch) data are duly required to accurately estimate the contamination of carbohydrates by organic compounds because of the abundance of carbohydrates over lipids in crops and plants. To overcome the current lack of reliable K(ch) data for organic compounds, a close correlation of log K(ch) with log K(ow) has been established for predicting the unavailable K(ch) data for low-polarity compounds.

  9. Indium triflate catalyzed peracetylation of carbohydrates.

    PubMed

    Bizier, Nicholas P; Atkins, Shannon R; Helland, Luke C; Colvin, Shane F; Twitchell, Joseph R; Cloninger, Mary J

    2008-07-21

    Peracetylation is a very common protection strategy that is widely implemented in carbohydrate synthesis. Here, a method for the peracetylation of carbohydrates using catalytic In(OTf)(3) in neat acetic anhydride is reported. In(OTf)(3) has low toxicity and is mild and water tolerant, and the reactions are high yielding and efficient. Details regarding the scope and mechanism of the reaction are briefly discussed.

  10. Computer Simulations Reveal Multiple Functions for Aromatic Residues in Cellulase Enzymes (Fact Sheet)

    SciTech Connect

    Not Available

    2012-07-01

    NREL researchers use high-performance computing to demonstrate fundamental roles of aromatic residues in cellulase enzyme tunnels. National Renewable Energy Laboratory (NREL) computer simulations of a key industrial enzyme, the Trichoderma reesei Family 6 cellulase (Cel6A), predict that aromatic residues near the enzyme's active site and at the entrance and exit tunnel perform different functions in substrate binding and catalysis, depending on their location in the enzyme. These results suggest that nature employs aromatic-carbohydrate interactions with a wide variety of binding affinities for diverse functions. Outcomes also suggest that protein engineering strategies in which mutations are made around the binding sites may require tailoring specific to the enzyme family. Cellulase enzymes ubiquitously exhibit tunnels or clefts lined with aromatic residues for processing carbohydrate polymers to monomers, but the molecular-level role of these aromatic residues remains unknown. In silico mutation of the aromatic residues near the catalytic site of Cel6A has little impact on the binding affinity, but simulation suggests that these residues play a major role in the glucopyranose ring distortion necessary for cleaving glycosidic bonds to produce fermentable sugars. Removal of aromatic residues at the entrance and exit of the cellulase tunnel, however, dramatically impacts the binding affinity. This suggests that these residues play a role in acquiring cellulose chains from the cellulose crystal and stabilizing the reaction product, respectively. These results illustrate that the role of aromatic-carbohydrate interactions varies dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, the results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for

  11. A study of the influence of charged residues on β-hairpin formation by nuclear magnetic resonance and molecular dynamics.

    PubMed

    Makowska, Joanna; Zmudzińska, Wioletta; Uber, Dorota; Chmurzyński, Lech

    2014-12-01

    Chain reversals are often nucleation sites in protein folding. The β-hairpins of FBP28 WW domain and IgG are stable and have been proved to initiate the folding and are, therefore, suitable for studying the influence of charged residues on β-hairpin conformation. In this paper, we carried out NMR examination of the conformations in solution of two fragments from the FPB28 protein (PDB code: 1E0L) (N-terminal part) namely KTADGKT-NH2 (1E0L 12-18, D7) and YKTADGKTY-NH2 (1E0L 11-19, D9), one from the B3 domain of the protein G (PDB code: 1IGD), namely DDATKT-NH2 (1IGD 51-56) (Dag1), and three variants of Dag1 peptide: DVATKT-NH2 (Dag2), OVATKT-NH2 (Dag3) and KVATKT-NH2 (Dag4), respectively, in which the original charged residue were replaced with non-polar residues or modified charged residues. It was found that both the D7 and D9 peptides form a large fraction bent conformations. However, no hydrophobic contacts between the terminal Tyr residues of D9 occur, which suggests that the presence of a pair of like-charged residues stabilizes chain reversal. Conversely, only the Dag1 and Dag2 peptides exhibit some chain reversal; replacing the second aspartic-acid residue with a valine and the first one with a basic residue results in a nearly extended conformation. These results suggest that basic residues farther away in sequence can result in stabilization of chain reversal owing to screening of the non-polar core. Conversely, smaller distance in sequence prohibits this screening, while the presence oppositely-charged residues can stabilize a turn because of salt-bridge formation.

  12. Carbohydrate ligands for endothelial - Leukocyte adhesion molecule 1

    SciTech Connect

    Tiemeyer, M.; Swiedler, S.J.; Ishihara, Masayuki; Moreland, M.; Schweingruber, H.; Hirtzer, P.; Brandley, B.K. )

    1991-02-15

    The acute inflammatory response requires that circulating leukocytes bind to and penetrate the vascular wall to access the site of injury. Several receptors have been implicated in this interaction, including a family of putative carbohydrate-binding proteins. The authors report here the identification of an endogenous carbohydrate ligand for one of these receptors, endothelial-leukocyte adhesion molecule 1 (ELAM-1). Radiolabeled COS cells transfected with a plasmid containing the cDNA for ELAM-1 were used as probes to screen glycolipids extracted from human leukocytes. COS cells transfected with this plasmid adhered to a subset of sialylated glycolipids resolved on TLC plates or adsorbed on polyvinyl chloride microtiter wells. Adhesion to these glycolipids required calcium but was not inhibited by heparin, chondroitin sulfate, keratan sulfate, or yeast phosphomannan. Monosaccharide composition, linkage analysis, and fast atom bombardment mass spectrometry of the glycolipids indicate that the ligands for ELAM-1 are terminally sialylated lactosylceramides with a variable number of N-acetyllactosamine repeats and at least one fucosylated N-acetylglucosamine residue.

  13. Glycoprotein labeling with click chemistry (GLCC) and carbohydrate detection.

    PubMed

    Wu, Zhengliang L; Huang, Xinyi; Burton, Andrew J; Swift, Karl A D

    2015-08-14

    Molecular labeling and detection techniques are essential to research in life science. Here, a method for glycoprotein labeling/carbohydrate detection through glycan replacement, termed glycoprotein labeling with click chemistry (GLCC), is described. In this method, a glycoprotein is first treated with specific glycosidases to remove certain sugar residues, a procedure that creates acceptor sites for a specific glycosyltransferase. A 'clickable' monosaccharide is then installed onto these sites by the glycosyltransferase. This modified glycoprotein is then conjugated to a reporter molecule using a click chemistry reaction. For glycoproteins that already contain vacant glycosylation sites, deglycosylation is not needed before the labeling step. As a demonstration, labeling on fetal bovine fetuin, mouse immunoglobulin IgG and bacterial expressed human TNFα and TNFβ are shown. Compared to traditional ways of protein labeling, labeling at glycosylation sites with GLCC is considerably more specific and less likely to have adverse effects, and, when utilized as a method for carbohydrate detection, this method is also highly specific and sensitive.

  14. Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects.

    PubMed

    Fadda, Elisa; Woods, Robert J

    2010-08-01

    The characterization of the 3D structure of oligosaccharides, their conjugates and analogs is particularly challenging for traditional experimental methods. Molecular simulation methods provide a basis for interpreting sparse experimental data and for independently predicting conformational and dynamic properties of glycans. Here, we summarize and analyze the issues associated with modeling carbohydrates, with a detailed discussion of four of the most recently developed carbohydrate force fields, reviewed in terms of applicability to natural glycans, carbohydrate-protein complexes and the emerging area of glycomimetic drugs. In addition, we discuss prospectives and new applications of carbohydrate modeling in drug discovery.

  15. The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.

    PubMed

    Kikuchi, Norihiro; Kameyama, Akihiko; Nakaya, Shuuichi; Ito, Hiromi; Sato, Takashi; Shikanai, Toshihide; Takahashi, Yoriko; Narimatsu, Hisashi

    2005-04-15

    Bioinformatics resources for glycomics are very poor as compared with those for genomics and proteomics. The complexity of carbohydrate sequences makes it difficult to define a common language to represent them, and the development of bioinformatics tools for glycomics has not progressed. In this study, we developed a carbohydrate sequence markup language (CabosML), an XML description of carbohydrate structures. The language definition (XML Schema) and an experimental database of carbohydrate structures using an XML database management system are available at http://www.phoenix.hydra.mki.co.jp/CabosDemo.html kikuchi@hydra.mki.co.jp.

  16. Carbohydrates and gibberellins relationship in potato tuberization.

    PubMed

    Ševčíková, Hana; Mašková, Petra; Tarkowská, Danuše; Mašek, Tomáš; Lipavská, Helena

    2017-07-01

    Potato represents the third most important crop worldwide and therefore to understand regulations of tuber onset is crucial from both theoretical and practical points of view. Photosynthesis and related carbohydrate status along with phytohormone balance belong to the essential factors in regulation of plant development including storage organ formation. In our work we used potato (Solanum tuberosum) cv. Lada and its spontaneously tuberizing mutant (ST plants) grown in vitro under low carbohydrate availability (non-inductive conditions). Small plant phenotype and readiness to tuberization of ST plants was, however, not accompanied by lower gibberellins levels, as determined by UHPLC-MS/MS. Therefore, we focused on the other inducing factor, carbohydrate status. Using HPLC, we followed changes in carbohydrate distribution under mixotrophic (2.5% sucrose in medium) and photoautotrophic conditions (no sucrose addition and higher gas and light availability) and observed changes in soluble carbohydrate allocation and starch deposition, favouring basal stem part in mutants. In addition, the determination of tuber-inducing marker gene expressions revealed increased levels of StSP6A in ST leaves. Collectively these data point towards the possibility of two parallel cross-talking pathways (carbohydrate - and gibberellin- dependent ones) with the power of both to outcompete the other one when its signal is for some reason extraordinary strong. Copyright © 2017 Elsevier GmbH. All rights reserved.

  17. Carbohydrate Nutrition and Team Sport Performance.

    PubMed

    Williams, Clyde; Rollo, Ian

    2015-11-01

    The common pattern of play in 'team sports' is 'stop and go', i.e. where players perform repeated bouts of brief high-intensity exercise punctuated by lower intensity activity. Sprints are generally 2-4 s long and recovery between sprints is of variable length. Energy production during brief sprints is derived from the degradation of intra-muscular phosphocreatine and glycogen (anaerobic metabolism). Prolonged periods of multiple sprints drain muscle glycogen stores, leading to a decrease in power output and a reduction in general work rate during training and competition. The impact of dietary carbohydrate interventions on team sport performance have been typically assessed using intermittent variable-speed shuttle running over a distance of 20 m. This method has evolved to include specific work to rest ratios and skills specific to team sports such as soccer, rugby and basketball. Increasing liver and muscle carbohydrate stores before sports helps delay the onset of fatigue during prolonged intermittent variable-speed running. Carbohydrate intake during exercise, typically ingested as carbohydrate-electrolyte solutions, is also associated with improved performance. The mechanisms responsible are likely to be the availability of carbohydrate as a substrate for central and peripheral functions. Variable-speed running in hot environments is limited by the degree of hyperthermia before muscle glycogen availability becomes a significant contributor to the onset of fatigue. Finally, ingesting carbohydrate immediately after training and competition will rapidly recover liver and muscle glycogen stores.

  18. Oral carbohydrate sensing and exercise performance.

    PubMed

    Jeukendrup, Asker E; Chambers, Edward S

    2010-07-01

    Carbohydrate during exercise has been demonstrated to improve exercise performance even when the exercise is of high intensity (>75% VO2max) and relatively short duration (approximately 1 h). It has become clear that the underlying mechanisms for the ergogenic effect during this type of activity are not metabolic but may reside in the central nervous system. Carbohydrate mouth rinses have been shown to result in similar performance improvements. This would suggest that the beneficial effects of carbohydrate feeding during exercise are not confined to its conventional metabolic advantage but may also serve as a positive afferent signal capable of modifying motor output. These effects are specific to carbohydrate and are independent of taste. The receptors in the oral cavity have not (yet) been identified and the exact role of various brain areas is not clearly understood. Further research is warranted to fully understand the separate taste transduction pathways for simple and complex carbohydrates and how these differ between mammalian species, particularly in humans. Carbohydrate is detected in oral cavity by unidentified receptors and this can be linked to improvements in exercise performance.

  19. Techniques for visualization of carbohydrate molecules.

    PubMed

    Kuttel, Michelle; Gain, James; Burger, Anton; Eborn, Ian

    2006-11-01

    Standard molecular visualizations, such as the classic ball-and-stick model, are not suitable for large, complex molecules because the overall molecular structure is obscured by the atomic detail. For proteins, the more abstract ribbon and cartoon representations are instead used to reveal large scale molecular conformation and connectivity. However, there is currently no accepted convention for simplifying oligo- and polysaccharide structures. We introduce two novel visualization algorithms for carbohydrates, incorporated into a visualization package, CarboHydra. Both algorithms highlight the sugar rings and backbone conformation of the carbohydrate chain, ignoring ring substituents. The first algorithm, termed PaperChain, emphasizes the type and conformation of the carbohydrate rings. The second, Twister, emphasizes the relative orientation of the rings. We further include two rendering enhancements to augment these visualizations: silhouettes edges and a translucent overlay of the ball-and-stick atomic representation. To demonstrate their utility, the algorithms and visualization enhancements are here applied to a variety of carbohydrate molecules. User evaluations indicate that they present a more useful view of carbohydrate structure than the standard ball-and-stick representation. The algorithms were found to be complementary, with PaperChain particularly effective for smaller carbohydrates and Twister useful at larger scales for highlighting the backbone twist of polysaccharides.

  20. Carbohydrate metabolism of schistosoma mansoni.

    PubMed

    BUEDING, E

    1950-05-20

    1. Schistosoma mansoni utilizes in 1 hour an amount of glucose equivalent to one-sixth to one-fifth of its dry weight. Over 80 per cent of the metabolized glucose is converted to lactic acid by this organism. 2. The rates of glucose utilization and of lactic acid production by S. mansoni are the same under aerobic and under anaerobic conditions. 3. A high rate of lactic acid production and the absence of a postanaerobic increase in the oxygen uptake differentiate S. mansoni from most other parasitic helminths whose metabolism has been studied. 4. Arsenite and p-chloromercuric benzoate inhibit in low concentrations the oxygen uptake and the rate of glycolysis of S. mansoni. This inhibition is not prevented or reversed by an excess of glutathione or of thioglycollate. 5. Fluoride inhibits the removal of glucose and the production of lactic acid by S. mansoni to the same degree. 6. Low concentrations of quinacrine (atabrine) do not affect the respiration or the carbohydrate metabolism of the schistosomes. 7. The inhibitory effect of aldehydes on the metabolism of S. mansoni has been measured. Among this group of compounds dl-glyceraldehyde and o-nitrobenzaldehyde are the most effective inhibitors of glycolysis. 8. In a concentration of 2.6 x 10(-6)M (1:1,000,000) a cyanine dye inhibits almost completely the respiration of the schistosomes, but has no effect on their rate of glycolysis. The oxygen uptake of the worms is inhibited by fuadin to a greater degree than their rate of glycolysis. 2-methyl-1,4-napthoquinone is a much more effective inhibitor of glycolysis than of the respiration of S. mansoni. The latter compound interacts with plasma albumin and, therefore, its inhibitory action on the metabolism of the schistosomes is greatly reduced in human serum or plasma. 9. Evidence is discussed which indicates that, in contrast to glycolysis, respiratory metabolism is not essential for the survival of S. mansoni.

  1. Carbohydrate intake, glycemic index, glycemic load, and risk of postmenopausal breast cancer in a prospective study of French women.

    PubMed

    Lajous, Martin; Boutron-Ruault, Marie-Christine; Fabre, Alban; Clavel-Chapelon, Françoise; Romieu, Isabelle

    2008-05-01

    Diets high in carbohydrates may result in chronically elevated insulin concentrations and may affect breast cancer risk by stimulation of insulin receptors or through insulin-like growth factor I (IGF-I)-mediated mitogenesis. Insulin response to carbohydrate intake is increased in insulin-resistant states such as obesity. We sought to evaluate carbohydrate intake, glycemic index (GI), and glycemic load (GL) and subsequent overall and hormone-receptor-defined breast cancer risk among postmenopausal women. A prospective cohort analysis of dietary carbohydrate and fiber intakes was conducted among 62 739 postmenopausal women from the E3N French study who had completed a validated dietary history questionnaire in 1993. During a 9-y period, 1812 cases of pathology-confirmed breast cancer were documented through follow-up questionnaires. Nutrients were categorized into quartiles and energy-adjusted with the regression-residual method. Cox model-derived relative risks (RRs) were adjusted for known determinants in breast cancer. Dietary carbohydrate and fiber intakes were not associated with overall breast cancer risk. Among overweight women, we observed an association between GI and breast cancer (RR(Q1-Q4): 1.35; 95% CI: 1.00, 1.82; P for trend = 0.04). For women in the highest category of waist circumference, the RR(Q1-Q4) was 1.28 (95% CI: 0.98, 1.67; P for trend = 0.10) for carbohydrates, 1.35 (95% CI: 1.04, 1.75; P for trend = 0.01) for GI, and 1.37 (95% CI: 1.05, 1.77; P for trend = 0.003) for GL. We also observed a direct association between carbohydrate intake, GL, and estrogen receptor-negative breast cancer risk. Rapidly absorbed carbohydrates are associated with postmenopausal breast cancer risk among overweight women and women with large waist circumference. Carbohydrate intake may also be associated with estrogen receptor-negative breast cancer.

  2. Effects of exercise and carbohydrate composition on gastric emptying.

    PubMed

    Neufer, P D; Costill, D L; Fink, W J; Kirwan, J P; Fielding, R A; Flynn, M G

    1986-12-01

    To examine the gastric emptying characteristics of selected test drinks varying in carbohydrate composition and concentration, twenty-five runners ingested 400 ml of a solution in one or more of a series of trials followed by either 15 min seated rest or 15 min running (50 to 70% VO2 max). The solutions tested at rest included water, 5.0% maltodextrin, 3.0% maltodextrin + 2% glucose (MG5.0), and 4.5% maltodextrin + 2.6% fructose (MF7.1). Solutions tested during running included water, MG5.0, MF7.1, 5.5% maltodextrin + 2% glucose, and 5.5% maltodextrin + 2% fructose. At rest and during running, water emptied significantly (P less than 0.5) faster than all other drinks. In the running trials, the volume of gastric residue of 5.5% maltodextrin + 2% fructose (221.7 +/- 11.0 ml) was significantly greater than water (103.4 +/- 19.0 ml), MG5.0 (153.3 +/- 16.8 ml), and MF7.1 (167.3 +/- 14.8), suggesting an inhibitory role of glucose on gastric emptying. Running resulted in a significantly lower volume of gastric residue of water, MG5.0, and MF7.1 (103.4 +/- 19.0, 153.3 +/- 16.8, and 167.3 +/- 14.8 ml, respectively) as compared to the corresponding drinks at rest (209.3 +/- 12.6, 287.7 +/- 16.0, and 271.0 +/- 17.8 ml, respectively). These results suggest a possible advantage for including maltodextrin and fructose as carbohydrate sources in athletic drinks. Furthermore, the rate of gastric emptying is enhanced while running, possibly due to increased mechanical movement of fluid within the stomach.

  3. Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii.

    PubMed

    Zurawski, Jeffrey V; Khatibi, Piyum A; Akinosho, Hannah O; Straub, Christopher T; Compton, Scott H; Conway, Jonathan M; Lee, Laura L; Ragauskas, Arthur J; Davison, Brian H; Adams, Michael W W; Kelly, Robert M

    2017-09-01

    Improving access to the carbohydrate content of lignocellulose is key to reducing recalcitrance for microbial deconstruction and conversion to fuels and chemicals. Caldicellulosiruptor bescii completely solubilizes naked microcrystalline cellulose, yet this transformation is impeded within the context of the plant cell wall by a network of lignin and hemicellulose. Here, the bioavailability of carbohydrates to C. bescii at 70°C was examined for reduced lignin transgenic switchgrass lines COMT3(+) and MYB Trans, their corresponding parental lines (cultivar Alamo) COMT3(-) and MYB wild type (WT), and the natural variant cultivar Cave-in-Rock (CR). Transgenic modification improved carbohydrate solubilization by C. bescii to 15% (2.3-fold) for MYB and to 36% (1.5-fold) for COMT, comparable to the levels achieved for the natural variant, CR (36%). Carbohydrate solubilization was nearly doubled after two consecutive microbial fermentations compared to one microbial step, but it never exceeded 50% overall. Hydrothermal treatment (180°C) prior to microbial steps improved solubilization 3.7-fold for the most recalcitrant line (MYB WT) and increased carbohydrate recovery to nearly 50% for the least recalcitrant lines [COMT3(+) and CR]. Alternating microbial and hydrothermal steps (T→M→T→M) further increased bioavailability, achieving carbohydrate solubilization ranging from 50% for MYB WT to above 70% for COMT3(+) and CR. Incomplete carbohydrate solubilization suggests that cellulose in the highly lignified residue was inaccessible; indeed, residue from the T→M→T→M treatment was primarily glucan and inert materials (lignin and ash). While C. bescii could significantly solubilize the transgenic switchgrass lines and natural variant tested here, additional or alternative strategies (physical, chemical, enzymatic, and/or genetic) are needed to eliminate recalcitrance.IMPORTANCE Key to a microbial process for solubilization of plant biomass is the organism's access

  4. Gastric residual volume by magnetic ressonance after intake of maltodextrin and glutamine: a randomized double-blind, crossover study.

    PubMed

    Brianez, Luigi R; Caporossi, Cervantes; de Moura, Yure W; Dias, Lorena A; Leal, Regis V; de Aguilar-Nascimento, José E

    2014-01-01

    The addition of glutamine in preoperative drinks may enhance the benefits of carbohydrate alone. To evaluate the gastric residual volume after the intake of a beverage containing carbohydrate plus glutamine. Eleven healthy volunteers (24-30 years-old) were randomized in a crossover fashion to intake 400 mL (4h before) and 200 mL (2h before) of a beverage containing either 12.5% maltodextrin (carbohydrate group) or 12.5% maltodextrin plus 15 g of glutamine (glutamine group) in two different moments 7 days apart. Magnetic ressonance was performed to measure the gastric residual volume (mL) 120 and 180 minutes after the last ingestion. Gastric residual volume similar to basal condition was found after 2h and 3h of the intake of beverages. There was no difference in the mean ±SD GRV (mL) found at 120 minutes (carbohydrate group: 22.9±16.6 and glutamine group: 19.7±10.7) and at 180 minutes (carbohydrate group: 21.5±24.1 and glutamine group: 15.1±10.1) between the two drinks. Gastric emptying is efficient, and occurs in up to two hours after the intake of a beverage containing either carbohydrate alone or carbohydrate associated with glutamine. The addition of glutamine to carbohydrate-enriched drink seems to be safe for the use up to 2h before an operation.

  5. Screening method of carbohydrate-binding proteins in biological sources by capillary affinity electrophoresis and its application to determination of Tulipa gesneriana agglutinin in tulip bulbs.

    PubMed

    Nakajima, Kazuki; Kinoshita, Mitsuhiro; Oda, Yasuo; Masuko, Takashi; Kaku, Hanae; Shibuya, Naoto; Kakehi, Kazuaki

    2004-09-01

    We developed capillary affinity electrophoresis (CAE) to analyze the molecular interaction between carbohydrate chains and proteins in solution state. A mixture of oligosaccharides derived from a glycoprotein was labeled with 8-aminopyrene-1,3,6-trisulfonate (APTS), and used as glycan library without isolation. Interaction of a carbohydrate-binding protein with each oligosaccharide in the mixture could be simultaneously observed, and relative affinities of oligosaccharides toward the protein were accurately determined. In this study, we applied CAE to detect the presence of lectins in some plants (Japanese elderberry bark and tulip bulb). In the crude extract of the elderberry bark, binding activity toward sialo-carbohydrate chains could be easily detected. We also examined the presence of lectins in the crude extract of tulip bulbs and determined the detailed carbohydrate-binding specificity of Tulipa gesneriana agglutinin (TGA), one of the lectins from tulip bulbs. Kinetic studies demonstrated that TGA showed novel carbohydrate-binding specificity and preferentially recognized triantennary oligosaccharides with Gal residues at nonreducing termini and a Fuc residue linked through alpha(1-6) linkage at chitobiose portion of the reducing termini but not tetraantennary carbohydrates. The results described here indicate that CAE will be a valuable method for both screening of lectins in natural sources and determination of their detailed carbohydrate-binding specificities.

  6. Carbohydrate sources in a coastal marine environment

    NASA Astrophysics Data System (ADS)

    Cowie, Gregory L.; Hedges, John I.

    1984-10-01

    Individual neutral sugars in sediments, sediment trap materials and major biological sources of a coastal marine environment (Dabob Bay, Washington State) were analyzed by capillary gas chromatography of equilibrated isomeric mixtures. Plankton, bacteria, and vascular plant tissues of different types yielded reproducible and biochemically consistent compositional patterns. These patterns, when expressed in simple parameters, allowed distinctions between marine and terrestrial carbohydrate sources as well as among the major different types of vascular plant tissues. Plankton and bacteria, due to their compositional diversity, were not further distinguishable by carbohydrate compositions alone. Carbohydrate compositions of Dabob Bay sediments and sediment trap materials, interpreted using source-indicator parameters, indicate a predominantly marine origin with increased relative input of terrestrially-derived carbohydrates in winter periods of low phytoplankton productivity. Both plankton and grasses are indicated as major carbohydrate sources during spring. Glucose yield enhancement factors, determined by comparative acid pretreatments, confirm the general predominance of α-cellulose-poor marine polysaccharides and increased levels of α-cellulose-rich vascular plant remains in winter sediment trap samples.

  7. Potential effect of ultrasound on carbohydrates.

    PubMed

    Bera, Smritilekha; Mondal, Dhananjoy; Martin, Jacob T; Singh, Man

    2015-06-17

    The use of ultrasound has emerged as one of the most useful alternative energy sources for the synthesis of carbohydrate-derived biologically and pharmaceutically potential compounds. Spectacular advances have been made in the field of sonication-assisted organic reactions, which are known for producing superior yields, enhanced reactivity of the reactant, improved stereoselectivity, and shortened reaction times. Orthogonal protection-deprotection reactions and/or modification and manipulation of functional groups in carbohydrates are common synthetic steps in carbohydrate chemistry. These reaction steps can be driven by the ultrasonic energy generated by acoustic cavitation via the formation and subsequent collapse of ultrasound-induced bubbles. The ultrasound-assisted synthesis of differently functionalised monosaccharides is useful in a wide variety of applications of carbohydrate chemistry such as the glycosylation of oligosaccharides, one pot domino reactions, thioglycoside syntheses, azidoglycoside syntheses, 1,3-dipolar cycloaddition reactions, and syntheses of natural products. This review article covers ultrasound-mediated reactions on carbohydrates that have been described in the literature since 2000.

  8. Coming of age: carbohydrates and immunity.

    PubMed

    Cobb, Brian A; Kasper, Dennis L

    2005-02-01

    Adaptive immune responses have long been considered the "territory" of antigenic proteins, whereas carbohydrates are characterized as T-cell-independent antigens that are not typically recognized by the complete adaptive machinery. The current modus operandi when searching for dominant epitopes is the use of synthetic peptides designed from the primary structure of interesting target proteins; however, there is growing evidence that sugars can also play a critical role in immune recognition. Findings reported in this issue of the European Journal of Immunology begin to shed light on the differences in protein glycosylation that can occur in association with disorders like rheumatoid arthritis and the effect these changes have on collagen recognition by the immune system. Other recent studies have shown that immunodominant glycopeptide "remnant" epitopes as well as glycosylation changes on self-proteins can generate autoimmunity. Finally, some types of carbohydrates are now known to be processed and presented to T cells by class II MHC. Taken together, these advances illustrate a clear importance for carbohydrate recognition in foreign and self antigens by the adaptive immune system. With the common presence of carbohydrate molecules on eukaryotic, prokaryotic, and viral surfaces, the impact of carbohydrates on adaptive immunity is now indisputable.

  9. Carbohydrates and T cells: a sweet twosome.

    PubMed

    Avci, Fikri Y; Li, Xiangming; Tsuji, Moriya; Kasper, Dennis L

    2013-04-01

    Carbohydrates as T cell-activating antigens have been generating significant interest. For many years, carbohydrates were thought of as T-independent antigens, however, more recent research had demonstrated that mono- or oligosaccharides glycosidically linked to peptides can be recognized by T cells. T cell recognition of these glycopeptides depends on the structure of both peptide and glycan portions of the antigen. Subsequently, it was discovered that natural killer T cells recognized glycolipids when presented by the antigen presenting molecule CD1d. A transformative insight into glycan-recognition by T cells occurred when zwitterionic polysaccharides were discovered to bind to and be presented by MHCII to CD4+ T cells. Based on this latter observation, the role that carbohydrate epitopes generated from glycoconjugate vaccines had in activating helper T cells was explored and it was found that these epitopes are presented to specific carbohydrate recognizing T cells through a unique mechanism. Here we review the key interactions between carbohydrate antigens and the adaptive immune system at the molecular, cellular and systems levels exploring the significant biological implications in health and disease.

  10. Carbohydrates and T cells: A sweet twosome

    PubMed Central

    Avci, Fikri Y.; Li, Xiangming; Tsuji, Moriya; Kasper, Dennis L.

    2013-01-01

    Carbohydrates as T cell-activating antigens have been generating significant interest. For many years, carbohydrates were thought of as T-independent antigens, however, more recent research had demonstrated that mono- or oligosaccharides glycosidically-linked to peptides can be recognized by T cells. T cell recognition of these glycopeptides depends on the structure of both peptide and glycan portions of the antigen. Subsequently, it was discovered that natural killer T cells recognized glycolipids when presented by the antigen presenting molecule CD1d. A transformative insight into glycan-recognition by T cells occurred when zwitterionic polysaccharides were discovered to bind to and be presented by MHCII to CD4+ T cells. Based on this latter observation, the role that carbohydrate epitopes generated from glycoconjugate vaccines had in activating helper T cells was explored and it was found that these epitopes are presented to specific carbohydrate recognizing T cells through a unique mechanism. Here we review the key interactions between carbohydrate antigens and the adaptive immune system at the molecular, cellular and systems levels exploring the significant biological implications in health and disease. PMID:23757291

  11. Neurobiologic basis of craving for carbohydrates.

    PubMed

    Ventura, Tamara; Santander, Jaime; Torres, Rafael; Contreras, Ana María

    2014-03-01

    There is a relationship between emotional disorders, obesity, and craving for carbohydrates. This relationship complicates the success of treatments aimed at combatting obesity, which is considered to be the epidemic of the twenty-first century. We conducted a review of the neurobiologic basis for carbohydrate craving, with the hope that this understanding will enable the design of more efficient therapeutic strategies. We conducted a non-systematic literature search in PubMed using MeSH. Research on the basis of carbohydrate craving is varied, but may be grouped into five main areas: the serotonergic system, palatability and hedonic response, the motivational system, stress response systems, and gene-environment interaction. The models that integrate motivational systems with palatability and hedonic response studies are the ones that we believe can best explain both craving for carbohydrates and related addictive phenomena. Research has contributed to a greater understanding of the neurobiologic basis of carbohydrate craving. The latter, in turn, contributes to an understanding of the implications, challenges, and possible therapies that might be put in place to cope with this phenomenon. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Saturated fat, carbohydrate, and cardiovascular disease.

    PubMed

    Siri-Tarino, Patty W; Sun, Qi; Hu, Frank B; Krauss, Ronald M

    2010-03-01

    A focus of dietary recommendations for cardiovascular disease (CVD) prevention and treatment has been a reduction in saturated fat intake, primarily as a means of lowering LDL-cholesterol concentrations. However, the evidence that supports a reduction in saturated fat intake must be evaluated in the context of replacement by other macronutrients. Clinical trials that replaced saturated fat with polyunsaturated fat have generally shown a reduction in CVD events, although several studies showed no effects. An independent association of saturated fat intake with CVD risk has not been consistently shown in prospective epidemiologic studies, although some have provided evidence of an increased risk in young individuals and in women. Replacement of saturated fat by polyunsaturated or monounsaturated fat lowers both LDL and HDL cholesterol. However, replacement with a higher carbohydrate intake, particularly refined carbohydrate, can exacerbate the atherogenic dyslipidemia associated with insulin resistance and obesity that includes increased triglycerides, small LDL particles, and reduced HDL cholesterol. In summary, although substitution of dietary polyunsaturated fat for saturated fat has been shown to lower CVD risk, there are few epidemiologic or clinical trial data to support a benefit of replacing saturated fat with carbohydrate. Furthermore, particularly given the differential effects of dietary saturated fats and carbohydrates on concentrations of larger and smaller LDL particles, respectively, dietary efforts to improve the increasing burden of CVD risk associated with atherogenic dyslipidemia should primarily emphasize the limitation of refined carbohydrate intakes and a reduction in excess adiposity.

  13. Saturated fat, carbohydrate, and cardiovascular disease1234

    PubMed Central

    Siri-Tarino, Patty W; Sun, Qi; Hu, Frank B; Krauss, Ronald M

    2010-01-01

    A focus of dietary recommendations for cardiovascular disease (CVD) prevention and treatment has been a reduction in saturated fat intake, primarily as a means of lowering LDL-cholesterol concentrations. However, the evidence that supports a reduction in saturated fat intake must be evaluated in the context of replacement by other macronutrients. Clinical trials that replaced saturated fat with polyunsaturated fat have generally shown a reduction in CVD events, although several studies showed no effects. An independent association of saturated fat intake with CVD risk has not been consistently shown in prospective epidemiologic studies, although some have provided evidence of an increased risk in young individuals and in women. Replacement of saturated fat by polyunsaturated or monounsaturated fat lowers both LDL and HDL cholesterol. However, replacement with a higher carbohydrate intake, particularly refined carbohydrate, can exacerbate the atherogenic dyslipidemia associated with insulin resistance and obesity that includes increased triglycerides, small LDL particles, and reduced HDL cholesterol. In summary, although substitution of dietary polyunsaturated fat for saturated fat has been shown to lower CVD risk, there are few epidemiologic or clinical trial data to support a benefit of replacing saturated fat with carbohydrate. Furthermore, particularly given the differential effects of dietary saturated fats and carbohydrates on concentrations of larger and smaller LDL particles, respectively, dietary efforts to improve the increasing burden of CVD risk associated with atherogenic dyslipidemia should primarily emphasize the limitation of refined carbohydrate intakes and a reduction in excess adiposity. PMID:20089734

  14. Low-carbohydrate diets and performance.

    PubMed

    Cook, Chad M; Haub, Mark D

    2007-07-01

    Athletes are continually searching for means to optimize their performance. Within the past 20 years, athletes and scientists have reported or observed that consuming a carbohydrate-restricted diet may improve performance. The original theories explaining the purported benefits centered on the fact that fat oxidation increases, thereby "sparing" muscle glycogen. More recent concepts that explain the plausibility of the ergogenicity of low-carbohydrate, or high-fat, diets on exercise performance pertain to an effect similar to altitude training. We and others have observed that although fat oxidation may be increased, the ability to maintain high-intensity exercise (above the lactate threshold) seems to be compromised or at least indifferent when compared with consumption of more carbohydrate. That said, clinical studies clearly demonstrate that ad libitum low-carbohydrate diets elicit greater decreases in body weight and fat than energy-equivalent low-fat diets, especially over a short duration. Thus, although low-carbohydrate and high-fat diets appear detrimental or indifferent relative to performance, they may be a faster means to achieve a more competitive body composition.

  15. Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction.

    PubMed

    Zhao, Huiying; Yang, Yuedong; von Itzstein, Mark; Zhou, Yaoqi

    2014-11-15

    Carbohydrate-binding proteins (CBPs) are potential biomarkers and drug targets. However, the interactions between carbohydrates and proteins are challenging to study experimentally and computationally because of their low binding affinity, high flexibility, and the lack of a linear sequence in carbohydrates as exists in RNA, DNA, and proteins. Here, we describe a structure-based function-prediction technique called SPOT-Struc that identifies carbohydrate-recognizing proteins and their binding amino acid residues by structural alignment program SPalign and binding affinity scoring according to a knowledge-based statistical potential based on the distance-scaled finite-ideal gas reference state (DFIRE). The leave-one-out cross-validation of the method on 113 carbohydrate-binding domains and 3442 noncarbohydrate binding proteins yields a Matthews correlation coefficient of 0.56 for SPalign alone and 0.63 for SPOT-Struc (SPalign + binding affinity scoring) for CBP prediction. SPOT-Struc is a technique with high positive predictive value (79% correct predictions in all positive CBP predictions) with a reasonable sensitivity (52% positive predictions in all CBPs). The sensitivity of the method was changed slightly when applied to 31 APO (unbound) structures found in the protein databank (14/31 for APO versus 15/31 for HOLO). The result of SPOT-Struc will not change significantly if highly homologous templates were used. SPOT-Struc predicted 19 out of 2076 structural genome targets as CBPs. In particular, one uncharacterized protein in Bacillus subtilis (1oq1A) was matched to galectin-9 from Mus musculus. Thus, SPOT-Struc is useful for uncovering novel carbohydrate-binding proteins. SPOT-Struc is available at http://sparks-lab.org.

  16. Structural Basis for Carbohydrate Recognition and Anti-inflammatory Modulation by Gastrointestinal Nematode Parasite Toxascaris leonina Galectin.

    PubMed

    Hwang, Eun Young; Jeong, Mi Suk; Park, Sang Kyun; Ha, Sung Chul; Yu, Hak Sun; Jang, Se Bok

    2016-12-02

    Toxascaris leonina galectin (Tl-gal) is a galectin-9 homologue protein isolated from an adult worm of the canine gastrointestinal nematode parasite, and Tl-gal-vaccinated challenge can inhibit inflammation in inflammatory bowel disease-induced mice. We determined the first X-ray structures of full-length Tl-gal complexes with carbohydrates (lactose, N-acetyllactosamine, lacto-N-tetraose, sialyllactose, and glucose). Bonds were formed on concave surfaces of both carbohydrate recognition domains (CRDs) in Tl-gal. All binding sites were found in the HXXXR and WGXEER motifs. Charged Arg(61)/Arg(196) and Glu(80)/Glu(215) on the conserved motif of Tl-gal N-terminal CRD and C-terminal CRD are critical amino acids for recognizing carbohydrate binding, and the residues can affect protein folding and structure. The polar amino acids His, Asn, and Trp are also important residues for the interaction with carbohydrates through hydrogen bonding. Hemagglutination activities of Tl-gal were inhibited by interactions with carbohydrates and mutations. We found that the mutation of Tl-gal (E80A/E215A) at the carbohydrate binding region induced protein aggregation and could be caused in many diseases. The short linker region between the N-terminal and C-terminal CRDs of Tl-gal was very stable against proteolysis and maintained its biological activity. This structural information is expected to elucidate the carbohydrate recognition mechanism of Tl-gal and improve our understanding of anti-inflammatory mediators and modulators of immune response.

  17. Carbohydrate-protein interactions that drive processive polysaccharide translocation in enzymes revealed from a computational study of cellobiohydrolase processivity.

    PubMed

    Knott, Brandon C; Crowley, Michael F; Himmel, Michael E; Ståhlberg, Jerry; Beckham, Gregg T

    2014-06-18

    Translocation of carbohydrate polymers through protein tunnels and clefts is a ubiquitous biochemical phenomenon in proteins such as polysaccharide synthases, glycoside hydrolases, and carbohydrate-binding modules. Although static snapshots of carbohydrate polymer binding in proteins have long been studied via crystallography and spectroscopy, the molecular details of polysaccharide chain processivity have not been elucidated. Here, we employ simulation to examine how a cellulose chain translocates by a disaccharide unit during the processive cycle of a glycoside hydrolase family 7 cellobiohydrolase. Our results demonstrate that these biologically and industrially important enzymes employ a two-step mechanism for chain threading to form a Michaelis complex and that the free energy barrier to chain threading is significantly lower than the hydrolysis barrier. Taken with previous studies, our findings suggest that the rate-limiting step in enzymatic cellulose degradation is the glycosylation reaction, not chain processivity. Based on the simulations, we find that strong electrostatic interactions with polar residues that are conserved in GH7 cellobiohydrolases, but not in GH7 endoglucanases, at the leading glucosyl ring provide the thermodynamic driving force for polysaccharide chain translocation. Also, we consider the role of aromatic-carbohydrate interactions, which are widespread in carbohydrate-active enzymes and have long been associated with processivity. Our analysis suggests that the primary role for these aromatic residues is to provide tunnel shape and guide the carbohydrate chain to the active site. More broadly, this work elucidates the role of common protein motifs found in carbohydrate-active enzymes that synthesize or depolymerize polysaccharides by chain translocation mechanisms coupled to catalysis.

  18. Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase.

    PubMed

    Ohlin, Mats; von Schantz, Laura; Schrader, Tobias E; Ostermann, Andreas; Logan, Derek T; Fisher, S Zoë

    2015-08-01

    Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that bind specific types of carbohydrates. Ultra high-resolution X-ray crystallographic studies of CBMs have helped to decipher the basis for specificity in carbohydrate-protein interactions. However, additional studies are needed to better understand which structural determinants confer which carbohydrate-binding properties. To address these issues, neutron crystallographic studies were initiated on one experimentally engineered CBM derived from a xylanase, X-2 L110F, a protein that is able to bind several different plant carbohydrates such as xylan, β-glucan and xyloglucan. This protein evolved from a CBM present in xylanase Xyn10A of Rhodothermus marinus. The protein was complexed with a branched xyloglucan heptasaccharide. Large single crystals of hydrogenous protein (∼1.6 mm(3)) were grown at room temperature and subjected to H/D exchange. Both neutron and X-ray diffraction data sets were collected to 1.6 Å resolution. Joint neutron and X-ray refinement using phenix.refine showed significant density for residues involved in carbohydrate binding and revealed the details of a hydrogen-bonded water network around the binding site. This is the first report of a neutron structure of a CBM and will add to the understanding of protein-carbohydrate binding interactions.

  19. Investigation of Carbohydrate Recognition via Computer Simulation.

    PubMed

    Johnson, Quentin R; Lindsay, Richard J; Petridis, Loukas; Shen, Tongye

    2015-04-28

    Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Recently, interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. We focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We review the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.

  20. Boronic acids for fluorescence imaging of carbohydrates.

    PubMed

    Sun, Xiaolong; Zhai, Wenlei; Fossey, John S; James, Tony D

    2016-02-28

    "Fluorescence imaging" is a particularly exciting and rapidly developing area of research; the annual number of publications in the area has increased ten-fold over the last decade. The rapid increase of interest in fluorescence imaging will necessitate the development of an increasing number of molecular receptors and binding agents in order to meet the demand in this rapidly expanding area. Carbohydrate biomarkers are particularly important targets for fluorescence imaging given their pivotal role in numerous important biological events, including the development and progression of many diseases. Therefore, the development of new fluorescent receptors and binding agents for carbohydrates is and will be increasing in demand. This review highlights the development of fluorescence imaging agents based on boronic acids a particularly promising class of receptors given their strong and selective binding with carbohydrates in aqueous media.

  1. Nutraceutical and pharmacological implications of marine carbohydrates.

    PubMed

    Pallela, Ramjee

    2014-01-01

    Current day's research has been focusing much on the potential pharmacological or nutraceutical agents of selective health benefits with less toxicity. As a consequence of increased demand of nutritional supplements of great medicinal values, development of therapeutic agents from natural sources, in particular, marine environment are being considered much important. A diverse array of marine natural products containing medicinally useful nutritional substances, i.e., marine nutraceuticals have been focused to the benefit of mankind. Carbohydrates, by being constituted in considerable amount of many marine organisms display several nutraceutical and pharmaceutical behavior to defend from various diseases. Moreover, the carbohydrates from algae as well as from shellfish wastes, like chitosan and its derivatives, showed tremendous applications in biology and biomedicine. In the current chapter, several of marine carbohydrates from various marine flora and fauna have been covered with their applications and prospects in the development of nutraceuticals and pharmaceuticals. © 2014 Elsevier Inc. All rights reserved.

  2. Investigation of Carbohydrate Recognition via Computer Simulation

    DOE PAGES

    Johnson, Quentin R.; Lindsay, Richard J.; Petridis, Loukas; ...

    2015-04-28

    Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. Here, we focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We reviewmore » the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.« less

  3. Investigation of Carbohydrate Recognition via Computer Simulation

    SciTech Connect

    Johnson, Quentin R.; Lindsay, Richard J.; Petridis, Loukas; Shen, Tongye

    2015-04-28

    Carbohydrate recognition by proteins, such as lectins and other (bio)molecules, can be essential for many biological functions. Interest has arisen due to potential protein and drug design and future bioengineering applications. A quantitative measurement of carbohydrate-protein interaction is thus important for the full characterization of sugar recognition. Here, we focus on the aspect of utilizing computer simulations and biophysical models to evaluate the strength and specificity of carbohydrate recognition in this review. With increasing computational resources, better algorithms and refined modeling parameters, using state-of-the-art supercomputers to calculate the strength of the interaction between molecules has become increasingly mainstream. We review the current state of this technique and its successful applications for studying protein-sugar interactions in recent years.

  4. Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network

    PubMed Central

    Malik, Adeel; Ahmad, Shandar

    2007-01-01

    Background Protein-Carbohydrate interactions are crucial in many biological processes with implications to drug targeting and gene expression. Nature of protein-carbohydrate interactions may be studied at individual residue level by analyzing local sequence and structure environments in binding regions in comparison to non-binding regions, which provide an inherent control for such analyses. With an ultimate aim of predicting binding sites from sequence and structure, overall statistics of binding regions needs to be compiled. Sequence-based predictions of binding sites have been successfully applied to DNA-binding proteins in our earlier works. We aim to apply similar analysis to carbohydrate binding proteins. However, due to a relatively much smaller region of proteins taking part in such interactions, the methodology and results are significantly different. A comparison of protein-carbohydrate complexes has also been made with other protein-ligand complexes. Results We have compiled statistics of amino acid compositions in binding versus non-binding regions- general as well as in each different secondary structure conformation. Binding propensities of each of the 20 residue types and their structure features such as solvent accessibility, packing density and secondary structure have been calculated to assess their predisposition to carbohydrate interactions. Finally, evolutionary profiles of amino acid sequences have been used to predict binding sites using a neural network. Another set of neural networks was trained using information from single sequences and the prediction performance from the evolutionary profiles and single sequences were compared. Best of the neural network based prediction could achieve an 87% sensitivity of prediction at 23% specificity for all carbohydrate-binding sites, using evolutionary information. Single sequences gave 68% sensitivity and 55% specificity for the same data set. Sensitivity and specificity for a limited galactose

  5. Engineered xyloglucan specificity in a carbohydrate-binding module.

    PubMed

    Gunnarsson, Lavinia Cicortas; Zhou, Qi; Montanier, Cedric; Karlsson, Eva Nordberg; Brumer, Harry; Ohlin, Mats

    2006-12-01

    The field of plant cell wall biology is constantly growing and consequently so is the need for more sensitive and specific probes for individual wall components. Xyloglucan is a key polysaccharide widely distributed in the plant kingdom in both structural and storage tissues that exist in both fucosylated and non-fucosylated variants. Presently, the only xyloglucan marker available is the monoclonal antibody CCRC-M1 that is specific to terminal alpha-1,2-linked fucosyl residues on xyloglucan oligo- and polysaccharides. As a viable alternative to searches for natural binding proteins or creation of new monoclonal antibodies, an approach to select xyloglucan-specific binding proteins from a combinatorial library of the carbohydrate-binding module, CBM4-2, from xylanase Xyn10A of Rhodothermus marinus is described. Using phage display technology in combination with a chemoenzymatic method to anchor xyloglucan to solid supports, the selection of xyloglucan-binding modules with no detectable residual wild-type xylan and beta-glucan-binding ability was achieved.

  6. Oxygen solubility and permeability of carbohydrates.

    PubMed

    Whitcombe, Michael J; Parker, Roger; Ring, Stephen G

    2005-06-13

    The saturated oxygen concentration in a series of aqueous solutions of sorbitol (up to 35% w/w) and maltitol (up to 50% w/w) was measured using colorimetric reagent vials based on Rhodazine D. The results indicate that the solubility of oxygen in low-water carbohydrates is considerably lower than its solubility in pure water. It was concluded that the low-oxygen solubility is a major factor contributing to the barrier properties of low-water content carbohydrates used in the encapsulation of flavours, lipids, peptides and other oxidisable species.

  7. Capillary electrophoresis-mass spectrometry of carbohydrates

    PubMed Central

    Zaia, Joseph

    2014-01-01

    The development of methods for capillary electrophoresis (CE) with on-line mass spectrometric detection (CE/MS) is driven by the need for accurate, robust and sensitive glycomics analysis for basic biomedicine, biomarker discovery, and analysis of recombinant protein therapeutics. One important capability is to profile glycan mixtures with respect to the patterns of substituents including sialic acids, acetate, sulfate, phosphate, and other groups. There is additional need for an MS-compatible separation system capable of resolving carbohydrate isomers. This review summarizes applications of CS/MS to analysis of carbohydrates, glycoproteins and glycopeptides that have appeared since 2008. Readers are referred to recent comprehensive reviews covering earlier publications. PMID:23386333

  8. Capillary electrophoresis-mass spectrometry of carbohydrates.

    PubMed

    Zaia, Joseph

    2013-01-01

    The development of methods for capillary electrophoresis (CE) with on-line mass spectrometric detection (CE/MS) is driven by the need for accurate, robust, and sensitive glycomics analysis for basic biomedicine, biomarker discovery, and analysis of recombinant protein therapeutics. One important capability is to profile glycan mixtures with respect to the patterns of substituents including sialic acids, acetate, sulfate, phosphate, and other groups. There is additional need for an MS-compatible separation system capable of resolving carbohydrate isomers. This chapter summarizes applications of CS/MS to analysis of carbohydrates, glycoproteins, and glycopeptides that have appeared since 2008. Readers are referred to recent comprehensive reviews covering earlier publications.

  9. Fructose-derived carbohydrates from Alisma orientalis.

    PubMed

    Zhang, Zhen; Wang, Dong; Zhao, Yun; Gao, Hong; Hu, Ying-He; Hu, Jin-Feng

    2009-01-01

    Nine fructose-derived carbohydrates were obtained from the methanol extract from the rhizome of Alisma orientalis. On the basis of spectroscopic analysis, their structures were determined to be alpha-D-fructofuranose (1), beta-D-fructofuranose (2), ethyl alpha-D-fructofuranoside (3), ethyl beta-D-fructofuranoside (4), 5-hydroxymethyl-furaldehyde (5), sucrose (6), raffinose (7), stachyose (8) and verbascose (9), along with two oligosaccharides of manninotriose (10) and verbascotetraose (11). Compounds 3, 4 and 7-11 were isolated from this plant for the first time. A hypothetical biosynthesis pathway among these isolated carbohydrates (1-11) was briefly introduced.

  10. Minimally refined biomass fuel. [carbohydrate-water-alcohol mixture

    SciTech Connect

    Pearson, R.K.; Hirschfeld, T.B.

    1981-03-26

    A minimally refined fluid composition, suitable as a fuel mixture and derived from biomass material, is comprised of one or more water-soluble carbohydrates such as sucrose, one or more alcohols having less than four carbons, and water. The carbohydrate provides the fuel source; water-solubilizes the carbohydrate; and the alcohol aids in the combustion of the carbohydrate and reduces the viscosity of the carbohydrate/water solution. Because less energy is required to obtain the carbohydrate from the raw biomass than alcohol, an overall energy savings is realized compared to fuels employing alcohol as the primary fuel.

  11. Dietary intakes, attitudes toward carbohydrates of postmenopausal women following low carbohydrate diets.

    PubMed

    Winham, Donna M; Collins, Courtney B; Hutchins, Andrea M

    2009-01-01

    Middle-aged women have the highest levels of obesity and comprise the largest group of dieters. Few investigators have examined how women apply weight-loss diet principles in an unsupervised setting. Dietary intakes and attitudes toward carbohydrates were examined in women who were self-reported low carbohydrate dieters (SRLCDs); these intakes and attitudes were compared with those of women who were following their normal diet (non-dieters [NDs]). A convenience sample of 29 postmenopausal women aged 45 to 65 was recruited. Data were obtained by interview, questionnaire, and direct anthropometric measurement. Descriptive statistics, chi-square analysis, and analysis of variance were used to compare groups. Although total energy and protein intakes were similar, SRLCDs consumed significantly more fat and less carbohydrate (expressed as a percentage of total energy) and more cholesterol and less fibre than did NDs. Both groups had unfavourable attitudes toward carbohydrates. The SRLCDs ate more fat than recommended. Women who are considering following a low carbohydrate diet need to know the nutritional risks of unbalanced self-designed low carbohydrate diets. Negative attitudes toward carbohydrates were not confined to dieters. Nutrition education is necessary to help consumers understand basic nutrition principles and to be more skeptical of fad diets.

  12. Carbohydrate mouth rinse and caffeine improves high-intensity interval running capacity when carbohydrate restricted.

    PubMed

    Kasper, Andreas M; Cocking, Scott; Cockayne, Molly; Barnard, Marcus; Tench, Jake; Parker, Liam; McAndrew, John; Langan-Evans, Carl; Close, Graeme L; Morton, James P

    2016-08-01

    We tested the hypothesis that carbohydrate mouth rinsing, alone or in combination with caffeine, augments high-intensity interval (HIT) running capacity undertaken in a carbohydrate-restricted state. Carbohydrate restriction was achieved by performing high-intensity running to volitional exhaustion in the evening prior to the main experimental trials and further refraining from carbohydrate intake in the post-exercise and overnight period. On the subsequent morning, eight males performed 45-min steady-state (SS) exercise (65% [Formula: see text]) followed by HIT running to exhaustion (1-min at 80% [Formula: see text]interspersed with 1-min walking at 6 km/h). Subjects completed 3 trials consisting of placebo capsules (administered immediately prior to SS and immediately before HIT) and placebo mouth rinse at 4-min intervals during HIT (PLACEBO), placebo capsules but 10% carbohydrate mouth rinse (CMR) at corresponding time-points or finally, caffeine capsules (200 mg per dose) plus 10% carbohydrate mouth rinse (CAFF + CMR) at corresponding time-points. Heart rate, capillary glucose, lactate, glycerol and NEFA were not different at exhaustion during HIT (P > 0.05). However, HIT capacity was different (P < 0.05) between all pair-wise comparisons such that CAFF + CMR (65 ± 26 min) was superior to CMR (52 ± 23 min) and PLACEBO (36 ± 22 min). We conclude that carbohydrate mouth rinsing and caffeine ingestion improves exercise capacity undertaken in carbohydrate-restricted states. Such nutritional strategies may be advantageous for those athletes who deliberately incorporate elements of training in carbohydrate-restricted states (i.e. the train-low paradigm) into their overall training programme in an attempt to strategically enhance mitochondrial adaptations of skeletal muscle.

  13. The mean hydration of carbohydrates as studied by normalized two-dimensional radial pair distributions.

    PubMed

    Andersson, C; Engelsen, S B

    1999-04-01

    The hydration of carbohydrates plays a key role in many biological processes. Molecular dynamics simulations provide an effective tool for investigating the hydration of complex solutes such as carbohydrates. In this article we devise an algorithm for the calculation of two-dimensional radial pair distributions describing the probability of finding a water molecule in a site defined by two reference atoms. The normalized 2D radial pair distribution is proposed as an effective tool for investigating and comparing localized or ordered water sites around flexible molecules such as carbohydrates when analyzing molecular dynamics simulations and the utility of 2D radial pair distributions is demonstrated using sucrose as an example. In this relatively simple structure, 2D radial pair distributions were able to characterize and quantify the importance of two unique interresidue hydration sites in which a water molecule is forming a bridge between the glycopyranosyl and fructofuranosyl residues. The approach is proposed to be a valuable tool for comparing and understanding the hydration of flexible biomolecules such as carbohydrates.

  14. Effects of carbohydrate, protein and lipid content of organic waste on hydrogen production and fermentation products.

    PubMed

    Alibardi, Luca; Cossu, Raffaello

    2016-01-01

    Organic waste from municipalities, food waste and agro-industrial residues are ideal feedstocks for use in biological conversion processes in biorefinery chains, representing biodegradable materials containing a series of substances belonging to the three main groups of the organic matter: carbohydrates, proteins and lipids. Biological hydrogen production by dark fermentation may assume a central role in the biorefinery concept, representing an up-front treatment for organic waste capable of hydrolysing complex organics and producing biohydrogen. This research study was aimed at evaluating the effects of carbohydrate, protein and lipid content of organic waste on hydrogen yields, volatile fatty acid production and carbon-fate. Biogas and hydrogen productions were linearly correlated to carbohydrate content of substrates while proteins and lipids failed to produce significant contributions. Chemical composition also produced effects on the final products of dark fermentation. Acetic and butyric acids were the main fermentation products, with their ratio proving to correlate with carbohydrate and protein content. The results obtained in this research study enhance the understanding of data variability on hydrogen yields from organic waste. Detailed information on waste composition and chemical characterisation are essential to clearly identify the potential performances of the dark fermentation process.

  15. Pyrolysis characteristics and pathways of protein, lipid and carbohydrate isolated from microalgae Nannochloropsis sp.

    PubMed

    Wang, Xin; Sheng, Lili; Yang, Xiaoyi

    2017-04-01

    Microalgal components were isolated gradually to get lipid-rich, protein-rich and carbohydrate-rich components. The aim of this work was to study pyrolysis mechanism of microalgae by real isolated real algae components. Thermogrametric analysis (DTG) curve of microalgae was fitted by single pyrolysis curves of protein, lipid and carbohydrate except special zones, which likely affected by cell disruption and hydrolysis mass loss. Experimental microalgae liquefaction without water index N was 0.6776, 0.3861 and 0.2856 for isolated lipid, protein and carbohydrate. Pyrolysis pathways of lipid are decarboxylation, decarbonylation, fragmentation of glycerin moieties and steroid to form hydrocarbons, carboxylic acids and esters. Pyrolysis pathways of protein are decarboxylation, deamination, hydrocarbon residue fragmentation, dimerization and fragmentation of peptide bonds to form amide/amines/nitriles, esters, hydrocarbons and N-heterocyclic compounds, especially diketopiperazines (DKPs). Pyrolysis pathways of carbohydrate are dehydrated reactions and further fragmentation to form ketones and aldehyde, decomposition of lignin to form phenols, and fragmentation of lipopolysaccharides. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. A Universal Protocol for Photochemical Covalent Immobilization of Intact Carbohydrates for the Preparation of Carbohydrate Microarrays

    PubMed Central

    Wang, Huibin; Zhang, Yiming; Yuan, Xun; Chen, Yi; Yan, Mingdi

    2010-01-01

    A universal photochemical method has been established for the immobilization of intact carbohydrates and their analogues, and for the fabrication of carbohydrate microarrays. The method features the use of perfluorophenyl azide (PFPA)-modified substrates and the photochemical reaction of surface azido groups with printed carbohydrates. Various aldoses, ketoses, non-reducing sugars such as alditols and their derivatives can be directly arrayed on the PFPA-modified chips. The lectin-recognition ability of arrayed mannose, glucose and their oligo- and polysaccharides were confirmed using surface plasmon resonance imaging and laser-induced fluorescence imaging. PMID:21138274

  17. Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects

    PubMed Central

    Fadda, Elisa; Woods, Robert J.

    2014-01-01

    The characterization of the 3D structure of oligosaccharides, their conjugates and analogs is particularly challenging for traditional experimental methods. Molecular simulation methods provide a basis for interpreting sparse experimental data and for independently predicting conformational and dynamic properties of glycans. Here, we summarize and analyze the issues associated with modeling carbohydrates, with a detailed discussion of four of the most recently developed carbohydrate force fields, reviewed in terms of applicability to natural glycans, carbohydrate–protein complexes and the emerging area of glycomimetic drugs. In addition, we discuss prospectives and new applications of carbohydrate modeling in drug discovery. PMID:20594934

  18. CD44 receptor unfolding enhances binding by freeing basic amino acids to contact carbohydrate ligand.

    PubMed

    Favreau, Amanda J; Faller, Christina E; Guvench, Olgun

    2013-09-03

    The extracellular carbohydrate-binding domain of the Type I transmembrane receptor CD44 is known to undergo affinity switching, where change in conformation leads to enhanced binding of its carbohydrate ligand hyaluronan. Separate x-ray crystallographic and NMR experiments have led to competing explanations, with the former supporting minor conformational changes at the binding site and the latter a major order-to-disorder unfolding transition distant from the binding site. Here, all-atom explicit-solvent molecular dynamics studies employing adaptive biasing force sampling revealed a substantial favorable free-energy change associated with contact formation between the Arg(41) side chain and hyaluronan at the binding site, independent of whether the distant site was ordered or disordered. Analogous computational experiments on Arg(41)Ala mutants showed loss of this favorable free-energy change, consistent with existing experimental data. More provocatively, the simulation data revealed the molecular mechanism by which the order-to-disorder transition enhances hyaluronan binding: in the disordered state, a number of basic residues gain sufficient conformational freedom-lacking in the ordered state-to spontaneously form side-chain contacts with hyaluronan. Mutation of these residues to Ala had been known to decrease binding affinity, but there had previously been no structural explanation, given their lack of proximity to the carbohydrate-binding site in existing structures of the complex.

  19. Analyses of extracellular carbohydrates in oomycetes unveil the existence of three different cell wall types.

    PubMed

    Mélida, Hugo; Sandoval-Sierra, Jose V; Diéguez-Uribeondo, Javier; Bulone, Vincent

    2013-02-01

    Some of the most devastating plant and animal pathogens belong to the oomycete class. The cell walls of these microorganisms represent an excellent target for disease control, but their carbohydrate composition is elusive. We have undertaken a detailed cell wall analysis in 10 species from 2 major oomycete orders, the Peronosporales and the Saprolegniales, thereby unveiling the existence of 3 clearly different cell wall types: type I is devoid of N-acetylglucosamine (GlcNAc) but contains glucuronic acid and mannose; type II contains up to 5% GlcNAc and residues indicative of cross-links between cellulose and 1,3-β-glucans; type III is characterized by the highest GlcNAc content (>5%) and the occurrence of unusual carbohydrates that consist of 1,6-linked GlcNAc residues. These 3 cell wall types are also distinguishable by their cellulose content and the fine structure of their 1,3-β-glucans. We propose a cell wall paradigm for oomycetes that can serve as a basis for the establishment of cell wall architectural models and the further identification of cell wall subtypes. This paradigm is complementary to morphological and molecular criteria for taxonomic grouping and provides useful information for unraveling poorly understood cell wall carbohydrate biosynthetic pathways through the identification and characterization of the corresponding enzymes.

  20. Analyses of Extracellular Carbohydrates in Oomycetes Unveil the Existence of Three Different Cell Wall Types

    PubMed Central

    Mélida, Hugo; Sandoval-Sierra, Jose V.; Diéguez-Uribeondo, Javier

    2013-01-01

    Some of the most devastating plant and animal pathogens belong to the oomycete class. The cell walls of these microorganisms represent an excellent target for disease control, but their carbohydrate composition is elusive. We have undertaken a detailed cell wall analysis in 10 species from 2 major oomycete orders, the Peronosporales and the Saprolegniales, thereby unveiling the existence of 3 clearly different cell wall types: type I is devoid of N-acetylglucosamine (GlcNAc) but contains glucuronic acid and mannose; type II contains up to 5% GlcNAc and residues indicative of cross-links between cellulose and 1,3-β-glucans; type III is characterized by the highest GlcNAc content (>5%) and the occurrence of unusual carbohydrates that consist of 1,6-linked GlcNAc residues. These 3 cell wall types are also distinguishable by their cellulose content and the fine structure of their 1,3-β-glucans. We propose a cell wall paradigm for oomycetes that can serve as a basis for the establishment of cell wall architectural models and the further identification of cell wall subtypes. This paradigm is complementary to morphological and molecular criteria for taxonomic grouping and provides useful information for unraveling poorly understood cell wall carbohydrate biosynthetic pathways through the identification and characterization of the corresponding enzymes. PMID:23204192

  1. Low-carbohydrate diets and all-cause and cause-specific mortality: Two cohort Studies

    PubMed Central

    Fung, Teresa T.; van Dam, Rob M.; Hankinson, Susan E.; Stampfer, Meir; Willett, Walter C.; Hu, Frank B.

    2010-01-01

    Background Data on the long-term association between low-carbohydrate diets and mortality are sparse. Objective To examine the association of low-carbohydrate diets with mortality during 26 years of follow-up in women and 20 years in men. Design A prospective cohort study of women and men, followed from 1980 (women) or 1986 (men) until 2006. Low-carbohydrate diets, either animal-based (emphasizing animal sources of fat and protein), or vegetable-based (emphasizing vegetable sources of fat and protein) were computed from multiple validated food frequency questionnaire assessed during follow-up. Setting Nurses' Health Study and Health Professionals' Follow-up Study Participants 85,168 women (aged 34-59 years at baseline) and 44,548 men (aged 40-75 years at baseline) without heart disease, cancer, or diabetes. Measurement Investigator documented 12,555 deaths (2,458 cardiovascular, 5,780 cancer) in women and 8,678 deaths (2,746 cardiovascular, 2,960 cancer) in men. Results The overall low-carbohydrate score was associated with a modest increase in overall mortality in pooled analysis (Hazard Ratio, HR, comparing extreme deciles=1.12 (95% CI=1.01-1.24, p-trend=0.14). The animal low-carbohydrate score was associated with a higher all-cause mortality (pooled HR comparing extreme deciles=1.23, 95% CI=1.11-1.37, p-trend=0.05), cardiovascular mortality (corresponding HR=1.14, 95% CI=1.01-1.29, p-trend=0.029), and cancer mortality (corresponding HR=1.28, 95% CI 1.02-1.60, p for trend = 0.09). In contrast, a higher vegetable low-carbohydrate score was associated with lower all-cause (HR=0.80, 95% CI=0.75-0.85, p-trend<0.001) and cardiovascular mortality (HR=0.77, 95% CI=0.68-0.87, p-trend<0.001). Limitations Diet and lifestyle characteristics were assessed with some degree of error, however, sensitivity analyses indicated that results were not unlikely to be substantially affected by residual or confounding or an unmeasured confounder. In addition, participants were not a

  2. The isolation, and amino acid and carbohydrate composition, of polymeric collagens prepared from various human tissues.

    PubMed

    Schofield, J D; Freeman, I L; Jackson, D S

    1971-09-01

    1. Insoluble polymeric collagens from various human tissues were prepared by the EDTA method. Almost all of the collagen from simple soft tissues such as dermis, tendon, submucosa, sclera and cornea could be extracted, whereas the more complex tissues such as intercostal cartilage and intervertebral disc yielded only small amounts of collagen. Amino acid and carbohydrate analysis indicated that most of the preparations were highly purified on the basis of their tyrosine, hexosamine, mannose, xylose and fucose contents. 2. Wide variation in the total hexose content was observed, the lowest being 8.5 residues/3000 amino acid residues for collagen from dermis and the highest being 42.1 residues/3000 in corneal collagen. The molar ratios of sugars also varied, submucosal collagen having a galactose/glucose ratio of 1.0 and corneal collagen having a ratio of 2.3. 3. The presence of glucosylgalactosylhydroxylysine was confirmed in submucosal collagen by compositional and chromatographic analysis of this component after its isolation from alkaline hydrolysates of the collagen. Evidence was also obtained for the presence of galactosylhydroxylysine. 4. Determination of the hydroxylysyl glycosides was carried out and it was observed that the amounts of these components varied widely from tissue to tissue. Corneal collagen contained 19.1 hydroxylysine-linked carbohydrate units/3000 amino acid residues, whereas tendon collagen contained only 4.1 units/3000. Variation in the ratio disaccharide unit/monosaccharide unit was also observed, the ratio being 1.2 in intercostal cartilage collagen and 4.1 in submucosal collagen. The proportion of the total hydroxylysine that was substituted by carbohydrate also varied from tissue to tissue.

  3. The isolation, and amino acid and carbohydrate composition, of polymeric collagens prepared from various human tissues

    PubMed Central

    Schofield, J. D.; Freeman, I. L.; Jackson, D. S.

    1971-01-01

    1. Insoluble polymeric collagens from various human tissues were prepared by the EDTA method. Almost all of the collagen from simple soft tissues such as dermis, tendon, submucosa, sclera and cornea could be extracted, whereas the more complex tissues such as intercostal cartilage and intervertebral disc yielded only small amounts of collagen. Amino acid and carbohydrate analysis indicated that most of the preparations were highly purified on the basis of their tyrosine, hexosamine, mannose, xylose and fucose contents. 2. Wide variation in the total hexose content was observed, the lowest being 8.5 residues/3000 amino acid residues for collagen from dermis and the highest being 42.1 residues/3000 in corneal collagen. The molar ratios of sugars also varied, submucosal collagen having a galactose/glucose ratio of 1.0 and corneal collagen having a ratio of 2.3. 3. The presence of glucosylgalactosylhydroxylysine was confirmed in submucosal collagen by compositional and chromatographic analysis of this component after its isolation from alkaline hydrolysates of the collagen. Evidence was also obtained for the presence of galactosylhydroxylysine. 4. Determination of the hydroxylysyl glycosides was carried out and it was observed that the amounts of these components varied widely from tissue to tissue. Corneal collagen contained 19.1 hydroxylysine-linked carbohydrate units/3000 amino acid residues, whereas tendon collagen contained only 4.1 units/3000. Variation in the ratio disaccharide unit/monosaccharide unit was also observed, the ratio being 1.2 in intercostal cartilage collagen and 4.1 in submucosal collagen. The proportion of the total hydroxylysine that was substituted by carbohydrate also varied from tissue to tissue. PMID:5002672

  4. Separation and quantification of microalgal carbohydrates.

    PubMed

    Templeton, David W; Quinn, Matthew; Van Wychen, Stefanie; Hyman, Deborah; Laurens, Lieve M L

    2012-12-28

    Structural carbohydrates can constitute a large fraction of the dry weight of algal biomass and thus accurate identification and quantification is important for summative mass closure. Two limitations to the accurate characterization of microalgal carbohydrates are the lack of a robust analytical procedure to hydrolyze polymeric carbohydrates to their respective monomers and the subsequent identification and quantification of those monosaccharides. We address the second limitation, chromatographic separation of monosaccharides, here by identifying optimum conditions for the resolution of a synthetic mixture of 13 microalgae-specific monosaccharides, comprised of 8 neutral, 2 amino sugars, 2 uronic acids and 1 alditol (myo-inositol as an internal standard). The synthetic 13-carbohydrate mix showed incomplete resolution across 11 traditional high performance liquid chromatography (HPLC) methods, but showed improved resolution and accurate quantification using anion exchange chromatography (HPAEC) as well as alditol acetate derivatization followed by gas chromatography (for the neutral- and amino-sugars only). We demonstrate the application of monosaccharide quantification using optimized chromatography conditions after sulfuric acid analytical hydrolysis for three model algae strains and compare the quantification and complexity of monosaccharides in analytical hydrolysates relative to a typical terrestrial feedstock, sugarcane bagasse.

  5. Genetics of carbohydrate accumulation in onion

    USDA-ARS?s Scientific Manuscript database

    Fructans are soluble carbohydrates composed of fructose chains attached to a basal sucrose molecule and act both as health-enhancing pro- and pre-biotics. In onion, higher fructan concentrations are correlated with greater soluble solids content, dry weights, and pungency. We analyzed dry weights ...

  6. Carbohydrate modified phenol-formaldehyde resins

    Treesearch

    Anthony H. Conner; Linda F. Lorenz

    1986-01-01

    For adhesive self-sufficiency, the wood industry needs new adhesive systems in which all or part of the petroleum-derived phenolic component is replaced by a renewable material without sacrificing high durability or ease of bonding. We tested the bonding of wood veneers, using phenolic resins in which part of the phenol-formaldehyde was replaced with carbohydrates. Our...

  7. Carbohydrate Metabolism in Bifidobacteria: Human Symbiotic Bacteria

    USDA-ARS?s Scientific Manuscript database

    Bifidobacterium ssp. constitute up to 90% of microbial gut flora in the infant colon, but considerably less in adults. Carbohydrate metabolism in these bacteria is highly unusual. Data from four Bifidobacterium genomes indicates genes missing from glycolysis, gluconeogenesis, and the TCA cycle, in...

  8. The clinical impact of carbohydrate malabsorption.

    PubMed

    Born, Peter

    2011-03-01

    Malabsorption of carbohydrates such as fructose, lactose or sorbitol can often be detected among patients suffering from so-called non specific abdominal complaints. Sometimes the differential diagnosis may be difficult. So far successful treatment consists of dietary interventions only. Nevertheless, many questions are remaining still unanswered. Copyright © 2011 Arab Journal of Gastroenterology. Published by Elsevier Ltd. All rights reserved.

  9. Carbohydrate-Based Lactones: Synthesis and Applications

    NASA Astrophysics Data System (ADS)

    Xavier, Nuno M.; Rauter, Amélia P.; Queneau, Yves

    The synthesis and uses of different kinds of carbohydrate-based lactones are described. This group of compounds includes aldonolactones, other related monocyclic lactones and bicyclic systems. The latter can arise from uronic acids, carboxymethyl ethers or glycosides, or from C-branched sugars.

  10. General Properties, Occurrence, and Preparation of Carbohydrates

    NASA Astrophysics Data System (ADS)

    Robyt, John F.

    D-Glucose and its derivatives and analogues, N-acetyl-D-glucosamine, N-acetyl-D-muramic acid, D-glucopyranosyl uronic acid, and D-glucitol represent 99.9% of the carbohydrates on the earth. D-Glucose is found in the free state in human blood and in the combined state in disaccharides, sucrose, lactose, and α,α-trehalose, in cyclic dextrins, and in polysaccharides, starch, glycogen, cellulose, dextrans; N-acetyl-D-glucosamine and an analogue N-acetyl-D-muramic acid are found in bacterial cell wall polysaccharide, murein, along with teichoic acids made up of poly-glycerol or -ribitol phosphodiesters. Other carbohydrates, D-mannose, D-mannuronic acid, D-galactose, N-acetyl-D-galactosamine, D-galacturonic acid, D-iduronic acid, L-guluronic acid, L-rhamnose, L-fucose, D-xylose, and N-acetyl-D-neuraminic acid are found in glycoproteins, hemicelluloses, glycosaminoglycans, and polysaccharides of plant exudates, bacterial capsules, alginates, and heparin. D-Ribofuranose-5-phosphate is found in many coenzymes and is the backbone of RNAs (ribonucleic acid), and 2-deoxy-D-ribofuranose-5-phosphate is the backbone of DNA (deoxyribonucleic acid). D-Fructofuranose is found in sucrose, inulin, and levan. The general properties and occurrence of these carbohydrates and general methods of isolation and preparation of carbohydrates are presented.

  11. Indicators of normal carbohydrate digestion in children

    USDA-ARS?s Scientific Manuscript database

    More research is needed to determine the nutritional and clinical significance of the intermediate values of low but not deficient duodenal disaccharidase activities, but the Dahlqvist-method biopsy assay of activity serves as a gnomon of carbohydrate digestion, in the sense that Anaximander used a ...

  12. High Carbohydrate-Fiber Nutrition for Running and Health.

    ERIC Educational Resources Information Center

    Battinelli, Thomas

    1983-01-01

    The roles of carbohydrates, fats, proteins, and fiber in producing energy for health and exercise are discussed. Long-distance runners should have a high intake of complex carbohydrates and fiber. (PP)

  13. High Carbohydrate-Fiber Nutrition for Running and Health.

    ERIC Educational Resources Information Center

    Battinelli, Thomas

    1983-01-01

    The roles of carbohydrates, fats, proteins, and fiber in producing energy for health and exercise are discussed. Long-distance runners should have a high intake of complex carbohydrates and fiber. (PP)

  14. Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module

    PubMed Central

    Yao, Chaoxiang; Junaid, Muhammad; Lu, Zhenghui; Zhang, Houjin; Ma, Yanhe

    2015-01-01

    Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme. PMID:26562160

  15. Cancer vaccine with mimotopes of tumor-associated carbohydrate antigens.

    PubMed

    Kozbor, Danuta

    2010-03-01

    The GD2 ganglioside, displayed by five carbohydrate Neu5Acalpha2-8Neu5Acalpha2-3(GalNAcbeta1-4)Galbeta1-4Glcbeta residues attached to a ceramide chain that anchors the ganglioside in the cell membrane, is expressed on neuroectodermally derived tumors. GD2 has been used as a target for passive and active immunotherapy in patients with malignant melanoma and neuroblastoma. We have generated 47-LDA mimotope of GD2 by screening a phage display peptide library with anti-GD2 mAb 14G2a and reported that vaccination with the 47-LDA mimotope elicited GD2 cross-reactive IgG antibody responses as well as MHC class I-restricted CD8(+) T cells to syngeneic neuroblastoma tumor cells. The cytotoxic activity of the vaccine-induced CTLs was independent of GD2 expression, suggesting recognition of a novel tumor-associated antigen cross-reacting with 47-LDA. Immunoblotting studies using 14G2a mAb demonstrated that this antibody cross-reacts with a 105 kDa glycoprotein expressed by GD2(+) and GD2(-) neuroblastoma and melanoma cells. Functional studies of tumor cells grown in three-dimensional (3D) collagen cultures with 14G2a mAb showed decreases in matrix metalloproteinase-2 activation, a process regulated by 105 kDa activated leukocyte cell adhesion molecules (ALCAM/CD166). The CD166 glycoprotein was shown to be recognized by 14G2a antibody, and inhibition of CD166 expression by RNA interference ablated the cell sensitivity to lysis by 47-LDA-induced CD8(+) T cells in vitro and in vivo. These results suggest that the vaccine-induced CTLs recognize a 47-LDA cross-reactive epitope expressed by CD166 and reveal a novel mechanism of induction of potent tumor-specific cellular responses by mimotopes of tumor-associated carbohydrate antigens.

  16. Crystal structures of three bicyclic carbohydrate derivatives

    PubMed Central

    Schilde, Uwe; Kelling, Alexandra; Umbreen, Sumaira; Linker, Torsten

    2016-01-01

    The title compounds, [(1R,3R,4R,5R,6S)-4,5-bis­(acet­yloxy)-7-oxo-2-oxabi­cyclo[4.2.0]octan-3-yl]methyl acetate, C14H18O8, (I), [(1S,4R,5S,6R)-5-acet­yloxy-7-hy­droxy­imino-2-oxobi­cyclo­[4.2.0]octan-4-yl acetate, C11H15NO6, (II), and [(3aR,5R,6R,7R,7aS)-6,7-bis­(acet­yloxy)-2-oxo­octa­hydro­pyrano[3,2-b]pyrrol-5-yl]methyl acetate, C14H19NO8, (III), are stable bicyclic carbohydrate derivatives. They can easily be synthesized in a few steps from commercially available glycals. As a result of the ring strain from the four-membered rings in (I) and (II), the conformations of the carbohydrates deviate strongly from the ideal chair form. Compound (II) occurs in the boat form. In the five-membered lactam (III), on the other hand, the carbohydrate adopts an almost ideal chair conformation. As a result of the distortion of the sugar rings, the configurations of the three bicyclic carbohydrate derivatives could not be determined from their NMR coupling constants. From our three crystal structure determinations, we were able to establish for the first time the absolute configurations of all new stereocenters of the carbohydrate rings. PMID:27980845

  17. Carbohydrate Intake Considerations for Young Athletes

    PubMed Central

    Montfort-Steiger, Veronica; Williams, Craig A.

    2007-01-01

    Good nutritional practices are important for exercise performance and health during all ages. Athletes and especially growing children engaged in heavy training have higher energy and nutrient requirements compared to their non-active counterparts. Scientific understanding of sports nutrition for the young athlete is lacking behind the growing number of young athletes engaged in sports. Most of the sports nutrition recommendations given to athletic children and adolescents are based on adult findings due to the deficiency in age specific information in young athletes. Therefore, this review reflects on child specific sports nutrition, particularly on carbohydrate intake and metabolism that distinguishes the child athlete from the adult athlete. Children are characterised to be in an insulin resistance stage during certain periods of maturation, have different glycolytic/metabolic responses during exercise, have a tendency for higher fat oxidation during exercise and show different heat dissipation mechanisms compared to adults. These features point out that young athletes may need different nutritional advice on carbohydrate for exercise to those from adult athletes. Sport drinks for example may need to be adapted to children specific needs. However, more research in this area is warranted to clarify sports nutrition needs of the young athlete to provide better and healthy nutritional guidance to young athletes. Key pointsAthletic girls show lower carbohydrate intakes compared to boys.Substrate oxidation during exercise appears to be maturity related, fat being the preferred fuel for oxidation in younger athletic children.Children appear to have lower endogenous but greater exogenous carbohydrate oxidation rates during exercise.Carbohydrate intake during exercise appears to show no additional performance improvement in young athletes. Perhaps fat intake or a combination of both nutrients may be a better approach for nutrient supplementation during exercise

  18. Maternal carbohydrate intake and pregnancy outcome.

    PubMed

    Clapp, James F

    2002-02-01

    Experimental evidence indicates that the primary maternal environmental factor that regulates feto-placental growth is substrate delivery to the placental site, which is the product of maternal substrate levels and the rate of placental-bed blood flow. Thus, maternal factors which change either substrate level or flow alter feto-placental growth rate. The best-studied substrate in human pregnancy is glucose, and there is a direct relationship between maternal blood glucose levels and size at birth. Altering the type of carbohydrate eaten (high- v. low-glycaemic sources) changes postprandial glucose and insulin responses in both pregnant and non-pregnant women, and a consistent change in the type of carbohydrate eaten during pregnancy influences both the rate of feto-placental growth and maternal weight gain. Eating primarily high-glycaemic carbohydrate results in feto-placental overgrowth and excessive maternal weight gain, while intake of low-glycaemic carbohydrate produces infants with birth weights between the 25th and the 50th percentile and normal maternal weight gain. The calculated difference in energy retention with similar total energy intakes is of the order of 80,000 kJ. Preliminary information from subsequent metabolic studies indicates that the mechanisms involved include changes in: daily digestible energy requirements (i.e. metabolic efficiency), substrate utilization (glucose oxidation v. lipid oxidation), and insulin resistance and sensitivity. Thus, altering the source of maternal dietary carbohydrate may prove to be a valuable tool in the management of pregnancies at risk for anomalous feto-placental growth and for the prevention and/or treatment of obesity and insulin resistance in the non-pregnant state.

  19. Exercise and Regulation of Carbohydrate Metabolism

    PubMed Central

    Mul, Joram D.; Stanford, Kristin I.; Hirshman, Michael F.; Goodyear, Laurie J.

    2016-01-01

    Carbohydrates are the preferred substrate for contracting skeletal muscles during high-intensity exercise and are also readily utilized during moderate intensity exercise. This use of carbohydrates during physical activity likely played an important role during the survival of early Homo sapiens, and genes and traits regulating physical activity, carbohydrate metabolism, and energy storage have undoubtedly been selected throughout evolution. In contrast to the life of early H. sapiens, modern lifestyles are predominantly sedentary. As a result, intake of excessive amounts of carbohydrates due to the easy and continuous accessibility to modern high-energy food and drinks has not only become unnecessary but also led to metabolic diseases in the face of physical inactivity. A resulting metabolic disease is type 2 diabetes, a complex endocrine disorder characterized by abnormally high concentrations of circulating glucose. This disease now affects millions of people worldwide. Exercise has beneficial effects to help control impaired glucose homeostasis with metabolic disease, and is a well-established tool to prevent and combat type 2 diabetes. This chapter focuses on the effects of exercise on carbohydrate metabolism in skeletal muscle and systemic glucose homeostasis. We will also focus on the molecular mechanisms that mediate the effects of exercise to increase glucose uptake in skeletal muscle. It is now well established that there are different proximal signaling pathways that mediate the effects of exercise and insulin on glucose uptake, and these distinct mechanisms are consistent with the ability of exercise to increase glucose uptake in the face of insulin resistance in people with type 2 diabetes. Ongoing research in this area is aimed at defining the precise mechanism by which exercise increases glucose uptake and insulin sensitivity and the types of exercise necessary for these important health benefits. PMID:26477909

  20. Exercise and Regulation of Carbohydrate Metabolism.

    PubMed

    Mul, Joram D; Stanford, Kristin I; Hirshman, Michael F; Goodyear, Laurie J

    2015-01-01

    Carbohydrates are the preferred substrate for contracting skeletal muscles during high-intensity exercise and are also readily utilized during moderate intensity exercise. This use of carbohydrates during physical activity likely played an important role during the survival of early Homo sapiens, and genes and traits regulating physical activity, carbohydrate metabolism, and energy storage have undoubtedly been selected throughout evolution. In contrast to the life of early H. sapiens, modern lifestyles are predominantly sedentary. As a result, intake of excessive amounts of carbohydrates due to the easy and continuous accessibility to modern high-energy food and drinks has not only become unnecessary but also led to metabolic diseases in the face of physical inactivity. A resulting metabolic disease is type 2 diabetes, a complex endocrine disorder characterized by abnormally high concentrations of circulating glucose. This disease now affects millions of people worldwide. Exercise has beneficial effects to help control impaired glucose homeostasis with metabolic disease, and is a well-established tool to prevent and combat type 2 diabetes. This chapter focuses on the effects of exercise on carbohydrate metabolism in skeletal muscle and systemic glucose homeostasis. We will also focus on the molecular mechanisms that mediate the effects of exercise to increase glucose uptake in skeletal muscle. It is now well established that there are different proximal signaling pathways that mediate the effects of exercise and insulin on glucose uptake, and these distinct mechanisms are consistent with the ability of exercise to increase glucose uptake in the face of insulin resistance in people with type 2 diabetes. Ongoing research in this area is aimed at defining the precise mechanism by which exercise increases glucose uptake and insulin sensitivity and the types of exercise necessary for these important health benefits. © 2015 Elsevier Inc. All rights reserved.

  1. Influence of Grape Maturity on Complex Carbohydrate Composition of Red Sparkling Wines.

    PubMed

    Martínez-Lapuente, Leticia; Apolinar-Valiente, Rafael; Guadalupe, Zenaida; Ayestarán, Belén; Pérez-Magariño, Silvia; Williams, Pascale; Doco, Thierry

    2016-06-22

    This paper studied how grape maturity affected complex carbohydrate composition during red sparkling wine making and wine aging. Grape ripening stage (premature and mature grapes) showed a significant impact on the content, composition, and evolution of polysaccharides and oligosaccharides of sparkling wines. Polysaccharides rich in arabinose and galactose, mannoproteins, rhamnogalacturonans II, and oligosaccharides in base wines increased with maturity. For both maturity stages, polysaccharides rich in arabinose and galactose, and the glucuronic acid glycosyl residue of the oligosaccharides were the major carbohydrates detected in all vinification stages. The total glycosyl content of oligosaccharides decreased during the whole period of aging on yeast lees. The reduction of polysaccharides rich in arabinose and galactose and rhamnogalacturonans type II during the aging was more pronounced in mature samples. To our knowledge, this is the first report of the polysaccharide and oligosaccharide composition of red sparkling wines.

  2. X-ray radiation-induced addition of oxygen atoms to protein residues.

    PubMed

    Wang, Jimin

    2016-08-01

    The additions of oxygen and peroxide to residues that result when proteins are exposed to the free radicals produced using the Fenton reaction or X-rays have been studied for over a century. Nevertheless little is known about the impact these modifications have on protein crystal structures. Here evidence is presented that both kinds of modifications occur in protein crystals on a significant scale during the collection of X-ray diffraction data. For example, at least 538 of the 5,351 residues of protein molecules in the crystal used to obtain the structure for photosystem II described by the PDB accession number 3ARC became oxygenated during data collection. © 2016 The Protein Society.

  3. Analysis of carbohydrate-protein interactions with synthetic N-linked neoglycoconjugate probes.

    PubMed Central

    Wong, S Y; Manger, I D; Guile, G R; Rademacher, T W; Dwek, R A

    1993-01-01

    Recently we have describe a simple efficient chemical method of generating an asparagine side-chain linker with beta-stereochemistry at the anomeric position of neutral oligosaccharides. We now report the 1-N-glycyl beta-derivatization of sialylated saccharides. Several neoglycoconjugates formed using these N-linked inter-mediates were investigated for their usefulness in probing carbohydrate-protein interactions. First, biotinyl derivatives of two xylose/fucose class plant-type oligosaccharides purified from horseradish peroxidase were effective in demonstrating the carbohydrate specificity of polyclonal anti-(horseradish peroxidase) antibodies. Secondly, a fluorescein-labelled asialo- and digalactosylated biantennary complex sugar was synthesized and shown to bind to a Ricinus communis agglutinin column. This galactose-specific recognition was abolished by treating this fluorescein-labelled oligosaccharide with jack bean beta-galactosidase. Finally, two 1-N-glycyl beta-saccharide derivatives were modified with thiophosgene to form their corresponding isothiocyanate derivatives. Coupling of these isothiocyanate derivatives of sugars to BSA, amino-derivatized polystyrene plates and glass-fibre discs resulted in multiple sugar presentation. The binding of an anti-N-acetylglucosamine monoclonal antibody to N,N'-diacetylchitobiose residues presented on BSA and solid supports was shown by e.l.i.s.a. Similarly the binding of concanavalin A to asialo-, agalactosylated biantennary complex oligosaccharide residues attached to BSA was demonstrated by a competitive e.l.i.s.a. Our results demonstrate that N-linked neoglycoconjugates could be made readily available and they are valuable tools for the detailed analyses of carbohydrates and carbohydrate-binding proteins. Images Figure 2 Figure 6 Figure 9 PMID:7506528

  4. Identification and Characterization of Sulfated Carbohydrate-Binding Protein from Lactobacillus reuteri

    PubMed Central

    Nishiyama, Keita; Ochiai, Ayaka; Tsubokawa, Daigo; Ishihara, Kazuhiko; Yamamoto, Yuji; Mukai, Takao

    2013-01-01

    We previously purified a putative sulfated-galactosylceramide (sulfatide)-binding protein with a molecular weight of 47 kDa from the cell surface of Lactobacillus reuteri JCM1081. The aim of this study was to identify the 47-kDa protein, examine its binding to sulfated glycolipids and mucins, and evaluate its role in bacterial adhesion to mucosal surfaces. By cloning and sequencing analysis, the 47-kDa protein was identified as elongation factor-Tu (EF-Tu). Adhesion properties were examined using 6×Histidine-fused EF-Tu (His6-EF-Tu). Surface plasmon resonance analysis demonstrated pH-dependent binding of His6-EF-Tu to sulfated glycolipids, but not to neutral or sialylated glycolipids, suggesting that a sulfated galactose residue was responsible for EF-Tu binding. Furthermore, His6-EF-Tu was found to bind to porcine gastric mucin (PGM) by enzyme-linked immunosorbent assay. Binding was markedly reduced by sulfatase treatment of PGM and in the presence of acidic and desialylated oligosaccharide fractions containing sulfated carbohydrate residues prepared from PGM, demonstrating that sulfated carbohydrate moieties mediated binding. Histochemical staining revealed similar localization of His6-EF-Tu and high iron diamine staining in porcine mucosa. These results indicated that EF-Tu bound PGM via sulfated carbohydrate moieties. To characterize the contribution of EF-Tu to the interaction between bacterial cells and PGM, we tested whether anti-EF-Tu antibodies could inhibit the interaction. Binding of L. reuteri JCM1081 to PGM was significantly blocked in a concentration-dependent matter, demonstrating the involvement of EF-Tu in bacterial adhesion. In conclusion, the present results demonstrated, for the first time, that EF-Tu bound sulfated carbohydrate moieties of sulfated glycolipids and sulfomucin, thereby promoting adhesion of L. reuteri to mucosal surfaces. PMID:24391811

  5. Potential Role for a Carbohydrate Moiety in Anti-Candida Activity of Human Oral Epithelial Cells

    PubMed Central

    Steele, Chad; Leigh, Janet; Swoboda, Rolf; Ozenci, Hatice; Fidel, Paul L.

    2001-01-01

    Candida albicans is both a commensal and a pathogen at the oral mucosa. Although an intricate network of host defense mechanisms are expected for protection against oropharyngeal candidiasis, anti-Candida host defense mechanisms at the oral mucosa are poorly understood. Our laboratory recently showed that primary epithelial cells from human oral mucosa, as well as an oral epithelial cell line, inhibit the growth of blastoconidia and/or hyphal phases of several Candida species in vitro with a requirement for cell contact and with no demonstrable role for soluble factors. In the present study, we show that oral epithelial cell-mediated anti-Candida activity is resistant to gamma-irradiation and is not mediated by phagocytosis, nitric oxide, hydrogen peroxide, and superoxide oxidative inhibitory pathways or by nonoxidative components such as soluble defensin and calprotectin peptides. In contrast, epithelial cell-mediated anti-Candida activity was sensitive to heat, paraformaldehyde fixation, and detergents, but these treatments were accompanied by a significant loss in epithelial cell viability. Treatments that removed existing membrane protein or lipid moieties in the presence or absence of protein synthesis inhibitors had no effect on epithelial cell inhibitory activity. In contrast, the epithelial cell-mediated anti-Candida activity was abrogated after treatment of the epithelial cells with periodic acid, suggesting a role for carbohydrates. Adherence of C. albicans to oral epithelial cells was unaffected, indicating that the carbohydrate moiety is exclusively associated with the growth inhibition activity. Subsequent studies that evaluated specific membrane carbohydrate moieties, however, showed no role for sulfated polysaccharides, sialic acid residues, or glucose- and mannose-containing carbohydrates. These results suggest that oral epithelial cell-mediated anti-Candida activity occurs exclusively with viable epithelial cells through contact with C. albicans by

  6. GlycomeDB – integration of open-access carbohydrate structure databases

    PubMed Central

    Ranzinger, René; Herget, Stephan; Wetter, Thomas; von der Lieth, Claus-Wilhelm

    2008-01-01

    Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource. PMID:18803830

  7. Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms

    PubMed Central

    Diago, Luis A; Morell, Persy; Aguilera, Longendri; Moreno, Ernesto

    2007-01-01

    Background The number of algorithms available to predict ligand-protein interactions is large and ever-increasing. The number of test cases used to validate these methods is usually small and problem dependent. Recently, several databases have been released for further understanding of protein-ligand interactions, having the Protein Data Bank as backend support. Nevertheless, it appears to be difficult to test docking methods on a large variety of complexes. In this paper we report the development of a new database of protein-ligand complexes tailored for testing of docking algorithms. Methods Using a new definition of molecular contact, small ligands contained in the 2005 PDB edition were identified and processed. The database was enriched in molecular properties. In particular, an automated typing of ligand atoms was performed. A filtering procedure was applied to select a non-redundant dataset of complexes. Data mining was performed to obtain information on the frequencies of different types of atomic contacts. Docking simulations were run with the program DOCK. Results We compiled a large database of small ligand-protein complexes, enriched with different calculated properties, that currently contains more than 6000 non-redundant structures. As an example to demonstrate the value of the new database, we derived a new set of chemical matching rules to be used in the context of the program DOCK, based on contact frequencies between ligand atoms and points representing the protein surface, and proved their enhanced efficiency with respect to the default set of rules included in that program. Conclusion The new database constitutes a valuable resource for the development of knowledge-based docking algorithms and for testing docking programs on large sets of protein-ligand complexes. The new chemical matching rules proposed in this work significantly increase the success rate in DOCKing simulations. The database developed in this work is available at . PMID:17718923

  8. Organotin-catalyzed highly regioselective thiocarbonylation of nonprotected carbohydrates and synthesis of deoxy carbohydrates in a minimum number of steps.

    PubMed

    Muramatsu, Wataru; Tanigawa, Satoko; Takemoto, Yuki; Yoshimatsu, Hirofumi; Onomura, Osamu

    2012-04-16

    Nonprotected carbohydrates: The catalytic regioselective thiocarbonylation of carbohydrates by using organotin dichloride under mild conditions was demonstrated. The reaction afforded various deoxy saccharides in high yields and excellent regioselectivity in a minimum number of steps. The regioselectivity of the thiocarbonylation is attributed to the intrinsic character of the carbohydrates based on the stereorelationship of their hydroxy groups (see scheme).

  9. From 'pleasure to chemistry': the experience of carbohydrate counting with and without carbohydrate restriction for people with Type 1 diabetes.

    PubMed

    Cresswell, Pip; Krebs, Jeremy; Gilmour, Jean; Hanna, Aoife; Parry-Strong, Amber

    2015-12-01

    Matching carbohydrate intake with insulin dosage is recommended management for people with Type 1 diabetes. However, international interest in restricted carbohydrate diets is growing. General practitioners and practice nurses need to know how to advise people with Type 1 diabetes regarding low-carbohydrate diets. This study aimed to explore the carbohydrate counting experiences of people with Type 1 diabetes in a trial with and without a diet restricted to 75 g of carbohydrate per day. Eight participants were interviewed by focus group or interview 12 weeks after a carbohydrate counting course with individual dietary choice or the same course with information on restricted carbohydrate eating and a daily maximum intake of 75 g of carbohydrate. Data were analysed using a qualitative thematic analysis approach. Themes included the need for insulin management skills, impact of the dietary experience, and need for dietary knowledge. The restricted-carbohydrate group encountered mealtime insulin resistance and difficulty managing insulin dosages when transitioning on and off the low-carbohydrate diet. The diet impacted on mood, feelings of satiety and it was reported that food changed from being 'a pleasure to chemistry'. Both groups described feeling empowered to manage their diabetes as a result of the carbohydrate counting course. Participants reported increased knowledge and challenging insulin management. The restricted-carbohydrate group reported mealtime insulin resistance and a strong dietary impact. Extra health professional support may be required, especially at dietary transition periods. More research is warranted into the reported mealtime insulin resistance.

  10. Carbohydrate and the regulation of blood glucose and metabolism.

    PubMed

    Wolever, Thomas M S

    2003-05-01

    Classifying the glycemic responses of carbohydrate foods using the glycemic index (GI) requires standardized methodology for valid results. Dietary carbohydrates influence metabolism by at least four mechanisms: nature of the monosaccharides absorbed, amount of carbohydrate consumed, rate of absorption, and colonic fermentation. Reducing glycemic responses by reducing carbohydrate intake increases postprandial serum free-fatty acids (FFA) and does not improve overall glycemic control in diabetic subjects. By contrast, low-GI diets reduce serum FFA and improve glycemic control. Thus, current evidence supports FAO/WHO recommendations to maintain a high-carbohydrate diet and choose low-GI starchy foods.

  11. Glycosylated Conductive Polymer: A Multimodal Biointerface for Studying Carbohydrate-Protein Interactions.

    PubMed

    Zeng, Xiangqun; Qu, Ke; Rehman, Abdul

    2016-09-20

    polymerization but also enable the simultaneous analysis of the binding events with orthogonal electrical, optical, or mass sensing label-free readouts. We established this approach using polyaniline and polythiophene as examples. Two general methods were demonstrated for glycosylated polymer fabrications (i.e., electropolymerization of monomer bearing α-mannoside residues or click chemistry based mannose conjugation to electrochemically preformed quinone fused polymer with potential to introduce different carbohydrate moieties and construct glycan arrays in a similar manner). Their conjugated π system extending over a large number of recurrent monomer units renders them sensitive optoelectronic materials. The carbohydrate-protein interactions on the side chain could disrupt the electrostatic, H-bonding, steric, or van der Waals interactions within or between polymers, leading to a change of conductivity or optical absorption of the conductive polymers. This will allow concurrent interrogation of these interactions with adjoining biological processes and mechanisms in multimodal fashion. Furthermore, the functionalized glycosylated conductive polymers can be designed and synthesized with controlled oxidation states, desired ionic dopants, and the imperative density and orientation of the sugar ligands that enable the assessment of differential receptor binding profiles of carbohydrate-protein interactions with much more detailed information and high accuracy. Finally, the glycosylated biosensing interfaces were successfully validated for their applications in Gram-negative bacterial detection, antibiotic resistance studies, and antimicrobial susceptibility assays, all based on inferring carbohydrate-protein interactions directly on cell surfaces, thus illustrating their potential uses in infectious disease research, clinical diagnostics, and environmental monitoring of harmful pathogens.

  12. Carbohydrate engineered cells for regenerative medicine.

    PubMed

    Du, Jian; Yarema, Kevin J

    2010-06-15

    Carbohydrates are integral components of the stem cell niche on several levels; proteoglycans are a major constituent of the extracellular matrix (ECM) surrounding a cell, glycosoaminoglycans (GAGs) help link cells to the ECM and the neighboring cells, and small but informationally-rich oligosaccharides provide a "sugar code" that identifies each cell and provides it with unique functions. This article samples roles that glycans play in development and then describes how metabolic glycoengineering - a technique where monosaccharide analogs are introduced into the metabolic pathways of a cell and are biosynthetically incorporated into the glycocalyx - is overcoming many of the long-standing barriers to manipulating carbohydrates in living cells and tissues and is becoming an intriguing new tool for tissue engineering and regenerative medicine.

  13. Carbohydrate Engineered Cells for Regenerative Medicine

    PubMed Central

    Du, Jian; Yarema, Kevin J.

    2010-01-01

    Carbohydrates are integral components of the stem cell niche on several levels; proteoglycans are a major constituent of the extracellular matrix (ECM) surrounding a cell, glycosoaminoglycans (GAGs) help link cells to the ECM and the neighboring cells, and small but informationally-rich oligosaccharides provide a “sugar code” that identifies each cell and provides it with unique functions. This article samples roles that glycans play in development and then describes how metabolic glycoengineering – a technique where monosaccharide analogs are introduced into the metabolic pathways of a cell and are biosynthetically incorporated into the glycocalyx – is overcoming many of the long-standing barriers to manipulating carbohydrates in living cells and tissues and is becoming an intriguing new tool for tissue engineering and regenerative medicine. PMID:20117158

  14. Solubility of carbohydrates in heavy water.

    PubMed

    Cardoso, Marcus V C; Carvalho, Larissa V C; Sabadini, Edvaldo

    2012-05-15

    The solubility of several mono-(glucose and xylose), di-(sucrose and maltose), tri-(raffinose) and cyclic (α-cyclodextrin) saccharides in H(2)O and in D(2)O were measured over a range of temperatures. The solution enthalpies for the different carbohydrates in the two solvents were determined using the vant' Hoff equation and the values in D(2)O are presented here for the first time. Our findings indicate that the replacement of H(2)O by D(2)O remarkably decreases the solubilities of the less soluble carbohydrates, such as maltose, raffinose and α-cyclodextrin. On the other hand, the more soluble saccharides, glucose, xylose, and sucrose, are practically insensitive to the H/D replacement in water.

  15. Functionalized carbon nanomaterials derived from carbohydrates.

    PubMed

    Jagadeesan, Dinesh; Eswaramoorthy, Muthusamy

    2010-02-01

    A tremendous growth in the field of carbon nanomaterials has led to the emergence of carbon nanotubes, fullerenes, mesoporous carbon and more recently graphene. Some of these materials have found applications in electronics, sensors, catalysis, drug delivery, composites, and so forth. The high temperatures and hydrocarbon precursors involved in their synthesis usually yield highly inert graphitic surfaces. As some of the applications require functionalization of their inert graphitic surface with groups like -COOH, -OH, and -NH(2), treatment of these materials in oxidizing agents and concentrated acids become inevitable. More recent works have involved using precursors like carbohydrates to produce carbon nanostructures rich in functional groups in a single-step under hydrothermal conditions. These carbon nanostructures have already found many applications in composites, drug delivery, materials synthesis, and Li ion batteries. The review aims to highlight some of the recent developments in the application of carbohydrate derived carbon nanostructures and also provide an outlook of their future prospects.

  16. Carbohydrates and the human gut microbiota.

    PubMed

    Chassard, Christophe; Lacroix, Christophe

    2013-07-01

    Due to its scale and its important role in maintaining health, the gut microbiota can be considered as a 'new organ' inside the human body. Many complex carbohydrates are degraded and fermented by the human gut microbiota in the large intestine to both yield basic energy salvage and impact gut health through produced metabolites. This review will focus on the gut microbes and microbial mechanisms responsible for polysaccharides degradation and fermentation in the large intestine. Gut microbes and bacterial metabolites impact the host at many levels, including modulation of inflammation, and glucose and lipid metabolisms. A complex relationship occurs in the intestine between the human gut microbiota, diet and the host. Research on carbohydrates and gut microbiota composition and functionality is fast developing and will open opportunities for prevention and treatment of obesity, diabetes and other related metabolic disorders through manipulation of the gut ecosystem.

  17. Synthesis of chiral dopants based on carbohydrates.

    PubMed

    Tsuruta, Toru; Koyama, Tetsuo; Yasutake, Mikio; Hatano, Ken; Matsuoka, Koji

    2014-07-01

    Chiral dopants based on carbohydrates for nematic liquid crystals were synthesized from D-glucose, and their helical twisting power (HTP) values were evaluated. The chiral dopants induced helices in the host nematic liquid crystals. An acetyl derivative having an ether-type glycosidic linkage between carbohydrate and a mesogenic moiety showed the highest HTP value of 10.4 μm(-1), while an acetyl derivative having an anomeric ester-type linkage did not show any HTP. It was surprising that this molecule had no HTP despite the presence of chirality in the molecule. A relationship between HTP and specific rotation was not observed in this study. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Carbohydrate immobilized on a dendrimer-coated colloidal gold surface for fabrication of a lectin-sensing device based on localized surface plasmon resonance spectroscopy.

    PubMed

    Ogiso, Masayo; Kobayashi, Junko; Imai, Tomoko; Matsuoka, Koji; Itoh, Miki; Imamura, Takeshi; Okada, Tomoko; Miura, Hiroshi; Nishiyama, Toshinori; Hatanaka, Kenichi; Minoura, Norihiko

    2013-03-15

    Carbohydrate-mediated functions in biological systems have generated considerable interest in recent years. We have developed a device bearing immobilized carbohydrates on a colloidal gold surface and applied this device to the detection of carbohydrate-binding molecules by using localized surface plasmon resonance (LSPR) spectroscopy. The sensing device was constructed by using cyanuric chloride as an amine-linker between an amino residue of a polyamidoamine (PAMAM) dendrimer-coated colloidal gold surface and the amino residue of a 12-aminododecyl glycoside. After optimizing the construction of the device, we characterized its LSPR-based sensing capability. Binding specificity with lectins and linear range responses were obtained with the device. Our LSPR-based sensing device thus provides a label-free, low-cost detection method for use as a laboratory research tool or in medical glycan arrays. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Gastrointestinal effects of low-digestible carbohydrates.

    PubMed

    Grabitske, Hollie A; Slavin, Joanne L

    2009-04-01

    Low-digestible carbohydrates (LDCs) are carbohydrates that are incompletely or not absorbed in the small intestine but are at least partly fermented by bacteria in the large intestine. Fiber, resistant starch, and sugar alcohols are types of LDCs. Given potential health benefits (including a reduced caloric content, reduced or no effect on blood glucose levels, non-cariogenic effect) the prevalence of LDCs in processed foods is increasing. Many of the benefits of LDCs are related to the inability of human digestive enzymes to break down completely the carbohydrates into absorbable saccharides and the subsequent fermentation of unabsorbed carbohydrates in the colon. As a result, LDCs may affect laxation and cause gastrointestinal effects, including abdominal discomfort, flatus, and diarrhea, especially at higher or excessive intakes. Such responses, though transient, affect the perception of the well-being of consumers and their acceptance of food products containing LDCs. Current recommendations for fiber intake do not consider total LDC consumption nor recommend an upper limit for LDC intake based on potential gastrointestinal effects. Therefore, a review of published studies reporting gastrointestinal effects of LDCs was conducted. We included only studies published in refereed journals in English. Additionally, we excluded studies of subjects with incomplete or abnormal functioning gastrointestinal tracts or where antibiotics, stimulant laxatives, or other drugs affecting motility were included. Only in studies with a control period, either placebo treatment or no LDC treatment, were included. Studies must have included an acceptable measure of gastrointestinal effect. Sixty-eight studies and six review articles were evaluated. This review describes definitions, classifications, and mechanisms of LDCs, evaluates published human feeding studies of fifteen LDCs for associations between gastrointestinal effects and levels of LDC intake, and presents recommendations

  20. Small-Molecule Carbohydrate-Based Immunostimulants.

    PubMed

    Marzabadi, Cecilia H; Franck, Richard W

    2017-02-03

    In this review, we discuss small-molecule, carbohydrate-based immunostimulants that target Toll-like receptor 4 (TLR-4) and cluster of differentiation 1D (CD1d) receptors. The design and use of these molecules in immunotherapy as well as results from their use in clinical trials are described. How these molecules work and their utilization as vaccine adjuvants are also discussed. Future applications and extensions for the use of these analogues as therapeutic agents will be outlined.

  1. Crystallisation and crystal forms of carbohydrate derivatives

    NASA Astrophysics Data System (ADS)

    Lennon, Lorna

    This thesis is focused on the synthesis and solid state analysis of carbohydrate derivatives, including many novel compounds. Although the synthetic chemistry surrounding carbohydrates is well established in the literature, the crystal chemistry of carbohydrates is less well studied. Therefore this research aims to improve understanding of the solid state properties of carbohydrate derivatives through gaining more information on their supramolecular bonding. Chapter One focuses on an introduction to the solid state of organic compounds, with a background to crystallisation, including issues that can arise during crystal growth. Chapter Two is based on glucopyranuronate derivatives which are understudied in terms of their solid state forms. This chapter reports on the formation of novel glucuronamides and utilising the functionality of the amide bond for crystallisation. TEMPO oxidation was completed to form glucopyranuronates by oxidation of the primary alcohol groups of glucosides to the carboxylic acid derivatives, to increase functionality for enhanced crystal growth. Chapter Three reports on the synthesis of glucopyranoside derivatives by O-glycosylation reactions and displays crystal structures, including a number of previously unsolved acetate protected and deprotected crystal structures. More complex glycoside derivatives were also researched in an aim to study the resultant supramolecular motifs. Chapter Four contains the synthesis of aryl cellobioside derivatives including the novel crystal structures that were solved for the acetate protected and deprotected compounds. Research was carried out to determine if 1-deoxycellodextrins could act as putative isostructures for cellulose. Our research displays the presence of isostructural references with 1-deoxycellotriose shown to be similar to cellulose III11, 1-deoxycellotetraose correlates with cellulose IV11 and 1-deoxycellopentose shows isostructurality similar to that of cellulose II. Chapter Five contains

  2. Direct synthesis of methyl phosphoramidates in carbohydrates.

    PubMed

    Dhurandhare, Vijay M; Mishra, Girija Prasad; Lam, Sarah; Wang, Cheng-Chung

    2015-09-28

    A direct installation of a methyl phosphoramidate group by using methyl benzylphosphoramidochloridate into carbohydrates and amino acid is described. This one-step synthesis is efficient for both primary and secondary alcohols and exhibited excellent regioselectivity and functional group compatibility. Formation of a single diastereomer is observed in certain cases. The N-benzyl protecting group on methyl phosphoramidates is easily removed under mild conditions.

  3. Antibodies reactive with cell surface carbohydrates.

    PubMed Central

    Sela, B A; Wang, J L; Edelman, G M

    1975-01-01

    Normal and immune sera from various animal species were fractionated on columns of Sepharose covalently coupled with the glycoprotein fetuin. Elution of the material bound to fetuin yielded low but reproducible amounts of protein, ranging from 0.02 to 0.2% of the protein mass of the input sera. This material has been identified by immunoelectrophoresis in agar and by zone electrophoresis on cellulose acetate as immunoglobulin. The Ig fractions bound and agglutinated erythrocytes of various species, and also bound to cells from various mouse tissues including heart, kidney, thymus, and spleen. In all cases, the binding was inhibited by glycoproteins such as fetuin and thyroglobulin, by a glycopeptide isolated from fetuin, and by some bacterial lipopolysaccharides. When the binding of these Ig fractions to mouse splenocytes was tested in the presence of 17 saccharides, no inhibition of binding was observed except by sialic acid, D-galactose, N-acetyl-D-glucosamine, and D-mannose, all of which showed partial inhibition. Inasmuch as these four saccharides are present on the carbohydrate moiety of fetuin, the results suggest that the isolated material is a carbohydrate-specific Ig (CS-Ig) fraction of serum capable of binding to the carbohydrate portion of cell surface receptors and glycoproteins. When bound to lymphocytes, these CS-Ig molecules induced redistribution (patching and capping) of cell surface receptors. Moreover, the CS-Ig fractions from chicken and rabbit sera were weakly mitogenic for mouse splenic lymphocytes. CS-Ig fractions are useful new reagents for studying glycoproteins and the interactions and activities of cell surface carbohydrates. Images PMID:48249

  4. A quick look at biochemistry: carbohydrate metabolism.

    PubMed

    Dashty, Monireh

    2013-10-01

    In mammals, there are different metabolic pathways in cells that break down fuel molecules to transfer their energy into high energy compounds such as adenosine-5'-triphosphate (ATP), guanosine-5'-triphosphate (GTP), reduced nicotinamide adenine dinucleotide (NADH2), reduced flavin adenine dinucleotide (FADH2) and reduced nicotinamide adenine dinucleotide phosphate (NADPH2). This process is called cellular respiration. In carbohydrate metabolism, the breakdown starts from digestion of food in the gastrointestinal tract and is followed by absorption of carbohydrate components by the enterocytes in the form of monosaccharides. Monosaccharides are transferred to cells for aerobic and anaerobic respiration via glycolysis, citric acid cycle and pentose phosphate pathway to be used in the starvation state. In the normal state, the skeletal muscle and liver cells store monosaccharides in the form of glycogen. In the obesity state, the extra glucose is converted to triglycerides via lipogenesis and is stored in the lipid droplets of adipocytes. In the lipotoxicity state, the lipid droplets of other tissues such as the liver, skeletal muscle and pancreatic beta cells also accumulate triacylglycerol. This event is the axis of the pathogenesis of metabolic dysregulation in insulin resistance, metabolic syndrome and type 2 diabetes. In this paper a summary of the metabolism of carbohydrates is presented in a way that researchers can follow the biochemical processes easily. Copyright © 2013 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  5. Hearing Loss, Dizziness, and Carbohydrate Metabolism

    PubMed Central

    Albernaz, Pedro L. Mangabeira

    2015-01-01

    Introduction  Metabolic activity of the inner ear is very intense, and makes it sensitive to changes in the body homeostasis. This study involves a group of patients with inner ear disorders related to carbohydrate metabolism disturbances, including hearing loss, tinnitus, dizziness, and episodes of vertigo. Objectives  To describe the symptoms of metabolic inner ear disorders and the examinations required to establish diagnoses. These symptoms are often the first to allow for an early diagnosis of metabolic disorders and diabetes. Methods  Retrospective study of 376 patients with inner ear symptoms suggestive of disturbances of carbohydrate metabolism. The authors present patientś clinical symptoms and clinical evaluations, with emphasis on the glucose and insulin essays. Results  Authors based their conclusions on otolaryngological findings, diagnostic procedures and treatment principles. They found that auditory and vestibular symptoms usually occur prior to other manifestations of metabolic changes, leading to an early diagnosis of hyperinsulinemia, intestinal sugar malabsorption or diabetes. Previously undiagnosed diabetes mellitus type II was found in 39 patients. Conclusions  The identification of carbohydrate metabolism disturbances is important not only to minimize the patients' clinical symptoms, but also to help maintain their general health. PMID:27413410

  6. Carbohydrate oxidation disorders of skeletal muscle.

    PubMed

    Vorgerd, Matthias; Zange, Jochen

    2002-11-01

    The major energy sources for muscle contraction are glycogen, glucose and fatty acids, and defects in their oxidative pathways cause metabolic myopathies. Eleven specific enzyme deficiencies of carbohydrate oxidation affect skeletal muscle alone or in combination with other tissues, such as liver, heart or red blood cells. These hereditary glycogen storage diseases cause two major clinical presentations: one characterized by fixed, often progressive muscle weakness, and the other by acute, intermittent, and reversible muscle dysfunction manifesting as exercise intolerance (myalgia on exertion, muscle contractures, myoglobinuria). The focus of this review is on recent developments in: clinical features, including a brief description of the newest identified glycogen storage disease type XIII; molecular genetic studies discussing genotype-phenotype correlations in some carbohydrate oxidation disorders; pathophysiological mechanisms, especially those assessed by non-invasive P magnetic resonance spectroscopy; and therapeutic approaches such as nutritional supplementation and gene therapy, including recombinant enzyme replacement. Although major progress has been made in an understanding of the molecular genetic bases of carbohydrate oxidation defects, the pathophysiology of exercise intolerance and muscle weakness remains to be further clarified. Gene therapy and dietary therapeutic regimes appear promising, but need to be actively investigated in the future.

  7. Extraction and analysis of soluble carbohydrates.

    PubMed

    Maness, Niels

    2010-01-01

    Soluble sugars are a universal component of most living organisms and a fundamental building block in biosynthetic processes. It is no wonder that both qualitative and quantitative changes in carbohydrates often accompany plant's responses to stress. Depending on the speed of onset of stress, plant tissues can exhibit rapid and very site-specific shifts in their soluble carbohydrate pool - rapid and precise tissue collection and stabilization are necessary if analytical results are to truly represent the sugar composition at the instant of harvest. Since soluble carbohydrates are, by definition, soluble in the cell's aqueous environment, they may be analyzed directly from liquids obtained from plants or they may require extraction from the plant matrix. During extraction and prior to analysis, steps should be taken to avoid change in form or quantity of sugars by endogenous active enzyme conversion or by contaminating microbial growth. Many procedures for soluble sugar analysis exist; the choice of the most appropriate analytical protocol is ultimately dictated by the depth of information required to substantiate findings for a particular purpose.

  8. Impact of carbohydrates on weight regain.

    PubMed

    Bosy-Westphal, Anja; Müller, Manfred J

    2015-07-01

    Research on obesity treatment has shifted its focus from weight loss to weight-loss maintenance strategies. The conventional approach of a low-fat diet is challenged by insights from glycemic effects of carbohydrates on body weight regulation. Metabolic and endocrine adaptations to weight loss that contribute to weight regain involve reduced energy expenditure, increased insulin sensitivity, and enhanced orexigenic signals. This review summarizes the impact of carbohydrates on energetic efficiency, partitioning of weight regain as fat and lean mass, and appetite control. Both the amount and frequency of postprandial glycemia add to body weight regulation after weight loss and strengthen the concept of glycemic index and glycemic load. In addition, dietary fiber and slowly or poorly absorbable functional sugars modify gastrointestinal peptides involved in appetite and metabolic regulation and exert prebiotic effects. Current evidence suggests that a low-glycemic load diet with a preference for low-glycemic index foods and integration of slowly digestible, poorly absorbable carbohydrates may improve weight-loss maintenance. Future studies should investigate the health benefits of low glycemic functional sweeteners (e.g., isomaltulose and tagatose).

  9. Lectin binding patterns and carbohydrate mediation of sperm binding to llama oviductal cells in vitro.

    PubMed

    Apichela, Silvana A; Valz-Gianinet, Jorge N; Schuster, Stefanie; Jiménez-Díaz, María A; Roldán-Olarte, Eugenia M; Miceli, Dora C

    2010-04-01

    Sperm binding to oviductal epithelium would be involved in sperm reservoir formation in the utero tubal junction (UTJ). Although in other mammals sperm-oviduct interaction has been proved to be mediated by carbohydrate-recognition mechanisms, the factors implicated in the sperm adhesion to oviductal epithelium of llama are still unknown. In order to assess the role of carbohydrates present in the mucosa surface, we examined the distribution of glycoconjugates in the llama oviduct by confocal lectin-histochemistry. Mannosyl, glucosyl, N-acetylglucosaminyl, galactosyl, N-acetylgalactosaminyl and sialic acid residues were detected in the oviductal mucose glycocalyx. By incubation of UTJ oviductal explants with LCA, DBA, UEA-1 or PNA lectin previous to co-culture with sperm, we observed a significant decrease in sperm binding only with LCA lectin. In the mucosa surface there were numerous d-glucosyl and D-manosyl residues, which were spotted by this lectin. Probably, this fact promotes the whole covering of the oviduct luminal surface by the sugar-lectin complex, preventing sperm access and adhesion of further residues. However, sperm incubation with mannose or glucose does not significantly prevent binding, which means that glucose and mannose would not be involved in a specific sperm-oviduct interaction. On the other hand, we observed a high reduction in sperm binding to UTJ explants with N-acetylgalactosamine and galactose (p<0.001). Coincidentally, binding sites for N-acetylgalactosamine-PAA-FITC conjugate were observed on the whole surface of the sperm, supporting the concept that llama sperm have lectin-like molecules in their surface, as is the case in other mammals. Probably, these lectin-like molecules, by means of N-acetylgalactosamine and galactose recognition, could link the sperm to the oviductal mucosa with the purpose of forming storing sites in the UTJ. Our results support the idea that more than one carbohydrate could participate in sperm reservoir

  10. Renewable Hydrogen Carrier Carbohydrate: Constructing the Carbon-Neutral Carbohydrate Economy

    SciTech Connect

    Zhang, Y.-H. Percival; Mielenz, Jonathan R

    2011-01-01

    Abstract The hydrogen economy presents an appealing energy future but its implementation must solve numerous problems ranging from low-cost sustainable production, high-density storage, costly infrastructure, to eliminating safety concern. The use of renewable carbohydrate as a high-density hydrogen carrier and energy source for hydrogen production is possible due to emerging cell-free synthetic biology technology called cell-free synthetic pathway biotransformation (SyPaB). Assembly of numerous enzymes and co-enzymes in vitro can create complicated set of biological reactions or pathways that microorganisms cannot complete, for example, C6H10O5 (aq) + 7 H2O (l) 12 H2 (g) + 6 CO2 (g) (PLoS One 2007, 2:e456). Thanks to 100% selectivity of enzymes, modest reaction conditions, and high-purity of generated hydrogen, carbohydrate is a promising hydrogen carrier for end users. Gravimetric density of carbohydrate is 14.8 H2 mass% if water can be recycled from PEM fuel cells or 8.33% H2 mass% without water recycling. Renewable carbohydrate can be isolated from plant biomass or would be produced from a combination of solar electricity/hydrogen and carbon dioxide fixation mediated by high-efficiency artificial photosynthesis mediated by SyPaB. The construction of this carbon-neutral carbohydrate economy would address numerous sustainability challenges, such as electricity and hydrogen storage, CO2 fixation and long-term storage, water conservation, transportation fuel production, plus feed and food production.

  11. Designing carbohydrate nanoparticles for prolonged efficacy of antimicrobial peptide.

    PubMed

    Bi, Lin; Yang, Lei; Narsimhan, Ganesan; Bhunia, Arun K; Yao, Yuan

    2011-03-10

    In this work, carbohydrate nanoparticles were created to prolong the efficacy of antimicrobial peptide against pathogens. Nisin and Listeria monocytogenes were used as the peptide and pathogen models, respectively, and phytoglycogen (PG)-based nanoparticles were developed as carriers of nisin. PG from su1 mutant maize was subjected to β-amylolysis as well as subsequent succinate or octenyl succinate substitutions. The goal was to minimize the loss of peptide during storage and meanwhile realize an effective release in the presence of bacteria. The capabilities of PG derivatives as carriers of nisin were evaluated using centrifugal ultrafiltration, zeta-potential, and the initial availability of nisin against L. monocytogenes. All methods indicated that nisin loading was favored by a high degree of substitution (DS), presence of hydrophobic octenyl moiety, and β-amylolysis of PG nanoparticles. To evaluate the prolonged nisin efficacy, preparations containing nisin and PG derivatives were loaded into a BHI-agar deep-well model (mimicking nisin depletion at the nutrient-containing surface). The residual inhibitory activities of preparations against L. monocytogenes were monitored during 21 days of storage at 4 °C. The results showed that all PG derivatives led to the prolonged retention of nisin activity and the longest retention was associated with high DS, β-amylolysis, and octenyl succinate. Evidently, both electrostatic and hydrophobic interactions are the driving forces of nisin adsorption, and the glucan structure at the nanoparticle surface also affects nisin loading and retention during storage.

  12. The long underestimated carbonyl function of carbohydrates – an organocatalyzed shot into carbohydrate chemistry.

    PubMed

    Mahrwald, R

    2015-09-21

    The aggressive and strong development of organocatalysis provides several protocols for the convenient utilization of the carbonyl function of unprotected carbohydrates in C-C-bond formation processes. These amine-catalyzed mechanisms enable multiple cascade-protocols for the synthesis of a wide range of carbohydrate-derived compound classes. Several, only slightly different protocols, have been developed for the application of 1,3-dicarbonyl compounds in the stereoselective chain-elongation of unprotected carbohydrates and the synthesis of highly functionalized C-glycosides of defined configuration. In addition, C-glycosides can also be accessed by amine-catalyzed reactions with methyl ketones. By a one-pot cascade reaction of isocyanides with unprotected aldoses and amino acids access to defined configured glycopeptide mimetics is achieved. Depending on the reaction conditions different origins to control the installation of configuration during the bond-formation process were observed.

  13. Easy Identification of Residues Involved on Structural Differences Between Nonphosphorylated and Phosphorylated CDK2Cyclin A Complexes Using Two-Dimensional Networks.

    PubMed

    Riadi, Gonzalo; Caballero, Julio

    2014-02-01

    The structures of proteins in Protein Data Bank (PDB) contain a lot of information that can be revealed through the use of tools to facilitate their organization and analysis. The increase in available structural data of nonphosphorylated and phosphorylated CDK2cyclin A (npCDK2cycA and pCDK2cycA) complexes has enabled a more realistic description of the fine structural details of the interface residues of these proteins. This work reports the application of two-dimensional network representations (TDNRs) to the structures deposited in PDB to distinguish the differences in the surface between both complexes due to phosphorylation. As a result, a detailed map of the hydrogen bonds (HBs) and hydrophobic interactions between the T-loop residues of CDK2 and the residues of cycA that are different among nonphosphorylated and phosphorylated complexes were described. In addition, we found some interesting subtle differences in the CDK2cycA interface between nonphosphorylated and phosphorylated complexes due to residues that are not located at the T-loop of CDK2. We noted that some HB interactions in CDK2cycA complex are reinforced when the CDK2 is phosphorylated.

  14. Analysis of Phyllostachys pubescens bamboo residues for liquefaction: chemical components, infrared spectroscopy, and thermogravimetry

    Treesearch

    Jinqiu Qi; Chung-Yun Hse; Todd F. Shupe

    2013-01-01

    Residues of Phyllostachys pubescens bamboo obtained from central Louisiana, USA, were comprehensively investigated for use in liquefaction. The results showed that bamboo branches had the highest Klason lignin and ash content, about 26% and 2.75%, respectively. The epidermis layer sample had relatively higher carbohydrate content, while the wax layer sample had the...

  15. Ketogenic low-carbohydrate diets have no metabolic advantage over nonketogenic low-carbohydrate diets.

    PubMed

    Johnston, Carol S; Tjonn, Sherrie L; Swan, Pamela D; White, Andrea; Hutchins, Heather; Sears, Barry

    2006-05-01

    Low-carbohydrate diets may promote greater weight loss than does the conventional low-fat, high-carbohydrate diet. We compared weight loss and biomarker change in adults adhering to a ketogenic low-carbohydrate (KLC) diet or a nonketogenic low-carbohydrate (NLC) diet. Twenty adults [body mass index (in kg/m(2)): 34.4 +/- 1.0] were randomly assigned to the KLC (60% of energy as fat, beginning with approximately 5% of energy as carbohydrate) or NLC (30% of energy as fat; approximately 40% of energy as carbohydrate) diet. During the 6-wk trial, participants were sedentary, and 24-h intakes were strictly controlled. Mean (+/-SE) weight losses (6.3 +/- 0.6 and 7.2 +/- 0.8 kg in KLC and NLC dieters, respectively; P = 0.324) and fat losses (3.4 and 5.5 kg in KLC and NLC dieters, respectively; P = 0.111) did not differ significantly by group after 6 wk. Blood beta-hydroxybutyrate in the KLC dieters was 3.6 times that in the NLC dieters at week 2 (P = 0.018), and LDL cholesterol was directly correlated with blood beta-hydroxybutyrate (r = 0.297, P = 0.025). Overall, insulin sensitivity and resting energy expenditure increased and serum gamma-glutamyltransferase concentrations decreased in both diet groups during the 6-wk trial (P < 0.05). However, inflammatory risk (arachidonic acid:eicosapentaenoic acid ratios in plasma phospholipids) and perceptions of vigor were more adversely affected by the KLC than by the NLC diet. KLC and NLC diets were equally effective in reducing body weight and insulin resistance, but the KLC diet was associated with several adverse metabolic and emotional effects. The use of ketogenic diets for weight loss is not warranted.

  16. Carbohydrate-protein interactions and their biosensing applications.

    PubMed

    Zeng, Xiangqun; Andrade, Cesar A S; Oliveira, Maria D L; Sun, Xue-Long

    2012-04-01

    Carbohydrate recognition is clearly present throughout nature, playing a major role in the initial attachment of one biological entity to another. The important question is whether these prevalent interactions could provide a real suitable alternative to the use of antibodies or nucleic acid for detection and identification. Currently, examples of carbohydrates being employed in biological detection systems are limited. The challenges of using carbohydrate recognition for detection mainly come from the weak affinity of carbohydrate-protein interactions, the lack of versatile carbohydrate scaffolds with well-defined structures, and the less developed high-information-content, real-time, and label-free assay technology. In this review, we focus on discussing the characteristics of carbohydrate-protein interactions in nature and the methods for carbohydrate immobilization based on surface coupling chemistry in terms of their general applicability for developing carbohydrate- and lectin-based label-free sensors. Furthermore, examples of innovative design of multivalent carbohydrate-protein interactions for sensor applications are given. We limit our review to show the feasibility of carbohydrate and lectin as recognition elements for label-free sensor development in several representative cases to formulate a flexible platform for their use as recognition elements for real-world biosensor applications.

  17. Multivalent interaction based carbohydrate biosensors for signal amplification

    PubMed Central

    Wang, Yanyan; Chalagalla, Srinivas; Li, Tiehai; Sun, Xue-long; Zhao, Wei; Wang, Peng; Zeng, Xiangqun

    2010-01-01

    Multivalent interaction between boronic acids immobilized on Quartz Crystal Microbalance (QCM) sensor surface and the carbohydrates modified Au - nanoparticle (AuNP) has been demonstrated for the development of a sensitive carbohydrate biosensor. Briefly, a boronic acid - containing polymer (boropolymer) as multivalent carbohydrate receptor was oriented immobilized on the cysteamine coated electrode through isourea bond formation. Carbohydrates were conjugated to AuNPs to generate a multivalent carbohydrates moiety to amplify the response signal. Thus, the binding of the carbohydrate conjugated AuNPs to the boropolymer surface are multivalent which could simultaneously increase the binding affinity and specificity. We systematically studied the binding between five carbohydrate conjugated AuNPs and the boropolymer. Our studies show that the associate constant (Ka) was in the order of fucose < glucose < mannose < galactose < maltose. A linear response in the range from 23 µM to 3.83 mM was observed for mannose conjugated AuNPs and the boropolymer recognition elements, with the lower detection limit of 1.5 µM for the carbohydrate analytes. Furthermore, the multivalent binding between carbohydrates and boronic acids are reversible and allow the regeneration of boropolymer surface by using 1M acetic acid so as to sequentially capture and release the carbohydrate analytes. PMID:20863680

  18. Blood Triglycerides Levels and Dietary Carbohydrate Indices in Healthy Koreans.

    PubMed

    Min, Hye Sook; Kang, Ji Yeon; Sung, Joohon; Kim, Mi Kyung

    2016-05-01

    Previous studies have obtained conflicting findings regarding possible associations between indices measuring carbohydrate intake and dyslipidemia, which is an established risk factor of coronary heart disease. In the present study, we examined cross-sectional associations between carbohydrate indices, including the dietary glycemic index (GI), glycemic load (GL), total amount of carbohydrates, and the percentage of energy from carbohydrates, and a range of blood lipid parameters. This study included 1530 participants (554 men and 976 women) from 246 families within the Healthy Twin Study. We analyzed the associations using a generalized linear mixed model to control for familial relationships. Levels of the Apo B were inversely associated with dietary GI, GL, and the amount of carbohydrate intake for men, but these relationships were not significant when fat-adjusted values of the carbohydrate indices were used. Triglyceride levels were positively associated with dietary GI and GL in women, and this pattern was more notable in overweight participants (body mass index [BMI] ≥25 kg/m(2)). However, total, low-density lipoprotein and high-density lipoprotein cholesterol levels were not significantly related with carbohydrate intake overall. Of the blood lipid parameters we investigated, only triglyceride levels were positively related with dietary carbohydrate indices among women participants in the Healthy Twin Study, with an interactive role observed for BMI. However, these associations were not observed in men, suggesting that the association between blood lipid levels and carbohydrate intake depends on the type of lipid, specific carbohydrate indices, gender, and BMI.

  19. Discovery and design of carbohydrate-based therapeutics.

    PubMed

    Cipolla, Laura; Araújo, Ana C; Bini, Davide; Gabrielli, Luca; Russo, Laura; Shaikh, Nasrin

    2010-08-01

    Till now, the importance of carbohydrates has been underscored, if compared with the two other major classes of biopolymers such as oligonucleotides and proteins. Recent advances in glycobiology and glycochemistry have imparted a strong interest in the study of this enormous family of biomolecules. Carbohydrates have been shown to be implicated in recognition processes, such as cell-cell adhesion, cell-extracellular matrix adhesion and cell-intruder recognition phenomena. In addition, carbohydrates are recognized as differentiation markers and as antigenic determinants. Due to their relevant biological role, carbohydrates are promising candidates for drug design and disease treatment. However, the growing number of human disorders known as congenital disorders of glycosylation that are being identified as resulting from abnormalities in glycan structures and protein glycosylation strongly indicates that a fast development of glycobiology, glycochemistry and glycomedicine is highly desirable. The topics give an overview of different approaches that have been used to date for the design of carbohydrate-based therapeutics; this includes the use of native synthetic carbohydrates, the use of carbohydrate mimics designed on the basis of their native counterpart, the use of carbohydrates as scaffolds and finally the design of glyco-fused therapeutics, one of the most recent approaches. The review covers mainly literature that has appeared since 2000, except for a few papers cited for historical reasons. The reader will gain an overview of the current strategies applied to the design of carbohydrate-based therapeutics; in particular, the advantages/disadvantages of different approaches are highlighted. The topic is presented in a general, basic manner and will hopefully be a useful resource for all readers who are not familiar with it. In addition, in order to stress the potentialities of carbohydrates, several examples of carbohydrate-based marketed therapeutics are given

  20. A step towards personalized sports nutrition: carbohydrate intake during exercise.

    PubMed

    Jeukendrup, Asker

    2014-05-01

    There have been significant changes in the understanding of the role of carbohydrates during endurance exercise in recent years, which allows for more specific and more personalized advice with regard to carbohydrate ingestion during exercise. The new proposed guidelines take into account the duration (and intensity) of exercise and advice is not restricted to the amount of carbohydrate; it also gives direction with respect to the type of carbohydrate. Studies have shown that during exercise lasting approximately 1 h in duration, a mouth rinse or small amounts of carbohydrate can result in a performance benefit. A single carbohydrate source can be oxidized at rates up to approximately 60 g/h and this is the recommendation for exercise that is more prolonged (2-3 h). For ultra-endurance events, the recommendation is higher at approximately 90 g/h. Carbohydrate ingested at such high ingestion rates must be a multiple transportable carbohydrates to allow high oxidation rates and prevent the accumulation of carbohydrate in the intestine. The source of the carbohydrate may be a liquid, semisolid, or solid, and the recommendations may need to be adjusted downward when the absolute exercise intensity is low and thus carbohydrate oxidation rates are also low. Carbohydrate intake advice is independent of body weight as well as training status. Therefore, although these guidelines apply to most athletes, they are highly dependent on the type and duration of activity. These new guidelines may replace the generic existing guidelines for carbohydrate intake during endurance exercise.

  1. Composition of the carbohydrate granules of the cyanobacterium, Cyanothece sp. strain ATCC 51142

    NASA Technical Reports Server (NTRS)

    Schneegurt, M. A.; Sherman, D. M.; Sherman, L. A.; Mitchell, C. A. (Principal Investigator)

    1997-01-01

    Cyanothece sp. strain ATCC 51142 is an aerobic, unicellular, diazotrophic cyanobacterium that temporally separates O2-sensitive N2 fixation from oxygenic photosynthesis. The energy and reducing power needed for N2 fixation appears to be generated by an active respiratory apparatus that utilizes the contents of large interthylakoidal carbohydrate granules. We report here on the carbohydrate and protein composition of the granules of Cyanothece sp. strain ATCC 51142. The carbohydrate component is a glucose homopolymer with branches every nine residues and is chemically identical to glycogen. Granule-associated protein fractions showed temporal changes in the number of proteins and their abundance during the metabolic oscillations observed under diazotrophic conditions. There also were temporal changes in the protein pattern of the granule-depleted supernatant fractions from diazotrophic cultures. None of the granule-associated proteins crossreacted with antisera directed against several glycogen-metabolizing enzymes or nitrogenase, although these proteins were tentatively identified in supernatant fractions. It is suggested that the granule-associated proteins are structural proteins required to maintain a complex granule architecture.

  2. Sweeter but deadlier: decoupling size, charge and capping effects in carbohydrate coated bactericidal silver nanoparticles.

    PubMed

    de Oliveira, Luciane França; Gonçalves, Julianna de Oliveira; Gonçalves, Kaliandra de Almeida; Kobarg, Jörg; Cardoso, Mateus Borba

    2013-11-01

    Silver nanoparticles are widely used due to their biomedical-antibacterial applications. At the same time, the stabilization of these nanoparticles is challenging and may be made using polymeric carbohydrates, based on the practice of avoiding toxic chemicals and undesirable residues. In this study, we synthesized silver nanoparticles (AgNPs) which were stabilized by carbohydrates (potato starch and chitosan) and characterized by UV-Vis spectroscopy, zeta potential and transmission electron microscopy techniques. Bactericidal efficiency of AgNPs capped with different carbohydrates was tested demonstrating that the synthesized materials were able to inhibit the growth of two clinical/medical relevant bacteria strains (Escherichia coil and Staphylococcus aureus). AgNPs stabilized by chitosan presented enhanced bactericidal activity if compared to the ones synthesized in presence of potato starch. This difference is mainly attributed to the known antibacterial properties of chitosan associated to overall positive charge of the nanoparticles capped by this polymer. Those nanoparticles obtained in presence of starch presented minor bactericidal effects since the starch-capping agent is not able to contribute to the avoidance of bacteria growth and confers a quasi-neutral charge to the nanoparticle.

  3. Composition of the carbohydrate granules of the cyanobacterium, Cyanothece sp. strain ATCC 51142

    NASA Technical Reports Server (NTRS)

    Schneegurt, M. A.; Sherman, D. M.; Sherman, L. A.; Mitchell, C. A. (Principal Investigator)

    1997-01-01

    Cyanothece sp. strain ATCC 51142 is an aerobic, unicellular, diazotrophic cyanobacterium that temporally separates O2-sensitive N2 fixation from oxygenic photosynthesis. The energy and reducing power needed for N2 fixation appears to be generated by an active respiratory apparatus that utilizes the contents of large interthylakoidal carbohydrate granules. We report here on the carbohydrate and protein composition of the granules of Cyanothece sp. strain ATCC 51142. The carbohydrate component is a glucose homopolymer with branches every nine residues and is chemically identical to glycogen. Granule-associated protein fractions showed temporal changes in the number of proteins and their abundance during the metabolic oscillations observed under diazotrophic conditions. There also were temporal changes in the protein pattern of the granule-depleted supernatant fractions from diazotrophic cultures. None of the granule-associated proteins crossreacted with antisera directed against several glycogen-metabolizing enzymes or nitrogenase, although these proteins were tentatively identified in supernatant fractions. It is suggested that the granule-associated proteins are structural proteins required to maintain a complex granule architecture.

  4. The structure of the carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-79104.

    PubMed

    Vinogradov, Evgeny; Li, Jianjun; Sadovskaya, Irina; Jabbouri, Said; Helander, Ilkka M

    2004-06-22

    The structure of the carbohydrate backbone of the lipopolysaccharide from Pectinatus frisingensis strain VTT E-79104 was analyzed using chemical degradations, NMR spectroscopy, mass spectrometry, and chemical methods. The LPS contains two major structural variants, differing in the presence or absence of an octasaccharide fragment. The largest structure of the carbohydrate backbone of the LPS, that could be deduced from experimental results, consists of 20 monosaccharides arranged in a nonrepetitive sequence: [carbohydrate structure: see text] where R is H or 4-O-Me-alpha-L-Fuc-(1-2)-4-O-Me-beta-Hep-(1-3)-alpha-GlcNAc-(1-2)-beta-Man-(1-3)-beta-ManNAc-(1-4)-alpha-Gal-(1-4)-beta-Hep-(1-3)-beta-GalNAc-(1- where Hep is a residue of D-glycero-D-galacto-heptose; all monosaccharides have the D-configuration except for 4-O-Me-L-Fuc and L-Ara4N. This structure is architecturally similar to the oligosaccharide system reported previously in P. frisingensis VTT E-82164 LPS, but differs from the latter in composition and also in the size of the outer region.

  5. [Malabsorption of carbohydrates in children (author's transl)].

    PubMed

    Vázquez, C; Escobar, H; Polanco, I; Codoceo, R; Vitoria, J C

    1975-01-01

    Physiological bases of digestion and absorption of carbohydrates are reviewed, as a preliminary step, in order to draw a general scheme of its patholophysiology. Clasification of different types of carbohydrate malabsorption is presented. Various exploration methods are discussed in terms of autors' own experiences. Relationship between a sugar screening test, faecal lactic acid contents and a simplified lactose tolerance test, is described in detail. Systematic diagnoses of these diseases are established. Different clinical pictures are reviewed. It is not yet well defined if a starch malabsorption can be caused by either a primary or secondary duodenal amylase deficiency. The clinical forms of congenital sucrose-isomaltose intolerance may be more attenuated than its classical form; incertain cases, secondary sucrose intolerance may also be present due to mucosa anatomic lesions. Maltose malabsorption has no clinical implications. As compared to other alpha-glycosidades, the trehalase activity has been not more affected by not using trehalose in feeding. Primary congenital lactase deficiency is not frequent, whereas secondary forms as much more usual and appear, in primary malabsorption syndromes and in the coeliac disease, very often along with clinical tolerance to lactose. In Spain, lactose nonabsorbers in 16.5% for adults 11.2% for adolescents and 18.3% for children, meaning, that it is being favored by environmental factors in the latter. The unspecified sugar malabsorption during the child's first year is still the most frequent cause of carbohydrate intolerance in children and, although certain progress has been achieved in its diagnosis and therapy, its pathogenic mechanism is not satisfactorily known yet.

  6. Radiofluorinated carbohydrates for positron emission tomography.

    PubMed

    Mun, Jiyoung

    2013-01-01

    2-Deoxy-2-[(18)F]fluoro-D-glucose (2-(18)FDG) has represented radiofluorinated carbohydrates as the most successful tracer for positron emission tomography (PET). 2-(18)FDG uptake depends on glucose metabolism, which is related to a disease progression. 2-(18)FDG has been widely used in oncology, neurology, cardiology, infectious diseases, and inflammation, to complement anatomical modalities such as CT and MRI. Followed by the success of 2-(18)FDG, various radiofluorinated carbohydrates have been evaluated as PET tracers, which include analogs of D-ribose, D-mannose, D-galactose, D-talose, D-fructose, D-allose, lactose, L-fucose, N-acetylneuraminic acid, and L-ascorbic acid. Among those radiofluorinated carbohydrates, several have implied potential for further development. 2-Deoxy-2-[(18)F]fluoro-D-galactose has been developed to assess liver function and diagnose hepatic carcinoma. 6-Deoxy-6-[(18)F]fluoro-D-fructose showed promising characteristics for diagnosis of breast cancer. Three radiofluorinated analogs of lactose have been designed as the substrates of the overexpressed hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein in peritumoral pancreatic tissue for early diagnosis of pancreatic cancer. The metabolism of 6-[(18)F]fluoro-L-fucose suggested that it is a bioactive analog of L-fucose in the synthesis of glycoconjugate macromolecules. 6-Deoxy-6-[(18)F]fluoro-L-ascorbic acid was evaluated to assess antioxidant function of L-ascorbic acid in rodent models of transient global ischemia and glutathione deficiency.

  7. Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance

    NASA Astrophysics Data System (ADS)

    Spiwok, Vojtěch; Lipovová, Petra; Skálová, Tereza; Vondráčková, Eva; Dohnálek, Jan; Hašek, Jindřich; Králová, Blanka

    2005-12-01

    Aromatic amino acid residues are often present in carbohydrate-binding sites of proteins. These binding sites are characterized by a placement of a carbohydrate moiety in a stacking orientation to an aromatic ring. This arrangement is an example of CH/π interactions. Ab initio interaction energies for 20 carbohydrate-aromatic complexes taken from 6 selected ultra-high resolution X-ray structures of glycosidases and carbohydrate-binding proteins were calculated. All interaction energies of a pyranose moiety with a side chain of an aromatic residue were calculated as attractive with interaction energy ranging from -2.8 to -12.3 kcal/mol as calculated at the MP2/6-311+G(d) level. Strong attractive interactions were observed for a wide range of orientations of carbohydrate and aromatic ring as present in selected X-ray structures. The most attractive interaction was associated with apparent combination of CH/π interactions and classical H-bonds. The failure of Hartree-Fock method (interaction energies from +1.0 to -6.9 kcal/mol) can be explained by a dispersion nature of a majority of the studied complexes. We also present a comparison of interaction energies calculated at the MP2 level with those calculated using molecular mechanics force fields (OPLS, GROMOS, CSFF/CHARMM, CHEAT/CHARMM, Glycam/AMBER, MM2 and MM3). For a majority of force fields there was a strong correlation with MP2 values. RMSD between MP2 and force field values were 1.0 for CSFF/CHARMM, 1.2 for Glycam/AMBER, 1.2 for GROMOS, 1.3 for MM3, 1.4 for MM2, 1.5 for OPLS and to 2.3 for CHEAT/CHARMM (in kcal/mol). These results show that molecular mechanics approximates interaction energies very well and support an application of molecular mechanics methods in the area of glycochemistry and glycobiology.

  8. Utilization of oak residues

    Treesearch

    Richard C. Allison

    1971-01-01

    Residues should be thought of as a raw material for specific uses rather than as a waste. Fines and solid wood residues are usually kept separated in waste-collection system, but species are rarely kept separated. The properties of each species dictate what uses can be made of them. Quantity, location, cost, moisture content, physical size, and presence of foreign...

  9. Carbohydrate nanotechnology: hierarchical assembly using nature's other information carrying biopolymers.

    PubMed

    Han, Xu; Zheng, Yeting; Munro, Catherine J; Ji, Yiwen; Braunschweig, Adam B

    2015-08-01

    Despite their central role in directing some of the most complex biological processes, carbohydrates--nature's other information carrying biopolymer--have been largely ignored as building blocks for synthetic hierarchical assemblies. The non-stoichiometric binding and astronomical diversity characteristic of carbohydrates could lead to tantalizingly complex assembly algorithms, but these attributes simultaneously increase the difficulty of preparing carbohydrate assemblies and anticipating their behavior. Convergences in biotechnology, nanotechnology, polymer chemistry, surface science, and supramolecular chemistry have led to many recent important breakthroughs in glycan microarrays and synthetic carbohydrate receptors, where the idiosyncrasies of carbohydrate structure and binding are increasingly considered. We hope to inspire more researchers to consider carbohydrate structure, diversity, and binding as attractive tools for constructing synthetic hierarchical assemblies.

  10. Chemical biology approaches to designing defined carbohydrate vaccines.

    PubMed

    Anish, Chakkumkal; Schumann, Benjamin; Pereira, Claney Lebev; Seeberger, Peter H

    2014-01-16

    Carbohydrate antigens have shown promise as important targets for developing effective vaccines and pathogen detection strategies. Modifying purified microbial glycans through synthetic routes or completely synthesizing antigenic motifs are attractive options to advance carbohydrate vaccine development. However, limited knowledge on structure-property correlates hampers the discovery of immunoprotective carbohydrate epitopes. Recent advancements in tools for glycan modification, high-throughput screening of biological samples, and 3D structural analysis may facilitate antigen discovery process. This review focuses on advances that accelerate carbohydrate-based vaccine development and various technologies that are driving these efforts. Herein we provide a critical overview of approaches and resources available for rational design of better carbohydrate antigens. Structurally defined and fully synthetic oligosaccharides, designed based on molecular understanding of antigen-antibody interactions, offer a promising alternative for developing future carbohydrate vaccines.

  11. Light period regulation of carbohydrate partitioning

    NASA Technical Reports Server (NTRS)

    Janes, Harry W.

    1994-01-01

    We have shown that the photosynthetic period is important in regulating carbon partitioning. Even when the same amount of carbon is fixed over a 24h period considerably more is translocated out of the leaf under the longer photosynthetic period. This is extremely important when parts of the plant other than the leaves are to be sold. It is also important to notice the amount of carbon respired in the short photosynthetic period. The light period effect on carbohydrate fixation, dark respiration, and translocation is shown in this report.

  12. A Carbohydrate-Derived Splice Modulator.

    PubMed

    Dhar, Sachin; La Clair, James J; León, Brian; Hammons, Justin C; Yu, Zhe; Kashyap, Manoj K; Castro, Januario E; Burkart, Michael D

    2016-04-20

    Small-molecule splice modulators have recently been recognized for their clinical potential for diverse cancers. This, combined with their use as tools to study the importance of splice-regulated events and their association with disease, continues to fuel the discovery of new splice modulators. One of the key challenges found in the current class of materials arises from their instability, where rapid metabolic degradation can lead to off-target responses. We now describe the preparation of bench-stable splice modulators by adapting carbohydrate motifs as a central scaffold to provide rapid access to potent splice modulators.

  13. Fluorescent carbohydrate probes for cell lectins

    NASA Astrophysics Data System (ADS)

    Galanina, Oxana; Feofanov, Alexei; Tuzikov, Alexander B.; Rapoport, Evgenia; Crocker, Paul R.; Grichine, Alexei; Egret-Charlier, Marguerite; Vigny, Paul; Le Pendu, Jacques; Bovin, Nicolai V.

    2001-09-01

    Fluorescein labeled carbohydrate (Glyc) probes were synthesized as analytical tools for the study of cellular lectins, i.e. SiaLe x-PAA-flu, Sia 2-PAA-flu, GlcNAc 2-PAA-flu, LacNAc-PAA-flu and a number of similar ones, with PAA a soluble polyacrylamide carrier. The binding of SiaLe x-PAA-flu was assessed using CHO cells transfected with E-selectin, and the binding of Sia 2-PAA-flu was assessed by COS cells transfected with siglec-9. In flow cytometry assays, the fluorescein probes demonstrated a specific binding to the lectin-transfected cells that was inhibited by unlabeled carbohydrate ligands. The intense binding of SiaLe x-PAA- 3H to the E-selectin transfected cells and the lack of binding to both native and permeabilized control cells lead to the conclusion that the polyacrylamide carrier itself and the spacer arm connecting the carbohydrate moiety with PAA did not contribute anymore to the binding. Tumors were obtained from nude mice by injection of CHO E-selectin or mock transfected cells. The fluorescent SiaLe x-PAA-flu probe could bind to the tumor sections from E-selectin positive CHO cells, but not from the control ones. Thus, these probes can be used to reveal specifically the carbohydrate binding sites on cells in culture as well as cells in tissue sections. The use of the confocal spectral imaging technique with Glyc-PAA-flu probes offered the unique possibility to detect lectins in different cells, even when the level of lectin expression was rather low. The confocal mode of spectrum recording provided an analysis of the probe localization with 3D submicron resolution. The spectral analysis (as a constituent part of the confocal spectral imaging technique) enabled interfering signals of the probe and intrinsic cellular fluorescence to be accurately separated, the distribution of the probe to be revealed and its local concentration to be measured.

  14. Multimodal CARS microscopy of structured carbohydrate biopolymers

    PubMed Central

    Slepkov, Aaron D.; Ridsdale, Andrew; Pegoraro, Adrian F.; Moffatt, Douglas J.; Stolow, Albert

    2010-01-01

    We demonstrate the utility of multimodal coherent anti-Stokes Raman scattering (CARS) microscopy for the study of structured condensed carbohydrate systems. Simultaneous second-harmonic generation (SHG) and spectrally-scanned CARS microscopy was used to elucidate structure, alignment, and density in cellulose cotton fibers and in starch grains undergoing rapid heat-moisture swelling. Our results suggest that CARS response of the O-H stretch region (3000 cm−1–3400 cm−1), together with the commonly-measured C-H stretch (2750 cm−1–2970 cm−1) and SHG provide potentially important structural information and contrast in these materials. PMID:21258555

  15. Liquid crystals based on fluorinated carbohydrates.

    PubMed

    Miethchen, R; Hein, M

    2000-07-10

    Fluorine introduced in the hydrophilic or the hydrophobic region of amphiphiles influences the thermomesomorphy of amphiphilic and monophilic fluorosugars in a very specific manner. This paper is the first review about chiral mesogens based on fluorinated carbohydrates. It covers the literature published so far. Analytical objectives are given to: (i) Effects of fluorine atoms on the H-bonding network of the hydrophilic region of sugar amphiphiles; (ii) Effects of perfluoroalkyl chains compared to alkyl chains; (iii) Polymorphism, e.g., also formation of smectic S(C)* phases.

  16. Targeting carbohydrate antigens in HIV vaccine development.

    PubMed

    Pashov, Anastas; Canziani, Gabriela; Macleod, Stewart; Plaxco, Jason; Monzavi-Karbassi, Behjatolah; Kieber-Emmons, Thomas

    2005-03-18

    Peptide mimotopes provide a strategy to augment human immunodeficiency virus 1 (HIV-1) specific carbohydrate reactive immune responses. Their antigenic and immunological properties will depend on the optimization of motif clustering and multimerization. We observe that structural variants of the same mimetic motif, linear versus cyclic, can be used to tune the properties of the antibodies elicited. The expansion of the database of mimotope sequence motifs can be increased by analyzing structures that bind to HIV directed monoclonal antibody 2G12 and the lectin Concanavalin A (Con A), fostering new mimotope designs. Such analysis indicates that these reagents bind to subsets of mannosyl antigens on the envelope (env) protein.

  17. Carbohydrates/nucleosides/RNA-DNA-ligand interactions

    SciTech Connect

    Kaptein, R.; McConnell, B.; Serianni, A.S.; Silks, L.A. III

    1994-12-01

    Carbohydrate and nucleotide structural determination using modern spectroscopic techniques is dependent on our ability to label oligonucleotides and oligosaccharides with stable isotopes. Uniform Carbon 13 and Nitrogen 15 labeling of oligonucleotides is important to present-day efforts, which are focused on determining the structure of relatively small oligosaccharides and oligonucleotides, which form the elements of larger structures. Because of the relatively recent interest in three-dimensional structure, the development of techniques used to label them has lagged behind parallel techniques used to label peptides and proteins. Therefore, this group`s discussion focused primarily on problems faced today in obtaining oligonucleotides labeled uniformly with carbon 13 and nitrogen 15.

  18. Alternatingly twisted β-hairpins and nonglycine residues in the disallowed II' region of the Ramachandran plot.

    PubMed

    Torshin, Ivan Yu; Esipova, Natalya G; Tumanyan, Vladimir G

    2014-01-01

    The structure of the SH3 domain of α-spectrin (PDB code 1SHG) features Asn47 in the II' area of the Ramachandran plot, which as a rule admits only glycine residues, and this phenomenon still awaits its explanation. Here, we undertook a computational study of this particular case by means of molecular dynamics and bioinformatics approaches. We found that the region of the SH3 domain in the vicinity of Asn47 remains relatively stable during denaturing molecular dynamics simulations of the entire domain and of its parts. This increased stability may be connected with the dynamic hydrogen bonding that is susceptible to targeted in silico mutations of Arg49. Bioinformatics analysis indicated that Asn47 is in the β-turn of a distinctive structural fragment we called 'alternatingly twisted β-hairpin.' Fragments of similar conformation are quite abundant in a nonredundant set of PDB chains and are distinguished from ordinary β-hairpins by some surplus of glycine in their β-turns, lack of certain interpeptide hydrogen bonds, and an increased chirality index. Thus, the disallowed conformation of residues other than glycine is realized in the β-turns of alternatingly twisted β-hairpins.

  19. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

    PubMed Central

    Lipska, Agnieszka G.; Sieradzan, Adam K.; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A.

    2016-01-01

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models. PMID:27179474

  20. Engineering Cel7A carbohydrate binding module and linker for reduced lignin inhibition.

    PubMed

    Strobel, Kathryn L; Pfeiffer, Katherine A; Blanch, Harvey W; Clark, Douglas S

    2016-06-01

    Non-productive binding of cellulases to lignin inhibits enzymatic hydrolysis of biomass, increasing enzyme requirements and the cost of biofuels. This study used site-directed mutagenesis of the Trichoderma Cel7A carbohydrate binding module (CBM) and linker to investigate the mechanisms of adsorption to lignin and engineer a cellulase with increased binding specificity for cellulose. CBM mutations that added hydrophobic or positively charged residues decreased the specificity for cellulose, while mutations that added negatively charged residues increased the specificity. Linker mutations that altered predicted glycosylation patterns selectively impacted lignin affinity. Beneficial mutations were combined to generate a mutant with 2.5-fold less lignin affinity while fully retaining cellulose affinity. This mutant was uninhibited by added lignin during hydrolysis of Avicel and generated 40% more glucose than the wild-type enzyme from dilute acid-pretreated Miscanthus. Biotechnol. Bioeng. 2016;113: 1369-1374. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  1. Carbohydrate secretion by phototrophic communities in tidal sediments

    NASA Astrophysics Data System (ADS)

    de Winder, B.; Staats, N.; Stal, L. J.; Paterson, D. M.

    1999-09-01

    Two different benthic phototrophic communities on tidal flats were investigated for their carbohydrate content and distribution. Carbohydrates were analysed as two operationally defined fractions, related to the difficulty of extraction from the sediment matrix. Water-soluble (colloidal) and EDTA-extractable (capsular) carbohydrates were measured in a cyanobacterial mat and a diatom biofilm. The chlorophyll-specific carbohydrate content of the two communities was very different. The diatom biofilm contained up to 100 times more colloidal carbohydrate than the cyanobacterial mat. The concentrations of colloidal carbohydrates in the diatom biofilm correlated with biomass (chlorophyll-a), but this was not the case with the carbohydrate in the EDTA extract. It is proposed that the capsular carbohydrates were probably recalcitrant to mineralisation and therefore accumulated in the sediment. Neither colloidal nor EDTA-extractable carbohydrate in the cyanobacterial mat correlated with chlorophyll-a. This was probably an artefact caused by the fact that approximately 50% of the chlorophyll-a in the mat was attributed to diatoms. The characteristics of extracellular polysaccharides were investigated in laboratory cultures of the dominant organisms. Extracellular polysaccharides of the cyanobacterium Microcoleus chthonoplastes and of the diatom Navicula menisculus did not contain uronic acids. However, carboxylated sugars were found in large quantities in the capsular polysaccharides of the cyanobacterium and were present in equal ratios in the extracellular and capsular carbohydrate of the diatom Cylindrotheca closterium. Both in laboratory model systems of diatom biofilms and in situ, enhanced colloidal carbohydrate production was observed in the light. No light-dependent increase in carbohydrate concentration was found for the cyanobacterial mat. The cyanobacteria formed a mat in which the filamentous organisms entangled sand grains and attached firmly to the substratum

  2. Structure-function relations of carbohydrates by neoglycolipid arrays.

    PubMed

    Huang, Gang-Liang; Huang, Hua-Liang; Zhang, Hou-Cheng; Wang, Peng-George

    2006-06-01

    The work presented herein is a new noncovalent glycoarray assembly method for microplates created by simply mixing together a carbohydrate and a tetradecylamine. alpha-D-Mannopyranoside, alpha-D-glucopyranoside, and alpha-D-galactopyranoside were utilized in model studies and product formations were detected by lectin binding. The method can be extended to study the steric hindrance effect of carbohydrate-protein interactions, namely the structure-function relations of carbohydrates.

  3. Maximizing Immune Response to Carbohydrate Antigens on Breast Tumors

    DTIC Science & Technology

    2004-08-01

    means to eradicate tumor cells would therefore be an advantage in vaccine development (manuscript #2 submitted). Choice of peptide mimotope Arrays of...peptide mimotopes of carbohydrate antigens formulated as multiple antigen peptides or as DNA vaccines can elicit carbohydrate reactive IgM serum...specific CTL. Immunity 1999; 10:51-61. 1. Kieber-Emmons T, Luo P, Qiu J, et al. Vaccination with carbohydrate peptide mimotopes promotes anti-tumor

  4. Distribution of structural carbohydrates in corn plants as influenced by corn residue management

    USDA-ARS?s Scientific Manuscript database

    As part of the Sun Grant Regional Partnership corn stover project, continuous corn (Zea mays L.) field studies incorporating stover removal management practices (0 and 100% removal) were established in both Alabama and South Carolina. Plots in both states were representative of major soil types in t...

  5. Carbohydrate-active enzymes from pigmented Bacilli: a genomic approach to assess carbohydrate utilization and degradation

    PubMed Central

    2011-01-01

    Background Spore-forming Bacilli are Gram-positive bacteria commonly found in a variety of natural habitats, including soil, water and the gastro-intestinal (GI)-tract of animals. Isolates of various Bacillus species produce pigments, mostly carotenoids, with a putative protective role against UV irradiation and oxygen-reactive forms. Results We report the annotation of carbohydrate active enzymes (CAZymes) of two pigmented Bacilli isolated from the human GI-tract and belonging to the Bacillus indicus and B. firmus species. A high number of glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) were found in both isolates. A detailed analysis of CAZyme families, was performed and supported by growth data. Carbohydrates able to support growth as the sole carbon source negatively effected carotenoid formation in rich medium, suggesting that a catabolite repression-like mechanism controls carotenoid biosynthesis in both Bacilli. Experimental results on biofilm formation confirmed genomic data on the potentials of B. indicus HU36 to produce a levan-based biofilm, while mucin-binding and -degradation experiments supported genomic data suggesting the ability of both Bacilli to degrade mammalian glycans. Conclusions CAZy analyses of the genomes of the two pigmented Bacilli, compared to other Bacillus species and validated by experimental data on carbohydrate utilization, biofilm formation and mucin degradation, suggests that the two pigmented Bacilli are adapted to the intestinal environment and are suited to grow in and colonize the human gut. PMID:21892951

  6. Carbohydrate-active enzymes from pigmented Bacilli: a genomic approach to assess carbohydrate utilization and degradation.

    PubMed

    Manzo, Nicola; D'Apuzzo, Enrica; Coutinho, Pedro M; Cutting, Simon M; Henrissat, Bernard; Ricca, Ezio

    2011-09-05

    Spore-forming Bacilli are gram-positive bacteria commonly found in a variety of natural habitats, including soil, water and the gastro-intestinal (GI)-tract of animals. Isolates of various Bacillus species produce pigments, mostly carotenoids, with a putative protective role against UV irradiation and oxygen-reactive forms. We report the annotation of carbohydrate active enzymes (CAZymes) of two pigmented Bacilli isolated from the human GI-tract and belonging to the Bacillus indicus and B. firmus species. A high number of glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) were found in both isolates. A detailed analysis of CAZyme families, was performed and supported by growth data. Carbohydrates able to support growth as the sole carbon source negatively effected carotenoid formation in rich medium, suggesting that a catabolite repression-like mechanism controls carotenoid biosynthesis in both Bacilli. Experimental results on biofilm formation confirmed genomic data on the potentials of B. indicus HU36 to produce a levan-based biofilm, while mucin-binding and -degradation experiments supported genomic data suggesting the ability of both Bacilli to degrade mammalian glycans. CAZy analyses of the genomes of the two pigmented Bacilli, compared to other Bacillus species and validated by experimental data on carbohydrate utilization, biofilm formation and mucin degradation, suggests that the two pigmented Bacilli are adapted to the intestinal environment and are suited to grow in and colonize the human gut.

  7. A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations.

    PubMed

    Flores, David I; Sotelo-Mundo, Rogerio R; Brizuela, Carlos A

    2014-01-01

    The automatic identification of catalytic residues still remains an important challenge in structural bioinformatics. Sequence-based methods are good alternatives when the query shares a high percentage of identity with a well-annotated enzyme. However, when the homology is not apparent, which occurs with many structures from the structural genome initiative, structural information should be exploited. A local structural comparison is preferred to a global structural comparison when predicting functional residues. CMASA is a recently proposed method for predicting catalytic residues based on a local structure comparison. The method achieves high accuracy and a high value for the Matthews correlation coefficient. However, point substitutions or a lack of relevant data strongly affect the performance of the method. In the present study, we propose a simple extension to the CMASA method to overcome this difficulty. Extensive computational experiments are shown as proof of concept instances, as well as for a few real cases. The results show that the extension performs well when the catalytic site contains mutated residues or when some residues are missing. The proposed modification could correctly predict the catalytic residues of a mutant thymidylate synthase, 1EVF. It also successfully predicted the catalytic residues for 3HRC despite the lack of information for a relevant side chain atom in the PDB file.

  8. A Simple Extension to the CMASA Method for the Prediction of Catalytic Residues in the Presence of Single Point Mutations

    PubMed Central

    Flores, David I.; Sotelo-Mundo, Rogerio R.; Brizuela, Carlos A.

    2014-01-01

    The automatic identification of catalytic residues still remains an important challenge in structural bioinformatics. Sequence-based methods are good alternatives when the query shares a high percentage of identity with a well-annotated enzyme. However, when the homology is not apparent, which occurs with many structures from the structural genome initiative, structural information should be exploited. A local structural comparison is preferred to a global structural comparison when predicting functional residues. CMASA is a recently proposed method for predicting catalytic residues based on a local structure comparison. The method achieves high accuracy and a high value for the Matthews correlation coefficient. However, point substitutions or a lack of relevant data strongly affect the performance of the method. In the present study, we propose a simple extension to the CMASA method to overcome this difficulty. Extensive computational experiments are shown as proof of concept instances, as well as for a few real cases. The results show that the extension performs well when the catalytic site contains mutated residues or when some residues are missing. The proposed modification could correctly predict the catalytic residues of a mutant thymidylate synthase, 1EVF. It also successfully predicted the catalytic residues for 3HRC despite the lack of information for a relevant side chain atom in the PDB file. PMID:25268770

  9. Reduction of myocardial infarct size in vivo by carbohydrate-based glycomimetics.

    PubMed

    Kilgore, K S; Tanhehco, E J; Park, J L; Naylor, K B; Anderson, M B; Lucchesi, B R

    1998-01-01

    One of the foremost mechanisms involved in the pathogenesis of myocardial reperfusion injury is the adhesion of neutrophils within the myocardium. The initial neutrophil-endothelial cell interactions are mediated by the selectin family of adhesion molecules. Blockade of this group of adhesion molecules, through the use of synthetic carbohydrate analogs to the selectin ligand sialyl Lewisx and glycomimetics, has been beneficial in reducing neutrophil influx and infarct size. In the present study, glycyrrhizin (GM1292), a natural structural glycomimetic, was analyzed for the ability to decrease myocardial infarct size after regional myocardial ischemia/reperfusion. To determine the structural requirements for optimal cardioprotective activity, two additional compounds related to glycyrrhizin, GM3290 and GM1658 (glycyrrhetinic acid), were studied. The molecular structures of the latter two compounds differ in the number of glucuronic acid residues in their respective molecules. Open-chest, anesthetized rabbits were subjected to 30 min occlusion of the left coronary artery followed by 5 hr of reperfusion. Vehicle or glycomimetic (10 mg/kg/hr) was administered intravenously immediately before the onset of reperfusion and every hour during the reperfusion period. Myocardial infarct size in rabbits treated with GM1292 (two glucuronic acid residues) and GM3290 (one glucuronic acid residue) was reduced significantly when compared with vehicle-treated animals (P < .05). GM1658, which lacks glucuronic acid residues, did not provide a protective effect in vivo. The data suggest that GM1292 and GM3290, which contain carbohydrate moieties, are effective in reducing the degree of myocardial injury after an acute period of ischemia/reperfusion.

  10. Carbohydrate recognition by boronolectins, small molecules, and lectins.

    PubMed

    Jin, Shan; Cheng, Yunfeng; Reid, Suazette; Li, Minyong; Wang, Binghe

    2010-03-01

    Carbohydrates are known to mediate a large number of biological and pathological events. Small and macromolecules capable of carbohydrate recognition have great potentials as research tools, diagnostics, vectors for targeted delivery of therapeutic and imaging agents, and therapeutic agents. However, this potential is far from being realized. One key issue is the difficulty in the development of "binders" capable of specific recognition of carbohydrates of biological relevance. This review discusses systematically the general approaches that are available in developing carbohydrate sensors and "binders/receptors," and their applications. The focus is on discoveries during the last 5 years.

  11. Physicochemical Characterization of Iron Carbohydrate Colloid Drug Products.

    PubMed

    Zou, Peng; Tyner, Katherine; Raw, Andre; Lee, Sau

    2017-07-31

    Iron carbohydrate colloid drug products are intravenously administered to patients with chronic kidney disease for the treatment of iron deficiency anemia. Physicochemical characterization of iron colloids is critical to establish pharmaceutical equivalence between an innovator iron colloid product and generic version. The purpose of this review is to summarize literature-reported techniques for physicochemical characterization of iron carbohydrate colloid drug products. The mechanisms, reported testing results, and common technical pitfalls for individual characterization test are discussed. A better understanding of the physicochemical characterization techniques will facilitate generic iron carbohydrate colloid product development, accelerate products to market, and ensure iron carbohydrate colloid product quality.

  12. Carbohydrate Recognition by Boronolectins, Small Molecules, and Lectins

    PubMed Central

    Jin, Shan; Cheng, Yunfeng; Reid, Suazette; Li, Minyong; Wang, Binghe

    2009-01-01

    Carbohydrates are known to mediate a large number of biological and pathological events. Small and macromolecules capable of carbohydrate recognition have great potentials as research tools, diagnostics, vectors for targeted delivery of therapeutic and imaging agents, and therapeutic agents. However, this potential is far from being realized. One key issue is the difficulty in the development of “binders” capable of specific recognition of carbohydrates of biological relevance. This review discusses systematically the general approaches that are available in developing carbohydrate sensors and “binders/receptors,” and their applications. The focus is on discoveries during the last five years. PMID:19291708

  13. Carbohydrate Analysis: Can We Control the Ripening of Bananas?

    NASA Astrophysics Data System (ADS)

    Deal, S. Todd; Farmer, Catherine E.; Cerpovicz, Paul F.

    2002-04-01

    We have developed an experiment for nutritional/introductory biochemistry courses that focuses on carbohydrate analysis--specifically, the carbohydrates found in bananas and the change in carbohydrate composition as the banana ripens. Pairs of students analyze the starch and reducing sugar content of green, ripe, and overripe bananas. Using the techniques and knowledge gained from these analyses, they then investigate the influence of various storage methods on the ripening process. While this experiment was developed for an introductory-level biochemistry lab, it can easily be adapted for use in other laboratory programs that seek to teach the fundamentals of carbohydrate analysis.

  14. Carbohydrate and lipid metabolism in farm animals.

    PubMed

    Nafikov, Rafael A; Beitz, Donald C

    2007-03-01

    Much research on carbohydrate and lipid metabolism in farm animals conducted over the second half of the 20th century has focused primarily on increasing the production efficiency and improving the quality and acceptability of animal-derived foods. Research was also performed with the express interest in greater understanding of biochemistry and metabolism of livestock species with ultimate application in the food industry. Knowledge about basic nutritional concepts and differences in metabolism among farm animals, however, has been accumulated and has been used successfully to better understand different health problems in humans such as obesity, atherosclerosis, diabetes, and others that are associated with disturbances in metabolism and nutrition. Here we focus on researchers who made major contributions to our understanding of the synthesis and degradation including digestion of carbohydrates and lipids during the past half-century and to our understanding of the growth and development of meat-producing animals (e.g., pigs and cattle) and milk-producing dairy cattle. These findings will serve as the basis for current and future animal biologists to develop newer concepts and methods for use in improving the efficiency of conversion of animal feed to food and the healthfulness of that food for human consumers.

  15. Bridging lectin binding sites by multivalent carbohydrates.

    PubMed

    Wittmann, Valentin; Pieters, Roland J

    2013-05-21

    Carbohydrate-protein interactions are involved in a multitude of biological recognition processes. Since individual protein-carbohydrate interactions are usually weak, multivalency is often required to achieve biologically relevant binding affinities and selectivities. Among the possible mechanisms responsible for binding enhancement by multivalency, the simultaneous attachment of a multivalent ligand to several binding sites of a multivalent receptor (i.e. chelation) has been proven to have a strong impact. This article summarizes recent examples of chelating lectin ligands of different size. Covered lectins include the Shiga-like toxin, where the shortest distance between binding sites is ca. 9 Å, wheat germ agglutinin (WGA) (shortest distance between binding sites 13-14 Å), LecA from Pseudomonas aeruginosa (shortest distance 26 Å), cholera toxin and heat-labile enterotoxin (shortest distance 31 Å), anti-HIV antibody 2G12 (shortest distance 31 Å), concanavalin A (ConA) (shortest distance 72 Å), RCA120 (shortest distance 100 Å), and Erythrina cristagalli (ECL) (shortest distance 100 Å). While chelating binding of the discussed ligands is likely, experimental proof, for example by X-ray crystallography, is limited to only a few cases.

  16. Impact of dietary polyphenols on carbohydrate metabolism.

    PubMed

    Hanhineva, Kati; Törrönen, Riitta; Bondia-Pons, Isabel; Pekkinen, Jenna; Kolehmainen, Marjukka; Mykkänen, Hannu; Poutanen, Kaisa

    2010-03-31

    Polyphenols, including flavonoids, phenolic acids, proanthocyanidins and resveratrol, are a large and heterogeneous group of phytochemicals in plant-based foods, such as tea, coffee, wine, cocoa, cereal grains, soy, fruits and berries. Growing evidence indicates that various dietary polyphenols may influence carbohydrate metabolism at many levels. In animal models and a limited number of human studies carried out so far, polyphenols and foods or beverages rich in polyphenols have attenuated postprandial glycemic responses and fasting hyperglycemia, and improved acute insulin secretion and insulin sensitivity. The possible mechanisms include inhibition of carbohydrate digestion and glucose absorption in the intestine, stimulation of insulin secretion from the pancreatic beta-cells, modulation of glucose release from the liver, activation of insulin receptors and glucose uptake in the insulin-sensitive tissues, and modulation of intracellular signalling pathways and gene expression. The positive effects of polyphenols on glucose homeostasis observed in a large number of in vitro and animal models are supported by epidemiological evidence on polyphenol-rich diets. To confirm the implications of polyphenol consumption for prevention of insulin resistance, metabolic syndrome and eventually type 2 diabetes, human trials with well-defined diets, controlled study designs and clinically relevant end-points together with holistic approaches e.g., systems biology profiling technologies are needed.

  17. Impact of Dietary Polyphenols on Carbohydrate Metabolism

    PubMed Central

    Hanhineva, Kati; Törrönen, Riitta; Bondia-Pons, Isabel; Pekkinen, Jenna; Kolehmainen, Marjukka; Mykkänen, Hannu; Poutanen, Kaisa

    2010-01-01

    Polyphenols, including flavonoids, phenolic acids, proanthocyanidins and resveratrol, are a large and heterogeneous group of phytochemicals in plant-based foods, such as tea, coffee, wine, cocoa, cereal grains, soy, fruits and berries. Growing evidence indicates that various dietary polyphenols may influence carbohydrate metabolism at many levels. In animal models and a limited number of human studies carried out so far, polyphenols and foods or beverages rich in polyphenols have attenuated postprandial glycemic responses and fasting hyperglycemia, and improved acute insulin secretion and insulin sensitivity. The possible mechanisms include inhibition of carbohydrate digestion and glucose absorption in the intestine, stimulation of insulin secretion from the pancreatic β–cells, modulation of glucose release from the liver, activation of insulin receptors and glucose uptake in the insulin-sensitive tissues, and modulation of intracellular signalling pathways and gene expression. The positive effects of polyphenols on glucose homeostasis observed in a large number of in vitro and animal models are supported by epidemiological evidence on polyphenol-rich diets. To confirm the implications of polyphenol consumption for prevention of insulin resistance, metabolic syndrome and eventually type 2 diabetes, human trials with well-defined diets, controlled study designs and clinically relevant end-points together with holistic approaches e.g., systems biology profiling technologies are needed. PMID:20480025

  18. Carbohydrate vaccines as immunotherapy for cancer.

    PubMed

    Slovin, Susan F; Keding, Stacy J; Ragupathi, Govind

    2005-08-01

    Carbohydrates have established themselves as the most clinically relevant antigens of those tested and subsequently developed for vaccines against infectious diseases. However, in cancer patients, many of the defined carbohydrate antigens are really altered 'self' antigens and for unclear reasons, the body does not react to them immunologically. Although these self antigens have been found to be potentially suitable targets for immune recognition and killing, the development of vaccines for cancer treatment is actually more challenging compared with those for infectious diseases mainly because of the difficulty associated with breaking the body's immunological tolerance to the antigen. These antigens lack the inherent immunogenicity associated with bacterial antigens and, therefore, methods to enhance immunological recognition and induction of immunity in vivo are under investigation. These include defining the appropriate tumour-associated antigen, successfully synthesizing the antigen to mimic the original molecule, inducing an immune response, and subsequently enhancing the immunological reactivity so that all components can work together. This has been successfully accomplished with several glycolipid and glycoprotein antigens using carriers such as keyhole limpet haemocyanin (KLH) together with a saponin adjuvant, QS-21. Not only can high titre IgM and IgG antibodies be induced, which are specific for the antigen used for immunization, but the antibodies can mediate complement lysis. The approaches for synthesis, conjugation, clinical administration and immunological potential are discussed.

  19. Species-specificity of amphibia carbohydrate chains: the Bufo viridis case study.

    PubMed

    Coppin, Alexandra; Maes, Emmanuel; Strecker, Gérard

    2002-02-05

    The jelly coat surrounding the eggs of amphibia is composed of oviducal mucins and plays an important role in the fertilization process. From a structural and chemical point of view, these jellies are very different from one species to another. Bufo viridis is the 13th amphibia species studied in term of carbohydrate structural analysis. The oligosaccharides have been released from the oviducal mucins by reductive beta elimination, purified by various chromatography procedures and analyzed by (1)H and (13)C 1D-2D NMR spectroscopy. Among the 15 compounds, ten have novel structures, although they possess some well-known structural patterns as blood group epitopes (Le(x), Le(y)) or other sequences already observed in other amphibia species. These results reinforce our hypothesis about the strict species-specificity of these carbohydrate chains. It must be noted that such species-specificity does not depend on one particular monosaccharide but it is rather due to a set of particular tri- or tetrasaccharide sequences. Hence, B. viridis species could be characterized by the simultaneous presence of a 2,3,6-trisubstituted galactosyl residue, the GlcNAc(beta 1-3)[Fuc(alpha 1-4)]GlcNAc beta sequence and the Le(x), Le(y) or Cad determinants. The anionic charge of the oligosaccharides is carried only by sialic acid alpha-(2-->6)-linked to GalNAc-ol residue as in Bufo bufo or in Bufo arenarum.

  20. Biological butanol production from microalgae-based biodiesel residues by Clostridium acetobutylicum.

    PubMed

    Cheng, Hai-Hsuan; Whang, Liang-Ming; Chan, Kun-Chi; Chung, Man-Chien; Wu, Shu-Hsien; Liu, Cheng-Pin; Tien, Shih-Yuan; Chen, Shan-Yuan; Chang, Jo-Shu; Lee, Wen-Jhy

    2015-05-01

    This study conducted batch experiments to evaluate the potential of butanol production from microalgae biodiesel residues by Clostridium acetobutylicum. The results indicated that with 90 g/L of glucose as the sole substrate the highest butanol yield of 0.2 g/g-glucose was found, but the addition of butyrate significantly enhanced the butanol yield. The highest butanol yield of 0.4 g/g-glucose was found with 60 g/L of glucose and 18 g/L of butyrate. Using microalgae biodiesel residues as substrate, C. acetobutylicum produced 3.86 g/L of butanol and achieved butanol yield of 0.13 g/g-carbohydrate via ABE fermentation, but the results indicated that approximately one third of carbohydrate was not utilized by C. acetobutylicum. Biological butanol production from microalgae biodiesel residues can be possible, but further research on fermentation strategies are required to improve production yield.

  1. Acute Effects of Carbohydrate Supplementation on Intermittent Sports Performance.

    PubMed

    Baker, Lindsay B; Rollo, Ian; Stein, Kimberly W; Jeukendrup, Asker E

    2015-07-14

    Intermittent sports (e.g., team sports) are diverse in their rules and regulations but similar in the pattern of play; that is, intermittent high-intensity movements and the execution of sport-specific skills over a prolonged period of time (~1-2 h). Performance during intermittent sports is dependent upon a combination of anaerobic and aerobic energy systems, both of which rely on muscle glycogen and/or blood glucose as an important substrate for energy production. The aims of this paper are to review: (1) potential biological mechanisms by which carbohydrate may impact intermittent sport performance; (2) the acute effects of carbohydrate ingestion on intermittent sport performance, including intermittent high-intensity exercise capacity, sprinting, jumping, skill, change of direction speed, and cognition; and (3) what recommendations can be derived for carbohydrate intake before/during exercise in intermittent sports based on the available evidence. The most researched intermittent sport is soccer but some sport-specific studies have also been conducted in other sports (e.g., rugby, field hockey, basketball, American football, and racquet sports). Carbohydrate ingestion before/during exercise has been shown in most studies to enhance intermittent high-intensity exercise capacity. However, studies have shown mixed results with regards to the acute effects of carbohydrate intake on sprinting, jumping, skill, change of direction speed, and cognition. In most of these studies the amount of carbohydrate consumed was ~30-60 g/h in the form of a 6%-7% carbohydrate solution comprised of sucrose, glucose, and/or maltodextrin. The magnitude of the impact that carbohydrate ingestion has on intermittent sport performance is likely dependent on the carbohydrate status of the individual; that is, carbohydrate ingestion has the greatest impact on performance under circumstances eliciting fatigue and/or hypoglycemia. Accordingly, carbohydrate ingestion before and during a game

  2. Effects of disturbance regime on carbohydrate reserves in meadow plants

    PubMed Central

    Janeček, Štěpán; Bartušková, Alena; Bartoš, Michael; Altman, Jan; de Bello, Francesco; Doležal, Jiří; Latzel, Vít; Lanta, Vojtěch; Lepš, Jan; Klimešová, Jitka

    2015-01-01

    Carbohydrate storage enables plants to tolerate both seasonally unfavourable conditions and recover from disturbance. Although short-term changes in storage levels due to disturbance are fairly well known, less is known about long-term changes in storage levels, especially in response to cessation of repeated disturbance. Additionally, whereas it is presumably the total amount (pool) of storage carbohydrate reserves that is of importance, typically carbohydrate concentrations are measured instead, as a proxy. We assessed changes in carbohydrate concentrations and pools in storage organs and changes in above- versus belowground biomass in response to mowing cessation in nine herbs from two meadows (dry and wet) at the (June) peak of vegetation development and the (October) growing season end 1 and 3 years after the change in the disturbance regime. We tested three hypotheses: (1) storage will increase with abandonment of mowing only in the first year after disturbance cessation, but not further increase subsequently, as high storage would hinder competitive ability; (2) storage will increase towards the end of the season in both disturbed and undisturbed plants; and (3) changes in carbohydrate concentrations are accurate predictors of changes in pools. Although species-specific changes in carbohydrate reserves occurred in the wet meadow, more general trends appeared in the dry meadow. There, plants accumulated higher carbohydrate reserves at the end of the season, especially in unmown plots. However, the reserves for plants in both disturbance regimes were the same at the growing season peak (June) in both examined years. The increase in storage of carbohydrates on unmown plots in October was manifested by increases of both storage organ biomass and carbohydrate concentration, whereas in mown plots, it was due only to increased carbohydrate concentration. Although concentrations and pools represent different aspects of plant carbohydrate economy, concentrations will

  3. Acute Effects of Carbohydrate Supplementation on Intermittent Sports Performance

    PubMed Central

    Baker, Lindsay B.; Rollo, Ian; Stein, Kimberly W.; Jeukendrup, Asker E.

    2015-01-01

    Intermittent sports (e.g., team sports) are diverse in their rules and regulations but similar in the pattern of play; that is, intermittent high-intensity movements and the execution of sport-specific skills over a prolonged period of time (~1–2 h). Performance during intermittent sports is dependent upon a combination of anaerobic and aerobic energy systems, both of which rely on muscle glycogen and/or blood glucose as an important substrate for energy production. The aims of this paper are to review: (1) potential biological mechanisms by which carbohydrate may impact intermittent sport performance; (2) the acute effects of carbohydrate ingestion on intermittent sport performance, including intermittent high-intensity exercise capacity, sprinting, jumping, skill, change of direction speed, and cognition; and (3) what recommendations can be derived for carbohydrate intake before/during exercise in intermittent sports based on the available evidence. The most researched intermittent sport is soccer but some sport-specific studies have also been conducted in other sports (e.g., rugby, field hockey, basketball, American football, and racquet sports). Carbohydrate ingestion before/during exercise has been shown in most studies to enhance intermittent high-intensity exercise capacity. However, studies have shown mixed results with regards to the acute effects of carbohydrate intake on sprinting, jumping, skill, change of direction speed, and cognition. In most of these studies the amount of carbohydrate consumed was ~30–60 g/h in the form of a 6%–7% carbohydrate solution comprised of sucrose, glucose, and/or maltodextrin. The magnitude of the impact that carbohydrate ingestion has on intermittent sport performance is likely dependent on the carbohydrate status of the individual; that is, carbohydrate ingestion has the greatest impact on performance under circumstances eliciting fatigue and/or hypoglycemia. Accordingly, carbohydrate ingestion before and during a

  4. Association of carbohydrate and fat intake with metabolic syndrome.

    PubMed

    Kwon, Yu-Jin; Lee, Hye-Sun; Lee, Ji-Won

    2017-07-04

    In Asia, dietary pattern has been changed with increased intake of refined carbohydrates, sugar, and saturated fat, while the prevalence of metabolic syndrome (MetS) is on the rise. However, it remains unclear whether a high-carbohydrate or a high-fat diet is more metabolically harmful, and the optimal amount of carbohydrates and fat has not been determined. The aim of our study was to examine the role of carbohydrate and fat intake in MetS in a Korean population. Data were obtained from a large, population-based, cross-sectional study (6737 males and 8845 females). The subjects were divided into nine groups based on carbohydrate and fat proportion, and multiple logistic regression analysis was performed after adjusting for confounding variables. Regardless of fat intake, the risk of MetS significantly increased in males with higher carbohydrate proportions (of total energy intake). In females, the risk of MetS was significantly elevated only in those with both the highest carbohydrate proportion and lowest fat proportion. A high carbohydrate proportion was associated with a higher prevalence of MetS in males, and a high carbohydrate proportion combined with a low fat proportion was associated with MetS in females. Our results indicate that reduction of excessive carbohydrate intake paired with an adequate fat intake, taking into consideration optimal types of fat, is useful for MetS prevention. Longitudinal studies are needed to clarify the optimal types and amounts of carbohydrate and fat proportions as well as the mechanism underlying these relationships. Copyright © 2017 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

  5. A method for (13)C-labeling of metabolic carbohydrates within French bean leaves (Phaseolus vulgaris L.) for decomposition studies in soils.

    PubMed

    Girardin, Cyril; Rasse, Daniel P; Biron, Philippe; Ghashghaie, Jaleh; Chenu, Claire

    2009-06-01

    The molecular composition of plant residues is suspected to largely govern the fate of their constitutive carbon (C) in soils. Labile compounds, such as metabolic carbohydrates, are affected differently from recalcitrant and structural compounds by soil-C stabilisation mechanisms. Producing (13)C-enriched plant residues with specifically labeled fractions would help us to investigate the fate in soils of the constitutive C of these compounds. The objective of the present research was to test (13)C pulse chase labeling as a method for specifically enriching the metabolic carbohydrate components of plant residues, i.e. soluble sugars and starch. Bean plants were exposed to a (13)CO(2)-enriched atmosphere for 0.5, 1, 2, 3 and 21 h. The major soluble sugars were then determined on water-soluble extracts, and starch on HCl-hydrolysable extracts. The results show a quick differential labeling between water-soluble and water-insoluble compounds. For both groups, (13)C-labeling increased linearly with time. The difference in delta(13)C signature between water-soluble and insoluble fractions was 7 per thousand after 0.5 h and 70 per thousand after 21 h. However, this clear isotopic contrast masked a substantial labeling variability within each fraction. By contrast, metabolic carbohydrates on the one hand (i.e. soluble sugars + starch) and other fractions (essentially cell wall components) on the other hand displayed quite homogeneous signatures within fractions, and a significant difference in labeling between fractions: delta(13)C = 414 +/- 3.7 per thousand and 56 +/- 5.5 per thousand, respectively. Thus, the technique generates labeled plant residues displaying contrasting (13)C-isotopic signatures between metabolic carbohydrates and other compounds, with homogenous signatures within each group. Metabolic carbohydrates being labile compounds, our findings suggest that the technique is particularly appropriate for investigating the effect of compound lability on the long

  6. Elucidating the exact role of engineered CRABPII residues for the formation of a retinal protonated Schiff base

    SciTech Connect

    Vasileiou, Chrysoula; Wang, Wenjing; Jia, Xiaofei; Lee, Kin Sing Stephen; Watson, Camille T.; Geiger, James H.; Borhan, Babak

    2010-03-04

    Cellular Retinoic Acid Binding Protein II (CRABPII) has been reengineered to specifically bind and react with all-trans-retinal to form a protonated Schiff base. Each step of this process has been dissected and four residues (Lys132, Tyr134, Arg111, and Glu121) within the CRABPII binding site have been identified as crucial for imine formation and/or protonation. The precise role of each residue has been examined through site directed mutagenesis and crystallographic studies. The crystal structure of the R132K:L121E-CRABPII (PDB-3I17) double mutant suggests a direct interaction between engineered Glu121 and the native Arg111, which is critical for both Schiff base formation and protonation.

  7. Asparagine-linked carbohydrate chains of inducible rat parotid proline-rich glycoprotein contain terminal beta-linked N-acetylgalactosamine.

    PubMed

    Bedi, G S

    1997-12-01

    Rats treated with daily injection of DL-isoproterenol for 10 consecutive days (25 mg kg(-1) body weight) showed marked induction of a proline-rich glycoprotein (GPRP) of 220 kDa. Proteinase K digestion of GPRP produced a homogeneous glycopeptide with an average chemical composition as follows (residues per mol): Pro4, Glx3, Asx2, Gly1, His1, Thr1, Arg1, GlcNAc5, GalNac1, Man3, Gal2-3, and Fuc1. The structural analysis of the asparagine-linked carbohydrate unit was performed by methylation, periodate oxidation and enzymatic degradation. Methylation studies indicated that the three mannosyl residues were substituted at 1,2-, 1,2,4-, and 1,3,6-positions. Fucose, N-acetylgalactosamine, 1.5 residues of galactose and 0.35 residues of N-acetylglucosamine were terminally located and one galactose residue was 1,4-substituted. Approximately four of the 5 N-acetylglucosamine residues were substituted at 1,4-position and approximately 1 residue of N-acetylglucosamine was substituted at 1,4,6-positions. Periodate oxidation studies and exoglycosidase results were consistent with the methylation data. Based on the results of Smith degradation, methylation and sequential exoglycosidase digestions a triantennary oligosaccharide structure having terminal N-acetylgalactosamine in one of the branches is proposed for the major Asn-linked carbohydrate moiety of GPRP.

  8. The effect of the carbohydrate moiety upon the size and conformation of human plasma galactoglycoprotein as judged by electron microscopy and circular dichroism. Structural studies of a glycoprotein after stepwise enzymic carbohydrate removal.

    PubMed

    Watzlawick, H; Walsh, M T; Ehrhard, I; Slayter, H S; Haupt, H; Schwick, H G; Jourdian, G W; Hase, S; Schmid, K; Brossmer, R

    1991-08-01

    Galactoglycoprotein is a unique human plasma protein [76% carbohydrate (23% N-acetylneuraminic acid, 20% galactose, 3% mannose, 1% fucose and 29% N-acetylgalactosamine plus N-acetylglucosamine) and 24% polypeptide, a single polypeptide chain of about 200 amino acid residues that is high in serine and threonine content] [Schmid, Mao, Kimura, Hayashi & Binette (1980) J. Biol. Chem. 255, 3221-3226]. Highly purified exoglycosidases with well-defined specificities were used to prepare five derivatives of galactoglycoprotein in which sequential residues of N-acetylneuraminic acid, galactose, N-acetylglucosamine, a second galactose and N-acetylgalactosamine were removed with 83% of the total carbohydrate cleaved. C.d. shows that native galactoglycoprotein and all derivatives in aqueous buffer are predominantly random coil, suggesting that removal of a large number of electrostatic net charges, as well as the major portion of the carbohydrate moiety, does not alter the secondary structure of the polypeptide chain. Examination of the size and conformation of tungsten-shadowed galactoglycoprotein and asialo and agalacto derivatives by electron microscopy shows the size and conformation of all three preparations to be similar, with only minor differences in particle length and width.

  9. The effect of the carbohydrate moiety upon the size and conformation of human plasma galactoglycoprotein as judged by electron microscopy and circular dichroism. Structural studies of a glycoprotein after stepwise enzymic carbohydrate removal.

    PubMed Central

    Watzlawick, H; Walsh, M T; Ehrhard, I; Slayter, H S; Haupt, H; Schwick, H G; Jourdian, G W; Hase, S; Schmid, K; Brossmer, R

    1991-01-01

    Galactoglycoprotein is a unique human plasma protein [76% carbohydrate (23% N-acetylneuraminic acid, 20% galactose, 3% mannose, 1% fucose and 29% N-acetylgalactosamine plus N-acetylglucosamine) and 24% polypeptide, a single polypeptide chain of about 200 amino acid residues that is high in serine and threonine content] [Schmid, Mao, Kimura, Hayashi & Binette (1980) J. Biol. Chem. 255, 3221-3226]. Highly purified exoglycosidases with well-defined specificities were used to prepare five derivatives of galactoglycoprotein in which sequential residues of N-acetylneuraminic acid, galactose, N-acetylglucosamine, a second galactose and N-acetylgalactosamine were removed with 83% of the total carbohydrate cleaved. C.d. shows that native galactoglycoprotein and all derivatives in aqueous buffer are predominantly random coil, suggesting that removal of a large number of electrostatic net charges, as well as the major portion of the carbohydrate moiety, does not alter the secondary structure of the polypeptide chain. Examination of the size and conformation of tungsten-shadowed galactoglycoprotein and asialo and agalacto derivatives by electron microscopy shows the size and conformation of all three preparations to be similar, with only minor differences in particle length and width. Images Fig. 2. PMID:1872812

  10. TENORM: Coal Combustion Residuals

    EPA Pesticide Factsheets

    Burning coal in boilers to create steam for power generation and industrial applications produces a number of combustion residuals. Naturally radioactive materials that were in the coal mostly end up in fly ash, bottom ash and boiler slag.

  11. The use of carbohydrates during exercise as an ergogenic aid.

    PubMed

    Cermak, Naomi M; van Loon, Luc J C

    2013-11-01

    Carbohydrate and fat are the two primary fuel sources oxidized by skeletal muscle tissue during prolonged (endurance-type) exercise. The relative contribution of these fuel sources largely depends on the exercise intensity and duration, with a greater contribution from carbohydrate as exercise intensity is increased. Consequently, endurance performance and endurance capacity are largely dictated by endogenous carbohydrate availability. As such, improving carbohydrate availability during prolonged exercise through carbohydrate ingestion has dominated the field of sports nutrition research. As a result, it has been well-established that carbohydrate ingestion during prolonged (>2 h) moderate-to-high intensity exercise can significantly improve endurance performance. Although the precise mechanism(s) responsible for the ergogenic effects are still unclear, they are likely related to the sparing of skeletal muscle glycogen, prevention of liver glycogen depletion and subsequent development of hypoglycemia, and/or allowing high rates of carbohydrate oxidation. Currently, for prolonged exercise lasting 2-3 h, athletes are advised to ingest carbohydrates at a rate of 60 g·h⁻¹ (~1.0-1.1 g·min⁻¹) to allow for maximal exogenous glucose oxidation rates. However, well-trained endurance athletes competing longer than 2.5 h can metabolize carbohydrate up to 90 g·h⁻¹ (~1.5-1.8 g·min⁻¹) provided that multiple transportable carbohydrates are ingested (e.g. 1.2 g·min⁻¹ glucose plus 0.6 g·min⁻¹ of fructose). Surprisingly, small amounts of carbohydrate ingestion during exercise may also enhance the performance of shorter (45-60 min), more intense (>75 % peak oxygen uptake; VO(₂peak)) exercise bouts, despite the fact that endogenous carbohydrate stores are unlikely to be limiting. The mechanism(s) responsible for such ergogenic properties of carbohydrate ingestion during short, more intense exercise bouts has been suggested to reside in the central nervous

  12. Synthesis of Chiral Spiroacetals from Carbohydrates.

    PubMed

    Martín, Angeles; Salazar, José A.; Suárez, Ernesto

    1996-06-14

    Chiral spiroacetals of the 1,7-dioxaspiro[5.5]undecane, 1,6-dioxaspiro[4.5]decane, and 1,6-dioxaspiro[4.4]nonane types have been prepared from carbohydrates in pyranose or furanose forms. The spirocyclization reaction has been accomplished from a conveniently homologated carbohydrate by an intramolecular hydrogen abstraction reaction promoted by alkoxy radicals. Thus, 2,3,4,6-tetra-O-benzyl-1-deoxy-1-(3'-hydroxypropyl)-alpha-D-glucopyranose (2) was photolyzed with visible light in the presence of (diacetoxyiodo)benzene and iodine to give a mixture of (1R)-(3) and (1S)-2,3,4,6-tetra-O-benzyl-1-deoxy-D-glucopyranose-1-spiro-2'-tetrahydrofuran (4). The photolysis of methyl 6-deoxy-6-(2'-hydroxyethyl)-2,3,4-tri-O-methyl-alpha-D-glucopyranoside (8) gave the isomeric spiroacetals methyl (5S)- (9) and (5R)-6-deoxy-5,2'-epoxy-6-ethyl-2,3,4-tri-O-methyl-alpha-D-glucopyranoside (10) in which the spirocenter is now located at C-5. The spiroacetals of the [5.5]undecane series: methyl (5R)- (19) and (5S)-6-deoxy-5,3'-epoxy-2,3,4-tri-O-methyl-6-propyl-beta-D-glucopyranoside (20) have been prepared starting from methyl 6-deoxy-6-(3'-hydroxypropyl)-2,3,4-tri-O-methyl-beta-D-glucopyranoside (18). The reaction has also been applied to hexofuranoses and 1-deoxy-1-(3'-hydroxypropyl)-2,3:5,6-di-O-isopropylidene-alpha-D-mannofuranose (21) gave rise to (1S)- (22) and (1R)-1-deoxy-2,3:5,6-di-O-isopropylidene-D-mannofuranose-1-spiro-2'-tetrahydrofuran (23); and 1-deoxy-1-(4'-hydroxybutyl)-2,3:5,6-di-O-isopropylidene-alpha-D-mannofuranose (28) to (1R)- (30) and (1S)-1-deoxy-2,3:5,6-di-O-isopropylidene-D-mannofuranose-1-spiro-2'-tetrahydropyran (32). Both spiroacetal enantiomers are formally available from the same carbohydrate.

  13. A single-amino-acid substitution eliminates the stringent carbohydrate requirement for intracellular transport of a viral glycoprotein.

    PubMed

    Pitta, A M; Rose, J K; Machamer, C E

    1989-09-01

    In this report, we have investigated the contribution of primary sequence to the carbohydrate requirement for intracellular transport of two closely related glycoproteins, the G proteins of the San Juan and Orsay strains of vesicular stomatitis virus. We used site-directed mutagenesis of the coding sequence to eliminate the two consensus sites for glycosylation in the Orsay G protein. Whereas the nonglycosylated San Juan G protein required at least one of its two asparagine-linked oligosaccharides for transport to the plasma membrane at 37 degrees C, a fraction of the Orsay G protein was transported without carbohydrate. Of the 10 amino acid differences between these two proteins, residue 172 (tyrosine in San Juan, aspartic acid in Orsay) played the major role in determining the stringency for the carbohydrate requirement. The rates at which the glycosylated and nonglycosylated Orsay G proteins were transported to the cell surface were the same, although a smaller fraction of the nonglycosylated protein was transported. These results suggest that the carbohydrate does not promote intracellular transport directly but influences a polypeptide folding or oligomerization step which is critical for transport.

  14. Formation of insoluble, nonhydrolyzable, sulfur-rich macromolecules via incorporation of inorganic sulfur species into algal carbohydrates

    NASA Astrophysics Data System (ADS)

    Kok, Marika D.; Schouten, Stefan; Sinninghe Damsté, Jaap S.

    2000-08-01

    The process of sulfur incorporation into organic matter was simulated in the laboratory by sulfurization of cell material of the prymnesiophyte alga Phaeocystis in sea water with inorganic polysulfides at 50°C. Flash pyrolysis of the residue, obtained after extraction and several hydrolysis steps, yielded mainly C 1-C 4 alkylbenzenes and C 1-C 4 alkylphenols and, in contrast to control and blank experiments, relatively high amounts of C 0-C 4 alkylthiophenes. The distribution of the thiophenes is very similar to that in pyrolysates of type II-S kerogens. The formation of high-molecular-weight sulfur-rich macromolecules co-occurs with a marked drop in the content of hydrolyzable carbohydrates. This indicates that sulfurization results in the preservation of algal carbohydrate carbon in a macromolecular structure composed of (poly)sulfidic cross-linked carbohydrate skeletons, which upon pyrolysis yields alkylthiophenes. Sulfurization of glucose under similar conditions resulted in the formation of a nonhydrolyzable, solid material, which yielded high amounts of organic sulfur compounds upon pyrolysis, mainly short-chain alkylthiophenes, although with a different distribution than that in the pyrolysate of the sulfurized algal material. The carbon numbers of these organic sulfur compounds extend beyond six, indicating that the length of the carbon skeleton of the pyrolysis products is not limited by the length of the carbon skeleton of the substrate. These results suggest that the sulfurization of carbohydrates may be an important pathway in the preservation of organic matter in euxinic depositional environments.

  15. Carbohydrate-responsive gene expression in adipose tissue of rats

    USDA-ARS?s Scientific Manuscript database

    Although obesity is often associated with high fat diets, it can develop from a variety of meal patterns. Excessive intake of simple carbohydrates is one consistent eating behavior leading to obesity. However, the impact of over-consumption of diets with high carbohydrate-to-fat ratios (C/F) on body...

  16. Reinforcement effect of soy protein and carbohydrates in polymer composites

    USDA-ARS?s Scientific Manuscript database

    The modulus of soft polymer material can be increased by filler reinforcement. A review of using soy protein and carbohydrates as alternative renewable reinforcement material is presented here. Dry soy protein and carbohydrates are rigid and can form strong filler networks through hydrogen-bonding...

  17. Chemical Changes in Carbohydrates Produced by Thermal Processing.

    ERIC Educational Resources Information Center

    Hoseney, R. Carl

    1984-01-01

    Discusses chemical changes that occur in the carbohydrates found in food products when these products are subjected to thermal processing. Topics considered include browning reactions, starch found in food systems, hydrolysis of carbohydrates, extrusion cooking, processing of cookies and candies, and alterations in gums. (JN)

  18. Genetic Analyses of Soluble Carbohydrate Concentrations in Onion Bulbs

    USDA-ARS?s Scientific Manuscript database

    Fructans are the primary soluble carbohydrate in onion (Allium cepa L.) bulbs and show significant correlations with dry weights and pungency. In this research, we estimated the genetic effects and interactions between two chromosome regions associated with higher amounts of soluble carbohydrates i...

  19. Identification of carbohydrate anomers using ion mobility-mass spectrometry

    NASA Astrophysics Data System (ADS)

    Hofmann, J.; Hahm, H. S.; Seeberger, P. H.; Pagel, K.

    2015-10-01

    Carbohydrates are ubiquitous biological polymers that are important in a broad range of biological processes. However, owing to their branched structures and the presence of stereogenic centres at each glycosidic linkage between monomers, carbohydrates are harder to characterize than are peptides and oligonucleotides. Methods such as nuclear magnetic resonance spectroscopy can be used to characterize glycosidic linkages, but this technique requires milligram amounts of material and cannot detect small amounts of coexisting isomers. Mass spectrometry, on the other hand, can provide information on carbohydrate composition and connectivity for even small amounts of sample, but it cannot be used to distinguish between stereoisomers. Here, we demonstrate that ion mobility-mass spectrometry--a method that separates molecules according to their mass, charge, size, and shape--can unambiguously identify carbohydrate linkage-isomers and stereoisomers. We analysed six synthetic carbohydrate isomers that differ in composition, connectivity, or configuration. Our data show that coexisting carbohydrate isomers can be identified, and relative concentrations of the minor isomer as low as 0.1 per cent can be detected. In addition, the analysis is rapid, and requires no derivatization and only small amounts of sample. These results indicate that ion mobility-mass spectrometry is an effective tool for the analysis of complex carbohydrates. This method could have an impact on the field of carbohydrate synthesis similar to that of the advent of high-performance liquid chromatography on the field of peptide assembly in the late 1970s.

  20. Blood brothers: carbohydrates in xenotransplantation and cancer immunotherapy.

    PubMed

    Ramsland, Paula

    2005-08-01

    Carbohydrate antigens have a central role in the hyperacute rejection of animal-to-human organ grafts (xenotransplantation) and they are emerging in importance in the immunotherapy of cancer. This article traces the historical origins of the discovery of key carbohydrate antigens and explores the future impact of recent technological advances of the field of glycobiology as it relates to xenotransplantation and cancer.

  1. Structural and Functional Studies of Peptide-Carbohydrate Mimicry

    NASA Astrophysics Data System (ADS)

    Johnson, Margaret A.; Pinto, B. Mario

    Certain peptides act as molecular mimics of carbohydrates in that they are specifically recognized by carbohydrate-binding proteins. Peptides that bind to anti-carbohydrate antibodies, carbohydrate-processing enzymes, and lectins have been identified. These peptides are potentially useful as vaccines and therapeutics; for example, immunologically functional peptide molecular mimics (mimotopes) can strengthen or modify immune responses induced by carbohydrate antigens. However, peptides that bind specifically to carbohydrate-binding proteins may not necessarily show the corresponding biological activity, and further selection based on biochemical studies is always required. The degree of structural mimicry required to generate the desired biological activity is therefore an interesting question. This review will discuss recent structural studies of peptide-carbohydrate mimicry employing NMR spectroscopy, X-ray crystallography, and molecular modeling, as well as relevant biochemical data. These studies provide insights into the basis of mimicry at the molecular level. Comparisons with other carbohydrate-mimetic compounds, namely proteins and glycopeptides, will be drawn. Finally, implications for the design of new therapeutic compounds will also be presented.

  2. Chemical Changes in Carbohydrates Produced by Thermal Processing.

    ERIC Educational Resources Information Center

    Hoseney, R. Carl

    1984-01-01

    Discusses chemical changes that occur in the carbohydrates found in food products when these products are subjected to thermal processing. Topics considered include browning reactions, starch found in food systems, hydrolysis of carbohydrates, extrusion cooking, processing of cookies and candies, and alterations in gums. (JN)

  3. Force fields and scoring functions for carbohydrate simulation.

    PubMed

    Xiong, Xiuming; Chen, Zhaoqiang; Cossins, Benjamin P; Xu, Zhijian; Shao, Qiang; Ding, Kai; Zhu, Weiliang; Shi, Jiye

    2015-01-12

    Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Why use DFT methods in the study of carbohydrates?

    USDA-ARS?s Scientific Manuscript database

    The recent advances in density functional theory (DFT) and computer technology allow us to study systems with more than 100 atoms routinely. This makes it feasible to study large carbohydrate molecules via quantum mechanical methods, whereas in the past, studies of carbohydrates were restricted to ...

  5. Carbohydrate levels in current-year shoots of sugar maple

    Treesearch

    John R. Donnelly

    1976-01-01

    Diurnal changes in carbohydrate concentrations in leaves and current-year stems of a mature sugar maple tree were studied in June and September. In leaves, alcohol-soluble sugar concentration was highest in the morning and lowest in late afternoon or early evening; diurnal changes in starch lagged about 5 hours behind changes in sugar. Carbohydrate concentrations in...

  6. Seasonal changes in carbohydrate levels in roots of sugar maple

    Treesearch

    Philip M. Wargo; Philip M. Wargo

    1971-01-01

    This study was done to determine the normal complement of individual carbohydrates present in roots of sugar maples duringthe year and to obtain, as a basis for future comparison, an estimate of the normal variation and range of concentrations of individual carbohydrates in the roots during the year.

  7. Regulation of low-density lipoprotein subfractions by carbohydrates.

    PubMed

    Gerber, Philipp A; Berneis, Kaspar

    2012-07-01

    This article aims at reviewing the recent findings that have been made concerning the crosstalk of carbohydrate metabolism with the generation of small, dense low-density lipoprotein (LDL) particles, which are known to be associated with an adverse cardiovascular risk profile. Studies conducted during the past few years have quite unanimously shown that the quantity of carbohydrates ingested is associated with a decrease of LDL particle size and an increase in its density. Conversely, diets that aim at a reduction of carbohydrate intake are able to improve LDL quality. Furthermore, a reduction of the glycaemic index without changing the amount of carbohydrates ingested has similar effects. Diseases with altered carbohydrate metabolism, for example, type 2 diabetes, are associated with small, dense LDL particles. Finally, even the kind of monosaccharide the carbohydrate intake consists of is important concerning LDL particle size: fructose has been shown to alter the LDL particle subclass profile more adversely than glucose in many recent studies. LDL particle quality, rather than its quantity, is affected by carbohydrate metabolism, which is of clinical importance, in particular, in the light of increased carbohydrate consumption in today's world.

  8. Soil amino compound and carbohydrate contents influenced by organic amendments

    USDA-ARS?s Scientific Manuscript database

    Amino compounds (i. e. amino acids and sugars), and carbohydrates are labile organic components and contribute to the improvement of soil fertility and quality. Animal manure and other organic soil amendments are rich in both amino compounds and carbohydrates, hence organic soil amendments might af...

  9. Identification of domains and domain interface residues in multidomain proteins from graph spectral method.

    PubMed

    Sistla, Ramesh K; K V, Brinda; Vishveshwara, Saraswathi

    2005-05-15

    We present a novel method for the identification of structural domains and domain interface residues in proteins by graph spectral method. This method converts the three-dimensional structure of the protein into a graph by using atomic coordinates from the PDB file. Domain definitions are obtained by constructing either a protein backbone graph or a protein side-chain graph. The graph is constructed based on the interactions between amino acid residues in the three-dimensional structure of the proteins. The spectral parameters of such a graph contain information regarding the domains and subdomains in the protein structure. This is based on the fact that the interactions among amino acids are higher within a domain than across domains. This is evident in the spectra of the protein backbone and the side-chain graphs, thus differentiating the structural domains from one another. Further, residues that occur at the interface of two domains can also be easily identified from the spectra. This method is simple, elegant, and robust. Moreover, a single numeric computation yields both the domain definitions and the interface residues. Copyright 2005 Wiley-Liss, Inc.

  10. The Structure of Physarum polycephalum hemagglutinin I suggests a minimal carbohydrate recognition domain of legume lectin fold.

    PubMed

    Kouno, Takahide; Watanabe, Nobuhisa; Sakai, Naoki; Nakamura, Takashi; Nabeshima, Yuko; Morita, Masashi; Mizuguchi, Mineyuki; Aizawa, Tomoyasu; Demura, Makoto; Imanaka, Tsuneo; Tanaka, Isao; Kawano, Keiichi

    2011-01-14

    Physarum polycephalum hemagglutinin I (HA1) is a 104-residue protein that is secreted to extracellular space. The crystal structure of HA1 has a β-sandwich fold found among lectin structures, such as legume lectins and galectins. Interestingly, the β-sandwich of HA1 lacks a jelly roll motif and is essentially composed of two simple up-and-down β-sheets. This up-and-down β-sheet motif is well conserved in other legume lectin-like proteins derived from animals, plants, bacteria, and viruses. It is more noteworthy that the up-and-down β-sheet motif includes many residues that make contact with the target carbohydrates. Our NMR data demonstrate that HA1 lacking a jelly roll motif also binds to its target glycopeptide. Taken together, these data show that the up-and-down β-sheet motif provides a fundamental scaffold for the binding of legume lectin-like proteins to the target carbohydrates, and the structure of HA1 suggests a minimal carbohydrate recognition domain. Copyright © 2010 Elsevier Ltd. All rights reserved.

  11. Compositional evaluation of selected agro-industrial wastes as valuable sources for the recovery of complex carbohydrates.

    PubMed

    Vojvodić, Aleksandra; Komes, Draženka; Vovk, Irena; Belščak-Cvitanović, Ana; Bušić, Arijana

    2016-11-01

    Re-utilization of various agro-industrial wastes is of growing importance from many aspects. Considering the variety and complexity of such materials, compositional data and compliant methodology is still undergoing many updates and improvements. Present study evaluated sugar beet pulp (SBP), walnut shell (WS), cocoa bean husk (CBH), onion peel (OP) and pea pods (PP) as potentially valuable materials for carbohydrate recovery. Macrocomponent analyses revealed carbohydrate fraction as the most abundant, dominating in dietary fibres. Upon complete acid hydrolysis of sample alcohol insoluble residues, developed procedures of high performance thin-layer chromatography (HPTLC) and high performance liquid chromatography (HPLC) coupled with 3-methyl-1-phenyl-2-pyrazolin-5-one pre-column derivatization (PMP-derivatization) were used for carbohydrate monomeric composition determination. HPTLC exhibited good qualitative features useful for multi-sample rapid analysis, while HPLC superior separation and quantification characteristics. Distinctive monomeric patterns were obtained among samples. OP, SBP and CBH, due to the high galacturonic acid content (20.81%, 13.96% and 6.90% dry matter basis, respectively), may be regarded as pectin sources, while WS and PP as materials abundant in xylan-rich hemicellulose (total xylan content 15.53%, 9.63% dry matter basis, respectively). Present study provides new and valuable compositional data for different plant residual materials and a reference for the application of established methodology. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Glycosidases: a key to tailored carbohydrates.

    PubMed

    Bojarová, Pavla; Kren, Vladimír

    2009-04-01

    In recent years, carbohydrate-processing enzymes have become the enzymes of choice in many applications thanks to their stereoselectivity and efficiency. This review presents recent developments in glycosidase-catalyzed synthesis via two complementary approaches: the use of wild-type enzymes with engineered substrates, and mutant glycosidases. Genetic engineering has recently produced glucuronyl synthases, an inverting xylosynthase and the first mutant endo-beta-N-acetylglucosaminidase. A thorough selection of enzyme strains and aptly modified substrates have resulted in rare glycostructures, such as N-acetyl-beta-galactosaminuronates, beta1,4-linked mannosides and alpha1,4-linked galactosides. The efficient selection of mutant enzymes is facilitated by high-throughput screening assays involving the co-expression of coupled enzymes or chemical complementation. Selective glycosidase inhibitors and highly specific glycosidases are finding attractive applications in biomedicine, biology and proteomics.

  13. Pasture nonstructural carbohydrates and equine laminitis.

    PubMed

    Longland, Annette C; Byrd, Bridgett M

    2006-07-01

    Fresh forages constitute a majority of the diet for many horses and ponies that graze on pastures during the growing season in many parts of the world. Grasses generally predominate in such pastures, with varying proportions of legumes. Nonstructural carbohydrates (NSC) (simple sugars, starch, and fructan) can induce laminitis experimentally, and NSC can accumulate to >400 g/kg of dry matter (DM) in pasture grasses. In this article we discuss the environmental factors affecting NSC accumulation in pastures and estimate the potential daily intakes of pasture NSC by grazing horses. We also discuss strategies for both reducing the NSC content of pastures and management practices that can help reduce intakes of pasture NSC by equines at risk of developing laminitis. This study reveals the importance of accurate forage analysis in the development of feeding regimens for equines at risk of laminitis.

  14. Genome of Bifidobacteria and Carbohydrate Metabolism

    PubMed Central

    2015-01-01

    In recent years, the knowledge about bifidobacteria has considerably evolved thanks to recent progress in molecular biology. The analysis of the whole genome sequences of 48 taxa of bifidobacteria offers new perspectives for their classification, especially to set up limit between two species. Indeed, several species are presenting a high homology and should be reclassified. On the other hand, some subspecies are presenting a low homology and should therefore be reclassified into different species. In addition, a better knowledge of the genome of bifidobacteria allows a better understanding of the mechanisms involved in complex carbohydrate metabolism. The genome of some species of bifidobacteria from human but also from animal origin demonstrates high presence in genes involved in the metabolism of complex oligosaccharides. Those species should be further tested to confirm their potential to metabolize complex oligosaccharides in vitro and in vivo. PMID:26761794

  15. Carbohydrate structure: the rocky road to automation.

    PubMed

    Agirre, Jon; Davies, Gideon J; Wilson, Keith S; Cowtan, Kevin D

    2016-12-08

    With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to 'protein standards' will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most.

  16. [Carbohydrate absorption and malabsorption (author's transl)].

    PubMed

    Caspary, W F

    1977-06-01

    Starch is digested intraluminally by alpha-amylase to maltose, maltotriose, and alpha-limit dextrins. These products, as well as the disaccharides sucrose and lactose, undergo enzymatic hydrolysis to monosaccharides at the brush border surface. The monosaccharides enter the absorbing cell by specific transport mechanisms ("carriers"). Primary carbohydrate (CH) intolerance is characterized by the congenital or acquired absence of individual brush border enzymes or of monosaccharide "carriers" without morphologic abnormalities of the intestinal villus: lactose, sucrose and trehalose intolerance and glucose-galactose malabsorption (brush border diseases). Secondary CH intolerance arises when surface digestion and absorption are reduced due to structural changes of the intestinal mucosa: e.g., decrease or absence of villi with sprue and reduction of the absorbing surface with intestinal resection. Watery diarrhea is the lead symptom. Many drugs delay or interfere with CH absorption. This action may be viewed either as an unwanted side effect or as a welcome therapeutic principle.

  17. Carbohydrate based materials for gamma radiation shielding

    NASA Astrophysics Data System (ADS)

    Tabbakh, F.; Babaee, V.; Naghsh-Nezhad, Z.

    2015-05-01

    Due to the limitation in using lead as a shielding material for its toxic properties and limitation in abundance, price or non-flexibility of other commonly used materials, finding new shielding materials and compounds is strongly required. In this conceptual study carbohydrate based compounds were considered as new shielding materials. The simulation of radiation attenuation is performed using MCNP and Geant4 with a good agreement in the results. It is found that, the thickness of 2 mm of the proposed compound may reduce up to 5% and 50% of 1 MeV and 35 keV gamma-rays respectively in comparison with 15% and 100% for the same thickness of lead.

  18. Carbohydrate supplementation improves stroke performance in tennis.

    PubMed

    Vergauwen, L; Brouns, F; Hespel, P

    1998-08-01

    The effect of carbohydrate supplementation on stroke quality during prolonged simulated tennis match-play was investigated. Well-trained tennis palyers reported to the test center three times. At each occasion they performed a pretest, consisting of the leuven Tennis Performance Test (LTPT) and a shuttle run (SHR), which they repeated (posttest) after a 2-h strenuous training session. Throughout the test session, they received in a double blind random order either a placebo drink (P), a carbohydrate solution (0.7 gxkg(-1) BWxh(-1); CHO), or CHO plus a dose of caffeine (5 mg per kg BW). Stroke quality was evaluated during the LTPT by means of measurements of error rate, ball velocity, precision of ball placement, and a velocity-precision (VP) and a velocity-precision-error (VPE) index. Pretest scores were similar during P and CHO. During P, compared with the pretest, stroke quality during the posttest deteriorated (P < 0.05) both for the first service and strokes during defensive rallies and for SHR performance. However, compared with P, the increase in error rate and number of nonreached balls indefensive rallies was smaller (P < 0.05) during CHO. Similarily, CHO attenuated (P < 0.05) the increase in error rate and the decrease in both the VP (P < 0.1) and VPE (P < 0.05) indices for the first service upon fatigue. Furthermore, CHO improved posttest SHR performance. Stroke quality and SHR time were similar during CHO alone and during combined CHO plus caffeine administration, both for the pretest and for the pretest and for the posttest. It is concluded that CHO supplementation improves stroke quality during the final stages of prolonged tennis play. The data prove that CHO intake may facilitate the maintenance of physical quality during long-lasting intermittent exercise to fatigue.

  19. Self-assembled carbohydrate-based vesicles for lectin targeting.

    PubMed

    Dos Santos, Marinalva Cardoso; Micheletto, Yasmine Miguel Serafini; da Silveira, Nadya Pesce; da Silva Pinto, Luciano; Giacomelli, Fernando Carlos; de Lima, Vânia Rodrigues; Frizon, Tiago Elias Allievi; Dal-Bó, Alexandre Gonçalves

    2016-12-01

    This study examined the physicochemical interactions between vesicles formed by phosphatidylcholine (PC) and glycosylated polymeric amphiphile N-acetyl-β-d-glucosaminyl-PEG900-docosanate (C22PEG900GlcNAc) conjugated with Bauhinia variegata lectin (BVL). Lectins are proteins or glycoproteins capable of binding glycosylated membrane components. Accordingly, the surface functionalization by such entities is considered a potential strategy for targeted drug delivery. We observed increased hydrodynamic radii (RH) of PC+C22PEG900GlcNAc vesicles in the presence of lectins, suggesting that this aggregation was due to the interaction between lectins and the vesicular glycosylated surfaces. Furthermore, changes in the zeta potential of the vesicles with increasing lectin concentrations implied that the vesicular glycosylated surfaces were recognized by the investigated lectin. The presence of carbohydrate residues on vesicle surfaces and the ability of the vesicles to establish specific interactions with BVL were further explored using atomic force microscopy (AFM) and small-angle X-ray scattering (SAXS) analysis. The results indicated that the thickness of the hydrophilic layer was to some extent influenced by the presence of lectins. The presence of lectins required a higher degree of polydispersity as indicated by the width parameter of the log-normal distribution of size, which also suggested more irregular structures. Reflectance Fourier transform infrared (HATR-FTIR), differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR) and ultraviolet-visible (UV-vis.) analyses revealed that the studied lectin preferentially interacted with the choline and carbonyl groups of the lipid, thereby changing the choline orientation and intermolecular interactions. The protein also discretely reduced the intermolecular communication of the hydrophobic acyl chains, resulting in a disordered state.

  20. FRET-based luminescence sensors for carbohydrates and glycoproteins analysis

    NASA Astrophysics Data System (ADS)

    Rosenzweig, Zeev; Rosenzweig, Nitsa; Blagoi, Gabriela

    2004-12-01

    This paper describes the development of novel particle-based fluorescence resonance energy transfer (FRET) biosensors. It describes the fundamentals of FRET in heterogeneous systems and the application of the new sensors in monitoring the binding affinity of carbohydrates and glycoproteins to lectins, which are carbohydrate binding proteins. The sensing approach is based on FRET between fluorescein (donor) labeled lectin molecules, adsorbed on the surface of micrometric polymeric beads, and polymeric dextran molecules labeled with Texas Red (acceptor). The FRET signal of the sensor decreases in the presence of carbohydrates or glycoproteins that inhibit the binding of Texas Red-labeled dextran molecules to the lectinic binding sites. The new FRET sensors could discriminate between carbohydrates and glycoproteins based on their binding affinity to the FRET sensing particles. Thery were also used for quantitative analysis of carbohydrates and glycoproteins in aqueous samples.

  1. Defined presentation of carbohydrates on a duplex DNA scaffold.

    PubMed

    Schlegel, Mark K; Hütter, Julia; Eriksson, Magdalena; Lepenies, Bernd; Seeberger, Peter H

    2011-12-16

    A new method for the spatially defined alignment of carbohydrates on a duplex DNA scaffold is presented. The use of an N-hydroxysuccinimide (NHS)-ester phosphoramidite along with carbohydrates containing an alkylamine linker allows for on-column labeling during solid-phase oligonucleotide synthesis. This modification method during solid-phase synthesis only requires the use of minimal amounts of complex carbohydrates. The covalently attached carbohydrates are presented in the major groove of the B-form duplex DNA as potential substrates for murine type II C-type lectin receptors mMGL1 and mMGL2. CD spectroscopy and thermal melting revealed only minimal disturbance of the overall helical structure. Surface plasmon resonance and cellular uptake studies with bone-marrow-derived dendritic cells were used to assess the capability of these carbohydrate-modified duplexes to bind to mMGL receptors.

  2. Single cell profiling of surface carbohydrates on Bacillus cereus

    PubMed Central

    Wang, Congzhou; Ehrhardt, Christopher J.; Yadavalli, Vamsi K.

    2015-01-01

    Cell surface carbohydrates are important to various bacterial activities and functions. It is well known that different types of Bacillus display heterogeneity of surface carbohydrate compositions, but detection of their presence, quantitation and estimation of variation at the single cell level have not been previously solved. Here, using atomic force microscopy (AFM)-based recognition force mapping coupled with lectin probes, the specific carbohydrate distributions of N-acetylglucosamine and mannose/glucose were detected, mapped and quantified on single B. cereus surfaces at the nanoscale across the entire cell. Further, the changes of the surface carbohydrate compositions from the vegetative cell to spore were shown. These results demonstrate AFM-based ‘recognition force mapping’ as a versatile platform to quantitatively detect and spatially map key bacterial surface biomarkers (such as carbohydrate compositions), and monitor in situ changes in surface biochemical properties during intracellular activities at the single cell level. PMID:25505137

  3. Carbohydrate CuAAC click chemistry for therapy and diagnosis.

    PubMed

    He, Xiao-Peng; Zeng, Ya-Li; Zang, Yi; Li, Jia; Field, Robert A; Chen, Guo-Rong

    2016-06-24

    Carbohydrates are important as signaling molecules and for cellular recognition events, therefore offering scope for the development of carbohydrate-mimetic diagnostics and drug candidates. As a consequence, the construction of carbohydrate-based bioactive compounds and sensors has become an active research area. While the advent of click chemistry has greatly accelerated the progress of medicinal chemistry and chemical biology, recent literature has seen an extensive use of such approaches to construct functionally diverse carbohydrate derivatives. Here we summarize some of the progress, covering the period 2010 to mid-2015, in Cu(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition CuAAC "click chemistry" of carbohydrate derivatives, in the context of potential therapeutic and diagnostic tool development. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. Relationship of carbohydrate molecular spectroscopic features in combined feeds to carbohydrate utilization and availability in ruminants

    NASA Astrophysics Data System (ADS)

    Zhang, Xuewei; Yu, Peiqiang

    To date, there is no study on the relationship between carbohydrate (CHO) molecular structures and nutrient availability of combined feeds in ruminants. The objective of this study was to use molecular spectroscopy to reveal the relationship between CHO molecular spectral profiles (in terms of functional groups (biomolecular, biopolymer) spectral peak area and height intensity) and CHO chemical profiles, CHO subfractions, energy values, and CHO rumen degradation kinetics of combined feeds of hulless barley with pure wheat dried distillers grains with solubles (DDGS) at five different combination ratios (hulless barley to pure wheat DDGS: 100:0, 75:25, 50:50, 25:75, 0:100). The molecular spectroscopic parameters assessed included: lignin biopolymer molecular spectra profile (peak area and height, region and baseline: ca. 1539-1504 cm-1); structural carbohydrate (STCHO, peaks area region and baseline: ca. 1485-1186 cm-1) mainly associated with hemi- and cellulosic compounds; cellulosic materials peak area (centered at ca. 1240 cm-1 with region and baseline: ca. 1272-1186 cm-1); total carbohydrate (CHO, peaks area region and baseline: ca. 1186-946 cm-1). The results showed that the functional groups (biomolecular, biopolymer) in the combined feeds are sensitive to the changes of carbohydrate chemical and nutrient profiles. The changes of the CHO molecular spectroscopic features in the combined feeds were highly correlated with CHO chemical profiles, CHO subfractions, in situ CHO rumen degradation kinetics and fermentable organic matter supply. Further study is needed to investigate possibility of using CHO molecular spectral features as a predictor to estimate nutrient availability in combined feeds for animals and quantify their relationship.

  5. Relationship of carbohydrate molecular spectroscopic features in combined feeds to carbohydrate utilization and availability in ruminants.

    PubMed

    Zhang, Xuewei; Yu, Peiqiang

    2012-06-15

    To date, there is no study on the relationship between carbohydrate (CHO) molecular structures and nutrient availability of combined feeds in ruminants. The objective of this study was to use molecular spectroscopy to reveal the relationship between CHO molecular spectral profiles (in terms of functional groups (biomolecular, biopolymer) spectral peak area and height intensity) and CHO chemical profiles, CHO subfractions, energy values, and CHO rumen degradation kinetics of combined feeds of hulless barley with pure wheat dried distillers grains with solubles (DDGS) at five different combination ratios (hulless barley to pure wheat DDGS: 100:0, 75:25, 50:50, 25:75, 0:100). The molecular spectroscopic parameters assessed included: lignin biopolymer molecular spectra profile (peak area and height, region and baseline: ca. 1539-1504 cm(-1)); structural carbohydrate (STCHO, peaks area region and baseline: ca. 1485-1186 cm(-1)) mainly associated with hemi- and cellulosic compounds; cellulosic materials peak area (centered at ca. 1240 cm(-1) with region and baseline: ca. 1272-1186 cm(-1)); total carbohydrate (CHO, peaks area region and baseline: ca. 1186-946 cm(-1)). The results showed that the functional groups (biomolecular, biopolymer) in the combined feeds are sensitive to the changes of carbohydrate chemical and nutrient profiles. The changes of the CHO molecular spectroscopic features in the combined feeds were highly correlated with CHO chemical profiles, CHO subfractions, in situ CHO rumen degradation kinetics and fermentable organic matter supply. Further study is needed to investigate possibility of using CHO molecular spectral features as a predictor to estimate nutrient availability in combined feeds for animals and quantify their relationship. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Metabolic response to high-carbohydrate and low-carbohydrate meals in a nonhuman primate model

    PubMed Central

    Fabbrini, Elisa; Higgins, Paul B.; Magkos, Faidon; Bastarrachea, Raul A.; Voruganti, V. Saroja; Comuzzie, Anthony G.; Shade, Robert E.; Gastaldelli, Amalia; Horton, Jay D.; Omodei, Daniela; Patterson, Bruce W.

    2013-01-01

    We established a model of chronic portal vein catheterization in an awake nonhuman primate to provide a comprehensive evaluation of the metabolic response to low-carbohydrate/high-fat (LCHF; 20% carbohydrate and 65% fat) and high-carbohydrate/low-fat (HCLF; 65% carbohydrate and 20% fat) meal ingestion. Each meal was given 1 wk apart to five young adult (7.8 ± 1.3 yr old) male baboons. A [U-13C]glucose tracer was added to the meal, and a [6,6-2H2]glucose tracer was infused systemically to assess glucose kinetics. Plasma areas under the curve (AUCs) of glucose, insulin, and C-peptide in the femoral artery and of glucose and insulin in the portal vein were higher (P ≤ 0.05) after ingestion of the HCLF compared with the LCHF meal. Compared with the LCHF meal, the rate of appearance of ingested glucose into the portal vein and the systemic circulation was greater after the HCLF meal (P < 0.05). Endogenous glucose production decreased by ∼40% after ingestion of the HCLF meal but was not affected by the LCHF meal (P < 0.05). Portal vein blood flow increased (P < 0.001) to a similar extent after consumption of either meal. In conclusion, a LCHF diet causes minimal changes in the rate of glucose appearance in both portal and systemic circulations, does not affect the rate of endogenous glucose production, and causes minimal stimulation of C-peptide and insulin. These observations demonstrate that LCHF diets cause minimal perturbations in glucose homeostasis and pancreatic β-cell activity. PMID:23269412

  7. Alcohol production from agricultural and forestry residues

    SciTech Connect

    Opilla, R.; Dale, L.; Surles, T.

    1980-05-01

    A variety of carbohydrate sources can be used as raw material for the production of ethanol. Section 1 is a review of technologies available for the production of ethanol from whole corn. Particular emphasis is placed on the environmental aspects of the process, including land utilization and possible air and water pollutants. Suggestions are made for technological changes intended to improve the economics of the process as well as to reduce some of the pollution from by-product disposal. Ethanol may be derived from renewable cellulosic substances by either enzymatic or acid hydrolysis of cellulose to sugar, followed by conventional fermentation and distillation. Section 2 is a review of the use of two agricultural residues - corn stover (field stalks remaining after harvest) and straw from wheat crops - as a cellulosic feedstock. Two processes have been evaluated with regard to environmental impact - a two-stage acid process developed by G.T. Tsao of Purdue University and an enzymatic process based on the laboratory findings of C.R. Wilke of the University of California, Berkeley. Section 3 deals with the environmental residuals expected from the manufacture of methyl and ethyl alcohols from woody biomass. The methanol is produced in a gasification process, whereas ethanol is produced by hydrolysis and fermentation processes similar to those used to derive ethanol from cellulosic materials.

  8. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures.

    PubMed

    Biro, Jan C; Fördös, Gergely

    2005-07-12

    The interacting residues of protein and nucleic acid sequences are close to each other - they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB) contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this purpose. SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The user: a. selects a structure from PDB; b. chooses an atom that is commonly present in every residues of the nucleic acid and/or protein structure(s). c. defines a distance from these atoms (3-15 A). The SeqX tool detects every residue that is located within the defined distances from the defined "backbone" atom(s); provides a DotPlot-like visualization (Residues Contact Map), and calculates the frequency of every possible residue pairs (Residue Contact Table) in the observed structure. It is possible to exclude +/- 1 to 10 neighbor residues in the same polymeric chain from detection, which greatly improves the specificity of detections (up to 60% when tested on dsDNA). Results obtained on protein structures showed highly significant correlations with results obtained from literature (p < 0.0001, n = 210, four different subsets). The co-location frequency of physico-chemically compatible amino acids is significantly higher than is calculated and expected in random protein sequences (p < 0.0001, n = 80). The tool is simple and easy to use and provides a quick and reliable visualization and analyses of residue co-locations in protein and nucleic acid structures. AVAILABILITY AND REQUIREMENTS: http://janbiro.com/Downloads.html SeqX, Java J2SE Runtime Environment 5.0 (available from [see Additional file 1] http://www.sun.com) and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors.

  9. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures

    PubMed Central

    Biro, Jan C; Fördös, Gergely

    2005-01-01

    Background The interacting residues of protein and nucleic acid sequences are close to each other – they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB) contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this purpose. Results SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The user a. selects a structure from PDB; b. chooses an atom that is commonly present in every residues of the nucleic acid and/or protein structure(s) c. defines a distance from these atoms (3–15 Å). The SeqX tool detects every residue that is located within the defined distances from the defined "backbone" atom(s); provides a DotPlot-like visualization (Residues Contact Map), and calculates the frequency of every possible residue pairs (Residue Contact Table) in the observed structure. It is possible to exclude +/- 1 to 10 neighbor residues in the same polymeric chain from detection, which greatly improves the specificity of detections (up to 60% when tested on dsDNA). Results obtained on protein structures showed highly significant correlations with results obtained from literature (p < 0.0001, n = 210, four different subsets). The co-location frequency of physico-chemically compatible amino acids is significantly higher than is calculated and expected in random protein sequences (p < 0.0001, n = 80). Conclusion The tool is simple and easy to use and provides a quick and reliable visualization and analyses of residue co-locations in protein and nucleic acid structures. Availability and requirements SeqX, Java J2SE Runtime Environment 5.0 (available from [see Additional file 1] ) and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors. PMID:16011796

  10. Comparative analysis of carbohydrate active enzymes in Clostridium termitidis CT1112 reveals complex carbohydrate degradation ability.

    PubMed

    Munir, Riffat I; Schellenberg, John; Henrissat, Bernard; Verbeke, Tobin J; Sparling, Richard; Levin, David B

    2014-01-01

    Clostridium termitidis strain CT1112 is an anaerobic, gram positive, mesophilic, cellulolytic bacillus isolated from the gut of the wood-feeding termite, Nasutitermes lujae. It produces biofuels such as hydrogen and ethanol from cellulose, cellobiose, xylan, xylose, glucose, and other sugars, and therefore could be used for biofuel production from biomass through consolidated bioprocessing. The first step in the production of biofuel from biomass by microorganisms is the hydrolysis of complex carbohydrates present in biomass. This is achieved through the presence of a repertoire of secreted or complexed carbohydrate active enzymes (CAZymes), sometimes organized in an extracellular organelle called cellulosome. To assess the ability and understand the mechanism of polysaccharide hydrolysis in C. termitidis, the recently sequenced strain CT1112 of C. termitidis was analyzed for both CAZymes and cellulosomal components, and compared to other cellulolytic bacteria. A total of 355 CAZyme sequences were identified in C. termitidis, significantly higher than other Clostridial species. Of these, high numbers of glycoside hydrolases (199) and carbohydrate binding modules (95) were identified. The presence of a variety of CAZymes involved with polysaccharide utilization/degradation ability suggests hydrolysis potential for a wide range of polysaccharides. In addition, dockerin-bearing enzymes, cohesion domains and a cellulosomal gene cluster were identified, indicating the presence of potential cellulosome assembly.

  11. Comparative Analysis of Carbohydrate Active Enzymes in Clostridium termitidis CT1112 Reveals Complex Carbohydrate Degradation Ability

    PubMed Central

    Munir, Riffat I.; Schellenberg, John; Henrissat, Bernard; Verbeke, Tobin J.; Sparling, Richard; Levin, David B.

    2014-01-01

    Clostridium termitidis strain CT1112 is an anaerobic, gram positive, mesophilic, cellulolytic bacillus isolated from the gut of the wood-feeding termite, Nasutitermes lujae. It produces biofuels such as hydrogen and ethanol from cellulose, cellobiose, xylan, xylose, glucose, and other sugars, and therefore could be used for biofuel production from biomass through consolidated bioprocessing. The first step in the production of biofuel from biomass by microorganisms is the hydrolysis of complex carbohydrates present in biomass. This is achieved through the presence of a repertoire of secreted or complexed carbohydrate active enzymes (CAZymes), sometimes organized in an extracellular organelle called cellulosome. To assess the ability and understand the mechanism of polysaccharide hydrolysis in C. termitidis, the recently sequenced strain CT1112 of C. termitidis was analyzed for both CAZymes and cellulosomal components, and compared to other cellulolytic bacteria. A total of 355 CAZyme sequences were identified in C. termitidis, significantly higher than other Clostridial species. Of these, high numbers of glycoside hydrolases (199) and carbohydrate binding modules (95) were identified. The presence of a variety of CAZymes involved with polysaccharide utilization/degradation ability suggests hydrolysis potential for a wide range of polysaccharides. In addition, dockerin-bearing enzymes, cohesion domains and a cellulosomal gene cluster were identified, indicating the presence of potential cellulosome assembly. PMID:25101643

  12. [Performance enhancement by carbohydrate intake during sport: effects of carbohydrates during and after high-intensity exercise].

    PubMed

    Beelen, Milou; Cermak, Naomi M; van Loon, Luc J C

    2015-01-01

    Endogenous carbohydrate availability does not provide sufficient energy for prolonged moderate to high-intensity exercise. Carbohydrate ingestion during high-intensity exercise can therefore enhance performance.- For exercise lasting 1 to 2.5 hours, athletes are advised to ingest 30-60 g of carbohydrates per hour.- Well-trained endurance athletes competing for longer than 2.5 hours at high intensity can metabolise up to 90 g of carbohydrates per hour, provided that a mixture of glucose and fructose is ingested.- Athletes participating in intermittent or team sports are advised to follow the same strategies but the timing of carbohydrate intake depends on the type of sport.- If top performance is required again within 24 hours after strenuous exercise, the advice is to supplement endogenous carbohydrate supplies quickly within the first few hours post-exercise by ingesting large amounts of carbohydrate (1.2 g/kg/h) or a lower amount of carbohydrate (0.8 g/kg/h) with a small amount of protein (0.2-0.4 g/kg/h).

  13. Carbohydrate Content in the GDM Diet: Two Views: View 1: Nutrition Therapy in Gestational Diabetes: The Case for Complex Carbohydrates

    PubMed Central

    2016-01-01

    IN BRIEF Restriction of dietary carbohydrate has been the cornerstone for treatment of gestational diabetes mellitus (GDM). However, there is evidence that a balanced liberalization of complex carbohydrate as part of an overall eating plan in GDM meets treatment goals and may mitigate maternal adipose tissue insulin resistance, both of which may promote optimal metabolic outcomes for mother and offspring. PMID:27182176

  14. Assessing carbohydrate-carbohydrate interactions by NMR spectroscopy: the trisaccharide epitope from the marine sponge Microciona prolifera.

    PubMed

    Santos, J Ignacio; Carvalho de Souza, Adriana; Cañada, F Javier; Martín-Santamaría, Sonsoles; Kamerling, Johannis P; Jiménez-Barbero, Jesús

    2009-02-13

    WEAK RECOGNITION PROCESSES: Weak calcium-mediated carbohydrate-carbohydrate interactions have been detected by DOSY and TRNOESY NMR methods by employing a gold glyconanoparticle as a multivalent system. In addition, 3D models of trisaccharide-Ca(II)-trisaccharide complexes based on results from molecular dynamics simulations are proposed. Diffusion-ordered NMR spectroscopy (DOSY-NMR) and TR-NOESY-NMR experiments are used to detect ligand binding to macromolecular receptors. These techniques have been applied to detect weak carbohydrate-carbohydrate self-recognition in solution, making use of sugar-decorated gold nanoparticles as the "macromolecule" and the same carbohydrate as the ligand. Changes in the diffusion coefficient of the free carbohydrate in the presence of the glyconanoparticle (only with Ca(II) ions in the sample solution), as well as changes in the sign of the sugar NOE peaks--positive for the free sugar (in the presence or absence of Ca(II)) and negative for the sugar only in the simultaneous presence of the glyconanoparticle and Ca(II) ions--have been taken as proof of weak Ca(II)-mediated carbohydrate-carbohydrate interactions in solution. Although different methods such as SPR, TEM, and AFM have been used in the past to detect carbohydrate-carbohydrate interactions with the aid of gold nanoparticles and gold selfassembled monolayers, they are restricted to high-affinity ranges. The methods used in this study allow expansion of the number of techniques to tackle this relevant biological problem, also for approaching ligand-receptor interactions below the high-affinity range. Additionally, 3D models of trisaccharide-Ca(II)-trisaccharide complexes based on results from molecular dynamics simulations are proposed.

  15. Health Effects of Low-Carbohydrate Diets: Where Should New Research Go?

    PubMed Central

    Wylie-Rosett, Judith; Aebersold, Karin; Conlon, Beth; Isasi, Carmen R.; Ostrovsky, Natania W.

    2013-01-01

    There has been considerable debate about the metabolic effects of restricting carbohydrate intake in weight and diabetes management. However, the American Diabetes Association has noted that weight and metabolic improvements can be achieved with low carbohydrate, low fat (implicitly higher carbohydrate), or a Mediterranean style diet (usually an intermediate level of carbohydrate). Our paper addresses variability in the definition for low or restricted carbohydrate, the effects of carbohydrate restriction on diabetes-related health outcomes, strategies for restricting carbohydrate intake, and potential genetic variability in response to dietary carbohydrate restriction. Issues for future research are also addressed. PMID:23266565

  16. Health effects of low-carbohydrate diets: where should new research go?

    PubMed

    Wylie-Rosett, Judith; Aebersold, Karin; Conlon, Beth; Isasi, Carmen R; Ostrovsky, Natania W

    2013-04-01

    There has been considerable debate about the metabolic effects of restricting carbohydrate intake in weight and diabetes management. However, the American Diabetes Association has noted that weight and metabolic improvements can be achieved with low carbohydrate, low fat (implicitly higher carbohydrate), or a Mediterranean style diet (usually an intermediate level of carbohydrate). Our paper addresses variability in the definition for low or restricted carbohydrate, the effects of carbohydrate restriction on diabetes-related health outcomes, strategies for restricting carbohydrate intake, and potential genetic variability in response to dietary carbohydrate restriction. Issues for future research are also addressed.

  17. Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity.

    PubMed

    Warda, Alicja K; Siezen, Roland J; Boekhorst, Jos; Wells-Bennik, Marjon H J; de Jong, Anne; Kuipers, Oscar P; Nierop Groot, Masja N; Abee, Tjakko

    2016-01-01

    We characterised carbohydrate utilisation of 20 newly sequenced Bacillus cereus strains isolated from food products and food processing environments and two laboratory strains, B. cereus ATCC 10987 and B. cereus ATCC 14579. Subsequently, genome sequences of these strains were analysed together with 11 additional B. cereus reference genomes to provide an overview of the different types of carbohydrate transporters and utilization systems found in B. cereus strains. The combined application of API tests, defined growth media experiments and comparative genomics enabled us to link the carbohydrate utilisation capacity of 22 B. cereus strains with their genome content and in some cases to the panC phylogenetic grouping. A core set of carbohydrates including glucose, fructose, maltose, trehalose, N-acetyl-glucosamine, and ribose could be used by all strains, whereas utilisation of other carbohydrates like xylose, galactose, and lactose, and typical host-derived carbohydrates such as fucose, mannose, N-acetyl-galactosamine and inositol is limited to a subset of strains. Finally, the roles of selected carbohydrate transporters and utilisation systems in specific niches such as soil, foods and the human host are discussed.

  18. T cell recognition of carbohydrates on type II collagen

    PubMed Central

    1994-01-01

    A critical event in an immune response is the T cell recognition of peptides bound to major histocompatibility complex (MHC) molecules on the surface of an antigen presenting cell (APC). Although the majority of eukaryotic proteins are glycosylated, it has not yet been shown that T cell recognition of such proteins involves recognition of the bound carbohydrates. Type II collagen (CII), the major protein constituent of joint cartilage, is posttranslationally modified by hydroxylation and glycosylation of lysines. In this report we show that posttranslational modifications of the immunodominant peptide CII(256-270) generate a structural determinant that is distinct from the determinant represented by the corresponding synthetic peptide. Elimination of carbohydrates, present on CII, by two different biochemical methods revealed that the carbohydrates, O-linked to the hydroxylysines within the CII(256-270) determinant, were crucial for the reactivity towards the posttranslationally modified peptide. Furthermore, a T cell hybridoma specific for the glycosylated determinant was stimulated by tryptic CII-peptides presented by fixed APCs, thus showing that the carbohydrates are involved in the trimolecular complex T cell receptor/peptide/MHC. Finally, the importance of the bound carbohydrates for the arthritogenicity of CII was investigated by comparing the development of arthritis after immunization with carbohydrate-depleted and glycosylated CII, respectively. Incidence, time of onset, and severity of the disease were significantly affected by the elimination of carbohydrates, whereas no significant difference in anti-CII antibody titers was seen. PMID:8046350

  19. Development of carbohydrate absorption in the fetus and neonate.

    PubMed

    Mobassaleh, M; Montgomery, R K; Biller, J A; Grand, R J

    1985-01-01

    Maturation of mechanisms for carbohydrate absorption occurs in a defined sequence during human fetal development. The intestinal enzymes, lactase, sucrase, maltase, isomaltase, and glucoamylase, are at mature levels in the term fetus. Mature levels of pancreatic amylase activity and glucose transport occur postnatally, and levels are low in both the term and preterm neonate. In the preterm infant, sucrase, maltase, and isomaltase are usually fully active, but lactase activity, which increases markedly from 24 to 40 weeks, may be low depending upon fetal age. Despite these developmental patterns, clinical lactose intolerance is uncommon. Postnatal adaptive responses to ingested carbohydrates lead to competent carbohydrate absorption. Inadequately absorbed carbohydrates are salvaged by colonic flora through fermentation of carbohydrates to hydrogen gas and short-chain fatty acids; the latter are readily absorbed by the colon. In this setting, carbohydrate tends to be absent from the stool. Noninvasive reflection of the status of carbohydrate absorption may be obtained from breath hydrogen testing, a technique of particular value in young infants.

  20. Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays

    PubMed Central

    Flannery, Andrea; Gerlach, Jared Q.; Joshi, Lokesh; Kilcoyne, Michelle

    2015-01-01

    Carbohydrates play a crucial role in host-microorganism interactions and many host glycoconjugates are receptors or co-receptors for microbial binding. Host glycosylation varies with species and location in the body, and this contributes to species specificity and tropism of commensal and pathogenic bacteria. Additionally, bacterial glycosylation is often the first bacterial molecular species encountered and responded to by the host system. Accordingly, characterising and identifying the exact structures involved in these critical interactions is an important priority in deciphering microbial pathogenesis. Carbohydrate-based microarray platforms have been an underused tool for screening bacterial interactions with specific carbohydrate structures, but they are growing in popularity in recent years. In this review, we discuss carbohydrate-based microarrays that have been profiled with whole bacteria, recombinantly expressed adhesins or serum antibodies. Three main types of carbohydrate-based microarray platform are considered; (i) conventional carbohydrate or glycan microarrays; (ii) whole mucin microarrays; and (iii) microarrays constructed from bacterial polysaccharides or their components. Determining the nature of the interactions between bacteria and host can help clarify the molecular mechanisms of carbohydrate-mediated interactions in microbial pathogenesis, infectious disease and host immune response and may lead to new strategies to boost therapeutic treatments. PMID:27600247