Conformations in polysaccharides and complex carbohydrates

A review is presented focussing attention on the structural molecular biology of polysaccharides and complex carbohydrates, using examples obtained from terraqueous plants, animals, bacteria and insects The type and sequence of the condensation linkages in polysaccharides dominate their conformation, flexibility and interactions The extensive variety of geometries is overlaid by the constituent saccharide units themselves, decoration by side appendages and post-polymerisation chemical and structural modification X-ray diffraction information from oriented samples and computerised modelling has been used to analyse molecular conformation and geometry In general the relationship between glycosidic linkage geometry and conformation for the chemically simpler polysaccharides is understood In the case of more complex carbohydrates, unique solutions using diffraction methods alone are harder to establish In mixed protein carbohydrate systems, such as the glycoprotein antifreezes and protein-polysaccharide fibrous composites in insect cuticle, novel features in structure, morphology and interactions can usefully be explored and examined.     

哺乳动物肠道微生物与碳水化合物的互作及其影响

肠道微生物具有调节宿主营养、免疫以及能量代谢等生理功能。饮食是影响哺乳动物的肠道微生物的一个重要因素。碳水化合物是哺乳动物食物能量的主要来源,因此研究肠道微生物与碳水化合物的代谢之间的关系及其影响具有重要意义。基于近年相关研究,本文从碳水化合物对肠道微生物组成的影响、肠道微生物对碳水化合物的代谢机制以及碳水化合物发酵产物短链脂肪酸对宿主的影响3个方面进行了综述。研究表明,肠道微生物可用于发酵的碳水化合物类型主要是抗性淀粉和非淀粉多糖;不同类型的碳水化合物会导致肠道菌群发生适应性变化;复杂多糖发酵产生的短链脂肪酸在调节宿主能量平衡和免疫应答方面发挥了重要作用。总结近年来相关研究,可加深对肠道菌群对宿主碳水化合物代谢贡献的理解,为哺乳动物机体健康状况的营养调控策略提供参考。     

A general and sensitive chemical method for sequencing the glycosyl residues of complex carbohydrates

This paper describes a new glycosyl-sequencing method. This method was made possible by the ability to fractionate complex mixtures of peralkylated oligosaccharides by reversed-phase, high-pressure liquid chromatography. The fractionation ability of the reversed-phase system allows the isolation and subsequent unambiguous identification by g.l.c.-m.s. of disaccharides, almost all trisaccharides, and, in some cases, tetrasaccharides generated by successive partial acid hydrolysis, reduction, and ethylation of a permethylated, complex carbohydrate. As these small oligosaccharides overlap within the unhydrolyzed, complex carbohydrate, the oligosaccharide sequences may be pieced together, and, with the glycosyl-linkage composition of the intact complex carbohydrate, can be used to determine the glycosyl sequence of the complex carbohydrate. The details of the sequencing method are illustrated by the elucidation of the glycosyl sequences of three complex carbohydrates. These examples demonstrate the wide variety of complex carbohydrates whose structures can be ascertained by the new sequencing technique. Two of the examples are the commercially available polysaccharides, lichenan and xanthan, whose structures have already been reported. The other example is a nonasaccharide derived from xyloglucan, a structural polymer of plant cell-walls. The glycosyl residues of the complex carbohydrates studied include hexosyl, deoxyhexosyl, pentosyl, glycosyluronic, and pyruvic acetal-substituted hexosyl residues. It will be demonstrated that the new glycosyl-sequencing technique is not compromise by the presence, in the carbohydrate to be analyzed, of glycosyl linkages possessing very different acid labilities. Two major advantages of this sequencing technique are that it is relatively rapid and that it requires only milligram quantities of carbohydrate.     

Modeling protein recognition of carbohydrates

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.     

Conformational studies of the O-specific polysaccharide of Shigella flexneri 5a and of four related synthetic pentasaccharide fragments using NMR and molecular modeling

As part of a program for the development of synthetic vaccines against the pathogen Shigella flexneri, we used a combination of NMR and molecular modeling methods to study the conformations of the O-specific polysaccharide (O-SP) of S. flexneri 5a and of four related synthetic pentasaccharide fragments. The NMR study, based on the analysis of 1H and 13C chemical shifts, the evaluation of inter-residue distances, and the measurement of one- and three-bond heteronuclear coupling constants, showed that the conformation of one of the four pentasaccharides is similar to that of the native O-SP in solution. Interestingly, inhibition enzyme-linked immunosorbent assay demonstrated that a protective monoclonal antibody specific for S. flexneri 5a has a greater affinity for this pentasaccharide than for the others. We carried out a complete conformational search on the pentasaccharides using the CICADA algorithm interfaced with MM3 force field. We calculated Boltzmann-averaged inter-residue distances and 3JC,H coupling constants for the different conformational families and compared the results with NMR data for all pentasaccharides. Our experimental data are consistent with only one conformational family. We also used molecular modeling data to build models of the O-SP with the molecular builder program POLYS. The models that are in agreement with NMR data adopt right-handed 3-fold helical structures in which the branched glucosyl residue points outwards.     

Derivatization of carbohydrates for GC and GC-MS analyses

GC and GC-MS are excellent techniques for the analysis of carbohydrates; nevertheless the preparation of adequate derivatives is necessary. The different functional groups that can be found and the diversity of samples require specific methods. This review aims to collect the most important methodologies currently used, either published as new procedures or as new applications, for the analysis of carbohydrates. A high diversity of compounds with diverse functionalities has been selected: neutral carbohydrates (saccharides and polyalcohols), sugar acids, amino and iminosugars, polysaccharides, glycosides, glycoconjugates, anhydrosugars, difructose anhydrides and products resulting of Maillard reaction (osuloses, Amadori compounds). Chiral analysis has also been considered, describing the use of diastereomers and derivatives to be eluted on chiral stationary phases.     

3DSDSCAR—a three dimensional structural database for sialic acid-containing carbohydrates through molecular dynamics simulation

The inherent flexibility and lack of strong intramolecular interactions of oligosaccharides demand the use of theoretical methods for their structural elucidation. In spite of the developments of theoretical methods, not much research on glycoinformatics is done so far when compared to bioinformatics research on proteins and nucleic acids. We have developed three dimensional structural database for a sialic acid-containing carbohydrates (3DSDSCAR). This is an open-access database that provides 3D structural models of a given sialic acid-containing carbohydrate. At present, 3DSDSCAR contains 60 conformational models, belonging to 14 different sialic acid-containing carbohydrates, deduced through 10 ns molecular dynamics (MD) simulations. The database is available at the URL: http://www.3dsdscar.org.     

Insights into stereochemical features of sulphated carbohydrates: X-ray crystallographic and modelling investigations

The three-dimensional structures of the 2-, 3-, 4- and 6-monosulphatesof methyl -D-galactopyranoside have been determined by X-raycrystallography; the first two as the sodium salt, the thirdas both the sodium and potassium salts, and the fourth as apotassium salt. These represent the principal sulphated monomersof the carrageenan polysaccharides. The results extend our knowledgeof the stereochemical features, such as ring conformation, sulphategeometry, hydrogen bonding and cation co-ordination, which characterizesulphated monosaccharides. The stereochemical data have beenused to derive a mean geometry of the O-sulphate group and aset of force constants for use in molecular mechanics calculationson sulphated monosaccharides. These may be used in an extrapolationof the populations of stable conformers of related oligo- andpolysaccharides. crystal structures molecular mechanics O-sulphated carbohydrates X-ray diffraction     

A universal protocol for photochemical covalent immobilization of intact carbohydrates for the preparation of carbohydrate microarrays

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, nonreducing 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.     

The histochemistry of complex carbohydrates in the scrotum of the boar

Summary In the scrotal skin of the boar, the histochemistry of complex carbohydrates has been studied by means of a series of selected methods of light microscopy. The epidermis of the scrotal skin was found to contain neutral and acidic complex carbohydrates with different saccharide residues. The secretory epithelial cells and secretory substances of the saccular apocrine sweat glands contained sulfated, other acidic and neutral complex carbohydrates, whereas the secretory epithelial cells and secretory substances of the tubular apocrine sweat glands involved largely neutral complex carbohydrates. The two types of complex carbohydrates from the both glands were shown to contain commonly substantial amounts of various saccharide residues but were devoid of notable amounts of sialic acid residues. In addition, complex carbohydrates in the smooth muscle cells were reacted for relatively small amounts of saccharide residues. From the present results, the histophysiological significanses of complex carbohydrates in the particular histologic structures of the scrotum have been discussed with special reference to the functions of the skin in the boar.A major part of this work has been presented at the 6th International Histochemistry and Cytochemistry Congress, Brighton, United Kingdom, in 1980     

Versatile derivatives of carbohydrate-binding modules for imaging of complex carbohydrates approaching the molecular level of resolution

The innate binding specificity of different carbohydrate-binding modules (CBMs) offers a versatile approach for mapping the chemistry and structure of surfaces that contain complex carbohydrates. We have employed the distinct recognition properties of a double His-tagged recombinant CBM tagged with semiconductor quantum dots for direct imaging of crystalline cellulose at the molecular level of resolution, using transmission and scanning transmission electron microscopy. In addition, three different types of CBMs from families 3, 6, and 20 that exhibit different carbohydrate specificities were each fused with either green fluorescent protein (GFP) or red fluorescent protein (RFP) and employed for double-labeling fluorescence microscopy studies of primary cell walls and various mixtures of complex carbohydrate target molecules. CBM probes can be used for characterizing both native complex carbohydrates and engineered biomaterials.     

Practical tools for molecular modeling of complex carbohydrates and their interactions with proteins

Computer modeling has become a valuable component of studies of carbohydrate three-dimensional structures and their relationship to function and properties. In this paper we examine the methods required for conformational modeling of carbohydrates, and we present a series of tools that have been developed to this end. These tools can be integrated into three-dimensional real-time molecular modeling software. A data base of pre-optimized carbohydrate fragments has been established to be used further in the construction of much more complex molecules. In addition we describe some possible uses of a data base of three dimensional structures of the disaccharide fragments present in the glycan moiety ofN-glycoprotein. A molecular mechanical force field appropriate for the conformational analysis of oligosaccharides has been derived by the addition of new parameters to the Tripos force field and is compatible with protein simulations. The new parametrization has been assessed in three stages of increasing complexity: computations of potential energy surfaces, conformational refinement of relevant oligosaccharides, modeling at the atomic level of a protein/carbohydrate complex.     

Molecular simulations of complex carbohydrates and glycoconjugates

Complex carbohydrates (glycans) are the most abundant and versatile biopolymers in nature. The broad diversity of biochemical functions that carbohydrates cover is a direct consequence of the variety of 3D architectures they can adopt, displaying branched or linear arrangements, widely ranging in sizes, and with the highest diversity of building blocks of any other natural biopolymer. Despite this unparalleled complexity, a common denominator can be found in the glycans’ inherent flexibility, which hinders experimental characterization, but that can be addressed by high-performance computing (HPC)-based molecular simulations. In this short review, I present and discuss the state-of-the-art of molecular simulations of complex carbohydrates and glycoconjugates, highlighting methodological strengths and weaknesses, important insights through emblematic case studies, and suggesting perspectives for future developments.     

Molecular aggregation of nucleotides and carbohydrates—their implication to prebiotic polymerization

Hydrogen bonding pattern of nucleotides and carbohydrates has been analysed using Cambridge database. An analysis on ribonucleotides shows the 3′ …5′ hydrogen bond mediated aggregation to be the most common alignment. The 2′ …5′ alignment, which occurs under special circumstances in nature, is found to be the second choice. An analysis on carbohydrates suggests that self assembly of these molecules is not conducive to the formation of polysaccharides of the type which are found in present day living organisms. Further, the role of water molecules in the polymerization of three important biomolecules, namely nucleotides, carbohydrates and amino acids, has been analysed. Implication of these results to prebiotic polymerization is discussed DCB contribution No. 804.     

多糖修饰物及其抗肿瘤作用机制研究

多糖是指一类由十个以上单糖分子通过糖苷键连接而成的糖类物质,因其具有许多重要的生物学活性而备受关注,这其中最为突出的是其在抗肿瘤方面所表现出的效用。目前多糖抗肿瘤方面的主要研究课题集中在如何进一步提高多糖的抗肿瘤活性上。对多糖分子进行结构上的修饰能够使其抗肿瘤的活性得到一定程度地提高。本文对常见的多糖修饰方法,如硫酸化、羧甲基化、磷酸化、硒化、乙酰化等进行了总结,对经修饰后所得产物的抗肿瘤作用的不同机制进行了阐述,并对多糖化学修饰物的应用前景进行了展望,为未来多糖的开发与利用提供一定的理论依据。     

Role for fucose-sulfate-rich carbohydrates in the penetration of zona-pellucida-free hamster eggs by hamster spermatozoa

The interaction of acrosome-reacted hamster spermatozoa and zona-pellucida-free hamster eggs was investigated by incubating gametes in the presence of a variety of simple and complex carbohydrates. Significant inhibition of gamete fusion was achieved only in the presence of fucoidan and ascophyllin, two algal polysaccharides containing fucose sulfate. These compounds did not interfere with sperm motility, capacitation, or acrosome reactions. It is concluded that these two compounds share common structural features with putative cell-surface carbohydrates involved in sperm-oolemmal interaction.     

The histochemistry of complex carbohydrates in the testes of patients of idiopathic male infertility

Summary In testis tissues from patients with idiopathic male infertility, complex carbohydrates have been studied by means of light microscopic histochemical methods, comparisons being made with the normal testes. In the infertile testes, histochemical reactions for acidic and neutral complex carbohydrates were in general weaker in intensity than in the normal testes. In the seminiferous tubules and interstitium of the infertile testes, a histochemical finding of primary importance was obtained with the demonstration of galactose deficiency in the complex carbohydrates involved. These glycoproteins contained only small numbers of sulfhydryl and disulfide groups. The possible histophysiological significance of these complex carbohydrates is discussed, with special reference to their histochemical properties determined in the present study.     

Novel functions of complex carbohydrates elucidated by the mutant mice of glycosyltransferase genes

Complex carbohydrates consist of carbohydrate moieties and protein or lipid portions, resulting in the formation of glycoproteins, proteoglycans or glycosphingolipids. The polymorphic carbohydrate structures are believed to contain profound biological implications which are important in cell-cell or cell-extracellular matrix interactions. A number of studies to delineate the roles of carbohydrates have been performed, and demonstrated definite changes in their profiles, cellular phenotypic changes or, sometimes, morphological and functional changes in tissues after modification of their structures. Recent successes in the isolation of glycosyltransferase genes and their modification enzyme genes has enabled clearer demonstrations of the roles of complex carbohydrates. In particular, genetic modification of glycosyltransferase genes in mice can elucidate the biological significances of their products in vivo. Here, we summarize recent advances in the understanding of the roles of complex carbohydrates provided from studies of gene knock-out mice of glycosyltransferase and modification enzyme genes focusing on novel functions which had not been expected.     

Molecular modelling of MHC class I carbohydrates

In this article we present the results of molecular modelling of four complex carbohydrates which have been found in the MHC class I proteins. Though these proteins show diversity in their sequences, the glycosylation sites are highly conserved indicating a possible structural/functional role of the glycan chain. Similar glycan chains have been found linked with other proteins of completely different function, such as IgG, and erythropoeitin. Thus, the molecular modelling of these carbohydrates will not only provide structural/dynamic information of these complex molecules but will also provide conformational information which can be utilised to build the glycoprotein models. The results presented here indicate that although several linkages show less conformational flexibility, terminal linkages can be quite flexible.