Computation techniques in the conformational analysis of carbohydrates

A growing number of modern studies of carbohydrates is devoted to spatial mechanisms of their participation in the cell recognition processes and directed design of inhibitors of these processes. No progress in this field is possible without the development of theoretical conformational analysis of carbohydrates. In this review, we generalize literature data on the potentialities of using various molecular-mechanic force fields, the methods of quantum mechanics, and molecular dynamics to study the conformation of glycoside linkage. A possibility of analyzing the reactivity of carbohydrates with the computation techniques is also discussed in brief.     

Histochemical study of the myelin-associated carbohydrates.

Myelin-associated carbohydrates were studied by means of histochemical techniques in the central nervous system of birds and mammals. Polianions in the surface of myelin and in interfascicular oligodendroglia were detected using histochemical techniques. Glycoproteins were studied by means of concanavalin A. The Con-A-PO-DAB sequence was used. Concanavalin-A-binding sites were detected in oligodendroglia and on the myelin surface. Similar results were observed in both birds and mammals. The processes of the interfascicular oligodendroglia also contain carbohydrates. A close association between the carbohydrates of these glial processes and the myelin surface carbohydrates was demonstrated, and their probable identity is assumed.     

Nutrition--a factor in preventing arteriosclerosis, coronary disease and disorders of the blood coagulation system. I. An imbalance in food fats and carbohydrates and atherogenesis

The analysis of the literary data and the results of own research testifies that the lipids and carbohydrates metabolism disturbance in food is one of the decisive factors of pathogenetic arteriosclerosis and coronary disease. A long balanced diet in particular in fats and carbohydrates favours the normalization of the metabolic processes in stabilization of the organism.     

植物非结构性贮藏碳水化合物的生理生态学研究进展

非结构性碳水化合物是参与植物生命过程的重要物质。蔗糖不仅是植物体内碳水化合物运输的主要形式,而且可以在基因表达水平上对细胞内的代谢进行调节。果聚糖是植物营养组织碳水化合物的主要暂贮形式;淀粉是植物主要的长期贮存物质之一。植物体内非结构性碳水化合物的代谢在很大程度上影响着植株的生长发育和对环境因子的响应。综述了植物非结构性贮藏碳水化合物的生理生态学研究进展,着重介绍了蔗糖,果聚糖和淀粉代谢的生理过程及对环境因子（温度和水分）和人为因素的响应机制。     

Nectar formation and floral nectary anatomy of Anigozanthos flavidus: a combined magnetic resonance imaging and spectroscopy study

Metabolic processes underlying the formation of floral nectar carbohydrates, especially the generation of the proportions of fructose, glucose, and sucrose, are important for understanding ecological plant-pollinator interactions. The ratio of sucrose-derived hexoses, fructose and glucose, in the floral nectar of Anigozanthos flavidus (Haemodoraceae) was observed to be different from 1:1, which cannot be explained by the simple action of invertases. Various NMR techniques were used to investigate how such an unbalanced ratio of the two nectar hexoses can be formed. High-resolution (13)C NMR spectroscopy in solution was used to determine the proportion of carbohydrates in vascular bundles of excised inflorescences fed with (13)C-labelled carbohydrates. These experiments verified that feeding did not affect the metabolic processes involved in nectar formation. In vivo magnetic resonance imaging (e.g. cyclic J cross-polarization) was used to detect carbohydrates in vascular bundles and (1)H spin echo imaging non-invasively displayed the architecture of tepal nectaries and showed how they are connected to the vascular bundles. A model of the carbohydrate metabolism involved in forming A. flavidus floral nectar was established. Sucrose from the vascular bundles is not directly secreted into the lumen of the nectary but, either before or after invertase-catalysed hydrolyses, taken up by nectary cells and cycled at least partly through glycolysis, gluconeogenesis, and the pentose phosphate pathway. Secretion of the two hexoses in the cytosolic proportion could elegantly explain the observed fructose:glucose ratio of the nectar.     

Lack of significant long-term effect of dietary carbohydrates on hepatic glucose-6-phosphatase expression in rainbow trout (Oncorhynchus mykiss)

Hepatic glucose-6-phosphatase (G6Pase) plays an important role in glucose metabolism because it catalyzes the release of glucose to the circulatory system in the processes of glycogenolysis and gluconeogenesis. The present study was initiated to analyze the regulation of hepatic G6Pase expression by dietary carbohydrates in rainbow trout. The first step in our study was the identification of a partial G6Pase cDNA in rainbow trout that was highly homologous to that of mammals. Hepatic G6Pase activities and mRNA levels were measured in trout fed one of the experimental diets, with or without carbohydrates. We found no significant effect of intake of dietary carbohydrates on G6Pase expression (mRNA and activity) 6 hours and 24 hours after feeding. These results suggest that there is no control of G6Pase synthesis by dietary carbohydrates in rainbow trout and that the lack of regulation of gluconeogenesis by dietary carbohydrates could at least partially explain the postprandial hyperglycemia and the low dietary glucose utilization observed in this species.     

Ultrastructural localization of lectin-binding sites and laminin-like immunoreactivity in glial cells and neurites growing out from explant cultures of the central nervous system of embryonic locusts

Summary Lectins with different sugar specificities and labeled with horseradish peroxidase or gold were used to study, at the electron-microscopic level, surface glycoconjugates of glial cells and neurites growing out from explant cultures of the central nervous system of embryonic locusts. Differential binding to differentiating glial cells and to neurites was demonstrated. Concanavalin A (Con A) and wheat-germ agglutinin (WGA) bound to glial and neurite surfaces with different degrees of labeling. The formation of glial processes and junctional complexes was invariably accompanied by a corresponding increase of Con A- and WGA-receptors. Peanut agglutinin (PNA) failed to bind to glial cells but strongly stained the plasma membrane of neurite junctions. Lotus tetragonolobus a. (LTA) did not bind either to glial cells or to neurites. In addition, staining with an antibody against laminin showed labeling in areas of neurite outgrowth and neurite interactions; this resembled the localization of PNA receptors. These findings provide evidence for the presence of different carbohydrates at the surface of neurites and glial cells of locust. Their predominant localization in glial processes and neurite junctions suggests that these carbohydrates constitute part of a group adhesion glycoproteins that also includes laminin.     

Potential role of glycosidase inhibitors in industrial biotechnological applications

The nutrient content of food and animal feed may be improved through new knowledge about enzymatic changes in complex carbohydrates. Enzymatic hydrolysis of complex carbohydrates containing alpha or beta glycosidic bonds is very important in nutrition and in several technological processes. These enzymes are called glycosidases (Enzyme Class 3.2.1) and include amylases, pectinases and xylanases. They are present in many foods such as cereals, but their microbial analogues are often produced and added in many food processes, for instance to improve the shelf-life of bakery products, clear beer, produce glucose, fructose or dextrins, hydrolyse lactose, modify food pectins, or improve processes. However, many plant foods also contain endogenous inhibitors, which reduce the activity of glycosidases, in particular, proteins, peptides, complexing agents and phenolic compounds. The plant proteinaceous inhibitors of glycosidases are in focus in this review whose objective is to report the effect and implications of these inhibitors in industrial processes and applications. These studies will contribute to the optimisation of industrial processes by using modified enzymes not influenced by the natural inhibitors. They will also allow careful selection of raw material and reaction conditions, and future development of new genetic varieties low in inhibitors. These are all new and very promising concepts for the food and feed sector.     

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.     

Thermophilic,lignocellulolytic bacteria for ethanol production: current state and perspectives

Lignocellulosic biomass contains a variety of carbohydrates, and their conversion into ethanol by fermentation requires an efficient microbial platform to achieve high yield, productivity, and final titer of ethanol. In recent years, growing attention has been devoted to the development of cellulolytic and saccharolytic thermophilic bacteria for lignocellulosic ethanol production because of their unique properties. First of all, thermophilic bacteria possess unique cellulolytic and hemicellulolytic systems and are considered as potential sources of highly active and thermostable enzymes for efficient biomass hydrolysis. Secondly, thermophilic bacteria ferment a broad range of carbohydrates into ethanol, and some of them display potential for ethanologenic fermentation at high yield. Thirdly, the establishment of the genetic tools for thermophilic bacteria has allowed metabolic engineering, in particular with emphasis on improving ethanol yield, and this facilitates their employment for ethanol production. Finally, different processes for second-generation ethanol production based on thermophilic bacteria have been proposed with the aim to achieve cost-competitive processes. However, thermophilic bacteria exhibit an inherent low tolerance to ethanol and inhibitors in the pretreated biomass, and this is at present the greatest barrier to their industrial application. Further improvement of the properties of thermophilic bacteria, together with the optimization production processes, is equally important for achieving a realistic industrial ethanol production.     

Large-scale approaches for glycobiology

Glycosylation, the attachment of carbohydrates to proteins and lipids, influences many biological processes. Despite detailed characterization of the cellular components that carry out glycosylation, a complete picture of a cell's glycoconjugates remains elusive because of the challenges inherent in characterizing complex carbohydrates. This article reviews large-scale techniques for accelerating progress in glycobiology.     

Industrial carbohydrate biotransformations

Nearly all major industrial processes which involve carbohydrates, include biotechnological transformations. This is due to the complex nature of carbohydrates where stereo- and regioselectivity are highly complex and difficult to control. Enzymes and microorganisms work highly selectively and efficiently in water solution, and provide high yield in general. The article focuses on different types of reactions, including large-scale processes. Topics are hydrolytic reactions, including starch processing, oxidation and reduction transformations including organic acids, such as gluconic and ketogluconic acids and vitamin C synthesis, and isomerization and transfer reactions, which are established on a very large scale to produce glucose/fructose syrups and sucrose isomers. The article will further discuss some mechanistic aspects which are relevant for technology and present selected details of industrial-scale processing. Finally an outlook outlines perspectives of future processes.     

Concanavalin A-perioxidase-diaminobenzidine (Con-A-PO-DAB)-alcian blue (AB): a reliable method for dual staining of complex carbohydrates.

A method has been established for the dual staining of complex carbohydrates in light microscopy. It is a combined concanavalin A-peroxidase-diaminobenzidine (Con-A-PO-DAB)-alcian blue (AB) (pH 2.5) method, and with this method it is possible to color alpha-D-glucosyl and alpha-D-mannosyl residues and acidic groupings of complex carbohydrates in tissues brown and blue respectively. Histochemical experiments using histological sections with reactive complex carbohydrates and casein films containing carbohydrates of known chemical structure have substantiated the validity of the above significance of the dual staining. Thus, the present dual staining method is a reliable one and a new addition to a series of dual staining techniques hitherto employed in the light microscopic histochemistry of complex carbohydrates.     

Methylglyoxal: metabolism and biological activity

The enzymic formation of methylglyoxal from dihydroxyacetone phosphate and aminoacetone (metabolites of carbohydrates and proteins) is considered. Methylglyoxal transformation into lactic and pyruvic acids is related to energy metabolism, catabolism and anabolism dissociation processes in carbohydrates and proteins, and, probably, to maintenance of asymmetrical entropy in vivo on the constant level. Attention is paid to the methylglyoxal inhibition of enzymes, its interaction with glutathione and polyamines affecting the mechanisms regulating protein synthesis and cellular division. The methods for obtaining and quantitative determination of methylglyoxal are described.     

The effect of structural differences in the reducing terminus of sugars on the binding affinity of carbohydrates and proteins analyzed using photoaffinity labeling

Because carbohydrates and proteins bind with such low affinity, the nature of their interactions is not clear. Photoaffinity labeling with diazirin groups is useful for elucidating the roles of carbohydrates in these binding processes. However, when carbohydrate probes are synthesized according to this conventional method, the reducing terminus of the sugar is opened to provide an acyclic structure. Because greater elucidation of carbohydrate-protein interactions requires a closed-ring carbohydrate in addition to the photoreactive group, we synthesized new molecular tools. The carbohydrate ligands were synthesized in three steps (glycosylation with allyl alcohol, deprotection, and ozonolysis). Specific binding proteins for carbohydrate ligands were obtained by photoaffinity labeling. Closed ring-type carbohydrate ligands, in which the reducing sugar is closed, bound to lectins more strongly than open ring-type sugars. Carbohydrate to protein binding was observed using AFM.     

Oligosaccharide microarrays fabricated on aminooxyacetyl functionalized glass surface for characterization of carbohydrate-protein interaction

Carbohydrate-protein interactions play important biological roles in biological processes. But there is a lack of high-throughput methods to elucidate recognition events between carbohydrates and proteins. This paper reported a convenient and efficient method for preparing oligosaccharide microarrays, wherein the underivatized oligosaccharide probes were efficiently immobilized on aminooxyacetyl functionalized glass surface by formation of oxime bonding with the carbonyl group at the reducing end of the suitable carbohydrates via irreversible condensation. Prototypes of carbohydrate microarrays containing 10 oligosaccharides were fabricated on aminooxyacetyl functionalized glass by robotic arrayer. Utilization of the prepared carbohydrate microarrays for the characterization of carbohydrate-protein interaction reveals that carbohydrates with different structural features selectively bound to the corresponding lectins with relative binding affinities that correlated with those obtained from solution-based assays. The limit of detection (LOD) for lectin ConA on the fabricated carbohydrate microarrays was determined to be approximately 0.008 microg/mL. Inhibition experiment with soluble carbohydrates also demonstrated that the binding affinities of lectins to different carbohydrates could be analyzed quantitatively by determining IC(50) values of the soluble carbohydrates with the carbohydrate microarrays. This work provides a simple procedure to prepare carbohydrate microarray for high-throughput parallel characterization of carbohydrate-protein interaction.     

糖类药物

糖链作为重要的生物信息分子和高密度的信息载体,参与细胞生物几乎所有的生命过程,特别是在细胞分化、发育、免疫、老化、癌变、信息传递等生命基础活动和重大疾病过程中起着特异性的识别、介导与调控作用。由于糖类物质的多种多样的生物活性,糖类药物在抗肿瘤、老年痴呆、免疫、抗病毒等多个重大疾病领域广泛应用,而且其使用范围还在不断开拓中。因此,糖类药物生物活性多样,毒副作用低,具有广阔的发展前景。     

Glycoconjugates for the recognition of Bacillus spores

Carbohydrates act as ligands in many biological processes, including the folding and secretion of proteins, cell-cell recognition, adhesion, and sporulation in the Bacillus genus. Fluorescent-labeled disaccharide glycoconjugates have been applied to evaluate binding to bacterial spores assuming that the spore surface is covered with carbohydrates. This study has shown that specific recognition of bacterial spores is based on interactions between disaccharide glycoconjugates acting as ligands and monosaccharide units expressed on the exterior of bacterial spores. Using fluorophore-assisted carbohydrate electrophoresis (FACE), carbohydrates that are expressed on the exterior of the spores were enumerated. The findings have an impact on how to improve ligand selection, essential for sensor development. In addition, the findings provide new information for inhibition of bacterial spores, and in general, demonstrate how carbohydrates function as recognition signals in nature.     

Determination of carbohydrates in fermentation processes by high-performance liquid chromatography

Summary HPLC is a universal, fast, accurate and selective method for the quantification of carbohydrates during fermentation processes. HPLC is not affected by complex constituents of fermentation media, such as meat extract, soybean meal or distillers solubles. The detection limit of the different investigated carbohydrates by refractive index monitoring ranges between 20 and 40 mg/l using a cation-exchange resin and between 50 and 100 mg/l using amino- or diol-bonded phases.Offprint requests to: H.-P. Fiedler