Information capacity of the carbohydrate code

2000

The closing years of the second millennium have been uplifting for carbohydrate biology. Optimism that oligosaccharide sequences are bearers of crucial biological information has been borne out by the constellation of efforts of carbohydrate chemists, biochemists, immunochemists, and cell-and molecular biologists. The direct involvement of speci®c oligosaccharide sequences in protein targeting and folding, and in mechanisms of infection, in¯ammation and immunity is now unquestioned. With the emergence of families of proteins with carbohydrate-binding activities, assignments of information content for de®ned oligosaccharide sequences will become more common, but the pinpointing and elucidation of the bioactive domains on oligosaccharides will continue to pose challenges even to the most experienced carbohydrate biologists. The neoglycolipid technology incorporates some of the key requirements for this challenge: namely the resolution of complex glycan mixtures, and ligand binding coupled with sequence determination by mass spectrometry.

Journal of Biological Chemistry, 1993

The carbohydrate binding specificity of recombinant carbohydrate-binding protein 35 (rCBP35) has been investigated by quantitative precipitation using a series of glycoproteins and carbohydrate-protein conjugates and by inhibition of precipitation using well defined carbohydrate haptens. Synthetic glycoconjugates and glycoproteins containing terminal nonreducing galactosyl units in &linkage were capable of forming a precipitate with rCBP35. If the glycoprotein or glycoconjugate contained terminal Neu5Ac, or galactose in a-linkage, precipitate formation was not observed. We also found that murine laminin, which contains polylactosamine structures, reacted more strongly than did bovine fetuin. Using carbohydrate-bovine serum albumin (BSA) glycoconjugates, we found that the tetrasaccharide Gal/31,4GlcNAc~1,3Galj31,4-GlcNAc-BSA reacted more strongly than the disaccharide GalDl,.iGlcNAc-BSA conjugate, suggesting that the binding site accommodates carbohydrate ligands greater in size than a disaccharide. Equilibrium dialysis experiments using [3H]lactose showed that rCBP35 binds 1 mol (n = 0.84) of lactose/ 30,000 g atoms of protein, with an affinity constant of 2.07 X lo4 M-'. The binding site on the polypeptide appears to contain four subsites that recognize the sequence Galj31,4GlcNAc~l,Gal~l,X-. All disaccharides tested that contain a nonreducing &galactosyl unit behaved as inhibitors of precipitation at approximately the same concentration, suggesting that the reducing position of the tetrasaccharide does not play an important role in the specific binding to the fourth subsite. The reducing sugar may serve to hold the saccharide in a tunnel like binding pocket since methyl-@-D-galactoside itself is an extremely poor inhibitor. Lectins have now been isolated from a variety of animal tissues and species. Structural studies on these lectins have revealed that, at the level of amino acid sequence, each carbohydrate-binding polypeptide exhibits a characteristic carbohydrate recognition domain (CRD).' In addition, some lectins show sequences in which other domains are fused onto CA-20424, GM-29470, and GM-38740. The costs of publication of

ipcbee.com

Carbohydrate-binding proteins can interact with sugars but do not modify them, and play a pivotal role in a variety of important biological recognition processes. Most studies predict carbohydrate-binding sites, but not carbohydrate-binding proteins. The existing method of predicting carbohydrate-binding proteins with sequence identity 35% uses an amino acid based encoding method and support vector machine (SVM). The merits of this study are three-fold. First, we establish a large-scale data set of carbohydrate-binding proteins collected from three up-to-date databases, CAZy, CGF and Swiss-Prot. This data set CBPDS consists of 2380 positive and negative proteins with sequence identity 25% by removing sequence redundancy. Secondly, we propose an efficient SVMbased method for predicting carbohydrate-binding proteins using a small set of informative physicochemical properties obtained by using an inheritable bi-objective genetic algorithm. The prediction accuracy of independent test is 79.45% using 17 properties. Third, from the analysis of informative physicochemical properties, some interpretable knowledge of carbohydrate-binding and non-carbohydrate-binding proteins can be further discovered. The set of obtained physicochemical properties can also be used conveniently as the core for designing various predictors of carbohydrate-binding problems.

BioTechniques, 1998

Immobilized neoglycoconjugates covalently cross-linked into a polyacrylamide gel can be used to detect and characterize carbohydrate-binding proteins. The neoglycoconjugates comprise two active groups, saccharide and allyl, located on a poly(2-hydroxyethylacrylamide) backbone. The allyl group cross-links with the polyacrylamide gel matrix, while the saccharide groups are available for specific protein interactions. This neoglycoconjugate gel is prepared as a thin layer within the stacking region of a polyacrylamide gel, and electrophoresis is performed according to native, non-denaturing conditions. Carbohydrate-binding proteins, specific for the immobilized neoglycoconjugates, are thus retarded during electrophoresis, while simultaneously permitting the separation of nonbinding proteins according to size and charge. This new approach can be used to study carbohydrate-binding proteins in the pathology of disease or infection.

Applied Microbiology and Biotechnology, 2010

Insoluble polysaccharides can be degraded by a set of hydrolytic enzymes formed by catalytic modules appended to one or more non-catalytic carbohydrate-binding modules (CBM). The most recognized function of these auxiliary domains is to bind polysaccharides, bringing the biocatalyst into close and prolonged vicinity with its substrate, allowing carbohydrate hydrolysis. Examples of insoluble polysaccharides recognized by these enzymes include cellulose, chitin, β-glucans, starch, glycogen, inulin, pullulan, and xylan. Based on their amino acid similarity, CBMs are grouped into 55 families that show notable variation in substrate specificity; as a result, their biological functions are miscellaneous. Carbohydrate or polysaccharide recognition by CBMs is an important event for processes related to metabolism, pathogen defense, polysaccharide biosynthesis, virulence, plant development, etc. Understanding of the CBMs properties and mechanisms in ligand binding is of vital significance for the development of new carbohydrate-recognition technologies and provide the basis for fine manipulation of the carbohydrate–CBM interactions.

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.

Journal of the American Chemical Society

The existence of stabilizing carbohydrate-aromatic interactions is demonstrated from both the theoretical and experimental viewpoints. The geometry of experimentally based galactose-lectin complexes has been properly accounted for by using a MP2/6-31G(d,p) level of theory and by considering a counterpoise correction during optimization. In this case, the stabilizing interaction energy of the fucosebenzene complex amounts to 3.0 kcal/mol. The theoretical results obtained herein indicate that the carbohydrate-aromatic interactions are stabilizing interactions with an important dispersive component and that electronic density between the sugar hydrogens and the aromatic ring indeed exists, thus giving rise to three so-called nonconventional hydrogen bonds. Experimental evidence of the intrinsic tendency of aromatic moieties to interact with certain sugars has also been shown by simple NMR experiments in water solution. Benzene and phenol specifically interact with the clusters of C-H bonds of the alpha face of methyl-galactoside, without requiring the well-defined three-dimensional shape provided by a protein receptor, therefore resembling the molecular recognition features that are frequently observed in many carbohydrate-protein complexes.

Chemical Reviews, 1996

Matrix Biology, 1997

In spite of the great diversity of animal lectins, a common characteristic is their ability to bind sugars by means of discrete, modular carbohydrate recognition domains, CRDs. Three different groups of animal lectins -galectins, P-type and C-type lectins-have different types of CRDs which they arrange in a number of combinations, in three dimensions, in order to increase the affinity for oligosaccharides associated with glycoconjugates. The necessity of combining multiple CRDs in a native lectin molecule in order to increase the affinity for multiple ligands is of great importance physiologically, since many of the carbohydrate structures associated with proteins exist in a variety of different conformations. Recent work has clarified the structural basis for carbohydrate recognition by some of these lectins.