Studies on Molecular Recognition Patterns between Sugars and Amino Acids by Use of the Data Obtained from Single Crystal X-Ray Analysis

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Structural investigations of oligosaccharides and studies on recognition patterns between sugars and proteins are very essential to the understanding of biological functions sugars. In the present study we have undertaken the conformational analysis of one of the most biologically important oligosaccharides, sialyl Le^X, and the analysis of the interaction patterns between sugars and amino acids in protein structures which have been determined by X-ray analysis.1.Conformational analysis of sialy Le^X by molecular mechanicsSince suitable crystals of the sugar chain for diffraction experiments could not be obtained, the conformation of the sugar chain was investigated by molecular mechanics calculations. The initial models were constructed by docking X-ray structures of the component monosaccharides through glycosidic bonds and they were optimized by molecular mechanics. Two different docking modes were applied.It was shown that the docking mode influence the resultant stable conformations signficantly.2.Analysis of interaction patterns between sugars and amino acids in proteinsInteraction patterns between selected monosaccharides and amino acids in the proteins have been investigated by use of the X-ray data. All the X-ray data were taken from Protein Databank compiled at Brookhaven National Laboratory (USA). The monosaccharides which were taken into consideration are N-acetyl-glucosamine, arabinose, fucose, galactose, glucose, mannose, sialic acid, and zylose. Hydrogen bonds, non-bonded interactions, and interactions between sugars and aromatic rings were taken into account. The analysis showed that there is a specific common binding pocket for sugars in proteins. The pocket is consist of two layrs of amino acids. The inner layr in which amino acids participate in hydrogen bonds is made of mainly hydrophilic amino acids. The outer layr is chiefly consist of hydrophobic amino acids.