Diverse oligosaccharide structures that are generated with the help of specific glycosyltransferases from a relatively small number of saccharide units, have an enormous potential for encoding information. This information content for a given oligosaccharide is increased furthermore by the existence of several conformers which exist in equilibrium in solution that have been implicated in several biological functions. Most of the experimental studies in solution give a time averaged conformation, closely resembling the global energy minimum conformer, that however, need not be the bioactive conformer. To have a precise idea about the bioactive conformer, it is essential to have the information about all the conformers which are accessible by this particular oligosaccharide. We have applied molecular dynamics technique to study all the possible conformations of some bi- and triantennary oligosaccharides that are the ligands of glycosyltransferases and of asialoglycoprotein cell surface receptor (ASGP-R). Most of the earlier studies on the conformational behavior of oligosaccharides were limited to the study of individual di- and trisaccharide fragments which constitute the actual oligosaccharides present on glycoproteins. Molecular dynamics simulation of the molecules for one nano second by considering all the monosaccharides simultaneously has provided a wealth of information about the conformational preferences of these molecules. The results show that contrary to earlier beliefs oligosaccharides show considerable amount of flexibility. The relative distance and orientation of the galactose residues on the 1,2- and 1,4- branches of the 1,3-arm of triantennary oligosaccharide are invariant during most of the simulation period. Contrary to the 1,3 arm, the 1,6 arm is close to the GlcNAc residues of the core oligosaccharide structure. Binding of the 1,3-arm may bring about a conformational change in the 1,6- arm and lead to its interaction with a lectin, e.g ASGP-R, providing additional binding energy.
