The high degree of internal flexibility observed for an oligomannose oligosaccharide does not alter the overall topology of the molecule

The conformational properties of oligosaccharides are important in determin ing their biological properties, such as recognition by proteins. The struc tural and dynamic properties of many oligosaccharides are poorly understood both because of a lack of experimental data (usually obtained from solutio n NMR parameters) and because of gross approximations frequently invoked in theoretical models. To characterise the oligomannose oligosaccharide Man(9 )GlcNAc(2) we have acquired a more extensive NMR data set and performed the first unrestrained molecular dynamics (MD) simulation in water of this lar ge oligosaccharide (employing the GLYCAM_93 parameter set with the AMBER fo rce field). Good agreement is seen between the computed dynamics data and t he results of both an isolated spin pair (ISPA) analysis of short mixing ti me NOE data and NOE build-up curves for mixing times from 100 to 2000 ms. T he number of experimental conformational constraints obtained in this study are in principle sufficient to fully define a rigid structure. The fact th at this could not be done indicates a high degree of internal flexibility a nd/or the presence of multiple conformations about the glycosidic linkages. Independently, the same conclusions are reached from an analysis of the MD results. In addition, the theoretical results allow the overall topology o f the molecule and its intra-molecular and solvent-mediated hydrogen bondin g pattern to be defined. Extensive re-organisation of solvent and inter-res idue hydrogen bonds is shown to be required for significant conformational changes to occur, resulting in relatively long life-times for distinct glyc osidic linkage conformations, despite the high local flexibility of the gly cosidic linkages. This factor is also seen in the overall topology of the m olecule, where the considerable internal flexibility is not translated into gross changes in structure. The control exerted by the solvent over both t he flexibility and overall topology of an oligosaccharide has important imp lications for recognition processes and for the conformational properties o f glycans attached to glycoproteins.