Conformations of terminal sialyloligosaccharide fragments — a molecular dynamics study

Molecular dynamics simulations have been performed to understand the conformational features of the terminal sialyloligosaccharide fragments NeuNAcα(2-3)Gal, NeuNAcα(2-6)Gal, NeuNAcα(2-8)NeuNAc and NeuNAcα(2-9)NeuNAc. The conformational regions Ai, Bi and Ci were identified in the Ramachandran plot. Analysis of the 1000 ps trajectories collected through simulation (2000 ps in the case of NeuNAcα (2-9)NeuNAc) revealed that these molecules have conformational propensity in region Bi. The occurrence of these molecules in the common conformational space leads to a structural similarity between them. This structural similarity may be an essential requirement for the neuraminidase activity towards sialyloligosaccharides. The local change in the conformation of the active site residues of neuraminidases may contribute for the specificity differences between different linkages of sialyloligosaccharides. A highly conserved water-mediated hydrogen bond observed in these structures between the sugar residues, acts as an additional stabilizing force.