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 NeuNAc alpha(2-3)Gal, NeuNAc alpha(2-6)Gal, NeuNAc alpha(2-8)NeuNAc and NeuNAc alpha(2-9)NeuNAc. The conformational regions A(i), B(i) and C(i) were identified in the Ramachandran plot. Analysis of the 1000 ps trajectories collected through simulation (2000 ps in the case of NeuNAc alpha (2-9)NeuNAc) revealed that these molecules have conformational propensity in region B(i). 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.
Suresh
M Xavier
MX
Department of Physics, Manonmaniam Sundaranar University, Tirunelveli 627 012, India.
Veluraja
K
K
D002236:Carbohydrate Conformation; D019295:Computational Biology / Q000379:methods; D004187:Disaccharides / Q000737:chemistry; D009844:Oligosaccharides / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry
D004187:Disaccharides; D009844:Oligosaccharides; D010446:Peptide Fragments; C016735:sialooligosaccharides