Abstract
Molecular dynamics simulations of several Asn-linked oligosaccharides carried out recently have been summarized. These oligosaccharides are flexible and the core α1 → 3- and α1 → 6-linkages play important roles in determining the overall shape of the molecule. The orientation of the 1 → 6-arm is affected not only by changes in χ but also by changes in φ and ψ around the α1 → 6-linkage. The processing of Man 9GlcNAc 2 to Man 5GlcNAc 2 during the biosynthesis of Asn-linked oligosaccharides proceeds in well-defined ‘conformation driven’ pathways. These molecular dynamics studies rationalize spectroscopic and biochemical observations such as the rate of cleavage of α1 → 2-linked mannoses by α-mannosidases, the action of β-1 → 4-galactosyltransferase on biantennary oligosaccharides, and the binding affinities of oligosaccharide ligands to the asialoglycoprotein receptor.
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