The conformational analysis of asparagine-linked oligosaccharides by molecular dynamics (MD) simulations were further extended to the hybrid and complex type intermediate structures which are the substrates for various glycosyl-transferases and precursors in the biosynthesis of final hybrid and complex type oligosaccharides. The simulations show that in the presence of the bisecting GlcNAc, the fluctuations of the core Man-alpha 1,3-Man fragment are restricted to a region around (30 degrees,30 degrees) in both the hybrid and complex types, which is in agreement with the conclusions drawn from NMR studies. However, conformations greater than 0 percent of phi and psi around the Man alpha1,3-Man fragment are also accessed in bisected oligosaccharides, albeit occasionally, suggesting that the conformations that are accessible for the 1,3-arm in the absence of the bisecting GlcNAc, are not stereochemically eliminated. The orientation of the 1,6-arm is affected not only by changes in khi, but also by changes in phi and psi around the core Man-alpha1,6-Man linkage as was observed previously in the MD simulations of the heptasaccharide moiety of the Erythrina corallodendron lectin. The conformation around the core Man-alpha1,6-Man linkage is different in the hybrid and the two complex types suggesting that the preferred values of phi, psi, khi are affected by the addition or deletion of saccharides to the alpha1,6-linked mannose. These molecular dynamics studies rationalize spectroscopic and biochemical observations like rate of cleavage of alpha1,2-linked mannoses by alpha-mannosidases, action of beta-1,4-galactosyl-transferase on biantennary oligosaccharides, and the binding affinities of oligosaccharide ligands to the asialoglycoprotein receptor. The results of the present and our previous MD simulations have been summarized in an invited review article.
