Molecular dynamics simulations of high-mannose oligosaccharides

Conformations of several high-mannose-type oligosaccharides that are generated during the biosynthetic degradation of Man9GlcNAc2 to Man5GlcNAc2 have been studied by molecular dynamics (MD). Simulations were performed on NCI-FCRDC's Cray Y-MP 8D/8128 supercomputer using Biosym's CVFF force field for 1000 ps with different initial conformations. The conformations of the two alpha 1,3- and the two alpha 1,6-linkages in each oligomannose were different, suggesting that deriving oligosaccharide conformations based on the conformational preferences of the constituent disaccharide fragments will not always yield correct results. Unlike other oligomannoses, Man9GlcNAc2 appears to take more than one distinct conformation around the core alpha 1,6-linkage. These various conformations may play an important role in determining the processing pathways. Using the data on the preferred conformations of these oligomannoses and the available experimental results, possible pathways for processing Man9GlcNAc2 to Man5GlcNAc2 by alpha 1,2-linkage-specific mannosidases have been proposed. Conformational analysis of Man5GlcNAc2 indicates that the addition of beta 1,2-GlcNAc to the alpha 1,3-linked core mannose, besides serving as a prerequisite for mannosidase II action as suggested earlier, may also prevent the removal of alpha 1,3-mannose. The MD simulations also suggest that the processing of the precursor oligosaccharide during Asn-linked complex and hybrid glycan biosynthesis proceeds in a well-defined pathway involving more than one alpha 1,2-linkage-specific mannosidase. Knowledge of the conformation of the processing intermediates obtained from the present study can be used to design highly specific substrate analogues to inhibit a particular mannosidase, thereby blocking one processing pathway without interfering with the others.