Molecular dynamics simulations of high-mannose oligosaccharides |
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Authors: | Balaji, Petety V. Qasba, Pradman K. Rao, V.S.R. |
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Affiliation: | Laboratory of Mathematical Biology, National Cancer Institute, National Institutes of Health Building Park 5, Room 410, 9000 Rockville Pike, Bethesda, MD 20892, USA |
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Abstract: | Conformations of several high-mannose-type oligosaccharidesthat are generated during the biosynthetic degradation of Man9GlcNAc2to Man5GlcNAc2 have been studied by molecular dynamics (MD).Simulations were performed on NCI-FCRDC's Cray Y-MP 8D/8128supercomputer using Biosym's CVFF force field for 1000 Ps withdifferent initial conformations. The conformations of the two1,3- and the two 1,6-linkages in each oligomannose were different,suggesting that deriving oligosaccharide conformations basedon the conformational preferences of the constituent disaccharidefragments will not always yield correct results. Unlike otheroligomannoses, Man9GlcNAc2 appears to take more than one distinctconformation around the core 1,6-linkage. These various conformationsmay play an important role in determining the processing pathways.Using the data on the preferred conformations of these oligomannosesand the available experimental results, possible pathways forprocessing Man9GlcNAc2 to Man5GlcNAc2 by 1,2-linkage-specificmannosidases have been proposed. Conformational analysis ofMan5GlcNAc2 indicates that the addition of ß1,2-GlcNActo the 1,3-linked core mannose, besides serving as a prerequisitefor mannosidase II action as suggested earlier, may also preventthe removal of 1,3-mannose. The MD simulations also suggestthat the processing of the precursor oligosaccharide duringAsn-linked complex and hybrid glycan biosynthesis proceeds ina well-defined pathway involving more than one 1,2-linkage-specificmannosidase. Knowledge of the conformation of the processingintermediates obtained from the present study can be used todesign highly specific substrate analogues to inhibit a particularmannosidase, thereby blocking one processing pathway withoutinterfering with the others. carbohydrates conformation glycosidase inhibitors mannosidase oligosaccharide processing |
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