Studies on the solution conformation and dynamics of a polysaccharide from Sinorhizobium fredii HH103 and its monosaccharide repeating unit
The conformational behavior of the homopolysaccharide isolated from Sinorhizobium fredii HH103 and its monosaccharide repeating unit (5-acetamido-3,5, 7,9-tetradeoxy-7-(3-hydroxybutyra-mido)-L-glycero-L-manno-nonulosonic acid) was analyzed by nuclear magnetic resonance (NMR) spectroscopy and extensive molecular dynamics simulations (MD). The results indicate that the glycosidic linkages and lateral chains may adopt a variety of conformations. MD simulations using the generalized Born sol vent-accessible surface area (GB/SA) continuum solvent model for water and the MM3*force field provide a population distribution of conformers that satisfactorily agrees with the experimental NMR data for the torsional degrees of freedom of the molecule. (C) 2000 by Elsevier Science Inc.
polysaccharide nmr molecular dynamics k-antigen pseudaminic acid