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-hydroxybutyramido)-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 solvent-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.
Rodríguez-Carvajal
M A
MA
Departamento Química Orgánica, Facultad Química, University of Sevilla, Spain.
Bernabe
M
M
Espartero
J L
JL
Tejero-Mateo
P
P
Gil-Serrano
A
A
Jiménez-Barbero
J
J
D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009005:Monosaccharides / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D011135:Polysaccharides, Bacterial / Q000737:chemistry*; D020579:Sinorhizobium / Q000737:chemistry*; D012996:Solutions; D013816:Thermodynamics
D009005:Monosaccharides; D011135:Polysaccharides, Bacterial; D012996:Solutions