title: Studies on the solution conformation and dynamics of a polysaccharide from Sinorhizobium fredii HH103 and its monosaccharide repeating unit.
abstract: 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.
authors.affiliation: Departamento Química Orgánica, Facultad Química, University of Sevilla, Spain.
authors.forename: M A
authors.initials: MA
authors.lastname: Rodríguez-Carvajal
authors.forename: M
authors.initials: M
authors.lastname: Bernabe
authors.forename: J L
authors.initials: JL
authors.lastname: Espartero
authors.forename: P
authors.initials: P
authors.lastname: Tejero-Mateo
authors.forename: A
authors.initials: A
authors.lastname: Gil-Serrano
authors.forename: J
authors.initials: J
authors.lastname: Jiménez-Barbero
mesh_terms: 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
chemical_list: D009005:Monosaccharides; D011135:Polysaccharides, Bacterial; D012996:Solutions