title: The use of CVFF and CFF91 force fields in conformational analysis of carbohydrate molecules. Comparison with AMBER molecular mechanics and dynamics calculations for methyl alpha-lactoside.
abstract: The solution conformation of methyl alpha-lactoside has been studied through molecular mechanics calculations using the AMBER/Homans, CVFF and CFF91 force fields, and compared to NMR nuclear Overhauser data. Steady-state and transient nuclear Overhauser effects (NOEs) have been interpreted in terms of the ensemble average distribution of conformers. The NOEs have been analysed using the complete relaxation matrix approach for a rigid and isotropic motion model. The molecular mechanics calculations have been performed at two dielectric constants (i.e. epsilon = 1 and 80 debyes, or epsilon = r and 80 debyes) in an exhaustive way, and, in some cases, have been complemented by specific calculations at intermediate epsilon values. Relaxed energy maps and adiabatic surfaces have been generated for the different dielectric constants. The probability distribution of conformers has been estimated from these steric energy maps. Molecular dynamics simulations in vacuo have also been performed. Our results indicate that the beta-(1-->4) glycosidic linkage shows some fluctuations between three low-energy regions, although it spends about 90% of its time in the region close to the global minimum. The observed conformation of methyl alpha-lactoside seems to be closer to that predicted by CVFF, although the AMBER/Homans results are also in qualitative agreement with the experimental data.
authors.affiliation: Departamento de Química Orgánica Biológica, Instituto de Química Orgánica (CSIC), Madrid, Spain.
authors.forename: J L
authors.initials: JL
authors.lastname: Asensio
authors.forename: M
authors.initials: M
authors.lastname: Martin-Pastor
authors.forename: J
authors.initials: J
authors.lastname: Jimenez-Barbero
mesh_terms: D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D004563:Electrochemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008433:Mathematics; D008759:Methylglycosides / Q000737:chemistry*; D008958:Models, Molecular; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D011336:Probability; D012996:Solutions
chemical_list: D008759:Methylglycosides; D012996:Solutions; C034207:methyl lactoside