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  • Title: The use of the AMBER force field in conformational analysis of carbohydrate molecules: determination of the solution conformation of methyl alpha-lactoside by NMR spectroscopy, assisted by molecular mechanics and dynamics calculations.
    Author: Asensio JL, Jimenez-Barbero J.
    Journal: Biopolymers; 1995 Jan; 35(1):55-73. PubMed ID: 7696556.
    Abstract:
    The solution conformation of methyl alpha-lactoside has been studied through nmr spectroscopy and molecular mechanics calculations using the assisted model building with energy refinement (AMBER) force field. The nmr data have included nuclear Overhauser effect (NOE) measurements both in the laboratory and rotating frames, longitudinal relaxation times, and homonuclear and heteronuclear coupling constants. The steady-state and transient NOEs have been interpreted in terms of an ensemble average distribution of conformers, making use of the complete relaxation matrix approach. The molecular mechanics calculations have been performed at two dielectric constants [epsilon = 1*r and 80 Debyes (D)] in an exhaustive way, and have been complemented with 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. The experimental results indicate that the beta (1-->4)-glycosidic linkage shows some fluctuations among three low energy regions, although spends ca. 85% of its time in the region close to the global minimum. It is shown that the overestimation of the electrostatic contributions in AMBER is responsible for the failure of this force field to explain the experimental results when used at low dielectric constant (epsilon < 20 D). The matching between the expected and observed facts increases for epsilon > 40 D. Different conditions have been tested to perform temperature constant molecular dynamics simulations in vacuo, which have indicated that, when used without explicit solvent, this force field should only be employed in a qualitatively way when analyzing dynamical properties of oligosaccharides.
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