Journal Highlight: Sucrose in aqueous solution revisited, Part 2: Adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation

Sucrose in aqueous solution revisited, Part 2: Adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation

Biopolymers, 2012, 97, 289-302
Junchao Xia, David A. Case

Abstract: We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic and torsion angles. NMR relaxation parameters, including longitudinal (R₁) and transverse (R₂) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S₂) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80-90% of the conformations having glycosidic angle-torsion angle values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures.

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