Sucrose in aqueous solution revisited, Part 2: adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation |
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Authors: | Xia Junchao Case David A |
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Institution: | Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ 08854, USA. |
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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 Φ and ψ 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 ??ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO‐water mixtures. © 2011 Wiley Periodicals, Inc. Biopolymers 97: 289–302, 2012. |
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Keywords: | carbohydrates NMR molecular dynamics |
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