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

Authors

  • Junchao Xia,

    1. Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ 08854
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  • David A. Case

    Corresponding author
    1. Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ 08854
    • Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ 08854
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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley. com

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 ϕ−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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