Sucrose in aqueous solution revisited, Part 1: Molecular dynamics simulations and direct and indirect dipolar coupling analysis

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

Although the crystal structure of the disaccharide sucrose was solved more than 30 years ago, its conformational distribution in aqueous solution is still a matter of debate. We report here a variety of molecular dynamics simulations (mostly of 100 ns) using the GLYCAM06 force field and various water models, paying particular attention to comparisons to NMR measurements of residual dipolar couplings and electron-mediated spin–spin couplings. We focus on the glycosidic linkage conformation, the puckering phase angle of the fructose ring, and intramolecular hydrogen bonds between the two sugars. Our results show that sucrose is indeed a dynamic molecule, but the crystal conformation is qualitatively the dominant one in dilute solution. A second conformational basin, populated in many force fields, is probably overstabilized in the calculations. © 2011 Wiley Periodicals, Inc. Biopolymers 97: 276–288, 2012.

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