The water R1(ω) NMRD profiles of a hydrated protein from molecular dynamics simulation

Phys Chem Chem Phys. 2013 Sep 7;15(33):14089-97. doi: 10.1039/c3cp51147b. Epub 2013 Jul 18.

Abstract

The hydration of a protein, Peroxiredoxin 5, is obtained from a molecular dynamics simulation and compared with the picture of hydration which is obtained by analysing the water proton R1 NMRD profiles using a generally accepted relaxation model [K. Venu, V. P. Denisov and B. Halle, J. Am. Chem. Soc., 1997, 119, 3122]. The discrepancy between the hydration pictures derived from the water R1(ω0)-NMRD profiles and MD is relevant in a discussion of the factors behind the stretched NMRD profile, the distribution of orientational order parameters and residence times of buried water used in the NMRD model.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Molecular Dynamics Simulation*
  • Peroxiredoxins / chemistry*
  • Peroxiredoxins / metabolism
  • Protein Structure, Tertiary
  • Protons
  • Water / chemistry*

Substances

  • Protons
  • Water
  • Peroxiredoxins