Protein crowding affects hydration structure and dynamics.

Journal of the American Chemical Society
Ryuhei HaradaMichael Feig

Abstract

The effect of protein crowding on the structure and dynamics of water was examined from explicit solvent molecular dynamics simulations of a series of protein G and protein G/villin systems at different protein concentrations. Hydration structure was analyzed in terms of radial distribution functions, three-dimensional hydration sites, and preservation of tetrahedral coordination. Analysis of hydration dynamics focused on self-diffusion rates and dielectric constants as a function of crowding. The results show significant changes in both structure and dynamics of water under highly crowded conditions. The structure of water is altered mostly beyond the first solvation shell. Diffusion rates and dielectric constants are significantly reduced following linear trends as a function of crowding reflecting highly constrained water in crowded environments. The reduced dynamics of diffusion is expected to be strongly related to hydrodynamic properties of crowded cellular environments while the reduced dielectric constant under crowded conditions has implications for the stability of biomolecules in crowded environments. The results from this study suggest a prescription for modeling solvation in simulations of cellular environments.

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Citations

Sep 17, 2013·Journal of Molecular Graphics & Modelling·Michael Feig, Yuji Sugita
Feb 14, 2013·Journal of the American Chemical Society·Ryuhei HaradaMichael Feig
Dec 18, 2013·Journal of the American Chemical Society·John T KingKevin J Kubarych
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May 24, 2014·PLoS Computational Biology·Drazen Petrov, Bojan Zagrovic
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