Reconstructing the protein-water interface
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Updated: Oct 29, 2026

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Published on: January 16, 2016
V A Makarov1, B K Andrews, B M Pettitt
1Program in Structural and Computational Biology, and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
Abstract:
Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpendicular radial distribution functions for water molecules around globular proteins. These universal functions may be used to reconstruct the unique three-dimensional solvent density distribution around every individual protein with a modest error. We discuss potential applications of this solvent treatment in protein x-ray crystallographic refinements and in theoretical modeling. We also present a fast, grid-based algorithm for construction of the perpendicular solvent density distributions.
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