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Reconstructing the protein-water interface.

V A Makarov·B K Andrews·B M Pettitt
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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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AlgorithmsAzurinCrystallography, X-RayDatabases, FactualModels, MolecularMyoglobinProteinsSolventsWaterJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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V A Makarov, B K Andrews, B M Pettitt. 1998. Reconstructing the protein-water interface.. https://doi.org/10.1002/(sici)1097-0282(199806)45%3A7%3C469%3A%3Aaid-bip1%3E3.0.co%3B2-m

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