Placevent: An algorithm for prediction of explicit solvent atom distribution—Application to HIV‐1 protease and F‐ATP synthase |
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Authors: | Daniel J. Sindhikara Norio Yoshida Fumio Hirata |
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Affiliation: | 1. Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444‐8585, Japan;2. Department of Chemistry, Graduate School of Sciences, Kyushu University, Fukuoka 812‐8581, Japan;3. Institute for Advanced Study, Kyushu University, Fukuoka 812‐8581, Japan;4. Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki 444‐8585, Japan |
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Abstract: | We have created a simple algorithm for automatically predicting the explicit solvent atom distribution of biomolecules. The explicit distribution is coerced from the three‐dimensional (3D) continuous distribution resulting from a 3D reference interaction site model (3D‐RISM) calculation. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure and the solvent composition. We show examples of predicting water molecules near the KNI‐272 bound form of HIV‐1 protease and predicting both sodium ions and water molecules near the rotor ring of F‐adenosine triphosphate (ATP) synthase. Our results give excellent agreement with experimental structure with an average prediction error of 0.39–0.65 Å. Further, unlike experimental methods, this method does not suffer from the partial occupancy limit. Our method can be performed directly on 3D‐RISM output within minutes. It is extremely useful for examining multiple specific solvent–solute interactions, as a convenient method for generating initial solvent structures for molecular dynamics calculations, and may assist in refinement of experimental structures. © 2012 Wiley Periodicals, Inc. |
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Keywords: | explicit solvent water distribution HIV‐1 protease ATPase rotor three‐dimensional reference interaction site model solvent penetration solvent prediction ion coordination refinement water structure |
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