Placevent: An algorithm for prediction of explicit solvent atom distribution-Application to HIV-1 protease and F-ATP synthase

Daniel J. Sindhikara, Norio Yoshida, Fumio Hirata

    Research output: Contribution to journalArticlepeer-review

    70 Citations (Scopus)

    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.

    Original languageEnglish
    Pages (from-to)1536-1543
    Number of pages8
    JournalJournal of Computational Chemistry
    Volume33
    Issue number18
    DOIs
    Publication statusPublished - Jul 5 2012

    All Science Journal Classification (ASJC) codes

    • Chemistry(all)
    • Computational Mathematics

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