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 journalArticle

54 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

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Adenosine
Protease
Fibrinolysin
Adenosine Triphosphate
Atoms
Prediction
Molecules
Interaction
Ions
Rigid structures
Water
Optimal Location
Biomolecules
Continuous Distributions
Prediction Error
Molecular Dynamics
Sodium
Rotor
Molecular dynamics
Refinement

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Computational Mathematics

Cite this

Placevent : An algorithm for prediction of explicit solvent atom distribution-Application to HIV-1 protease and F-ATP synthase. / Sindhikara, Daniel J.; Yoshida, Norio; Hirata, Fumio.

In: Journal of Computational Chemistry, Vol. 33, No. 18, 05.07.2012, p. 1536-1543.

Research output: Contribution to journalArticle

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