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

Détails bibliographiques
Publié dans:	Journal of computational chemistry. - 1984. - 33(2012), 18 vom: 05. Juli, Seite 1536-43
Auteur principal:	Sindhikara, Daniel J (Auteur)
Autres auteurs:	Yoshida, Norio, Hirata, Fumio
Format:	Article en ligne
Langue:	English
Publié:	2012
Accès à la collection:	Journal of computational chemistry
Sujets:	Journal Article Research Support, Non-U.S. Gov't Oligopeptides Solvents HIV Protease EC 3.4.23.- Proton-Translocating ATPases EC 3.6.3.14 kynostatin 272 MUL0OE3YBF

Description
Résumé:	Copyright © 2012 Wiley Periodicals, Inc. 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
Description:	Date Completed 28.09.2012 Date Revised 16.11.2017 published: Print-Electronic Citation Status MEDLINE
ISSN:	1096-987X
DOI:	10.1002/jcc.22984