Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects
Copyright © 2011 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 32(2011), 12 vom: 01. Sept., Seite 2664-78 |
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| Weitere Verfasser: | , |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2011
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Solvents Methane OP0UW79H66 |
| Zusammenfassung: | Copyright © 2011 Wiley Periodicals, Inc. A revised and improved version of our efficient polarizable force-field/coarse grained solvent combined approach (Masella, Borgis, and Cuniasse, J. Comput. Chem. 2008, 29, 1707) is described. The polarizable pseudo-particle solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile pseudo-particles. In this study, we propose a new formulation of the energy term handling the nonelectrostatic interactions among the pseudo-particles. This term is now able to reproduce the energetic and structural response of liquid water due to the presence of a hydrophobic spherical cavity. Accordingly, the parameters of the energy term handling the nonpolar solute/solvent interactions have been refined to reproduce the free-solvation energy of small solutes, based on a standard thermodynamic integration scheme. The reliability of this new approach has been checked for the properties of solvated methane and of the solvated methane dimer, as well as by performing 10 × 20 ns molecular dynamics (MD) trajectories for three solvated proteins. A long-time stability of the protein structures along the trajectories is observed. Moreover, our method still provides a measure of the protein solvation thermodynamic at the same accuracy as standard Poisson-Boltzman continuum methods. These results show the relevance of our approach and its applicability to massively coupled MD schemes to accurately and intensively explore solvated macromolecule potential energy surfaces |
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| Beschreibung: | Date Completed 25.11.2011 Date Revised 21.11.2013 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.21846 |