Implicit treatment of solvent dispersion forces in protein simulations
Published 2014. This article is a U.S. Government work and is in the public domain in the USA.
| Publié dans: | Journal of computational chemistry. - 1984. - 35(2014), 22 vom: 15. Aug., Seite 1621-9 |
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| Auteur principal: | |
| Format: | Article en ligne |
| Langue: | English |
| Publié: |
2014
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| Accès à la collection: | Journal of computational chemistry |
| Sujets: | Journal Article Research Support, N.I.H., Intramural binding enthalpy dispersion interactions hydration implicit salvation protein-protein association Proteins Solvents Water |
| Résumé: | Published 2014. This article is a U.S. Government work and is in the public domain in the USA. A model is proposed for the evaluation of dispersive forces in a continuum solvent representation for use in large-scale computer simulations. The model captures the short- and long-range effects of water-exclusion in conditions of partial and anisotropic hydration. The model introduces three parameters, one of which represents the degree of hydration (water occupancy) at any point in the system, which depends on the solute conformation, and two that represent the strength of water-water and water-solute dispersive interactions. The model is optimized for proteins, using hydration data of a suboptimally hydrated binding site and results from dynamics simulations in explicit water. The model is applied to a series of aliphatic-alcohol/protein complexes and a set of binary and ternary complexes of various sizes. Implications for weak and ultra-weak protein-protein association and for simulation in crowded media are discussed |
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| Description: | Date Completed 23.09.2015 Date Revised 24.03.2024 published: Print-Electronic Citation Status MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.23655 |