| Autor: |
Kimura, S. Roy, Brower, Richard C., Zhang, Chao, Sugimori, Masamichi |
| Předmět: |
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| Zdroj: |
Journal of Chemical Physics; 5/1/2000, Vol. 112 Issue 17, 4 Diagrams, 5 Charts, 24 Graphs |
| Abstrakt: |
We present a strategy for solvating biomolecules in molecular dynamics or Monte Carlo simulations. The method employs a thin layer (often monomolecular) of explicit water with additional external forces representing the electrostatics, pressure, fluctuations, and dissipations caused by the neglected bulk. Long-range electrostatic corrections are supplied through a set of variable surface charges (polarons) that recreates the mean reaction field (or dielectric properties) of an infinite solvent. We refer to this "fictitious" boundary layer as a "surface of active polarons" (or SOAP). Test simulations of the solvation free energies of 15 amino acid analogs and nine ions are in good agreement with experiment (correlation coefficients: 0.995 and 1.000, respectively) despite the use of unaltered published force-fields with only one adjustable parameter. Dynamical capabilities of SOAP are illustrated by application to a six residue peptide with a stable conformation (SYPFDV), as well as a flexible nine residue HIV-1 gp120 peptide (TLTSCNTSV from PDB 1hhg). Future extensions, calibrations, and applications are discussed briefly. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR] |
| Databáze: |
Complementary Index |
| Externí odkaz: |
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