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GBr6NL: A generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation

J. Chem. Phys. 126, 195102 (2007); doi:10.1063/1.2735322

Published 18 May 2007

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Harianto Tjong and Huan-Xiang Zhou
Department of Physics and Institute of Molecular Biophysics, and School of Computational Science, Florida State University, Tallahassee, Florida 32306
The nonlinear Poisson-Boltzmann (NLPB) equation can provide accurate modeling of electrostatic effects for nucleic acids and highly charged proteins. Generalized Born methods have been developed to mimic the linearized Poisson-Boltzmann (LPB) equation at substantially reduced cost. The computer time for solving the NLPB equation is ~fivefold longer than for the LPB equation, thus presenting an even greater obstacle. Here we present the first generalized Born method, GBr6NL, for mimicking the NLPB equation. GBr6NL is adapted from GBr6, a generalized Born method recently developed to reproduce the solvation energy of the LPB equation [Tjong and Zhou, J. Phys. Chem. B 111, 3055 (2007)]. Salt effects predicted by GBr6NL on 55 proteins overall deviate from NLPB counterparts by 0.5  kcal/mol from ionic strengths from 10  to  1000  mM, which is ~10% of the average magnitudes of the salt effects. GBr6NL predictions for the salts effects on the electrostatic interaction energies of two protein:RNA complexes are very promising. ©2007 American Institute of Physics
History: Received 16 February 2007; accepted 4 April 2007; published 18 May 2007
Permalink: http://link.aip.org/link/?JCPSA6/126/195102/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.Rn
    Biochemical reactions and kinetics; polymerization
  • 87.10.+e
    General theory and mathematical aspects (biological/medical physics)
  • YEAR: 2007

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ISSN:
0021-9606 (print)   1089-7690 (online)
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