title: A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.
abstract: The Poisson-Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N- and C-terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules.
authors.affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-15 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; Laboratory for Computational Molecular Design, Quantitative Biology Center (QBiC), RIKEN, 1-6-5 Minatojima-Minatomachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
authors.forename: Junya
authors.initials: J
authors.lastname: Yamagishi
authors.forename: Noriaki
authors.initials: N
authors.lastname: Okimoto
authors.forename: Gentaro
authors.initials: G
authors.lastname: Morimoto
authors.forename: Makoto
authors.initials: M
authors.lastname: Taiji
mesh_terms: D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D012995:Solubility; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D010455:Peptides; D011506:Proteins; D012997:Solvents
keywords: Poisson-Boltzmann implicit solvent; continuum electrostatics; implicit solvent; molecular modeling; solvation-free energy