Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum

被引:73
作者
Schnieders, Michael J.
Baker, Nathan A.
Ren, Pengyu
Ponder, Jay W. [1 ]
机构
[1] Washington Univ, Sch Med, Dept Biochem & Mol Biophys, St Louis, MO 63110 USA
[2] Washington Univ, Dept Biomed Engn, St Louis, MO 63130 USA
[3] Washington Univ, Sch Med, Dept Biochem & Mol Biophys, St Louis, MO 63110 USA
[4] Univ Texas, Dept Biomed Engn, Austin, TX 78712 USA
关键词
D O I
10.1063/1.2714528
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solvent, due to polarization, has long been an interesting problem. In vacuum, experimental values for the dipole moments and polarizabilities of small, rigid molecules are known to high accuracy; however, it has generally been difficult to determine these quantities for a polar molecule in water. A theoretical approach introduced by Onsager [J. Am. Chem. Soc. 58, 1486 (1936)] used vacuum properties of small molecules, including polarizability, dipole moment, and size, to predict experimentally known permittivities of neat liquids via the Poisson equation. Since this important advance in understanding the condensed phase, a large number of computational methods have been developed to study solutes embedded in a continuum via numerical solutions to the Poisson-Boltzmann equation. Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here the authors describe the theory underlying a newly developed polarizable multipole Poisson-Boltzmann (PMPB) continuum electrostatics model, which builds on the atomic multipole optimized energetics for biomolecular applications (AMOEBA) force field. As an application of the PMPB methodology, results are presented for several small folded proteins studied by molecular dynamics in explicit water as well as embedded in the PMPB continuum. The dipole moment of each protein increased on average by a factor of 1.27 in explicit AMOEBA water and 1.26 in continuum solvent. The essentially identical electrostatic response in both models suggests that PMPB electrostatics offers an efficient alternative to sampling explicit solvent molecules for a variety of interesting applications, including binding energies, conformational analysis, and pK(a) prediction. Introduction of 150 mM salt lowered the electrostatic solvation energy between 2 and 13 kcal/mole, depending on the formal charge of the protein, but had only a small influence on dipole moments. (c) 2007 American Institute of Physics.
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页数:21
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