Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?

被引:34
作者
Cerutti, David S. [1 ]
Baker, Nathan A.
McCammon, J. Andrew
机构
[1] Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA
[2] Washington Univ, Dept Biochem & Mol Biophys, St Louis, MO 63110 USA
[3] Univ Calif San Diego, Howard Hughes Med Inst, La Jolla, CA 92093 USA
[4] Univ Calif San Diego, Dept Chem, La Jolla, CA 92093 USA
[5] Univ Calif San Diego, Dept Pharmacol, La Jolla, CA 92093 USA
基金
美国国家卫生研究院; 美国国家科学基金会;
关键词
D O I
10.1063/1.2771171
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
The solvent reaction field potential of an uncharged protein immersed in simple point charge/extended explicit solvent was computed over a series of molecular dynamics trajectories, in total 1560 ns of simulation time. A finite, positive potential of 13-24 k(b)Te(c)(-1) (where T=300 K), dependent on the geometry of the solvent-accessible surface, was observed inside the biomolecule. The primary contribution to this potential arose from a layer of positive charge density 1.0 A from the solute surface, on average 0.008 e(c)/A(3), which we found to be the product of a highly ordered first solvation shell. Significant second solvation shell effects, including additional layers of charge density and a slight decrease in the short-range solvent-solvent interaction strength, were also observed. The impact of these findings on implicit solvent models was assessed by running similar explicit solvent simulations on the fully charged protein system. When the energy due to the solvent reaction field in the uncharged system is accounted for, correlation between per-atom electrostatic energies for the explicit solvent model and a simple implicit (Poisson) calculation is 0.97, and correlation between per-atom energies for the explicit solvent model and a previously published, optimized Poisson model is 0.99. (C) 2007 American Institute of Physics.
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页数:12
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