COMPUTATION OF ELECTROSTATIC FORCES ON SOLVATED MOLECULES USING THE POISSON-BOLTZMANN EQUATION
COMPUTATION OF ELECTROSTATIC FORCES ON SOLVATED MOLECULES USING THE POISSON-BOLTZMANN EQUATION
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DOI：
10.1021/j100116a025
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发表时间：
1993-04-08
影响因子：
--
通讯作者：
MCCAMMON, JA
中科院分区：
文献类型：
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作者：
GILSON, MK;DAVIS, ME;MCCAMMON, JA
泊松-玻尔兹曼方程(PBE)的数值解在包括生物大分子在内的水合分子的静电能计算中得到了广泛的应用。然而，事实证明，求解静电力的PBE更加困难，这主要是因为计算高介电水溶液在溶质表面施加的压力是一项挑战。本文介绍了一种精确计算这些力的方法。首先，我们给出了一个由PBE管理的系统中作用力的新的推导。由此得到的表达式包含三个不同的项：电场对固定的原子电荷的影响；介电边界压，它解释了高介电性溶剂在电场存在的任何地方取代低介电溶质的趋势；以及离子边界压，它解释了溶解的电解液向非零静电势区域移动的趋势。然后描述了从溶剂化分子的PBE的有限差分解中提取这三种力贡献的技术。通过与解析结果和数值结果的对比试验，证明了该方法的准确性。最后，分析了作用于磷酸丙糖异构酶盐桥上两个成员的静电力。研究发现，介质边界压力对原子力有很大的贡献。事实上，它们的忽视导致了系统上显著的净静电力的非物理情况。相反，在生理离子强度下，离子边界力通常非常弱。
Numerical solutions of the Poisson-Boltzmann equation (PBE) have found wide application in the computation of electrostatic energies of hydrated molecules, including biological macromolecules. However, solving the PBE for electrostatic forces has proved more difficult, largely because of the challenge of computing the pressures exerted by a high dielectric aqueous solvent on the solute surface. This paper describes an accurate method for computing these forces. We begin by presenting a novel derivation of the forces acting in a system governed by the PBE. The resulting expression contains three distinct terms: the effect of electric fields on 'fixed'' atomic charges; the dielectric boundary pressure, which accounts for the tendency of the high dielectric solvent to displace the low dielectric solute wherever an electric field exists; and the ionic boundary pressure, which accounts for the tendency of the dissolved electrolyte to move into regions of nonzero electrostatic potential. Techniques for extracting each of these three force contributions from finite difference solutions of the PBE for a solvated molecule are then described. Tests of the methods against both analytic and numeric results demonstrate their accuracy. Finally, the electrostatic forces acting on the two members of a salt bridge in the enzyme triosephosphate isomerase are analyzed. The dielectric boundary pressures are found to make substantial contributions to the atomic forces. In fact, their neglect leads to the unphysical situation of a significant net electrostatic force on the system. In contrast, the ionic boundary forces are usually extremely weak at physiologic ionic strength.