Analytical electrostatics for biomolecules: Beyond the generalized Born approximation
Analytical electrostatics for biomolecules: Beyond the generalized Born approximation
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DOI：
10.1063/1.2177251
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发表时间：
2006-03-28
影响因子：
4.4
通讯作者：
Onufriev, A
中科院分区：
文献类型：
--
作者：
Sigalov, G;Fenley, A;Onufriev, A
溶液中大分子的建模和模拟通常受益于静电相互作用的快速分析近似。在我们之前的工作中[G.西加洛夫，J.化学。物理。 122, 094511 (2005)]，我们提出了一种基于球体线性化泊松-玻尔兹曼方程的近似解析解的方法。在当前的工作中，我们将该方法扩展到任意形状的生物分子，并提供计算有效的算法来估计模型的参数。这种方法（我们在此暂时将其称为 ALPB）针对标准数值泊松-玻尔兹曼 (NPB) 处理对一组 579 种代表性蛋白质、核酸和小肽进行了测试。这些测试是在各种溶剂/溶质电介质和生物学相关的盐浓度下进行的。在测试的溶剂和溶质参数范围内，ALPB 计算的溶剂化能的系统偏差（相对于 NPB 参考）为 0.5-3.5 kcal/mol，比在此背景下广泛使用的传统广义 Born 近似小 5-50 倍。同时，ALPB 的计算效率同样高。新模型被纳入 AMBER 分子建模包中，并在小蛋白质上进行了测试。 (c) 2006 年美国物理研究所。
The modeling and simulation of macromolecules in solution often benefits from fast analytical approximations for the electrostatic interactions. In our previous work [G. Sigalov , J. Chem. Phys. 122, 094511 (2005)], we proposed a method based on an approximate analytical solution of the linearized Poisson-Boltzmann equation for a sphere. In the current work, we extend the method to biomolecules of arbitrary shape and provide computationally efficient algorithms for estimation of the parameters of the model. This approach, which we tentatively call ALPB here, is tested against the standard numerical Poisson-Boltzmann (NPB) treatment on a set of 579 representative proteins, nucleic acids, and small peptides. The tests are performed across a wide range of solvent/solute dielectrics and at biologically relevant salt concentrations. Over the range of the solvent and solute parameters tested, the systematic deviation (from the NPB reference) of solvation energies computed by ALPB is 0.5-3.5 kcal/mol, which is 5-50 times smaller than that of the conventional generalized Born approximation widely used in this context. At the same time, ALPB is equally computationally efficient. The new model is incorporated into the AMBER molecular modeling package and tested on small proteins. (c) 2006 American Institute of Physics.