Electronic continuum model for molecular dynamics simulations of biological molecules.
Electronic continuum model for molecular dynamics simulations of biological molecules.
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DOI：
10.1021/ct9005807
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发表时间：
2010
影响因子：
5.5
通讯作者：
Stuchebrukhov, A. A.
中科院分区：
文献类型：
--
作者：
Leontyev, I. V.;Stuchebrukhov, A. A.
电子极化率是影响分子间相互作用的重要因素。然而，在传统的力场，如琥珀色或CHARMM，有不一致的库仑相互作用，固有的凝聚相介质的电子介电屏蔽的效果如何处理。也就是说，筛选似乎是占通过有效电荷仅为中性部分，而带电的残基被视为，如果他们在真空中。因此，电离基团之间的静电相互作用在分子模拟中被夸大了约2倍。本文讨论的MDEC（Molecular Dynamics in Electronic Continuum）模型为修正标准不可极化力场提供了一个理论框架，使之与部分原子电荷的均匀电子屏蔽的思想相一致。目前的理论指出，电离基团和离子的电荷应该按比例缩小，即减少约0.7倍。在几个例子中，包括Na+离子之间的相互作用，这是感兴趣的离子通道模拟，和一个重要的盐新娘在细胞色素c氧化酶的动力学，我们比较了标准的非极化MD模拟与MDEC模拟，并证明MDEC电荷缩放程序的结果更准确的相互作用。包括带电部分的电子屏蔽显示，导致蛋白质动力学的显着变化，并可以产生新的定性结果相比，传统的非极化力场模拟。
Electronic polarizability is an important factor in molecular interactions. In the conventional force fields such as AMBER or CHARMM, however, there is inconsistency in how the effect of electronic dielectric screening of Coulombic interactions, inherent for the condensed phase media, is treated. Namely, the screening appears to be accounted for via effective charges only for neutral moieties, whereas the charged residues are treated as if they were in vacuum. As a result, the electrostatic interactions between ionized groups are exaggerated in molecular simulations by the factor of about 2. The discussed here MDEC (Molecular Dynamics in Electronic Continuum) model provides a theoretical framework for modification of the standard non-polarizable force fields to make them consistent with the idea of uniform electronic screening of partial atomic charges. The present theory states that the charges of ionized groups and ions should be scaled; i.e. reduced by a factor of about 0.7. In several examples, including the interaction between Na+ ions, which is of interest for ion-channel simulations, and the dynamics of an important salt-bride in Cytochrome c Oxidase, we compared the standard non-polarizable MD simulations with MDEC simulations, and demonstrated that MDEC charge scaling procedure results in more accurate interactions. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force fields simulations.
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影响因子：
3.4
作者：
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