Role of Electrostatics in the Structure, Energy, and Dynamics of Biomolecules: A Model Study of N-Methylalanylacetamide
Role of Electrostatics in the Structure, Energy, and Dynamics of Biomolecules: A Model Study of N-Methylalanylacetamide
复制标题
静电在生物分子结构、能量和动力学中的作用：N-甲基丙氨酰乙酰胺的模型研究
DOI：
10.1021/ja00291a014
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发表时间：
1985
影响因子：
15
通讯作者：
M. Karplus
中科院分区：
文献类型：
--
作者：
B. Pettitt;M. Karplus
静电相互作用的丙氨酸二肽的结构，能量和动力学性质的范围contributionof静电相互作用进行检查。采用经验能量函数来表示二肽，并且部分原子电荷从零变化到用于氨基酸和蛋白质的标准模型中的值。它表明，虽然有很大的差异，具有不同的电荷的模型的绝对能量，各种二肽构象的相对能量是不太敏感的电荷。构象的最小能量结构仅弱依赖于电荷。一个正常的模式分析表明，只有少数模式是敏感的收费和热力学量，代表的总和模式，基本上是相同的所有themodels。谐波动力学的结果与那些从合奏的分子动力学轨迹的比较表明，静电的潜在表面的贡献引入非谐波效应。
The contributionof electrostatic interactions to a range of structural, energetic, and dynamic properties of the alanine dipeptide is examined. An empirical energy function is employed to represent the dipeptide, and the partial atomic charges are varied from zero to values used in standard models for aminoacids and proteins. It is demonstrated that, although there are large differences in the absolute energy of models with different charges, the relative energies of the various dipeptide conformers are less sensitive to the charges. The minimum energy structures of the conformers are only weakly dependent on the charges. A normal mode analysis shows that only a few modes are sensitive to the charges and that thermodynamic quantities, which represent sums over the modes, are essentially the same for all themodels. Comparison of the harmonic dynamics results with those from an ensemble of molecular dynamics trajectories reveals that the electrostatic contributions to the potential surface introduce anharmonic effects.