Reaction coordinates and rates from transition paths
Reaction coordinates and rates from transition paths
复制标题
DOI：
10.1073/pnas.0408098102
复制
发表时间：
2005-05-10
影响因子：
11.1
通讯作者：
Hummer, G
中科院分区：
文献类型：
--
作者：
Best, RB;Hummer, G
溶液中反应的分子机理反映在其过渡态系综和过渡路径中。我们使用贝叶斯公式有关的平衡和过渡路径合奏，以确定过渡状态，排名反应坐标，并估计速率系数。我们还介绍了一个变分过程来优化反应坐标。该理论说明与应用程序的蛋白质折叠和偶极重定向的有序水链内的碳纳米管。为了描述一个简单的三螺旋束蛋白质模型的折叠，我们变分优化的权重投影到矩阵的本地和非本地氨基酸接触。所得的一维反应坐标捕获折叠过渡态，螺旋2和3的形成和包装构成折叠的瓶颈。
The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. We use a Bayesian formula relating the equilibrium and transition-path ensembles to identify transition states, rank reaction coordinates, and estimate rate coefficients. We also introduce a variational procedure to optimize reaction coordinates. The theory is illustrated with applications to protein folding and the dipole reorientation of an ordered water chain inside a carbon nanotube. To describe the folding of a simple model of a three-helix bundle protein, we variationally optimize the weights of a projection onto the matrix of native and nonnative amino acid contacts. The resulting one-dimensional reaction coordinate captures the folding transition state, with formation and packing of helix 2 and 3 constituting the bottleneck for folding.