肽折叠动力学的分子交换分子动力学
Peptide Folding Kinetics from Replica Exchange Molecular Dynamics
摘要：
我们展示了如何从复制交换分子动力学（REMD）模拟中提取准确的动力学信息，如蛋白质折叠和展开的速率。从复制品交换之间的短暂和连续的轨迹段，我们估计短期传播子的构象空间，并使用它们来构建一个主方程。对于一个螺旋肽在明确的水，我们确定的过渡率既本地微观构象状态和全球性的折叠和展开。我们表明，在~1/（100 ns）到~1/（1 ns）范围内的准确率可以从REMD与交换时间为5 ps，在很好的协议与长平衡分子动力学的结果。
英文摘要：
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica exchanges, we estimate short-time propagators in conformation space and use them to construct a master equation. For a helical peptide in explicit water, we determine the rates of transitions both locally between microscopic conformational states and globally for folding and unfolding. We show that accurate rates in the ~1/(100 ns) to ~1/(1 ns) range can be obtained from REMD with exchange times of 5 ps, in excellent agreement with results from long equilibrium molecular dynamics.
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