Long-time protein folding dynamics from short-time molecular dynamics simulations
Long-time protein folding dynamics from short-time molecular dynamics simulations
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DOI：
10.1137/06065146x
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发表时间：
2006-01-01
影响因子：
1.6
通讯作者：
Dill, Ken A.
中科院分区：
文献类型：
--
作者：
Chodera, John D.;Swope, William C.;Dill, Ken A.
蛋白质折叠涉及物理时间尺度-微秒到几秒-太长了，无法直接用直接的分子动力学模拟来研究，其中基本的时间步长被限制在飞秒。在这里，我们展示了一个简单的溶剂化生物分子系统的长时间统计动力学如何通过一个离散状态的马尔可夫链模型来很好地描述，该模型由比系统的最长驰豫时间短一个数量级的轨道构造而成。这表明，从短分子动力学模拟中适当构建的这些模型在研究长时间构象动力学中可能是有用的。
Protein folding involves physical timescales - microseconds to seconds - that are too long to be studied directly by straightforward molecular dynamics simulation, where the fundamental timestep is constrained to femtoseconds. Here we show how the long-time statistical dynamics of a simple solvated biomolecular system can be well described by a discrete-state Markov chain model constructed from trajectories that are an order of magnitude shorter than the longest relaxation times of the system. This suggests that such models, appropriately constructed from short molecular dynamics simulations, may have utility in the study of long-time conformational dynamics.