Enhanced sampling and applications in protein folding in explicit solvent
Enhanced sampling and applications in protein folding in explicit solvent
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DOI：
10.1063/1.3435332
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发表时间：
2010-06-28
影响因子：
4.4
通讯作者：
Ma, Jianpeng
中科院分区：
文献类型：
--
作者：
Zhang, Cheng;Ma, Jianpeng
我们报告了一种模拟大型复杂系统的单副本回火方法。在广义系综中，该方法利用一种新的积分单位计算的热平均能量的运行时估计来指导连续的温度-空间随机漫步。我们首先在二维Ising模型和Lennard-Jones液体系统中验证了该方法。然后将其应用于三种小蛋白，trpzip2， trp-cage和绒毛头在显式溶剂中的折叠。在近似于1微秒的0.5秒内，所有三种体系都可逆地折叠成原子精度：对于trpzip2、trp-cage和villin headpiece，最佳折叠构象的α碳均方根偏差分别为0.2、0.4和0.4埃。(C) 2010年美国物理研究所。(doi: 10.1063/1.3435332)
We report a single-copy tempering method for simulating large complex systems. In a generalized ensemble, the method uses runtime estimate of the thermal average energy computed from a novel integral identity to guide a continuous temperature-space random walk. We first validated the method in a two-dimensional Ising model and a Lennard-Jones liquid system. It was then applied to folding of three small proteins, trpzip2, trp-cage, and villin headpiece in explicit solvent. Within 0.5 similar to 1 microsecond, all three systems were reversibly folded into atomic accuracy: the alpha carbon root mean square deviations of the best folded conformations from the native states were 0.2, 0.4, and 0.4 angstrom, for trpzip2, trp-cage, and villin headpiece, respectively. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3435332]