Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water
Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water
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DOI：
10.1063/1.2001648
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发表时间：
2005-09-15
影响因子：
4.4
通讯作者：
Pande, VS
中科院分区：
文献类型：
--
作者：
Elmer, SP;Park, S;Pande, VS
在这篇文章中，我们分析了聚苯乙炔(PPA)12-聚体在显性溶剂中的全原子模型在四种常见的有机和水溶剂中的折叠动力学。溶剂质量对PPA 12-MERS折叠的时间尺度有很大影响。乙腈具有理想的折叠条件，根据温度的不同，最佳折叠时间约为100-200 ns。相反，由于极端的溶剂化条件，氯仿和水阻碍了PPA 12-聚体的折叠；氯仿使低聚物变性，而水促进聚集和陷阱。PPA 12-聚体在纯甲醇溶液中的折叠时间在300K时类似于400 ns，而在1：1v/v四氢呋喃/甲醇溶液中测量的实验12-聚体折叠时间类似于160 ns。作为得出上述结论的必要条件，基于马尔可夫状态模型的分析技术被应用于多个短的独立轨迹，以外推12-聚体在每个相应溶剂中的长时间尺度动力学。我们回顾了马尔可夫链的理论，并推导出一种对由模拟数据计算的转移概率矩阵施加详细平衡的方法。(C)2005年美国物理研究所。
In this article, we analyze the folding dynamics of an all-atom model of a polyphenylacetylene (pPA) 12-mer in explicit solvent for four common organic and aqueous solvents: acetonitrile, chloroform, methanol, and water. The solvent quality has a dramatic effect on the time scales in which pPA 12-mers fold. Acetonitrile was found to manifest ideal folding conditions as suggested by optimal folding times on the order of similar to 100-200 ns, depending on temperature. In contrast, chloroform and water were observed to hinder the folding of the pPA 12-mer due to extreme solvation conditions relative to acetonitrile; chloroform denatures the oligomer, whereas water promotes aggregation and traps. The pPA 12-mer in a pure methanol solution folded in similar to 400 ns at 300 K, compared relative to the experimental 12-mer folding time of similar to 160 ns measured in a 1:1 v/v THF/methanol solution. Requisite in drawing the aforementioned conclusions, analysis techniques based on Markov state models are applied to multiple short independent trajectories to extrapolate the long-time scale dynamics of the 12-mer in each respective solvent. We review the theory of Markov chains and derive a method to impose detailed balance on a transition-probability matrix computed from simulation data. (c) 2005 American Institute of Physics.