Scrutinizing the squeezed exponential kinetics observed in the folding simulation of an off-lattice Go-like protein model
Scrutinizing the squeezed exponential kinetics observed in the folding simulation of an off-lattice Go-like protein model
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DOI：
10.1016/j.chemphys.2004.07.011
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发表时间：
2004-12-27
期刊：
影响因子：
2.3
通讯作者：
Takano, M
中科院分区：
文献类型：
--
作者：
Nakamura, HK;Sasai, M;Takano, M
我们研究了在之前蛋白质折叠晶格 Go 模型的蒙特卡罗模拟中发现的压缩指数动力学是否也可以在类离格 Go 模型的分子动力学模拟 (MD) 中观察到。结果表明，在类离格 Go 模型中确实观察到了挤压指数型折叠动力学。然后，研究了天然结构拓扑、折叠反应的初始条件、用于监测折叠反应的可观察量以及动力学数据的时间分辨率对观察到的压缩指数动力学的影响。时间分辨率效应分析表明，压缩指数动力学可以归因于折叠动力学早期的特征。这表明在侧重于折叠动力学早期阶段的实验中最有可能观察到压缩指数动力学。 (C) 2004 Elsevier B.V. 保留所有权利。
We investigated whether the squeezed exponential kinetics, which was found in the previous Monte Carlo simulation of a lattice Go model for protein folding, can be observed as well in the molecular dynamics simulation (MD) of an off-lattice Go-like model. It was shown that the squeezed-exponential-type folding kinetics is indeed observed in the off-lattice Go-like model. Then, the effects of the native structure topology, the initial condition of the folding reaction, the employed observable to monitor folding reaction, and the time resolution of the kinetics data, on the observed squeezed exponential kinetics were investigated. The analysis of the time-resolution effect showed that the squeezed exponential kinetics can be attributed to the characteristics of the early stage of folding kinetics. suggesting that the squeezed exponential kinetics is most likely to be observed in experiment which focuses on the early stage of folding kinetics. (C) 2004 Elsevier B.V. All rights reserved.