肽折叠的定向主成分动力学模拟。
A directed essential dynamics simulation of peptide folding.
作者信息
Chen Changjun, Xiao Yi, Zhang Linsen
机构信息
Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
出版信息
Biophys J. 2005 May;88(5):3276-85. doi: 10.1529/biophysj.104.046904. Epub 2005 Feb 24.
We present a directed essential dynamics (DED) method for peptide and protein folding. DED is a molecular dynamics method based on the essential dynamics sampling and the principal component analysis. The main idea of DED is to use principal component analysis to determine the direction of the most active collective motion of peptides at short intervals of time (20 fs) during the folding process and then add an additional force along it to adjust the folding direction. This method can make the peptides avoid being trapped in the local minima for a long time and enhance the sampling efficiency in conformational space during the simulation. An S-peptide with 15 amino acids is used to demonstrate the DED method. The results show that DED can lead the S-peptide to fold quickly into the native state, whereas traditional molecular dynamics needs more time to do this.
我们提出了一种用于肽和蛋白质折叠的定向本质动力学（DED）方法。DED是一种基于本质动力学采样和主成分分析的分子动力学方法。DED的主要思想是利用主成分分析来确定肽在折叠过程中短时间间隔（20飞秒）内最活跃的集体运动方向，然后沿该方向施加一个额外的力来调整折叠方向。这种方法可以使肽避免长时间被困在局部最小值中，并在模拟过程中提高构象空间中的采样效率。使用一个含有15个氨基酸的S肽来演示DED方法。结果表明，DED可以使S肽快速折叠成天然状态，而传统分子动力学则需要更多时间才能做到这一点。
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