A directed essential dynamics simulation of peptide folding

被引:24
作者
Chen, CJ
Xiao, Y [1 ]
Zhang, LS
机构
[1] Huazhong Univ Sci & Technol, Dept Phys, Biomol Phys & Modeling Grp, Wuhan 430074, Hubei, Peoples R China
[2] Chinese Acad Sci, Wuhan Inst Phys & Math, Wuhan 430071, Hubei, Peoples R China
基金
中国国家自然科学基金;
关键词
D O I
10.1529/biophysj.104.046904
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
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.
引用
收藏
页码:3276 / 3285
页数:10
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