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	Efficient and reproducible folding simulations of the Trp-cage protein with multiscale molecular dynamics
	Xia XueFeng ; Zhang Song ; Huang Bo ; Zhou Yun ; Sun ZhiRong
	2010-05-11 ; 2010-05-11
关键词	protein folding multiscale Trp-cage molecular dynamics structure prediction FREE-ENERGY LANDSCAPE NMR RESOLUTION FORCE-FIELD MODEL MECHANICS PEPTIDES KINETICS WATER Multidisciplinary Sciences
中文摘要	Folding simulations are often time-consuming or highly sensitive to the initial conformation of the simulation even for mini protein like the Trp-cage. Here, we present a multiscale molecular dynamics method which appears to be both efficient and insensitive to the starting conformation based on the testing results from the Trp-cage protein. In this method the simulated system is simultaneously modeled on atoms and coarse-grained particles with incremental coarsening levels. The dynamics of coarse-grained particles are adapted to the recent trajectories of finer-grained particles instead of fixed and parameterized energy functions as used in previous coarse-grained models. In addition, the compositions of coarse-grained particles are allowed to be updated automatically based on the coherence during its history. Starting from the fully extended conformation and other several different conformations of the Trp-cage protein, our method successfully finds out the native-like conformations of the Trp-cage protein in the largest cluster of the trajectories in all of the eight performed simulations within at most 10 ns simulation time. The results show that approaches based on multiscale modeling are promising for ab initio protein structure prediction.
语种	英语 ; 英语
出版者	SCIENCE CHINA PRESS ; BEIJING ; 16 DONGHUANGCHENGGEN NORTH ST, BEIJING 100717, PEOPLES R CHINA
内容类型	期刊论文
源URL	[http://hdl.handle.net/123456789/26986]
专题	清华大学
推荐引用方式 GB/T 7714	Xia XueFeng,Zhang Song,Huang Bo,et al. Efficient and reproducible folding simulations of the Trp-cage protein with multiscale molecular dynamics[J],2010, 2010.
APA	Xia XueFeng,Zhang Song,Huang Bo,Zhou Yun,&Sun ZhiRong.(2010).Efficient and reproducible folding simulations of the Trp-cage protein with multiscale molecular dynamics..
MLA	Xia XueFeng,et al."Efficient and reproducible folding simulations of the Trp-cage protein with multiscale molecular dynamics".(2010).

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