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	Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations
	Lei, Hongxing1,2,3; Wang, Zhi-Xiang1,2,4; Wu, Chun1,2; Duan, Yong1,2
刊名	Journal of chemical physics
	2009-10-28
卷号	131期号:16页码:7
ISSN号	0021-9606
DOI	10.1063/1.3238567
通讯作者	Duan, yong(duan@ucdavis.edu)
英文摘要	Successful ab initio folding of proteins with both alpha-helix and beta-sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any alpha/beta proteins to within experimental error has yet to be reported. here we demonstrate that it is an achievable goal to fold alpha/beta proteins with a force field emphasizing the balance between the two major secondary structures. using our newly developed force field, we conducted extensive ab initio folding simulations on an alpha/beta protein full sequence design (fsd) employing both conventional molecular dynamics and replica exchange molecular dynamics in combination with a generalized-born solvation model. in these simulations, the folding of fsd to the native state with high population (>64.2%) and high fidelity (c(alpha)-root mean square deviation of 1.29 angstrom for the most sampled conformation when compared to the experimental structure) was achieved. the folding of fsd was found to follow two pathways. in the major pathway, the folding started from the formation of the helix. in the minor pathway, however, folding of the beta-hairpin started first. further examination revealed that the helix initiated from the c-terminus and propagated toward the n-terminus. the formation of the hydrophobic contacts coincided with the global folding. therefore the hydrophobic force does not appear to be the driving force of the folding of this protein. (c) 2009 american institute of physics. [doi:10.1063/1.3238567]
WOS关键词	MOLECULAR-DYNAMICS SIMULATIONS ; VILLIN HEADPIECE SUBDOMAIN ; DIFFUSION-COLLISION MODEL ; SEQUENCE DESIGN PROTEIN ; FREE-ENERGY LANDSCAPE ; FORCE-FIELD ; BETA-HAIRPIN ; TRP-CAGE ; NUCLEIC-ACIDS ; BACKBONE
WOS研究方向	Physics
WOS类目	Physics, Atomic, Molecular & Chemical
语种	英语
出版者	AMER INST PHYSICS
WOS记录号	WOS:000271358400068
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2401814
专题	中国科学院大学
通讯作者	Duan, Yong
作者单位	1.Dept Appl Sci, Davis, CA 95616 USA 2.UC Davis Genome Ctr, Davis, CA 95616 USA 3.Chinese Acad Sci, Beijing Inst Genom, Beijing 100029, Peoples R China 4.Chinese Acad Sci, Grad Sch, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Lei, Hongxing,Wang, Zhi-Xiang,Wu, Chun,et al. Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations[J]. Journal of chemical physics,2009,131(16):7.
APA	Lei, Hongxing,Wang, Zhi-Xiang,Wu, Chun,&Duan, Yong.(2009).Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations.Journal of chemical physics,131(16),7.
MLA	Lei, Hongxing,et al."Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations".Journal of chemical physics 131.16(2009):7.

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