Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation

doi:10.1021/acs.jctc.6b00967

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	Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation
	Shao, Qiang1 ; Shi, Jiye 2; Zhu, Weiliang1
刊名	JOURNAL OF CHEMICAL THEORY AND COMPUTATION
	2017-03
卷号	13 期号:3 页码:1229-1243
ISSN号	1549-9618
DOI	10.1021/acs.jctc.6b00967
文献子类	Article
英文摘要	Replica exchange molecular dynamics (REMD) and integrated-tempering-sampling (ITS) are two representative enhanced sampling methods which utilize parallel and integrated tempering approaches, respectively. In this work, a partitioned integrated-tempering-sampling (P-ITS) method is proposed which takes advantage of the benefits of both parallel and integrated tempering approaches. Using P-ITS, the folding pathways of a series of proteins with diverse native structures are explored on multidimensional free-energy landscapes, and the associated thermodynamics are evaluated. In comparison to the original form of ITS, P-ITS improves the sampling efficiency and measures the folding/unfolding thermodynamic quantities more consistently with experimental data. In comparison to REMD, P-ITS significantly reduces the requirement of computational resources and meanwhile achieves similar simulation results. The observed structural characterizations of transition and intermediate states of the proteins under study are in good agreement with previous experimental and simulation studies on the same proteins and homologues. Therefore, the P-ITS method has great potential in simulating the structural dynamics of complex biomolecular systems.
资助项目	National Natural Science Foundation of China[21373258] ; National Basic Research Program[2014CB910400] ; Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund[00000000]
WOS关键词	MOLECULAR-DYNAMICS SIMULATIONS ; FREE-ENERGY LANDSCAPE ; REPLICA-EXCHANGE SIMULATIONS ; HELIX BUNDLE PROTEINS ; PARTICLE MESH EWALD ; BETA-HAIRPIN ; TRP-CAGE ; EXPLICIT-SOLVENT ; GENERALIZED BORN ; CONFORMATIONAL-CHANGES
WOS研究方向	Chemistry ; Physics
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000396638800026
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/272755]
专题	药物发现与设计中心
通讯作者	Shao, Qiang; Shi, Jiye
作者单位	1.Chinese Acad Sci, Drug Discovery & Design Ctr, CAS Key Lab Receptor Res, Shanghai Inst Mat Med, 555 Zuchongzhi Rd, Shanghai 201203, Peoples R China; 2.UCB Biopharma SPRL, Chemin Foriest, B-1420 Braine Lalleud, Belgium
推荐引用方式 GB/T 7714	Shao, Qiang,Shi, Jiye,Zhu, Weiliang. Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2017,13(3):1229-1243.
APA	Shao, Qiang,Shi, Jiye,&Zhu, Weiliang.(2017).Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,13(3),1229-1243.
MLA	Shao, Qiang,et al."Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13.3(2017):1229-1243.