Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

doi:http://dx.doi.org/10.1088/0253-6102/68/1/137

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	Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation
	Song, YS; Zhou, X; Zheng, WM; Wang, YT; Wang, YT (reprint author), Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China.; Wang, YT (reprint author), Chinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China.
	2017
发表期刊	COMMUNICATIONS IN THEORETICAL PHYSICS
卷号	68 期号:1 页码:137-148
文章类型	Article
摘要	To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one alpha-helix (seqB: KVFKQYAN), two beta-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one beta-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-mu s equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics.
关键词	Protein Folding Molecular Dynamics Simulation Structure Prediction
学科领域	Physics
资助者	National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project ; National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project
DOI	http://dx.doi.org/10.1088/0253-6102/68/1/137
关键词[WOS]	BETA-HAIRPIN FORMATION ; STRUCTURE PREDICTION ; HELICAL PEPTIDES ; CASP EXPERIMENTS ; ALPHA-HELIX ; 3(10)-HELIX ; PROGRESS ; POTENTIALS ; EXCHANGE ; SEQUENCE
语种	英语
资助者	National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project ; National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Basic Research Program of China [2013CB932804] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; National Natural Science Foundation of China [11421063] ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project ; CAS Biophysics Interdisciplinary Innovation Team Project
WOS类目	Physics, Multidisciplinary
引用统计
文献类型	期刊论文
条目标识符	http://ir.itp.ac.cn/handle/311006/22024
专题	理论物理所SCI论文
通讯作者	Wang, YT (reprint author), Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China.; Wang, YT (reprint author), Chinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China.
推荐引用方式 GB/T 7714	Song, YS,Zhou, X,Zheng, WM,et al. Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation[J]. COMMUNICATIONS IN THEORETICAL PHYSICS,2017,68(1):137-148.
APA	Song, YS,Zhou, X,Zheng, WM,Wang, YT,Wang, YT ,&Wang, YT .(2017).Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation.COMMUNICATIONS IN THEORETICAL PHYSICS,68(1),137-148.
MLA	Song, YS,et al."Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation".COMMUNICATIONS IN THEORETICAL PHYSICS 68.1(2017):137-148.

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