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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
DOIhttp://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
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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.
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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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