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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.
Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation
Source PublicationCOMMUNICATIONS IN THEORETICAL PHYSICS
Language英语
KeywordProtein Folding Molecular Dynamics Simulation Structure Prediction
AbstractTo 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.
2017
Volume68Issue:1Pages:137-148
Subject AreaPhysics
DOIhttp://dx.doi.org/10.1088/0253-6102/68/1/137
Funding OrganizationNational 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
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Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/22024
Collection理论物理所科研产出_SCI论文
Corresponding AuthorWang, 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.
Recommended Citation
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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