ITP OpenIR  > 理论物理所2015年知识产出
Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping
Gong, LC; Zhou, X; Ouyang, ZC; Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China.
2015
发表期刊PLOS ONE
卷号10期号:5页码:UNSP e0125932
文章类型Article
摘要Molecular dynamics (MD) simulation is an important tool for understanding bio-molecules in microscopic temporal/spatial scales. Besides the demand in improving simulation techniques to approach experimental scales, it becomes more and more crucial to develop robust methodology for precisely and objectively interpreting massive MD simulation data. In our previous work [J Phys Chem B 114, 10266 (2010)], the trajectory mapping (TM) method was presented to analyze simulation trajectories then to construct a kinetic transition network of metastable states. In this work, we further present a top-down implementation of TM to systematically detect complicate features of conformational space. We first look at longer MD trajectory pieces to get a coarse picture of transition network at larger time scale, and then we gradually cut the trajectory pieces in shorter for more details. A robust clustering algorithm is designed to more effectively identify the metastable states and transition events. We applied this TM method to detect the hierarchical structure in the conformational space of alanine-dodeca-peptide from microsecond to nanosecond time scales. The results show a downhill folding process of the peptide through multiple pathways. Even in this simple system, we found that single common-used order parameter is not sufficient either in distinguishing the metastable states or predicting the transition kinetics among these states.
学科领域Science & Technology - Other Topics
资助者National Science Foundation of China [11175250] ; National Science Foundation of China [11175250] ; Hundred of Talents Program in Chinese Academy of Sciences ; Hundred of Talents Program in Chinese Academy of Sciences ; National Science Foundation of China [11175250] ; National Science Foundation of China [11175250] ; Hundred of Talents Program in Chinese Academy of Sciences ; Hundred of Talents Program in Chinese Academy of Sciences
DOIhttp://dx.doi.org/10.1371/journal.pone.0125932
关键词[WOS]PROTEIN-FOLDING MECHANISMS ; FREE-ENERGY LANDSCAPES ; DIFFUSION MAPS ; DYNAMICS ; SIMULATIONS ; ALGORITHMS ; ENSEMBLE ; BEHAVIOR ; MODELS
收录类别SCI
语种英语
资助者National Science Foundation of China [11175250] ; National Science Foundation of China [11175250] ; Hundred of Talents Program in Chinese Academy of Sciences ; Hundred of Talents Program in Chinese Academy of Sciences ; National Science Foundation of China [11175250] ; National Science Foundation of China [11175250] ; Hundred of Talents Program in Chinese Academy of Sciences ; Hundred of Talents Program in Chinese Academy of Sciences
WOS类目Multidisciplinary Sciences
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文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/21006
专题理论物理所2015年知识产出
通讯作者Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China.
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GB/T 7714
Gong, LC,Zhou, X,Ouyang, ZC,et al. Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping[J]. PLOS ONE,2015,10(5):UNSP e0125932.
APA Gong, LC,Zhou, X,Ouyang, ZC,&Zhou, X .(2015).Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping.PLOS ONE,10(5),UNSP e0125932.
MLA Gong, LC,et al."Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping".PLOS ONE 10.5(2015):UNSP e0125932.
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