Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping
文献类型：期刊论文
| 作者 | Gong, LC; Zhou, X; Ouyang, ZC
|
| 刊名 | PLOS ONE
 |
| 出版日期 | 2015 |
| 卷号 | 10期号:5页码:UNSP e0125932 |
| 通讯作者 | Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China. |
| 英文摘要 | 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. |
| 学科主题 | Science & Technology - Other Topics |
| 类目[WOS] | Multidisciplinary Sciences |
| 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 |
| 源URL | [http://ir.itp.ac.cn/handle/311006/21006]  |
| 专题 | 理论物理研究所_理论物理所1978-2010年知识产出 |
| 推荐引用方式 GB/T 7714 | Gong, LC,Zhou, X,Ouyang, ZC. 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.(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. |
入库方式： OAI收割
来源：理论物理研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。