Multiscale simulations of protein folding: application to formation of secondary structures
文献类型：期刊论文
| 作者 | Xu, Ji1,2; Ren, Ying1; Li, Jinghai1 |
| 刊名 | JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
 |
| 出版日期 | 2013-07-01 |
| 卷号 | 31期号:7页码:779-787 |
| 关键词 | protein folding stability multiscale compromise mesoscale genetic algorithm molecular dynamics simulation |
| ISSN号 | 0739-1102 |
| 英文摘要 | A multiscale simulation method of protein folding is proposed, using atomic representation of protein and solvent, combing genetic algorithms to determine the key protein structures from a global view, with molecular dynamic simulations to reveal the local folding pathways, thus providing an integrated landscape of protein folding. The method is found to be superior to previously investigated global search algorithms or dynamic simulations alone. For secondary structure formation of a selected peptide, RN24, the structures and dynamics produced by this method agree well with corresponding experimental results. Three most populated conformations are observed, including hairpin, -sheet and -helix. The energetic barriers separating these three structures are comparable to the kinetic energy of the atoms of the peptide, implying that the transition between these states can be easily triggered by kinetic perturbations, mainly through electrostatic interactions between charged atoms. Transitions between -helix and -sheet should jump over at least two energy barriers and may stay in the energetic trap of hairpin. It is proposed that the structure of proteins should be jointly governed by thermodynamic and dynamic factors; free energy is not the exclusive dominant for stability of proteins. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 类目[WOS] | Biochemistry & Molecular Biology ; Biophysics |
| 研究领域[WOS] | Biochemistry & Molecular Biology ; Biophysics |
| 关键词[WOS] | MOLECULAR-DYNAMICS SIMULATIONS ; LINEAR CONSTRAINT SOLVER ; ARTIFICIAL PERIODICITY ; GENETIC ALGORITHM ; COMPLEX-SYSTEMS ; PEPTIDES ; TIME ; RIBONUCLEASE ; LINCS ; FLOW |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000320981700009 |
| 公开日期 | 2015-05-27 |
| 源URL | [http://ir.ipe.ac.cn/handle/122111/13324]  |
| 专题 | 过程工程研究所_研究所（批量导入） |
| 作者单位 | 1.Chinese Acad Sci, Inst Proc Engn, State Key Lab Multiphase Complex Syst, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China |
| 推荐引用方式 GB/T 7714 | Xu, Ji,Ren, Ying,Li, Jinghai. Multiscale simulations of protein folding: application to formation of secondary structures[J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS,2013,31(7):779-787. |
| APA | Xu, Ji,Ren, Ying,&Li, Jinghai.(2013).Multiscale simulations of protein folding: application to formation of secondary structures.JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS,31(7),779-787. |
| MLA | Xu, Ji,et al."Multiscale simulations of protein folding: application to formation of secondary structures".JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 31.7(2013):779-787. |
入库方式： OAI收割
来源：过程工程研究所
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