Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method
文献类型：期刊论文
| 作者 | Han, Mengzhi1,2; Xu, Ji1; Ren, Ying1 |
| 刊名 | JOURNAL OF MOLECULAR GRAPHICS & MODELLING
 |
| 出版日期 | 2017-03-01 |
| 卷号 | 72页码:136-147 |
| 关键词 | Intrinsically disordered protein Well-tempered ensemble Replica exchange with solute tempering Free energy surface Molecular dynamics |
| ISSN号 | 1093-3263 |
| 英文摘要 | Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent. Two-methods, parallel tempering well-tempered-ensemble-(PT-WTE) and replica-exchange-with solute tempering (REST), have been proposed to alleviate the computational expense of T-REMD. In this work, we select three different IDP systems to compare the sampling characteristics and efficiencies of the two methods Both the two methods could efficiently sample the conformational space of IDP and yield highly consistent results for all the three IDPs. The efficiencies of the two methods: are compatible, with about 5-6 times better than the plain T-REMD. Besides, the advantages and disadvantages of each method are also discussed. Specially, the PT-WTE method could provide temperature dependent data of the system which could not be achieved by REST, while the REST method could readily be used to a part of the system, which is quite efficient to simulate some biological processes. (C) 2016 Elsevier Inc. All rights reserved. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences |
| 类目[WOS] | Biochemical Research Methods ; Biochemistry & Molecular Biology ; Computer Science, Interdisciplinary Applications ; Crystallography ; Mathematical & Computational Biology |
| 研究领域[WOS] | Biochemistry & Molecular Biology ; Computer Science ; Crystallography ; Mathematical & Computational Biology |
| 关键词[WOS] | EXCHANGE MOLECULAR-DYNAMICS ; FREE-ENERGY LANDSCAPE ; PARTICLE MESH EWALD ; REPLICA-EXCHANGE ; C-TERMINUS ; SIMULATIONS ; PEPTIDE ; P53 ; EFFICIENT ; METADYNAMICS |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000395841700016 |
| 源URL | [http://ir.ipe.ac.cn/handle/122111/22064]  |
| 专题 | 过程工程研究所_多相复杂系统国家重点实验室 |
| 作者单位 | 1.Chinese Acad Sci, Inst Proc Engn, State Key Lab Multiphase Complex Syst, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Han, Mengzhi,Xu, Ji,Ren, Ying. Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method[J]. JOURNAL OF MOLECULAR GRAPHICS & MODELLING,2017,72:136-147. |
| APA | Han, Mengzhi,Xu, Ji,&Ren, Ying.(2017).Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method.JOURNAL OF MOLECULAR GRAPHICS & MODELLING,72,136-147. |
| MLA | Han, Mengzhi,et al."Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method".JOURNAL OF MOLECULAR GRAPHICS & MODELLING 72(2017):136-147. |
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来源：过程工程研究所
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