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Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method
Han, Mengzhi1,2; Xu, Ji1; Ren, Ying1
2017-03-01
发表期刊JOURNAL OF MOLECULAR GRAPHICS & MODELLING
ISSN1093-3263
卷号72页码:136-147
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.
关键词Intrinsically Disordered Protein Well-tempered Ensemble Replica Exchange With Solute Tempering Free Energy Surface Molecular Dynamics
文章类型Article
WOS标题词Science & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences
DOI10.1016/j.jmgm.2016.12.014
收录类别SCI
语种英语
关键词[WOS]EXCHANGE MOLECULAR-DYNAMICS ; FREE-ENERGY LANDSCAPE ; PARTICLE MESH EWALD ; REPLICA-EXCHANGE ; C-TERMINUS ; SIMULATIONS ; PEPTIDE ; P53 ; EFFICIENT ; METADYNAMICS
WOS研究方向Biochemistry & Molecular Biology ; Computer Science ; Crystallography ; Mathematical & Computational Biology
WOS类目Biochemical Research Methods ; Biochemistry & Molecular Biology ; Computer Science, Interdisciplinary Applications ; Crystallography ; Mathematical & Computational Biology
项目资助者National Natural Science Foundation of China(21103195 ; Ministry of Science and Technology of China(COM2015A003) ; 91434104)
WOS记录号WOS:000395841700016
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被引频次:2[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.ipe.ac.cn/handle/122111/22064
专题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
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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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