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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
Source PublicationJOURNAL OF MOLECULAR GRAPHICS & MODELLING
ISSN1093-3263
Volume72Pages:136-147
Abstract

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.

KeywordIntrinsically Disordered Protein Well-tempered Ensemble Replica Exchange With Solute Tempering Free Energy Surface Molecular Dynamics
SubtypeArticle
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences
DOI10.1016/j.jmgm.2016.12.014
Indexed BySCI
Language英语
WOS KeywordExchange Molecular-dynamics ; Free-energy Landscape ; Particle Mesh Ewald ; Replica-exchange ; C-terminus ; Simulations ; Peptide ; P53 ; Efficient ; Metadynamics
WOS Research AreaBiochemistry & Molecular Biology ; Computer Science ; Crystallography ; Mathematical & Computational Biology
WOS SubjectBiochemical Research Methods ; Biochemistry & Molecular Biology ; Computer Science, Interdisciplinary Applications ; Crystallography ; Mathematical & Computational Biology
Funding OrganizationNational Natural Science Foundation of China(21103195 ; Ministry of Science and Technology of China(COM2015A003) ; 91434104)
WOS IDWOS:000395841700016
Citation statistics
Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ipe.ac.cn/handle/122111/22064
Collection多相复杂系统国家重点实验室
Affiliation1.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
Recommended Citation
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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