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Compromise in competition between free energy and binding effect of intrinsically disordered protein p53 C-terminal domain
Han, Mengzhi1,2; Xu, Ji1; Ren, Ying1
2017
Source PublicationMOLECULAR SIMULATION
ISSN0892-7022
Volume43Issue:2Pages:110-120
Abstract

The C-terminal domain (CTD) of tumour suppressor p53 is an intrinsically disordered protein which has been shown to be able to bind multiple partner proteins and exercise diverse physiological functions in the cell. In this study, we performed molecular dynamics simulations on the isolated p53 CTD, as well as three regulatory binding complexes to investigate the conformational ensemble of isolated p53 CTD and its dynamic structures when different binding partner present. The results demonstrate that the isolated p53 CTD resembles a molten globule rather than extended structure. It mainly adopts random coil conformations with some tendency to form helical structures, which is consistent with experimental observations. For isolated p53 CTD, the dynamics is exclusively dominated by the intrinsic free energy and the p53 CTD could not folded spontaneously to each binding competent state which is located in high free energy region. However, when the binding partners present, the dynamics of p53 CTD are dominated by two mechanisms, the p53 CTD tending to adopt the structure with minimum free energy as isolate existed and the binding energy from partner protein tending to minimum. Each of them has an extreme tendency and corresponds to a possible characteristic state, the random coil state and each binding competent state. The compromise in competition between these two mechanisms results in alternate realisation of different characteristic states, while the relative strength of each mechanism determines the sampling frequency of each characteristic state.

KeywordTumour Suppressor P53 Multiple Mechanisms Dynamic Structures Compromise In Competition Free Energy Landscape Molecular Dynamics
SubtypeArticle
WOS HeadingsScience & Technology ; Physical Sciences
DOI10.1080/08927022.2016.1237023
Indexed BySCI
Language英语
WOS KeywordMOLECULAR-DYNAMICS METHOD ; GLYCOPROTEIN-IB-ALPHA ; PARTICLE MESH EWALD ; SECONDARY STRUCTURES ; BETA-SWITCH ; SIMULATIONS ; S100B(BETA-BETA) ; EFFICIENT ; CELL ; TRANSITION
WOS Research AreaChemistry ; Physics
WOS SubjectChemistry, Physical ; Physics, Atomic, Molecular & Chemical
Funding OrganizationNational Natural Science Foundation of China(21103195 ; Ministry of Science and Technology of China(COM2015A003) ; 91434104)
WOS IDWOS:000389435200005
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ipe.ac.cn/handle/122111/21834
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, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China
Recommended Citation
GB/T 7714
Han, Mengzhi,Xu, Ji,Ren, Ying. Compromise in competition between free energy and binding effect of intrinsically disordered protein p53 C-terminal domain[J]. MOLECULAR SIMULATION,2017,43(2):110-120.
APA Han, Mengzhi,Xu, Ji,&Ren, Ying.(2017).Compromise in competition between free energy and binding effect of intrinsically disordered protein p53 C-terminal domain.MOLECULAR SIMULATION,43(2),110-120.
MLA Han, Mengzhi,et al."Compromise in competition between free energy and binding effect of intrinsically disordered protein p53 C-terminal domain".MOLECULAR SIMULATION 43.2(2017):110-120.
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