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Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation
Yang, Ming-Jun2; Zhang, Xin1
关键词Signal Recognition Particle Gtpase Protein Interaction Molecular Dynamics
刊名PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
2011-06-01
DOI10.1002/prot.23000
79期:6页:1774-1785
收录类别SCI
文章类型Article
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]SIGNAL-RECOGNITION PARTICLE ; SRP GTPASES ; ENDOPLASMIC-RETICULUM ; PROTEIN TRANSLOCATION ; MESH EWALD ; NG DOMAIN ; COMPLEX ; RECEPTOR ; HYDROLYSIS ; SWITCH
英文摘要Two homologous GTPases (guanine-triphosphatases) in the signal recognition particle (SRP) and its receptor (SR) use their cumulative energy during GTP (guanine-triphosphate) hydrolysis to control the co-translational protein targeting process. Distinct from classical GTPases, which rely on external factors to hydrolyze GTP, SRP GTPases stimulate one another's activity in a self-sufficient manner upon SRP-SR complex association. Although both ground-state and putative transition-state GTP analogs have been used to recapitulate the state of GTPase activation, the underlying mechanism of the activated state still remains elusive. In particular, several residues that were placed in pending positions have been shown to be important to GTP hydrolysis in biochemical studies. Here, we examined the stability and dynamics of three interaction networks involving these residues and discovered that they contribute to the GTPase activation via well-tuned conformational changes. The crystallographically identified pending residues Ffh:R191/FtsY:R195 undergo extensive conformational rearrangements to form persisted interactions with FtsY: E284/Ffh:E274, explaining the biochemically observed defective effect of R191 mutant to the activation of both GTPases. In addition, the side chain of FtsY:R142, one of the most important catalytic residues, rotates to an extended conformation that could more efficiently maintain the electrostatic balance for GTP hydrolysis. Finally, the invariant residues Ffh: G190 and FtsY:G194, instead of the supposed auxiliary water molecules, are proposed to stabilize the nucleophilic waters during GTPase activation. In complementary to experimental observations, these findings suggest a more favorable interaction model for SRP GTPase activation and would thus benefit to our understanding of how SRP GTPases regulate the protein targeting pathway. Proteins 2011; 79:1774-1785. (C) 2011 Wiley-Liss, Inc.
语种英语
WOS记录号WOS:000290485500008
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文献类型期刊论文
条目标识符http://cas-ir.dicp.ac.cn/handle/321008/142631
专题中国科学院大连化学物理研究所
作者单位1.Scripps Res Inst, Dept Chem, La Jolla, CA 92037 USA
2.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian 116023, Peoples R China
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Yang, Ming-Jun,Zhang, Xin. Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2011,79(6):1774-1785.
APA Yang, Ming-Jun,&Zhang, Xin.(2011).Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,79(6),1774-1785.
MLA Yang, Ming-Jun,et al."Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 79.6(2011):1774-1785.
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