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Simulations of flow induced structural transition of the beta-switch region of glycoprotein Ib alpha
Han, Mengzhi1,2; Xu, Ji1; Ren, Ying1; Li, Jinghai1
2016-02-01
发表期刊BIOPHYSICAL CHEMISTRY
ISSN0301-4622
卷号209期号:FEB页码:9-20
摘要Binding of glycoprotein Ib alpha to von Willebrand factor induces platelet adhesion to injured vessel walls and initiates a multistep hemostatic process. It has been hypothesized that the flow condition could induce a loop to beta-sheet conformational change in the beta-switch region of glycoprotein Ib alpha, which regulates it binding to the von Willebrand factor and facilitates the blood clot formation and wound healing. In this work, direct molecular dynamics (MD), flow MD and metadynamics, were employed to investigate the mechanisms of this flow induced conformational transition process. Specifically, the free energy landscape of the whole transition process was drawn by metadynamics with the path collective variable approach. The results reveal that without flow, the free energy landscape has two main basins, including a random loop basin stabilized by large conformational entropy and a partially folded beta-sheet basin. The free energy barrier separating these two basins is relatively high and the beta-switch could not fold from loop to beta-sheet state spontaneously. The fully beta-sheet conformations located in high free energy regions, which are also unstable and gradually unfold into partially folded beta-sheet state with flow. Relatively weak flow could trigger some folding of the beta-switch but could not fold it into fully beta-sheet state. Under strong flow conditions, the beta-switch could readily overcome the high free energy barrier and fold into fully beta-sheet state. (C) 201 5 Elsevier B.V. All rights reserved.
关键词Glycoprotein Ib Alpha Protein Conformational Transition Metadynamics Free Energy Landscape Molecular Dynamics
文章类型Article
WOS标题词Science & Technology ; Life Sciences & Biomedicine ; Physical Sciences
DOI10.1016/j.bpc.2015.11.002
收录类别SCI
语种英语
关键词[WOS]VON-WILLEBRAND-FACTOR ; MOLECULAR-DYNAMICS SIMULATIONS ; LINEAR CONSTRAINT SOLVER ; FREE-ENERGY LANDSCAPES ; INTRINSIC DISORDER ; TETHER BOND ; A1 DOMAIN ; HAIRPIN ; COMPLEX ; DISEASE
WOS研究方向Biochemistry & Molecular Biology ; Biophysics ; Chemistry
WOS类目Biochemistry & Molecular Biology ; Biophysics ; Chemistry, Physical
项目资助者National Natural Science Foundation of China(21103195 ; 91434104)
WOS记录号WOS:000369462700002
引用统计
文献类型期刊论文
条目标识符http://ir.ipe.ac.cn/handle/122111/20611
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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GB/T 7714
Han, Mengzhi,Xu, Ji,Ren, Ying,et al. Simulations of flow induced structural transition of the beta-switch region of glycoprotein Ib alpha[J]. BIOPHYSICAL CHEMISTRY,2016,209(FEB):9-20.
APA Han, Mengzhi,Xu, Ji,Ren, Ying,&Li, Jinghai.(2016).Simulations of flow induced structural transition of the beta-switch region of glycoprotein Ib alpha.BIOPHYSICAL CHEMISTRY,209(FEB),9-20.
MLA Han, Mengzhi,et al."Simulations of flow induced structural transition of the beta-switch region of glycoprotein Ib alpha".BIOPHYSICAL CHEMISTRY 209.FEB(2016):9-20.
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