F-1-ATPase Stabilizes and Positions Adenosine Triphosphate Revealed by Molecular Dynamics Simulations

doi:http://dx.doi.org/10.3866/PKU.WHXB201508062

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	F-1-ATPase Stabilizes and Positions Adenosine Triphosphate Revealed by Molecular Dynamics Simulations
	Wu, SG; Gao, XT; Li, Q; Liao, J; Xu, CG; Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610068, Peoples R China.
	2015
发表期刊	ACTA PHYSICO-CHIMICA SINICA
卷号	31 期号:9 页码:1803-1809
文章类型	Article
摘要	F-1-ATPase makes extensive interactions with ATP through forming a network of interactions around ATP. These interactions create a steady environment for ATP synthesis/hydrolysis. Thus understanding these interactions between ATP and F-1-ATPase is essential for understanding ATP synthesis/hydrolysis mechanism. We performed all-atom molecular dynamics (MD) simulations to elucidate these interactions and attempted to identify key residues which play important roles in stabilizing and positioning ATP. By examining the non-bonded energies between ATP and residues of beta(TP) subunit in F-1-ATPase, it is found that residues 158-164, R189, Y345 have significant interactions with ATP. The loop segment (residues 158-164) and R189 surround ATP by a half and they interact with beta and gamma phosphates through forming a network of hydrogen bonds to constraint the motion of ATP triphosphate. The interaction network seals off the conformation of the catalytic site, creating a steady environment for ATP synthesis/hydrolysis. Additionally, ATP base is positioned by the pi-pi stacking interaction from Y345. However, ATP base can slide and move paralleling to the aromatic group of Y345. It is deduced that this motion may facilitate ATP hydrolysis.
关键词	F-1-atpase Hydrogen Bond Molecular Dynamics Mutation
学科领域	Chemistry
资助者	National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02]
DOI	http://dx.doi.org/10.3866/PKU.WHXB201508062
关键词[WOS]	BOVINE HEART-MITOCHONDRIA ; PARTICLE MESH EWALD ; FOF1-ATP SYNTHASE ; F0F1-ATP SYNTHASE ; ATP SYNTHASE ; FORCE-FIELD ; MECHANISM ; ROTATION ; SUBUNIT ; PHOSPHORYLATION
收录类别	SCI
语种	中文
资助者	National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02]
WOS类目	Chemistry, Physical
引用统计
文献类型	期刊论文
条目标识符	http://ir.itp.ac.cn/handle/311006/20880
专题	理论物理所SCI论文
通讯作者	Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610068, Peoples R China.
推荐引用方式 GB/T 7714	Wu, SG,Gao, XT,Li, Q,et al. F-1-ATPase Stabilizes and Positions Adenosine Triphosphate Revealed by Molecular Dynamics Simulations[J]. ACTA PHYSICO-CHIMICA SINICA,2015,31(9):1803-1809.
APA	Wu, SG,Gao, XT,Li, Q,Liao, J,Xu, CG,&Wu, SG .(2015).F-1-ATPase Stabilizes and Positions Adenosine Triphosphate Revealed by Molecular Dynamics Simulations.ACTA PHYSICO-CHIMICA SINICA,31(9),1803-1809.
MLA	Wu, SG,et al."F-1-ATPase Stabilizes and Positions Adenosine Triphosphate Revealed by Molecular Dynamics Simulations".ACTA PHYSICO-CHIMICA SINICA 31.9(2015):1803-1809.

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