Citation: WU Shao-Gui, GAO Xiao-Tong, LI Quan, LIAO Jie, XU Cheng-Gang. F₁-ATPase Stabilizes and Positions Adenosine Triphosphate Revealed by Molecular Dynamics Simulations[J]. Acta Physico-Chimica Sinica, ;2015, 31(9): 1803-1809. doi: 10.3866/PKU.WHXB201508062 shu

F₁-ATPase Stabilizes and Positions Adenosine Triphosphate Revealed by Molecular Dynamics Simulations

1.
1 College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, P. R. China;
2 State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, P. R. China

Received Date: 17 April 2015
Available Online: 6 August 2015
Fund Project: 国家自然科学基金(11405113) (11405113) 四川省科技厅项目(2010JY0122) (2010JY0122)四川师范大学科学研究基金(10MSL02)资助 (10MSL02)

F₁-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 F₁-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 βTP subunit in F₁-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 β and γ 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 π-π 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.
- F₁-ATPase,
- Hydrogen bond,
- Molecular dynamics,
- Mutation
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沈阳化工大学材料科学与工程学院沈阳 110142

F1-ATPase Stabilizes and Positions Adenosine Triphosphate Revealed by Molecular Dynamics Simulations

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通讯作者: 陈斌, bchen63@163.com

F₁-ATPase Stabilizes and Positions Adenosine Triphosphate Revealed by Molecular Dynamics Simulations