Acta Phys. -Chim. Sin. ›› 2015, Vol. 31 ›› Issue (9): 1803-1809.doi: 10.3866/PKU.WHXB201508062

• BIOPHYSICAL CHEMISTRY • Previous Articles     Next Articles

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

Shao-Gui. WU1,2(),Xiao-Tong. GAO1,Quan. LI1,Jie. LIAO1,Cheng-Gang. XU1   

  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:2015-04-17 Published:2015-09-06
  • Supported by:
    the National Natural Science Foundation of China(11405113);Science and Technology Plan of Sichuan Province,China(2010JY0122);Science Research Fund of Sichuan Normal University, China(10MSL02)

Abstract:

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.

Key words: F1-ATPase, Hydrogen bond, Molecular dynamics, Mutation

MSC2000: 

  • O641