The Missing Link between Thermodynamics and Structure in F1-ATPase

• Published in: Proceedings of the National Academy of Sciences - PNAS 2003-02, Vol.100 (3), p.874-879
• Main Authors: Yang, W., Gao, Y. Q., Cui, Q., Ma, J., Karplus, M.
• Format: Article
• Language: English
• Subjects: Adenosine Diphosphate - metabolism; Adenosine Triphosphate - metabolism; Animals; Atoms; Binding Sites; Biochemistry; Biological Sciences; Cattle; Crystal structure; Enzymes; Free energy; Hydrolysis; Ligands; Magnesium - metabolism; Mitochondria - enzymology; Models, Chemical; Models, Molecular; Neurotransmitters; Oxygen; Physical Sciences; Protein Binding; Protein Conformation; Proton-Translocating ATPases - chemistry; Reactants; Thermodynamics; Time Factors
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0337432100

F1F o-ATP synthase is the enzyme responsible for most of the ATP synthesis in living systems. The catalytic domain F1of the F1F ocomplex, F1-ATPase, has the ability to hydrolyze ATP. A fundamental problem in the development of a detailed mechanism for this enzyme is that it has not been possible to determine experimentally the relation between the ligand binding affinities measured in solution and the different conformations of the catalytic β subunits $(\beta_{TP},\>\beta_{DP},\>\beta_E)$ observed in the crystal structures of the mitochondrial enzyme, MF1. Using free energy difference simulations for the hydrolysis reaction ATP+H2O→ ADP+Piin the βTPand βDPsites and unisite hydrolysis data, we are able to identify βTPas the "tight" $(K_D = 10^{-12}\>M, \>MF_1)$ binding site for ATP and βDPas the "loose" site. An energy decomposition analysis demonstrates how certain residues, some of which have been shown to be important in catalysis, modulate the free energy of the hydrolysis reaction in the βTPand βDPsites, even though their structures are very similar. Combined with the recently published simulations of the rotation cycle of F1-ATPase, the present results make possible a consistent description of the binding change mechanism of F1-ATPase at an atomic level of detail.