F-ATPase is a membrane protein and catalyzes to synthesize ATP in the cell. It is well known that the ATPase (γ-subunit) rotates in coupling with hydrolysis of ATP. The rotating unit of ATPase for its function is α
3β
3γ subunit complex, and each of three β-subunits in the complex has the catalytic site. X-ray crystallographic study has revealed that there are three types of β-subunit conformations, ATP bound form (β
TP), ADP bound form (β
DP), and ligand free form (β
E). These three types of β-subunit conformations show different ligand (ATP and ADP) binding affinities, however, ADP binding affinities and the conformational change of them accompanying the rotation of γ-subunit have not been extensively investigated. Here, we estimated the ADP binding affinities of three types of the β-subunits by using molecular dynamics/free energy calculations. From simulations, the β
DP was the dominant β-subunit conformation to bind ADP with the highest affinity. Our free energy profile of the ATP hydrolysis by β-subunit supported thermodynamically the ATP hydrolysis model, which has been predicted from single molecule experiments. Furthermore, in our simulations, the conformational change of Phe418∼Gly426 was observed accompanying ligand change from ATP to ADP or vice versa. This result indicates that Phe418∼Gly426 are key residues to couple catalysis, conformational change and rotation of the F-ATPase.
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