Estimation of Ligand Binding Free Energies of F-ATPase by Using Molecular Dynamics/Free Energy Calculation

Atsushi SUENAGAa*, Osamu UMEZUb, Tadashi ANDOb, Ichiro YAMATOb, Takeshi MURATAc and Makoto TAIJIa

aHigh-performance Molecular Simulation Team, RIKEN Advanced Science Institute
61-1 Ono, Tsurumi, Yokohama, Kanagawa 230-0046, Japan
bDepartment of Biological Science and Technology, Tokyo University of Science
2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
cGraduate School of Medicine and Faculty of Medicine, University of Kyoto
Konoe-cho Yoshida, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan

(Received: May 20, 2008; Accepted for publication: August 18, 2008)

F-ATPase is a membrane protein and catalyzes to synthesize ATP in the cell. It is well known that the ATPase (g-subunit) rotates in coupling with hydrolysis of ATP. The rotating unit of ATPase for its function is a3b3g subunit complex, and each of three b-subunits in the complex has the catalytic site. X-ray crystallographic study has revealed that there are three types of b-subunit conformations, ATP bound form (bTP), ADP bound form (bDP), and ligand free form (bE). These three types of b-subunit conformations show different ligand (ATP and ADP) binding affinities, however, ADP binding affinities and the conformational change of them accompanying the rotation of g-subunit have not been extensively investigated. Here, we estimated the ADP binding affinities of three types of the b-subunits by using molecular dynamics/free energy calculations. From simulations, the bDP was the dominant b-subunit conformation to bind ADP with the highest affinity. Our free energy profile of the ATP hydrolysis by b-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.

Keywords: F-ATPase, Molecular dynamics, Free energy calculation, Molecular motor

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