Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor

Abstract

the f o motor in f o f 1 Atp synthase rotates its rotor driven by the proton motive force. While earlier studies elucidated basic mechanisms therein, recent advances in high-resolution cryo-electron microscopy enabled to investigate proton-transfer coupled F o rotary dynamics at structural details. Here, taking a hybrid Monte Carlo/molecular dynamics simulation method, we studied reversible dynamics of a yeast mitochondrial f o. We obtained the 36°-stepwise rotations of F o per one proton transfer in the ATP synthesis mode and the proton pumping in the ATP hydrolysis mode. In both modes, the most prominent path alternatively sampled states with two and three deprotonated glutamates in c-ring, by which the c-ring rotates one step. The free energy transduction efficiency in the model f o motor reached ~ 90% in optimal conditions. Moreover, mutations in key glutamate and a highly conserved arginine increased proton leakage and markedly decreased the coupling, in harmony with previous experiments. This study provides a simple framework of simulations for chemical-reaction coupled molecular dynamics calling for further studies in ATP synthase and others. F O F 1 ATP synthase is a ubiquitous protein complex that plays the central role in the energy generation of living cells 1,2. The enzyme complex is located at the inner membrane of mitochondria, the thylakoid membrane of chloroplast, and the bacterial membrane, working for most of ATP production in cells. Dysfunction in the ATP synthase causes severe diseases such as neuropathy, maternally inherited leigh syndrome, ataxia and retinitis pigmentosa syndrome 3-5. F O F 1 ATP synthase is composed of two regions, F O embedded in the membrane and F 1 protruded to the matrix solution (Fig. 1A); each of the regions works as a reversible rotary motor 2,6. Driven by the proton motive force, the proton flux through the F O motor from the inter membrane space (IMS) to the matrix generates a torque in the rotor. The torque is transmitted to the central rotor in F 1 where the rotary motion is used to synthesis ATP 7,8. Conversely, in vitro, and in vivo for bacteria, the F 1 motor can hydrolyze ATP to generate a torque in the inverse direction and drives F O to pump up protons. The motor function of F O arises from a complex of c-ring and a-subunit (Fig. 1B). The c-ring is made up of 8-15 c-subunits depending on the species 6,9-14. Here, we focus on yeast mitochondrial F O having 10 c-subunits in the c-ring, which we call c 10-ring 10,15. The c-subunit has a key glutamate (cE59, throughout, the residue number is for yeast F O F 1) nearly at the middle point in the membrane, which serves as the carrier of protons: A protonation in the cE59 allows c 10-ring to hold a proton, whereas it is deprotonated upon a proton release. It is experimentally confirmed that the bacterial ATP synthase activity drastically decreases when the corresponding key residue is mutated into the amino acids that cannot carry a proton 16,17. The a-subunit is considered to be a mediator between the aqueous envi...

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