Structural basis for efficient F_o motor rotation revealed by MCMD simulation and structural analysis

F_o domain of ATP synthase functions as a rotary molecular motor, coupling proton translocation with the rotation of the c-ring rotor. This process involves proton uptake at the entry half-channel, rotor rotation, and proton release to the exit half-channel. Although the overall coupling mechanism is established, the design principle for efficient rotation remains unclear. Here, we employed hybrid molecular simulations-combining coarse-grained modeling and Monte Carlo methods-to investigate the roles of side-chain flexibility at proton-binding residues and the angular mismatch between the proton uptake process and the proton release process. Our results indicate that both factors promote rotational activity, with side-chain flexibility playing a more significant role. Comparable analysis of F_o structures from different species revealed that the key residue geometry is conserved, and that the asymmetric geometry of the two half-channels aligns with the mechanism suggested by simulation. These findings highlight a conserved design principle that enhances rotational efficiency and offers a mechanistic basis for engineering synthetic rotary systems.