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bioRxiv · 10.1101/2025.06.28.662110

Structural Basis for Efficient Fo Motor Rotation Revealed by MCMD simulation and Structural Analysis

Kubo, S.·Noji, H.
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Abstract

Fo 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. While 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 Fo 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 offer a mechanistic basis for engineering synthetic rotary systems. Significance StatementFo motor is the proton-conducting unit of ATP synthase and a rotary molecular motor driven by proton translocation across the membrane. Previous biochemical and structural studies have established the "half-channel model," which explains how proton translocation is coupled with rotation. However, it remains unclear what structural features of Fo enable the smooth coordination of proton flow and rotation for kinetically efficient motion. In this study, we conducted a hybrid molecular simulation combining coarse-grained model calculations with Monte Carlo simulations. The present study found that the conformational flexibility of side chains in amino acid residues involved in proton translocation is one of the critical factors for kinetically efficient rotation. Furthermore, it is also found that the fundamental structural features are conserved across different species, suggesting that the principal mechanism and the design principles of Fo motor are well conserved across species.

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Kubo, S., Noji, H.. 2025-07-02. Structural Basis for Efficient Fo Motor Rotation Revealed by MCMD simulation and Structural Analysis. https://doi.org/10.1101/2025.06.28.662110

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