Understanding how molecular motors transduce energy is central to all living systems and is a fundamentally important area in biology and physical chemistry. However, the complex problems in unraveling their working mechanism have proved extremely challenging, given their molecular size (nm, with molecular mass up to a million daltons), timescale (fs to ms), and changes in multiple interactions and dynamics during their mechanochemical cycle. For systems that have a solid-state physical nature, i.e. where the machines are mechanical, it is suggested that engineering-based computational approaches afford simplification that make them amenable to physical analysis. In this spirit, Engineering Molecular Dynamics (EMD) simulations were performed on bovine mitochondrial F1 – ATPase, nature's smallest rotary motor. The bottom residues of the γ subunit interacting with the polar loop of the c subunits of FO were rotated counterclockwise as well as clockwise. The simulations verify previous proposals that the γ subunit of ATP synthase behaves in a torsional manner, and hence the top of γ does not move smoothly but rather rotates differentially with respect to the bottom. The torsional strain patterns in the central γ-shaft/rotor on counterclockwise rotation when viewed from F1 are visualized as a function of angle and time. Upon clockwise rotation of the bottom of the γ subunit when viewed from the F1 side, uncoiling of the left-handed coiled coil of γ was observed, indicating that ATP synthesis cannot occur when γ is rotated in the clockwise sense. The results have implications for molecular mechanisms of ATP synthesis. The work also offers a coarse-grained approach for simulation of mechanochemical processes that achieves a reduction in the degrees of freedom by focusing on the dynamical mechanical response and behavior of the biological system. Some potential applications in nanotechnology-based design of intrinsically nonequilibrium protein mechanochemical devices are discussed.
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