Molecular simulation and modeling of functional dynamics in biomolecular motor
F0F1 ATP synthase is one of the most important biomolecules, synthesizing most of ATP in the cell. Especially the catalytic part, F1-ATPase, has been extensively studied by both crystallography and single-molecule experiments, revealing atomistic structures and detailed mechanochemical coupling scheme, respectively. However, connection between these two aspects are not well established: structural basis of the functional cycle has been controversial. We previously performed systematic structural analysis [1] and molecular dynamics simulations [2] to clarify the connection. We have been recently working on multiscale dynamics of this rotary motor, to understand how the ATP hydrolysis reaction drives the large-scale rotational motion. For the whole F0F1 ATP synthase, we built a simple viscoelastic model to explain symmetry mismatch between F0 and F1 motors [3].
References:
[1] Mitsuhiro Sugawa, Kei-ichi Okazaki, et al. (2016) “F1-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements” Proc. Natl. Acad. Sci. USA, 113 (21): E2916-E2924
[2] Kei-ichi Okazaki and Gerhard Hummer (2013) “Phosphate release coupled to rotary motion of F1-ATPase” Proc. Natl. Acad. Sci. USA, 110 (41): 16468-16473
[3] Kei-ichi Okazaki and Gerhard Hummer (2015) “Elasticity, friction, and pathway of γ-subunit rotation in F0F1-ATP synthase” Proc. Natl. Acad. Sci. USA, 112 (34) 10720-10725