The distortion-push mechanism for the γ subunit rotation in F1-ATPase

• 成果类型: Article
• 署名作者: Motohashi, Masahiro; Oide, Mao; Kobayashi, Chigusa; Jung, Jaewoon; Muneyuki, Eiro; Sugita, Yuji
• 署名单位: Chuo University; University of Osaka; RIKEN; RIKEN
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-13111
• DOI: 10.1073/pnas.2502642122
• 发表日期: 2025-08-12
• 关键词: molecular-dynamics simulator; enhanced sampling algorithms; particle mesh ewald; atp hydrolysis; conformational-change; crystal-structure; hybrid-parallel; catalytic sites; rotary motion; f-1-atpase

摘要

F1-ATPase comprises the stator ring consisting of alpha 3 beta 3 subunits and the rotor gamma subunit. The gamma subunit rotation mechanism has been extensively investigated by biochemical analyses, structural studies, single-molecule measurements, and computational studies. Recent cryoelectron microscopy (cryo-EM) structures of F1-ATPase from the thermophilic bacterium Bacillus PS3 (TF1) provide us with further possibilities for a better understanding of the gamma-rotation mechanisms. Using cryo-EM structures having the gamma-rotation angles close to the binding dwell and catalytic dwell states, we investigate the relationships between the gamma subunit rotation, conformational changes of the stator alpha 3 beta 3 subunits, and the nucleotide-binding and release. We performed targeted molecular dynamics (MD) simulations with external forces on the alpha 3 beta 3 subunits and observed 80 degrees substep rotations of the gamma subunit. Then, we optimized the most probable transition pathway through the mean-force string method simulations with 64 images. Finally, using umbrella sampling, we calculated the potential of mean forces along the minimum free energy pathway during the 80 degrees substep rotation. Our MD simulations suggest that 80 degrees substep rotation is divided into the first rotation, resting, and the second rotation. Notably, the first rotation is driven by the distortion of the stator alpha 3 beta 3 subunits, and the second rotation is induced mainly by direct beta/gamma subunit interactions. This model, which we call the distortion-push mechanism, is consistent with the residue-level experimental analysis on F1-ATPase and the atomic structures determined by X-ray crystallography and cryo-EM.