生体分子モーターの回転駆動機構を原子レベルで解明～「歪み」と「押し出し」から成る駆動力～

2025-08-20 理化学研究所

図1 ATP合成酵素とF1-ATPaseの構造、およびサブステップ回転の模式図
(A)ATP合成酵素は、ミトコンドリア内膜(真核生物)や細胞膜(細菌)などの生体膜に存在する酵素複合体である。膜を貫通するF_o部分と、膜の外側に露出した可溶性のF₁部分から構成され、F₁がATP合成を担う。
(B)F₁-ATPaseは、それぞれ三つのαサブユニットとβサブユニットが交互に配置された六量体(α₃β₃)と、その中央に位置する回転子γサブユニットから成り、これらで回転機能の最小単位を構成する。ATPの加水分解に伴い、γサブユニットは固定子であるα₃β₃複合体に対して反時計回りに回転する。
(C)好熱菌由来のF₁-ATPaseは、γサブユニットが80度と40度のサブステップ回転で構成された120度のステップ回転を行う。80度サブステップには、ATP結合とアデノシン二リン酸(ADP)解離が関与し、40度サブステップにはATP加水分解と無機リン酸(P_i)解離が関与することが知られている。

<関連情報>

• https://www.riken.jp/press/2025/20250820_1/index.html
• https://www.pnas.org/doi/10.1073/pnas.2502642122

F1-ATPaseのγサブユニット回転における歪み–押しメカニズム The distortion–push mechanism for the γ subunit rotation in F1-ATPase

Masahiro Motohashi, Mao Oide, Chigusa Kobayashi, +2 , and Yuji Sugita
Proceedings of the National Academy of Sciences  Published:August 12, 2025
DOI:https://doi.org/10.1073/pnas.2502642122

Significance

F₁ -ATPase is a rotary molecular motor that forms part of the ATP synthase complex. The F₁ -ATPase from thermophilic Bacillus PS3 rotates in 120° steps upon ATP hydrolysis, consisting of two substeps of 80° and 40°. In this study, we analyzed the rotation mechanism of the 80° substep using all-atom molecular dynamics (MD) simulations. Transition path sampling and free energy analysis suggest that this rotation is driven by distortion of the stator and a pushing force acting into the rotor. This “distortion–push” mechanism improves our understanding of the chemo-mechanical energy conversion in F₁ -ATPase, providing detailed insight into how mechanical force is generated at the atomic level.

Abstract

F₁-ATPase comprises the stator ring consisting of α₃β₃ subunits and the rotor γ subunit. The γ 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 γ-rotation mechanisms. Using cryo-EM structures having the γ-rotation angles close to the binding dwell and catalytic dwell states, we investigate the relationships between the γ subunit rotation, conformational changes of the stator α₃β₃ subunits, and the nucleotide-binding and release. We performed targeted molecular dynamics (MD) simulations with external forces on the α₃β₃ subunits and observed 80° substep rotations of the γ 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° substep rotation. Our MD simulations suggest that 80° 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 α₃β₃ subunits, and the second rotation is induced mainly by direct β/γ 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.