中国物理B ›› 2026, Vol. 35 ›› Issue (2): 28702-028702.doi: 10.1088/1674-1056/ae2674

• • 上一篇    

Simulation on mechanochemical coupling of rotary biomotors F1 and V1

Liqiang Dai(戴立强)1, Yao-Gen Shu(舒咬根)1,†, and Zhong-Can Ouyang(欧阳钟灿)2,‡   

  1. 1 Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China;
    2 Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
  • 收稿日期:2025-10-01 修回日期:2025-11-17 接受日期:2025-12-02 发布日期:2026-01-21
  • 通讯作者: Yao-Gen Shu, Zhong-Can Ouyang E-mail:shuyaogen@ucas.ac.cn;oy@itp.ac.cn
  • 基金资助:
    This work was supported by the National Natural Science Foundation of China (Grant Nos. 22193032 and 32401033) and the Research Fund of Wenzhou Institute, Chinese Academy of Sciences (Grant Nos. WIUCASQD2020009, WIUCASQD2023005, XSZD2024004, 2021HZSY0061, and WIUCASICTP2022).

Simulation on mechanochemical coupling of rotary biomotors F1 and V1

Liqiang Dai(戴立强)1, Yao-Gen Shu(舒咬根)1,†, and Zhong-Can Ouyang(欧阳钟灿)2,‡   

  1. 1 Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China;
    2 Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
  • Received:2025-10-01 Revised:2025-11-17 Accepted:2025-12-02 Published:2026-01-21
  • Contact: Yao-Gen Shu, Zhong-Can Ouyang E-mail:shuyaogen@ucas.ac.cn;oy@itp.ac.cn
  • Supported by:
    This work was supported by the National Natural Science Foundation of China (Grant Nos. 22193032 and 32401033) and the Research Fund of Wenzhou Institute, Chinese Academy of Sciences (Grant Nos. WIUCASQD2020009, WIUCASQD2023005, XSZD2024004, 2021HZSY0061, and WIUCASICTP2022).

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摘要： The F$_1$-ATPase and V$_1$-ATPase are rotary biomotors. Alignment of their amino acid sequences, which originate from bovine heart mitochondria (1BMF) and Enterococcus hirae (3VR6), respectively, demonstrates that the segment forming the ATP catalytic pocket is highly conserved. Single-molecule experiments, however, have revealed subtle differences in efficiency between the F$_1$ and V$_1$ motors. Here, we perform both atomistic and coarse-grained molecular dynamics simulations to investigate the mechanochemical coupling and coordination in F$_1$ and V$_1$ ATPase. Our results show that the correlation between conformational changes in F$_1$ is stronger than that in V$_1$, indicating that the mechanochemical coupling in F$_1$ is tighter than in V$_1$. Moreover, the unidirectional rotation of F$_1$ is more processive than that of V$_1$, which accounts for the higher efficiency observed in F$_1$ and explains the occasional backward steps detected in single-molecule experiments on V$_1$.

关键词: rotary biomotor, correlation, mechanochemical coupling, simulation

Abstract: The F$_1$-ATPase and V$_1$-ATPase are rotary biomotors. Alignment of their amino acid sequences, which originate from bovine heart mitochondria (1BMF) and Enterococcus hirae (3VR6), respectively, demonstrates that the segment forming the ATP catalytic pocket is highly conserved. Single-molecule experiments, however, have revealed subtle differences in efficiency between the F$_1$ and V$_1$ motors. Here, we perform both atomistic and coarse-grained molecular dynamics simulations to investigate the mechanochemical coupling and coordination in F$_1$ and V$_1$ ATPase. Our results show that the correlation between conformational changes in F$_1$ is stronger than that in V$_1$, indicating that the mechanochemical coupling in F$_1$ is tighter than in V$_1$. Moreover, the unidirectional rotation of F$_1$ is more processive than that of V$_1$, which accounts for the higher efficiency observed in F$_1$ and explains the occasional backward steps detected in single-molecule experiments on V$_1$.

Key words: rotary biomotor, correlation, mechanochemical coupling, simulation

中图分类号:  (Motor proteins (myosin, kinesin dynein))

  • 87.16.Nn
87.15.ap (Molecular dynamics simulation) 87.15.hp (Conformational changes)