Development of a Soft Robotics-Based Physical Simulator Reproducing the Motion Mechanism of V1-ATPase
Ren NOBUSAWA *1, Ryudai YOKOKAWA2, Toru EKIMOTO1, Masao INOUE1, Tsutomu YAMANE3, Shingo MAEDA2, 4, Mitsunori IKEGUCHI1, 3
1Graduate School of Medical Life Science, Yokohama City University
2Department of Mechanical Engineering, Institute of Science Tokyo
3RIKEN R-CCS, RIKEN
4Research Center for Autonomous Systems Materialogy, Institute of Integrated Research, Institute of Science Tokyo
[Introduction]
In nature, biological molecular motors such as ATP synthase, kinesin, and myosin convert chemical energy into mechanical motion, enabling precise and coordinated movements within cells. These motors are known for their high efficiency and high-power output, and applying their operating principles to artificial systems could lead to novel driving sources for soft robotics as well as controllable motion mechanisms at the molecular scale. However, the operation of molecular motors depends on complex intermolecular interactions and stochastic processes, making their direct application to engineering design challenging. In this study, we aim to develop a fundamental technology for designing and controlling soft robotic mechanisms by constructing a simulator that reproduces the physical processes of biological molecular motors.
[Purpose]
This study focuses on the rotary motor protein V1-ATPase. By translating its structural changes and dynamic properties into mechanical characteristics through soft robotics technology, we aim to develop a physical simulator capable of reproducing the operation of V1-ATPase.
[Methods]
V1-ATPase consists of a hexameric A3B3 ring and a central stalk. We performed molecular dynamics (MD) simulations of the V1-ATPase complex and, based on the results, defined rigid and flexible regions to construct a prototype physical simulator. The simulator was first driven manually to reproduce the conformational transitions of an AB pair among the four states—empty, bindable, bound, and tight—and to evaluate their reproducibility. In addition, we examined the feasibility of reproducing rotary motion based on the contact between the hexameric ring and the central stalk.
[Results and Discussion]
Based on the MD simulation results, each A and B subunit was divided into three domains, with the boundaries treated as hinges, to construct the physical simulator. Manual driving successfully reproduced transitions among the four conformational states of an AB pair. Furthermore, when the three AB pairs opened and closed in a coordinated sequence, force transmission occurred at the contact points between the hexameric ring and the central stalk, enabling the conditions necessary for rotation. These results demonstrate that domain partitioning based on MD simulations, combined with the assignment of rigid and flexible regions, is effective for designing physical simulators.
[Conclusions]
We constructed a physical simulator of V1-ATPase by defining rigid and flexible regions based on MD simulations. The results demonstrate the feasibility of reproducing AB pair opening/closing motions and rotary motion mediated by contact between the hexameric ring and the central shaft. This approach holds promise for elucidating molecular motor mechanisms and for designing soft robotic driving sources.