Publications

Ilona Christy Unarta, Siqin Cao, Shintaroh Kubo, Wei Wang, Peter Pak-Hang Cheung, Xin Gao, Shoji Takada, Xuhui Huang (2021). Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model. Proceedings of the National Academy of Sciences.

Noriyo Mitome, Shintaroh Kubo, Sumie Ohta, Hikaru Takashima, Yuto Shigefuji, Toru Niina, Shoji Takada (2021). Cooperation among c-subunits of FoF1-ATP synthase in rotation-coupled proton translocation. bioRxiv.

Ahmad Abdelzaher Zaki Khalifa, Muneyoshi Ichikawa, Daniel Dai, Shintaroh Kubo, Corbin Steven Black, Katya Peri, Thomas S McAlear, Simon Veyron, Shun Kai Yang, Javier Vargas, others (2020). The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications. Elife.

Shintaroh Kubo, Suguru Kato, Kazuyuki Nakamura, Noriyuki Kodera, Shoji Takada (2020). Resolving the data asynchronicity in high-speed atomic force microscopy measurement via the Kalman Smoother. Scientific reports.

Shintaroh Kubo, Shun Kai Yang, Corbin Black, Daniel Dai, Melissa Valente, Jacek Gaertig, Muneyoshi Ichikawa, Khanh Huy Bui (2020). Remodeling and activation mechanisms of outer arm dynein revealed by cryo-electron microscopy. bioRxiv.

Shintaroh Kubo, Toru Niina, Shoji Takada (2020). Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor. Scientific Reports.

Shintaroh Kubo, Tomohiro Shima, Shoji Takada (2020). How cytoplasmic dynein couples ATP hydrolysis cycle to diverse stepping motions: kinetic modeling. Biophysical Journal.

Muneyoshi Ichikawa, Ahmad Abdelzaher Zaki Khalifa, Shintaroh Kubo, Daniel Dai, Kaustuv Basu, Mohammad Amin Faghfor Maghrebi, Javier Vargas, Khanh Huy Bui (2019). Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins. Proceedings of the National Academy of Sciences.

Shintaroh Kubo, Wenfei Li, Shoji Takada (2017). Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations. PLoS computational biology.