研究者業績

久保 稔

クボ ミノル  (Minoru Kubo)

基本情報

所属
兵庫県立大学 大学院理学研究科 教授
理化学研究所 客員研究員
学位
博士(理学)(2003年3月 北海道大学)

研究者番号
90392878
J-GLOBAL ID
200901071216606810
researchmap会員ID
1000309450

Minoru Kubo received his Ph.D. in computational chemistry from Hokkaido University in 2003 under the supervision of Prof. Etsuro Ito. After working on ultrafast spectroscopy as a JSPS Young Research Fellow (PD), he started time-resolved Raman spectroscopy with Prof. Teizo Kitagawa at Okazaki Institute for Integrative Bioscience in 2004. In 2006, he moved to Prof. Paul M. Champion's group at Northeastern University as a JSPS overseas research fellow. In 2008, he started time-resolved IR spectroscopy with Prof. Takashi Ogura at University of Hyogo as a research assistant professor. In 2012, he started time-resolved XFEL crystallography combined with time-resolved in-crystallo spectroscopy with Prof. Yoshitsugu Shiro at RIKEN as research scientist and senior research scientist. In 2018, he moved to University of Hyogo as a professor. His research interests include dynamic structural biology.


論文

 83
  • Sachiko Yanagisawa, Takuto Kamei, Atsuhiro Shimada, Stephanie Gladyck, Siddhesh Aras, Maik Hüttemann, Lawrence I. Grossman, Minoru Kubo
    Journal of Inorganic Biochemistry 260 112673-112673 2024年11月  査読有り責任著者
  • Kaho Ueda, Wataru Sato, Sachiko Yanagisawa, Minoru Kubo, Masahiko Hada, Hiroshi Fujii
    Journal of Inorganic Biochemistry 255 112544 2024年6月  査読有り
  • Hongjie Li, Yoshiki Nakajima, Eriko Nango, Shigeki Owada, Daichi Yamada, Kana Hashimoto, Fangjia Luo, Rie Tanaka, Fusamichi Akita, Koji Kato, Jungmin Kang, Yasunori Saitoh, Shunpei Kishi, Huaxin Yu, Naoki Matsubara, Hajime Fujii, Michihiro Sugahara, Mamoru Suzuki, Tetsuya Masuda, Tetsunari Kimura, Tran Nguyen Thao, Shinichiro Yonekura, Long-Jiang Yu, Takehiko Tosha, Kensuke Tono, Yasumasa Joti, Takaki Hatsui, Makina Yabashi, Minoru Kubo, So Iwata, Hiroshi Isobe, Kizashi Yamaguchi, Michihiro Suga, Jian-Ren Shen
    Nature 626(7999) 670-677 2024年1月31日  査読有り
    Abstract Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0–4) at the Mn4CaO5 cluster1–3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4–7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O–O bond formation.
  • Alexander M. Wolff, Eriko Nango, Iris D. Young, Aaron S. Brewster, Minoru Kubo, Takashi Nomura, Michihiro Sugahara, Shigeki Owada, Benjamin A. Barad, Kazutaka Ito, Asmit Bhowmick, Sergio Carbajo, Tomoya Hino, James M. Holton, Dohyun Im, Lee J. O’Riordan, Tomoyuki Tanaka, Rie Tanaka, Raymond G. Sierra, Fumiaki Yumoto, Kensuke Tono, So Iwata, Nicholas K. Sauter, James S. Fraser, Michael C. Thompson
    Nature Chemistry 15(11) 1549-1558 2023年9月18日  査読有り
    Abstract Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.
  • Shinya Ariyasu, Kai Yonemura, Chie Kasai, Yuichiro Aiba, Hiroki Onoda, Yuma Shisaka, Hiroshi Sugimoto, Takehiko Tosha, Minoru Kubo, Takashi Kamachi, Kazunari Yoshizawa, Osami Shoji
    ACS Catalysis 13 8613-8623 2023年6月14日  査読有り

MISC

 13

共同研究・競争的資金等の研究課題

 22