兵庫県立大学 大学院理学研究科 生命科学専攻
バイオダイナミクス研究センター
Bio-dynamics Research Center

研究業績

2024年度

  1. Yokomine, M., Morimoto, J., Fukuda, Y., Ueda, T., Takeuchi, K., Umezawa, K., Ago, H., Matsuura, H., Ueno, G., Senoo, A., Nagatoishi, S., Tsumoto K., Sando, S. A high-resolution structural characterization and physicochemical study of how a peptoid binds to an oncoprotein MDM2. Chem. Sci. 15, 7051-7060 (2024)
  2. Jenney, F. E., Jr., Wang, H., George, S. J., Xiong, J., Guo, Y., Gee, L. B., Marizcurrena, J. J., Castro-Sowinski, S., Staskiewicz, A., Yoda, Y., Hu, M. Y., Tamasaku, K., Nagasawa, N., Li, L., Matsuura, H., Doukov, T., Cramer, S. P. Temperature-dependent iron motion in extremophile rubredoxins - no need for ‘corresponding states’ Sci. Rep. 14, 12197 (2024)
  3. Ueda, K., Sato, W., Yanagisawa, S., Kubo, M., Hada, M., Fujii, H. Resonance Raman study of oxoiron(IV) porphyrin π-cation radical complex: Porphyrin ligand effect o v(Fe=O) frequency. J. Inorg. Biochem. 255, 112544 (2024)
  4. Orville, A. M., Nango, E., Iwata, S., Mous, S., Standfuss, J., Nogly, P., Suga, M., Shen, J.-R., Kubo, M. Chapter 15. Time-resolved studies of protein structural dynamics. Ultrafast Electronic and Structural Dynamics (Editor: Ueda, K.), Springer Nature Singapore, 439-476 (2024)
  5. Karafoulidi-Restou, C., Lorent, C., Katz, S., Rippers, Y., Matsuura, H., Higuchi, Y., Zebger, I., Horch, M. Light-induced electron transfer in a [NiFe] hydrogenase opens a photochemical shortcut for catalytic dihydrogen cleavage. Angew. Chem. 63, e202409065 (2024)
  6. Satoh, T., Yagi-Utsumi, M., Ishii, N., Mizushima, T., Yagi, H., Kato, R., Tachida, Y., Tateno, H., Matsuo, I., Kato, K., Suzuki, T., Yoshida, Y. Structural basis of sugar recognition by SCFFBS2 ubiquitin ligase involved in NGLY1 deficiency. FEBS Lett., 598, 2259-2268. (2024)
  7. Lee, H.-E., Okumura, T., Ooka, H., Adachi, K., Hikima, T., Hirata, K., Kawano, Y., Matsuura, H., Yamamoto, M., Yamamoto, M., Yamaguchi, A., Lee, J.-E., Takahashi, H., Nam, K. T., Ohara, Y., Hashizume, D., McGlynn, S. E., Nakamura, R. Osmotic energy conversion in serpentinite-hosted deep-sea hydrothermal vents. Nat. Commun. 15, 8193 (2024)
  8. Shimakawa, G., Demulder, M., Flori, S., Kawamoto, A., Tsuji, Y., Nawaly, H., Tanaka, A., Tohda, R., Ota, T., Matsui, H., Morishima, N., Okubo, R., Wietrzynski, W., Lamm, L., Righetto, R. D., Uwizeye, C., Gallet, B., Jouneau, P.-H., Gerle, C., Kurisu, G., Finazzi, G., Engel, B. D., Matsuda, Y. Diatom pyrenoids are encased in a protein shell that enables efficient CO2 fixation. Cell, 187, 1-16 (2024)
  9. Yanagisawa, S., Kamei, T., Shimada, A., Gladyck, S., Aras, S., Huttemann, M., Grossman, L. I., Kubo, M. Resonance Raman spectral analysis of the heme site structure of cytochrome c oxidase with its positive regulator CHCHD2. J. Inorg. Biochem. 260, 112673 (2024)
  10. Sato, W., Yamada, D., Kubo, M. Chapter 6. Time-resolved IR spectroscopy for monitoring protein dynamics in microcrystals. Methods Enzymol. 709: Time-Resolved Methods in Structural Biology (Editors: Moody, P. & Kwon, H.), Elsevier, 161-176 (2024)
  11. 柴田 直樹, 山口 真稔, 山口 友輔, 吉村 日向, 樋口 芳樹, Wnt シグナル因子Dickkopf-1 のＸ線結晶学的研究. SPring-8/SACLA利用研究成果集, 12, 382-385 (2024)
  12. Destan, E., Turkut, E., Aldeniz, A., Kang, J., Tosha, T., Yabashi, M., Yilmaz, B., Timucin, A. C., Matsuura, H., Kawano, Y., Cinkaya, I., DeMirci, H. Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap. Small Struct., 2400680 (2025)
  13. Nagao, S., Kuwano, W., Tosha, T., Yamashita, K., Stanfield, J. K., Kasai, C., Ariyasu, S., Hirata, K., Ueno, G., Murakami, H., Ago, H., Yamamoto, M., Shoji, O., Sugimoto, H., Kubo, M. XFEL crystallography reveals catalytic cycle dynamics during non-native substrate oxidation by cytochrome P450BM3. Commun. Chem. 8, 63 (2025)

2023年度

  1. Ariyasu, S., Yonemura, K., Kasai, C., Aiba, Y., Onoda, H., Shisaka, Y., Sugimoto, H., Tosha, T., Kubo, M., Kamachi, T., Yoshizawa, K., Shoji, O. Catalytic oxidation of methane by wild-type cytochrome P450BM3 with chemically evolved decoy molecules. ACS Catal. 13, 8613-8623 (2023)
  2. Hragi, K., Nishide, A., Takagi, K., Iwai, K., Kim, M., Mizushima T., Structural insight into the recognition of the linear ubiquitin assembly complex by Shigella E3 ligase IpaH1.4/2.5. J. Biochem. 173, 317-326 (2023)
  3. Nishio, K., Kawarasaki, T., Sugiura, Y., Matsumoto, S., Konoshima, A., Takano, Y., Hayashi, M., Okumura, F., Kamura, T., Mizushima, T., Nakatsukasa, K. Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress. Sci. Adv. 9, eadf1956 (2023)
  4. Takeda, H., Shimba, K., Horitani, M., Kimura, T., Nomura, T., Kubo, M., Shiro, Y., Tosha, T. Trapping of a mononitrosyl nonheme intermediate of nitric oxide reductase by cryo-photolysis of caged nitric oxide. J. Phys. Chem. B 127, 846-854 (2023)(Selected for Cover Picture)
  5. Chongdar, N., Rodríguez-Maciá, P., Reijerse, E. J., Lubitz, W., Ogata, H., Birrell, J. A. Redox tuning of the H-cluster by second coordination sphere amino acids in the sensory [FeFe] hydrogenase from Thermotoga maritima. Chemical Science 14, 3682-3692 (2023)
  6. Hiromoto, T., Nishikawa, K., Inoue, S., Ogata, H., Hori, Y., Kusaka, K., Hirano, Y., Kurihara, K., Shigeta, Y., Tamada, T., Higuchi Y., New insights into the oixdiation process from neutron and X-ray crystal structures of an O2-sensitive [NiFe]-hydrogenase.Chem. Sci., 14, 9306-9315 (2023)
  7. Kobayashi, A., Taketa, M., Sowa, K., Kano, K., Higuchi, Y., Ogata, H., Structure and function relationship of formate dehydrogenases: an overview of recent progress. IUCrJ, 10, 544-554 (2023)
  8. Sakai, T. Mashima, T., Kobayashi, N., Ogata, H., Duan, L., Fujiki, R., Hengphasatporn, K., Uda, T., Shigeta, Y., Hifumi, E., Hirota S., Structural and thermodynamic insights into antibody light chain tetramer formation through 3D domain swapping.Nature Commun., 14, 7807 (2023)
  9. Li, H., Nakajima, Y., Nango, E., Owada, S., Yamada, D., Hashimoto, K., Luo, F., Tanaka, R., Akita, F., Kato, K., Kang, J., Saitoh, Y., Kishi, S., Yu, H., Matsubara, N., Fujii, H., Sugahara, M., Suzuki, M., Masuda, T., Kimura, T., Thao, T. N., Yonekura, S., Yu, L.-J., Tosha, T., Tono, K., Joti, Y., Hatsui, T., Yabashi, M., Kubo, M., Iwata, S., Isobe, H., Yamaguchi, K., Suga, M., Shen, J.-R. Oxygen-evolving photosystem II structures during S1-S2-S3 transitions. Nature Vol. 626, 670-677 (2024)
  10. Wolff, A. M., Nango, E., Young, I. D., Brewster, A. S., Kubo, M., Nomura, T., Sugahara, M., Owada, S., Barad, B. A., Ito, K., Bhowmick, A., Carbajo, S., Hino, T., Holton, J. M., Im, D., O’Riordan, L. J., Tanaka, T., Tanaka, R., Sierra, R. G., Yumoto, F., Tono, K., Iwata, S., Sauter, N. K., Fraser, J. S., Thompson, M. C. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nat. Chem. Vol. 15, 1549-1558 (2023)
  11. Kokubo, Y., Tsuzuki, K., Sugiura, H., Yomura, S., Wasada-Tsutsui., Ozawa, T., Yanagisawa, S., Kubo, M., Takeyama, T., Yamaguchi, T., Shimazaki, Y., Kugimiya, S., Masuda, H., Kajita, Y. Syntheses, characterizations, crystal structures, and protonation reactions of dinitrogen chromium complexes supported with triamidoamine ligands. Inorg. Chem. Vol. 62, 5320-5333 (2023)
  12. Fadini, A., Hutchison, C., Morozov, D., Chang, J., Maghlaoui, K., Perrett, S., Luo, F., Kho, J., Romei, M., Morgan, R., Orr, C., Cordon-Preciado, V., Fujiwara, T., Nuemket, N., Tosha, T., Tanaka, R., Owada, S., Tono, K., Iwata, S., Boxer, S., Groenhof, G., Nango, E., van Thor, J., Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism. J. Am. Chem. Soc. 145, 15796-15808 (2023)
  13. Safari, C., Ghosh, S., Andersson, R., Johannesson, J., Båth, P., Uwangue, O., Dahl, P., Zoric, D., Sandelin, E., Vallejos, A., Nango, E., Tanaka, R., Bosman, R., Börjesson, P., Dunevall, E., Hammarin, G., Ortolani, G., Panman, M., Tanaka, T., Yamashita, A., Arima, T., Sugahara, M., Suzuki, M., Masuda, T., Takeda, H., Yamagiwa, R., Oda, K., Fukuda, M., Tosha, T., Naitow, H., Owada, S., Tono, K., Nureki, O., Iwata, S., Neutze, R., Brändén G., Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase. Sci. Adv. 9, eadh4179 (2023)
  14. Shimada, A., Baba, S., Nagao, S., Shinzawa-Itoh, K., Yamashita, E., Muramoto, K., Tsukihara, T., Yoshikawa, S. Crystallographic cyanide-probing for cytochrome c oxidase reveals structural bases suggesting that a putative proton transfer H-pathway pumps protons. J. Biol. Chem. 299, 105277 (2023)
  15. Bolton, R., Machelett, M., Stubbs, J., Axford, D., Caramello, N., Catapano, L., Maly, M., Rodrigues, M., Tizzard, G., MacMillan, F., Engilberge, S., von Stetten, D., Tosha, T., Sugimoto, H., Worrall, J., Zubkov, M., Coles, S., Mathieu, E., Steiner, R., Murshudov, G., Schrader, T., Orville, A., Royant, A., Evans, G., Hough, M., Owen, R., Tews I. A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron binding protein FutA from Prochlorococcus. Proc. Natl. Acad. Sci. USA 121, e2308478121 (2024)

2022年度

  1. Nishida, Y., Yanagisawa, S., Morita, R., Shigematsu, H., Shinzawa-Itoh, K., Yuki, S., Ogasawara, H., Shimuta, K., Iwamoto, T., Nakabayashi, C., Matsumura, W., Kato, H., Gopalasingam, C., Nagao, T., Qaqorh, T., Takahashi, Y., Yamazaki, S., Kamiya, K., Harada, R., Mizuno, N., Takahashi, H., Akeda, Y., Ohnishi, M., Ishii, Y., Kumasaka, T., Murata, T., Muramoto, K., Tosha, T., Shiro, Y., Honma, T., Shigeta, Y., Kubo, M., Takashima, S., Shintani, Y. Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nat. Commun. 13, 7591 (2022)
  2. Yoshida, Y., Shimizu, I., Shimada, A., Nakahara, K., Yanagisawa, S., Kubo, M., Fukuda, S., Ishii, C., Yamamoto, H., Ishikawa, T., Kano, K., Aoki, J., Katsuumi, G., Suda, M., Ozaki, K., Yoshida, Y., Okuda, S., Ohta, S., Okamoto, S., Minokoshi, Y., Oda, K., Sasaoka, T., Abe, M., Sakimura, K., Kubota, Y., Yoshimura, N., Kajimura, S., Zuriaga, M., Walsh, K., Soga, T., Minamino, T. Brown adipose tissue dysfunction promotes heart failure via a trimethylamine N-oxide-dependent mechanism. Sci. Rep. 12, 14883 (2022)
  3. Nagatomo, S., Shoji, M., Terada, T., Nakatani, K., Shigeta, Y., Hirota, S., Yanagisawa, S., Kubo, M., Kitagawa, T., Nagai, M., Ohki, M., Park, S.-Y., Shibayama, N. Heme-bound tyrosine vibrations in hemoglobin M: resonance Raman, crystallography and DFT calculation. Biophys. J. 121, 2767-2780 (2022)
  4. Hosaka, T., Nomura, T., Kubo, M., Nakane, T., Fangjia, L., Sekine, S., Ito, T., Murayama, K., Ihara, K., Ehara, H., Kashiwagi, K., Katsura, K., Akasaka, R., Hisano, T., Tanaka, T., Tanaka, R., Arima, T., Yamashita, A., Sugahara, M., Naitow, H., Matsuura, Y., Yoshizawa, S., Tono, K., Owada, S., Nureki, O., Kimura-Someya, T., Iwata, S., Nango, E., Shirouzu, M. Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers. Proc. Natl. Acad. Sci. USA 119, e2117433119 (2022)
  5. Lucic, M., Wilson, M., Tosha, T., Sugimoto, H., Shilova, A., Axford, D., Owen, R., Hough, M., Worrall, J. Serial femtosecond crystallography reveals the role of water in the one- or two-electron redox chemistry of Compound I in the catalytic cycle of a B-type dye-decolorizing peroxidase DtpB ACS Catal. Vol. 12, 13349-13359 (2022)
  6. Moreno-Chicano, T., Carey, L., Axford, D., Beale, J., Doak, R., Duyvesteyn, H., Ebrahim, A., Henning, R., Monteiro, D., Myles, D., Owada, S., Sherrell, D., Straw, M., Srajer, V., Sugimoto, H., Tono, K., Tosha, T., Tews, I., Trebbin, M., Strange, R., Weiss, K., Worrall, J., Meilleur, F., Owen, R., Ghiladi, R., Hough, M. Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature. IUCrJ Vol. 9, 610-624 (2022)
  7. Rose, S., Baba, S., Okumura, H., Antonyuk, S., Sasaki, D., Hedison, T., Shanmugam, M., Heyes, D., Scrutton, N., Kumasaka, T., Tosha, T., Eady, R., Yamamoto, M., Hasnain, S. Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases. Proc. Natl. Acad. Sci. USA 119, e2205664119 (2022)
  8. Nakamura, H., Hisano, T., Rahman, M, Tosha, T., Shirouzu, M., Shiro, Y. Structural insight into heme detoxification by an ABC-type efflux pump in Gram-positive bacteria. Proc. Natll Acad. Sci. USA 119, e2123385119 (2022)
  9. Matsumura, H., Faponle, A., Hegedoorn, P.-L., Tosha, T., de Visser, S., Moënne-Loccoz, P. Mechanism of substrate inhibition in cytochrome-c dependent NO reductases from denitrifying bacteria (cNORs). J. Inorg. Biochem. 231, 111781 (2022)
  10. Kwon, H., Basran, J., Pathak, C., Hussain, M., Freeman, S., Fielding, A., Bailey, A., Stefanou, N., Sparkes, H., Tosha, T., Yamashita, K., Hirata, K., Murakami, H., Ueno, G., Ago, H., Tono, K., Yamamoto, M., Sawai, H., Shiro, Y., Sugimoto, H., Moody, P., Raven E. XFEL Crystal Structures of Peroxidase Compound II. Angew. Chem. Int. Ed. 60, 14578-14585 (2022)
  11. Stripp, S., Duffus, B. R., Fourmond, V., Léger, C., Leimkühler, S., Hirota, S., Hu, Y., Jasniewski, A., Ogata, H., Ribbe, M. W. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chemical Reviews 122, 11900-11973 (2022)
  12. Furlan, C., Chongdar, N., Gupta, P., Lubitz, W., Ogata, H., Blaza, J. N., Birrell, J. A. Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase. eLife 11, e79361 (2022)

2021年度

  1. Li, H., Nakajima, Y., Nomura, T., Sugahara, M., Yonekura, S., Chan, S. K., Nakane, T., Yamane, T., Umena, Y., Suzuki, M., Masuda, T., Motomura, T., Naitow, H., Matsuura, Y., Kimura, T., Tono, K., Owada, S., Joti, Y., Tanaka, R., Nango, E., Akita, F., Kubo, M., Iwata, S., Shen, J.-R., Suga, M. Capturing structural changes of photosystem II using time-resolved serial femtosecond crystallography with proper flash excitations. IUCrJ 8, 431-443 (2021).
  2. Nomura, T., Kimura, T., Kanematsu, Y., Yamada, D., Yamashita, K., Hirata, K., Ueno, G., Murakami, H., Hisano, T., Yamagiwa, R., Takeda, H., Gopalasingam, C., Kousaka, R., Yanagisawa, S., Shoji, O., Kumasaka, T., Yamamoto, M., Takano, Y., Sugimoto, H., Tosha, T., Kubo, M., Shiro, Y.　Short-lived intermediate in N2O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography. Proc. Natl. Acad. Sci. USA Vol. 118, e2101481118 (2021).