Original Papers

​​​​​

​​

1. Yamada, D., Kadono, A., Maeno, T., Sato, W., Yanagisawa, S., Hamamura, T., Shigeta, Y., Yamamoto, J., Kubo, M.* Infrared and ultraviolet spectroscopic characterization of a key intermediate during DNA repair by (6-4) photolyase. Commun. Chem. Vol. 8, 256 (2025).​​

2. Tanaka, Y., Iwanaga, O., Fujikawa, K., Shinomiya, S., Kitagishi, H., Yanagisawa, S., Kubo, M., Kambe, T., Masaoka, S., Kodera, M.* Structural control of μ-hydroxo-μ-peroxodicobalt(III) complex with 6-hpa dinucleating ligand to enhance the O2-evolution activity in the catalytic water oxidation. Dalton Trans. Vol. 54, 12130-12134 (2025).​​

3. Nakagami, A., Tosha, T., Horitani, M., Oohora, K., Hayashi, T., Sato, W., Kubo, M., Kodera, M., Kitagishi, H.* Nitric oxide binding to ferric and ferrous porphyrins encapsulated in the cyclodextrin nanocavities in aqueous solution. Inorg. Chem. Vol. 64, 13973-13985 (2025).​

4. Kojima, T.*, Takaoka, T., Chiba, Y., Kotani, H., Fujisaki, H., Ishi-zuka, T., Yanagisawa, S., Kubo, M., Shiota, Y., Yoshizawa K. Mechanistic insight into water oxidation catalysis by a mononuclear ruthenium complex. Inorg. Chem. Vol. 64, 8620-8629 (2025).

5. 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. Vol. 8, 63 (2025).​​​

6. Yanagisawa, S.*, Kamei, T., Shimada, A., Gladyck, S., Aras, S., Hüttemann, 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. (Special Issue in Memory of Jim Kincaid) Vol. 260, 112673 (2024). ​​​​​​

7. 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 on ν(Fe = O) frequency. J. Inorg. Biochem. Vol. 255, 112544 (2024). ​​​​​

8. 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).​​​​​

9. 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. Nature Chem. Vol. 15, 1549-1558 (2023).​​​​​

10. 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. Vol. 13, 8613-8623 (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. 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 Vol. 127, 846-854 (2023)(Selected for Cover Picture). ​​​​​

13. 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. Vol. 13, 7591 (2022).​​​​​

14. 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. Vol 12, 14883 (2022).​​​​​

15. 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. Vol. 121, 2767-2780 (2022).​​​​​

16. Gupta, R., Li, X.-X., Lee, Y., Seo, M. S., Lee, Y.-M., Yanagisawa, S., Kubo, M., Sarangi, R.*, Cho, K.-B.*, Fukuzumi, S.*, Nam, W.* Heme compound II models in chemoselectivity and disproportionation reactions. Chem. Sci. Vol. 13, 5707-5717 (2022).​​​​​

17. 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 Vol. 119, e2117433119 (2022).​​​​​

18. Mikata, Y.*, Aono, Y., Yamamoto, C., Nakayama, H., Matsumoto, A., Kotegawa, F., Harada, M., Katano, H., Kobayashi, Y., Yanagisawa, S., Kubo, M., Kajiwara, A., Kodera, M. A synthetic model for the possible FeIV2(μ-O)2 core of methane monooxygenase intermediate Q derived from a structurally characterized FeIIIFeIV(μ-O)2 complex. Inorg. Chem. Vol. 61, 786-790 (2022).​​​​​

19. Shinke, T., Itoh, M., Wada, T., Morimoto, Y., Yanagisawa, S., Sugimoto, H., Kubo, M., Itoh S.* Revisiting alkane hydroxylation with m-CPBA (m-chloroperbenzoic acid) catalyzed by nickel(II) complexes. Chem. Eur. J. Vol. 27, 14730-14737 (2021).​​​​​

20. 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).​​​​​

21. 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 the S1 to S2 transition of photosystem II using time-resolved serial femtosecond crystallography. IUCrJ Vol. 8, 431-443 (2021).​​​​​

22. Oda, K., Nomura, T., Nakane, T., Yamashita, K., Inoue, K., Ito, S., Vierock, J., Hirata, K., Maturana, A. D., Katayama, K., Ikuta, T., Ishigami, I., Izume, T., Umeda, R., Eguma, R., Oishi, S., Kasuya, G., Kato, T., Kusakizako, T., Shihoya, W., Shimada, H., Takatsuji, T., Takemoto, M., Taniguchi, R., Tomita, A., Nakamura, R., Fukuda, M., Miyauchi, H., Lee, Y., Nango, E., Tanaka, R., Tanaka, T., Sugawara, M., Kimura, T., Shimamura, T., Fujiwara, T., Yamanaka, Y., Owada, S., Joti, Y., Tono, K., Ishitani, R., Hayashi, S., Kandori, H., Hegemann, P., Iwata, S., Kubo, M.*, Nishizawa, T.*, Nureki, O.* Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. eLife Vol. 10, e62389 (2021).​​​​​

23. Xue, S.-S., Li, X.-X., Lee, Y.-M., Seo, M. S., Kim, Y., Yanagisawa, S., Kubo, M., Jeon, Y.-K., Kim, W.-S., Sarangi, R., Kim, S. H.*, Fukuzumi, S.*, Nam, W.* Enhanced redox reactivity of a nonheme iron(V)‒oxo complex binding protons. J. Am. Chem. Soc. Vol. 142, 15305-15319 (2020).​​​​​

24. Fujieda, N.*, Umakoshi, K., Ochi, Y., Nishikawa, Y., Yanagisawa, S., Kubo, M., Kurisu, G., Itoh, S.* Copper-oxygen dynamics in tyrosinase mechanism. Angew. Chem. Int. Ed. Vol. 59, 13385-13390 (2020).

25. ​​​​​Takeda, H., Kimura, T., Nomura, T., Horitani, M., Yokota, A., Matsubayashi, A., Ishii, S., Shiro, Y., Kubo, M.*, Tosha, T.* Timing of NO binding and protonation in the catalytic reaction of bacterial nitric oxide reductase as established by time-resolved spectroscopy. Bull. Chem. Soc. Japan. Vol. 93, 825-833 (Selected paper) (2020). ​​​​​

26. Wolff, A. M., Young, I. D., Sierra, R. G., Brewster, A. S., Martynowycz, M. W., Nango, E., Sugahara, M., Nakane, T., Ito, K., Aquila, A., Bhowmick, A., Biel, J. T., Carbajo, S., Cohen, A. E., Cortez, S., Gonzalez, A., Hino, T., Im, D., Koralek, J. D., Kubo, M., Lazarou, T. S., Nomura, T., Owada, S., Samelson, A. J., Tanaka, T., Tanaka, R., Thompson, E. M., van den Bedem, H., Woldeyes, R. A., Yumoto, F., Zhao, W., Tono, K., Boutet, S., Iwata, S., Gonen, T., Sauter, N. K., Fraser, J. S., Thompson, M. C.* Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCrJ Vol. 7, 306-323 (2020).​​​​​

27. Kokubo, Y., Wasada-Tsutsui, Y., Yomura, S., Yanagisawa, S., Kubo, M., Kugimiya, S., Kajita, Y.*, Ozawa, T., Masuda, H. Syntheses, characterizations, and crystal Structures of dinitrogen-divanadium complexes bearing triamidoamine ligands. Eur. J. Inorg. Chem. Vol. 2020, 1456-1464 (2020).​​​​​

28. Suga, M.*, Akita, F., Yamashita, K., Nakajima, Y., Ueno, G., Li, H., Yamane, T., Hirata, K., Umena, Y., Yonekura, S., Yu, L.-J., Murakami, H., Nomura, T., Kimura, T., Kubo, M., Baba, S., Kumasaka, T., Tono, K., Yabashi, M., Isobe, H., Yamaguchi, K. Yamamoto, M., Ago, H.*, Shen, J.-R.* An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an X-ray free electron laser. Science Vol. 366, 334-338 (2019).​​​​​

29. Kadoya, Y., Fukui, K., Hata, M., Miyano, R., Hitomi, Y., Yanagisawa, S., Kubo, M., Kodera, M.* Oxidative DNA cleavage, formation of μ-1,1-hydroperoxo species, and cytotoxicity of dicopper(II) complex supported by a p-cresol-derived amide-tether ligand. Inorg. Chem. Vol. 58, 14294-14298 (2019).​

30. Kotani, H., Shimomura, H., Horimoto, M., Ishizuka, T., Shiota, Y., Yoshizawa, K., Yanagisawa, S., Kawahara-Nakagawa, Y., Kubo, M., Kojima, T.* Fundamental electron-transfer and proton-coupled electron-transfer properties of Ru(IV)-oxo complexes. Dalton Trans. Vol. 48, 13154-13161 (2019).

​​​​​​

​​​​​​​

Reviews, Books, etc

​​​​​​

1. Mizohata, E., Nango, E., Tosha, T., Iwata, S., Kubo, M. Tracking protein motions by serial femtosecond crystallography with X-ray Free-Electron Laser. Curr. Protoc. 5, e70212 (2025).​​​​

2. Sato, W., Yamada, D., Kubo, M. Chapter 6. Time-resolved IR spectroscopy for monitoring protein dynamics in microcrystals. Methods Enzymol. Vol. 709: Time-Resolved Methods in Structural Biology (Editors: Moody, P. & Kwon, H.), Elsevier, 161-176 (2024).​​

3. 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).​​​​

4. 片山哲郎, 木村哲就, 久保稔　第III章第6節 タンパク質微結晶を測定する時間分解顕微分光技術.　生体の科学 特集「高速分子動画：動的構造からタンパク質分子制御へ」, 医学書院, Vol. 75, 225-230 (2024).​​​​

5. 久保稔, 山田大智　第1章 第6節 ラマン分光法の構造生物学的利用.　タンパク質の構造解析手法とIn silicoスクリーニングの応用事例, 技術情報協会, 51-61 (2023).​​​

6. 久保稔　第1編 第5章 第2節 反応ダイナミクスの時間分解測定.　ヘムタンパク質の科学 (城宜嗣、青野重利、齋藤正男監修), エヌ・ティー・エス, 193-201 (2022). ​​​

7. 柳澤幸子　第1編 第2章 第3節 二原子酸素添加酵素.　ヘムタンパク質の科学 (城宜嗣、青野重利、齋藤正男監修), エヌ・ティー・エス, 69-76 (2022). ​​​

8. 久保稔　SACLA時分割結晶構造解析による動的構造生物学研究～酵素反応の可視化に向けた分子動画～.　放射光 Vol. 33, 266-270 (2020).​​​

9. 溝端栄一, 久保稔　第1編 第1章 X線自由電子レーザーによる膜タンパク質の構造解析.　膜タンパク質工学ハンドブック (津本浩平、浜窪隆雄監修), エヌ・ティー・エス, 11-15 (2020). ​​​

10. 柳澤幸子　第1編 第2章 第16節 ピコバイオロジー：振動分光法.　膜タンパク質工学ハンドブック (津本浩平、浜窪隆雄監修), エヌ・ティー・エス, 122-129 (2020). ​​​

11. Nango, E., Kubo, M., Tono, K., Iwata, S. Pump-probe time-resolved serial femtosecond crystallography at SACLA: Current status and data collection strategies. Appl. Sci., Vol. 9, 5505 (2019).

12. 當舎武彦, 久保稔　SACLAを利用した酵素反応の可視化.​　生物物理 Vol. 59, 205-207 (2019).

​​​

2018年度以前の久保の業績は → https://researchmap.jp/min00000

​​​

​​

​​

​