研究業績
Original Papers
[1] 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).
[2] 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).
[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 on ν(Fe = O) frequency.
J. Inorg. Biochem. Vol. 255, 112544 (2024).
[4] 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).
[5] 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).
[6] 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).
[7] 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).
[8] 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).
[9] 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).
[10] 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).
[11] 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).
[12] 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).
[13] 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).
[14] 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).
[15] 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).
[16] 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).
[17] 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) .
[18] 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).
[19] 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).
[20] 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) .
[21] 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).
[22] 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).
[23] 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).
[24] 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).
[25] 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).
[26] 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] Sato, W., Yamada, D., Kubo, M.
Chapter 4. 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).
[2] 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).
[3] 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).
[4] 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).
[5] 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).
[6] 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).
[7] 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).
[8] 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).
[9] 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).
[10] 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).
[11] 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).