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研究成果

謝辞の記載についてAcknowledgement remarks

雑誌論文Papers

  1. Miki Nakano, Osamu Miyashita, Yasumasa Joti, Akihiro Suzuki, Hideyuki Mitomo, Yoshiya Niida, Ying Yang, Hirokatsu Yumoto, Takahisa Koyama, Kensuke Tono, Haruhiko Ohashi, Makina Yabashi, Tetsuya Ishikawa, Yoshitaka Bessho, Kuniharu Ijiro, Yoshinori Nishino, Florence Tama
    Three-dimensional structure determination of gold nanotriangles in solution using X-ray free-electron laser single-particle analysis
    Optica , 9 , 7 , 776 (2022)
    DOI: https://doi.org/10.1364/optica.457352
    プレスリリース: https://www.riken.jp/press/2022/20220715_2/index.html
    A01:計画研究  C01:計画研究  B01:2022年公募班   A01 別所 義隆  C01 宮下 治  B01 鈴木 明大  
  2. Hosaka T, Nomura T, Kubo M, Nakane T, Fangjia L, Sekine SI, 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 U S A , 119 , 9 , e2117433119 (2022)
    DOI: https://doi.org/10.1073/pnas.2117433119
    プレスリリース: https://www.kyoto-u.ac.jp/ja/research-news/2022-02-28-2
    A01:計画研究  B01:計画研究  C01:計画研究  A01:2020年公募班   A01 岩田 想  B01 南後 恵理子  B01 大和田 成起  C01 久保 稔  A01 保坂 俊彰  
  3. Tiwari, S. P., Tama, F. & Miyashita, O.
    Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns.
    J Chem Inf Model , 61 , 8 , 4108-4119 (2021)
    DOI: https://doi.org/10.1021/acs.jcim.1c00602
    C01:計画研究   C01 宮下 治  
  4. Dasgupta, B., Miyashita, O., Uchihashi, T. & Tama, F.
    Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images.
    Front Mol Biosci , 8 , 704274 (2021)
    DOI: https://doi.org/10.3389/fmolb.2021.704274
    C01:計画研究   C01 宮下 治  
  5. SP Tiwari, S Chhabra, *Tama F, *Miyashita O.
    Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps
    J Chem Info Model , 60 , 5 , 2570-2580 (2020)
    DOI: 10.1021/acs.jcim.9b01107.
    C01:計画研究   C01 宮下 治  
  6. Oda K, Nomura T, Nakane T, Yamashita K, Inoue K, Ito S, Vierock J, Hirata K, Maturana AD, 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, Sugahara 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 , 23 , e62389 (2021)
    DOI: 10.7554/eLife.62389
    プレスリリース: https://www.s.u-tokyo.ac.jp/ja/press/2021/7284/
    A01:計画研究  B01:計画研究  C01:計画研究  A01:2020年公募班  C01:2020年公募班   A01 岩田 想  A01 草木迫 司  B01 南後 恵理子  B01 大和田 成起  C01 久保 稔  C01 木村 哲就  A01 志甫谷 渉  A01 片山 耕大  C01 林 重彦  
  7. 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. , 142 , 36 , 15305-15319 (2020)
    DOI: https://doi.org/10.1021/jacs.0c05108
    C01:計画研究   C01 久保 稔  
  8. 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. , 59 , 13385-13390 (2020)
    DOI: https://doi.org/10.1002/anie.202004733
    C01:計画研究   C01 久保 稔  
  9. 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 , 93 , 7 , 825-833 (2020)
    DOI: https://doi.org/10.1246/bcsj.20200038
    C01:計画研究  A01:2020年公募班   C01 久保 稔  C01 木村 哲就  A01 當舎 武彦  
  10. 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 , 366 , 6463 , 334-338 (2019)
    DOI: 10.1126/science.aax6998
    A01:計画研究  B01:計画研究  C01:計画研究  A01:2020年公募班   A01 梅名 泰史  B01 山本 雅貴  B01 熊坂 崇  C01 久保 稔  C01 木村 哲就  A01 菅 倫寛  
  11. Mitsuo Shoji, Yukihiro Abe, Mauro Boero, Yasuteru Shigeta and Yoshiaki Nishiya.
    Reaction Mechanism of Monomeric Sarcosine Oxidase with N-Cyclopropylglycine
    Phys Chem Chem Phys. , 22 , 29 , 16552-16561 (2020)
    DOI: https://doi.org/10.1039/D0CP01679A
    プレスリリース: https://www.ccs.tsukuba.ac.jp/release200730/
    C01:計画研究   C01 庄司 光男  
  12. 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. , 2020 , 1456-1464 (2020)
    DOI: https://doi.org/10.1002/ejic.201901123
    C01:計画研究   C01 久保 稔  
  13. 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. , 58 , (21) , 14294-14298 (2019)
    DOI: https://doi.org/10.1021/acs.inorgchem.9b02093
    C01:計画研究   C01 久保 稔  
  14. 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. , 48 , (35) , 13154-13161 (2019)
    DOI: https://doi.org/10.1039/C9DT02734C
    C01:計画研究   C01 久保 稔  
  15. 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 , 7 , 2 , 306-323 (2020)
    DOI: https://doi.org/10.1107/S205225252000072X
    A01:計画研究  B01:計画研究  C01:計画研究  C01:2020年公募班   A01 岩田 想  B01 南後 恵理子  B01 大和田 成起  C01 久保 稔  A01 日野 智也  
  16. Ashutosh Srivastava, Sandhya P Tiwari, Osamu Miyashita and Florence Tama
    Integrative/Hybrid Modeling Approaches for Studying Biomolecules
    Journal of Molecular Biology , In Press (2020)
    DOI: https://doi.org/10.1016/j.jmb.2020.01.039
    C01:計画研究   C01 宮下 治  

書籍Books

  1. 溝端栄一、久保稔
    膜タンパク質工学ハンドブック 『構造・解析―X線自由電子レーザーによる膜タンパク質の構造解析』
    (株)エヌ・ティー・エス page: 11-15 (2020)
    A01:計画研究  C01:計画研究   A01 溝端 栄一  C01 久保 稔  

学会発表Presentations, Lectures

  1. 久保稔
    XFEL結晶構造解析と振動分光法を用いたタンパク質の動的精密構造解析
    鳥取大学GSCセミナー, ( 2019 , 9 )
    C01:計画研究   C01 久保 稔  
  2. Osamu Miyashita
    Hybrid Approach for Structural Biology: Simulation and Experimental Data
    CBI Society Meeting, ( 2019 , 10 )
    C01:計画研究   C01 宮下 治