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謝辞の記載についてAcknowledgement remarks

雑誌論文Papers

  1. Akihiro Suzuki, Toshiyuki Moriya, Tairo Oshima, Ying Yang, Yoshiya Niida, Kensuke Tono, Makina Yabashi, Tetsuya Ishikawa, Yasumasa Joti, Yoshinori Nishino, Yoshitaka Bessho
    Thermus thermophilus polyploid cells directly imaged by X-ray laser diffraction
    The Journal of General and Applied Microbiology , 69 , 2 , 125 (2023)
    DOI: https://doi.org/10.2323/jgam.2023.06.002
    B01:2022   A01 Yoshitaka Bessho  B01 Akihiro Suzuki  
  2. Hirokatsu Yumoto, Takahisa Koyama, Akihiro Suzuki, Yasumasa Joti, Yoshiya Niida, Kensuke Tono, Yoshitaka Bessho, Makina Yabashi, Yoshinori Nishino, Haruhiko Ohashi
    High-fluence and high-gain multilayer focusing optics to enhance spatial resolution in femtosecond X-ray laser imaging
    Nature Communications , 13 , 5300 (2022)
    DOI: https://doi.org/10.1038/s41467-022-33014-4
    プレスリリース: http://www.spring8.or.jp/ja/news_publications/press_release/2022/220913_2/
    B01:2022   A01 Yoshitaka Bessho  B01 Akihiro Suzuki  
  3. 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:  C01:  B01:2022   A01 Yoshitaka Bessho  C01 Osamu Miyashita  B01 Akihiro Suzuki  
  4. Akihiro Suzuki, Hiromochi Tanaka, Hisao Yamashige, Yuki Orikasa, Yoshiya Niida, Takashi Kimura, Kensuke Tono, Makina Yabashi, Tetsuya Ishikawa, Yoshitaka Bessho, Yasumasa Joti, Yoshinori Nishino
    Femtosecond X-ray Laser Reveals Intact Sea–Island Structures of Metastable Solid-State Electrolytes for Batteries
    Nano Letters , 22 , 11 , 4603 (2022)
    DOI: https://doi.org/10.1021/acs.nanolett.1c04392
    プレスリリース: https://www.hokudai.ac.jp/news/2022/05/xx.html
    A01:  B01:2022   A01 Yoshitaka Bessho  B01 Akihiro Suzuki  
  5. Jinta Asami, Jae-Hyun Park, Yayoi Nomura, Chisa Kobayashi, Junki Mifune, Naito Ishimoto, Tomoko Uemura, Kehong Liu, Yumi Sato, Zhikuan Zhang, Masamichi Muramatsu, Takaji Wakita, David Drew, So Iwata, Toshiyuki Shimizu, Koichi Watashi, Sam-Yong Park, Norimichi Nomura, Umeharu Ohto
    Structural basis of hepatitis B virus receptor binding
    Nature Structural & Molecular Biology , 31 (2024)
    DOI: 10.1038/s41594-023-01191-5
    プレスリリース:
    A01:   A01 So Iwata  A01 Norimichi Nomura  A01 Sam-Yong Park  
  6. *Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, *Bessho Y, *Essen LO, *Tsai MD.
    Visualizing the DNA repair process by a photolyase at atomic resolution.
    J Science , 382 , 6674 , eadd7795 (2023)
    DOI: https://doi.org/10.1126/science.add7795
    プレスリリース: https://www.riken.jp/press/2023/20231201_2/index.html
    A01:  B01:   A01 So Iwata  A01 Yoshitaka Bessho  B01 Eriko Nango  B01 Sigeki Owada  
  7. Han Ba Bui, Satoshi Watanabe, Norimichi Nomura, Kehong Liu, Tomoko Uemura, Michio Inoue, Akihisa Tsutsumi, Hiroyuki Fujita, Kengo Kinoshita, Yukinari Kato, So Iwata, Masahide Kikkawa, Kenji Inaba
    Cryo-EM structures of human zinc transporter ZnT7 reveal the mechanism of Zn2+ uptake into the Golgi apparatus
    Nature Communications , 14 , 4770 (2023)
    DOI: 10.1038/s41467-023-40521-5
    A01:   A01 So Iwata  A01 Norimichi Nomura  
  8. Naito Ishimoto, Jae-Hyun Park, Kouki Kawakami, Michiko Tajiri, Kenji Mizutani, Satoko Akashi, Jeremy R. H. Tame, Asuka Inoue, Sam-Yong Park
    Structural basis of CXC chemokine receptor 1 ligand binding and activation
    Nat Commun. , 14 , 4107 (2023)
    DOI: https://doi.org/10.1038/s41467-023-39799-2
    プレスリリース: https://www.yokohama-cu.ac.jp/news/2023/20230728park.html
    A01:   A01 Sam-Yong Park  
  9. Titouan Jaunet-Lahary, Tatsuro Shimamura, Masahiro Hayashi, Norimichi Nomura, Kouta Hirasawa, Tetsuya Shimizu, Masao Yamashita, Naotaka Tsutsumi, Yuta Suehiro, Keiichi Kojima, Yuki Sudo, Takashi Tamura, Hiroko Iwanari, Takao Hamakubo, So Iwata, Kei-ichi Okazaki, Teruhisa Hirai, Atsuko Yamashita
    Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota
    Nature Communications , 14 , 1730 (2023)
    DOI: https://doi.org/10.1038/s41467-023-36883-5
    A01:   A01 So Iwata  A01 Norimichi Nomura  
  10. T. Katayama, T.-K. Choi, D. Khakhulin, A. O. Dohn, C. J. Milne, G. Vankó, Z. Németh, F. A. Lima, J. Szlachetko, T. Sato, S. Nozawa, S. Adachi, M. Yabashi, T. J. Penfold, W. Gawelda, G. Levi
    Atomic-scale observation of solvent reorganization influencing photoinduced structural dynamics in a copper complex photosensitizer
    Chemical Science , 14 , 10 , 2572–2584 (2023)
    DOI: https://doi.org/10.1039/D2SC06600A
    プレスリリース: http://www.spring8.or.jp/ja/news_publications/press_release/2023/230214/
    B01:   B01 Shinichi Adachi  B01 Tetsuo Katayama  
  11. Yonezawa, K., Takahashi, M.,Yatabe, K., Nagatani, Y. and Shimizu, N.
    MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV-visible spectroscopy combined with size-exclusion chromatography.
    Biophysics Physicobiology , 20 , 1 , e200001 (2023)
    DOI: 10.2142/biophysico.bppb-v20.0001
    B01:   B01 Nobutaka Shimizu  
  12. Daisuke Tsuboi, Takeshi Otsuka, Takushi Shimomura, Md Omar Faruk, Yukie Yamahashi, Mutsuki Amano, Yasuhiro Funahashi, Keisuke Kuroda, Tomoki Nishioka, Kenta Kobayashi, Hiromi Sano, Taku Nagai, Kiyofumi Yamada, Anastasios V Tzingounis, Atsushi Nambu, Yoshihiro Kubo, Yasuo Kawaguchi, Kozo Kaibuchi
    Dopamine drives neuronal excitability via KCNQ channel phosphorylation for reward behavior
    Cell Reports , 40 , 10 , 111309 (2022)
    DOI: https://doi.org/10.1016/j.celrep.2022.111309
    A01:2022   A01 Takushi Shimomura  
  13. Takushi Shimomura, Kiichi Hirazawa Yoshihiro Kubo
    Conformational rearrangements in the second voltage sensor domain switch PIP2- and voltage-gating modes in two-pore channels
    Proc Natl Acad Sci U S A , 120 , 6 , e2209569120 (2023)
    DOI: https://doi.org/10.1073/pnas.2209569120
    プレスリリース: https://www.nips.ac.jp/release/2023/02/20230203shimomura.html
    A01:2022   A01 Takushi Shimomura  
  14. Haruyo Hatanaka, Hiromi Toyonaga, Yukiko Ishida, Eiichi Mizohata, Eiichiro Ono
    Functional diversity and plasticity in the sugar preferences of Saccharomyces MALT transporters in domesticated yeasts
    FEMS Yeast Res. , 22 , 1 , foac055 (2022)
    DOI: 10.1093/femsyr/foac055.
    A01:   A01 Eiichi Mizohata  
  15. Muna Al-Habsi, Kenji Chamoto, Ken Matsumoto, Norimichi Nomura, Baihao Zhang, Yuki Sugiura, Kazuhiro Sonomura, Aprilia Maharani, Yuka Nakajima, Yibo Wu, Yayoi Nomura, Rosemary Menzies, Masaki Tajima, Koji Kitaoka, Yasuharu Haku, Sara Delghandi, Keiko Yurimoto, Fumihiko Matsuda, So Iwata, Toshihiko Ogura, Sidonia Fagarasan, Tasuku Honjo
    Spermidine activates mitochondrial trifunctional protein and improves antitumor immunity in mice
    Science , 378 , 6618 , eabj3510 (2022)
    DOI: 10.1126/science.abj3510
    A01:   A01 So Iwata  A01 Norimichi Nomura  
  16. Ryoji Suno, Yukihiko Sugita, Kazushi Morimoto, Hiroko Takazaki, Hirokazu Tsujimoto, Mika Hirose, Chiyo Suno-Ikeda, Norimichi Nomura, Tomoya Hino, Asuka Inoue, Kenji Iwasaki, Takayuki Kato, So Iwata, Takuya Kobayashi
    Structural insights into the G protein selectivity revealed by the human EP3-Gi signaling complex
    Cell Reports , 40 , 11 , 111323 (2022)
    DOI: 10.1016/j.celrep.2022.111323
    プレスリリース:
    A01:   A01 So Iwata  A01 Norimichi Nomura  A01 Tomoya Hino  
  17. Zhikuan Zhang, Norimichi Nomura, Yukiko Muramoto, Toru Ekimoto, Tomoko Uemura, Kehong Liu, Moeko Yui, Nozomu Kono, Junken Aoki, Mitsunori Ikeguchi, Takeshi Noda, So Iwata, Umeharu Ohto, Toshiyuki Shimizu
    Structure of SARS-CoV-2 membrane protein essential for virus assembly
    Nature Communications , 13 , 4399 (2022)
    DOI: 10.1038/s41467-022-32019-3
    プレスリリース:
    A01:   A01 So Iwata  A01 Norimichi Nomura  
  18. Daisuke Takahashi, Kento Yonezawa, Yuki Okizaki, Jose M. M. Caaveiro, Tadashi Ueda, Atsushi Shimada, Fumio Sakane, Nobutaka Shimizu
    Ca2+-induced structural changes and intramolecular interactions in N-terminal region of diacylglycerol kinase alpha
    Protein Science , 31 , 7 , e4365 (2022)
    DOI: 10.1002/pro.4365
    B01:   B01 Nobutaka Shimizu  
  19. Toshiaki Hosaka, Kazushige Katsura, Yoshiko Ishizuka-Katsura, Kazuharu Hanada, Kaori Ito, Yuri Tomabechi, Mio Inoue, Ryogo Akasaka, Chie Takemoto, and Mikako Shirouzu
    Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography
    International Journal of Molecular Sciences , 23 , 10399 (2022)
    DOI: https://doi.org/10.3390/ijms231810399
    A01:2022   A01 Toshiaki Hosaka  
  20. Kenichiro Takaba, Duy Phuoc Tran, Akio Kitao
    Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins
    The Journal of Chemical Physics , 152 , 22 , 225101 (2020)
    DOI: 10.1063/5.0004654
    C01:2022  C01:2020   C01 Akio Kitao  
  21. Hiroaki Hata, Duy Phuoc Tran, Mohamed Marzouk Sobeh, Akio Kitao
    Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model
    Biophysics and physicobiology , 18 , 305-316 (2021)
    DOI: 10.2142/biophysico.bppb-v18.037
    C01:2022  C01:2020   C01 Akio Kitao  
  22. Takeo Yamawaki, Misao Mizuno, Haruto Ishikawa, Kazuhiro Takemura, Akio Kitao, Yoshitsugu Shiro, Yasuhisa Mizutani
    Regulatory Switching by Concerted Motions on the Microsecond Time Scale of the Oxygen Sensor Protein FixL
    The Journal of Physical Chemistry B , 125 , 25 , 6847-6856 (2021)
    DOI: 10.1021/acs.jpcb.1c01885
    C01:2022  C01:2020   C01 Akio Kitao  
  23. Steven Hayward, Akio Kitao
    The role of the half-turn in determining structures of Alzheimer’s Aβ wild-type and mutants
    Journal of Structural Biology , 213 , 4 , 107792 (2021)
    DOI: 10.1016/j.jsb.2021.107792
    C01:2022  C01:2020   C01 Akio Kitao  
  24. Mohamed Marzouk Sobeh, Akio Kitao
    Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM
    Journal of Chemical Information and Modeling , 62 , 5 , 1294–1307 (2022)
    DOI: 10.1021/acs.jcim.1c01508
    プレスリリース: https://www.titech.ac.jp/news/2022/063638
    C01:2022  C01:2020   C01 Akio Kitao  
  25. Duy Phuoc Tran, Yuta Taira, Takumi Ogawa, Ryoga Misu, Yoshiki Miyazawa, Akio Kitao
    Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer
    Sci. Rep. , 12 , 3860 (2022)
    DOI: doi.org/10.1038/s41598-022-07792-2
    プレスリリース: https://www.titech.ac.jp/news/2022/063494
    C01:2022  C01:2020   C01 Akio Kitao  
  26. Satoshi Yamashita, Misao Mizuno, Kazuhiro Takemura, Akio Kitao, and Yasuhisa Mizutani
    Dependence of Vibrational Energy Transfer on Distance in a Four-Helix Bundle Protein: Equidistant Increments with the Periodicity of α Helices
    J. Phys. Chem. B , 126 , 17 , 3283–3290 (2022)
    DOI: 10.1021/acs.jpcb.2c00956
    C01:2022  C01:2020   C01 Akio Kitao  
  27. Akio Kitao
    Principal Component Analysis and Related Methods for Investigating the Dynamics of Biological Macromolecules
    J , 5 , 2 , 298-317 (2022)
    DOI: 10.3390/j5020021
    C01:2022  C01:2020   C01 Akio Kitao  
  28. Jinta Asami, Kanako Terakado Kimura, Yoko Fujita-Fujiharu, Hanako Ishida, Zhikuan Zhang, Yayoi Nomura, Kehong Liu, Tomoko Uemura, Yumi Sato, Masatsugu Ono, Masaki Yamamoto, Takeshi Noda, Hideki Shigematsu, David Drew, So Iwata, Toshiyuki Shimizu, Norimichi Nomura, Umeharu Ohto
    Structure of the bile acid transporter and HBV receptor NTCP
    Nature , 606 , 7916 , 1021 (1026)
    DOI: https://doi.org/10.1038/s41586-022-04845-4
    A01:  B01:   A01 So Iwata  A01 Norimichi Nomura  B01 Masaki Yamamoto  
  29. Jae-Hyun Park, Masashi Iwamoto, Ji-Hye Yun, Tomomi Uchikubo-Kamo, Donghwan Son, Zeyu Jin, Hisashi Yoshida, Mio Ohki, Naito Ishimoto, Kenji Mizutani, Mizuki Oshima, Masamichi Muramatsu, Takaji Wakita, Mikako Shirouzu, Kehong Liu, Tomoko Uemura, Norimichi Nomura, So Iwata, Koichi Watashi, Jeremy R. H. Tame, Tomohiro Nishizawa, Weontae Lee, Sam-Yong Park
    Structural insights into the HBV receptor and bile acid transporter NTCP
    Nature , 606 , 7916 , 1027-1031 (2022)
    DOI: https://doi.org/10.1038/s41586-022-04857-0
    プレスリリース: https://www.yokohama-cu.ac.jp/news/2022/20220518parksamyong.html
    A01:   A01 So Iwata  A01 Norimichi Nomura  A01 Sam-Yong Park  
  30. *Wakao Fukuda, Mamoru Osaki, Yusuke Yasuda, Ryota Hidese , Tsunehiko Higuchi, Naoki Umezawa, Shinsuke Fujiwara and *Eiichi Mizohata
    Substrate Specificity of an Aminopropyltransferase and the Biosynthesis Pathway of Polyamines in the Hyperthermophilic Crenarchaeon Pyrobaculum calidifontis
    Catalysts , 12 , 5 , 567 (2022)
    DOI: 10.3390/catal12050567
    A01:   A01 Eiichi Mizohata  
  31. J. Ono, U. Koshimizu, Y. Fukunishi, H. Nakai
    Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations
    Chem. Phys. Lett. , 794 , 139489 (2022)
    DOI: 10.1016/j.cplett.2022.139489
    C01:2020   C01 Junichi Ono  
  32. 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:  B01:  C01:  A01:2020   A01 So Iwata  B01 Eriko Nango  B01 Sigeki Owada  C01 Minoru Kubo  A01 Toshiaki Hosaka  
  33. Rei Matsuoka, Roman Fudim, Sukkyeong Jung, Chenou Zhang, Andre Bazzone, Yurie Chatzikyriakidou, Carol V. Robinson, Norimichi Nomura, So Iwata, Michael Landreh, Laura Orellana, Oliver Beckstein, David Drew
    Structure, mechanism and lipid-mediated remodeling of the mammalian Na+/H+ exchanger NHA2
    Nature Structural & Molecular Biology , 29 , 2 , 108-120 (2022)
    DOI: 10.1038/s41594-022-00738-2
    A01:   A01 So Iwata  A01 Norimichi Nomura  
  34. Koichiro E. Kishi, Yoon Seok Kim, Masahiro Fukuda, Masatoshi Inoue, Tsukasa Kusakizako, Peter Y. Wang, Charu Ramakrishnan, Eamon F.X. Byrne, Elina Thadhani, Joseph M. Paggi, Toshiki E. Matsui, Keitaro Yamashita, Takashi Nagata, Masae Konno, Sean Quirin, Maisie Lo, Tyler Benster, Tomoko Uemura, Kehong Liu, Mikihiro Shibata, Norimichi Nomura, So Iwata, Osamu Nureki, Ron O. Dror, Keiichi Inoue, Karl Deisseroth, Hideaki E. Kato
    Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine
    Cell , 185 , 4 , 672-689 (2022)
    DOI: 10.1016/j.cell.2022.01.007
    プレスリリース: https://www.u-tokyo.ac.jp/focus/ja/press/z0109_00034.html
    A01:   A01 So Iwata  A01 Norimichi Nomura  A01 Tsukasa Kusakizako  A01 Keitaro Yamashita  
  35. Akira Hirata, Keisuke Okada, Kazuaki Yoshii, Hiroyuki Shiraishi, Shinya Saijo, Kento Yonezawa, Nobutaka Shimizu, Hiroyuki Hori
    Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.
    Nucleic Acids Research , 47 , 20 , 10942-10955 (2019)
    DOI: 10.1093/nar/gkz856
    プレスリリース: https://www.kek.jp/ja/newsroom/attic/PR20191031.pdf
    B01:   B01 Nobutaka Shimizu  
  36. Ite, K., Yonezawa, K., Kitanishi, K., Shimizu, N., and Unno, M.
    Optimal Mutant Model of Human S100A3 Protein Citrullinated at Arg51 by Peptidylarginine Deiminase Type III and Its Solution Structural Properties
    ACS Omega , 5 , 8 , 4032-4042 (2020)
    DOI: 10.1021/acsomega.9b03618
    B01:   B01 Nobutaka Shimizu  
  37. Yuma Nagano , Aoi Sugiyama , Madoka Kimoto , Takuya Wakahara , Yasuyo Noguchi , Xinxin Jiang , Shinya Saijo , Nobutaka Shimizu , Nana Yabuno , Min Yao , Paul R. Gooley , Gregory W. Moseley , Takashi Tadokoro , Katsumi Maenaka , Toyoyuki Ose
    The Measles Virus V Protein Binding Site to STAT2 Overlaps That of IRF9
    Journal of Virology , 94 , 17 , e01169 (2020)
    DOI: 10.1128/jvi.01169-20
    B01:   B01 Nobutaka Shimizu  
  38. Sachiko Toma-Fukai , Ryota Hibi , Takao Naganuma , Mashito Sakai , Shinya Saijo , Nobutaka Shimizu , Michihiro Matsumoto , Toshiyuki Shimizu
    Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure
    Journal of Biological Chemistry , 295 , 43 , 14630-14639 (2020)
    DOI: 10.1074/jbc.ra120.013431
    B01:   B01 Nobutaka Shimizu  
  39. Karman Virk , Kento Yonezawa , Komal Choukate , Lucky Singh , Nobutaka Shimizu , Barnali Chaudhuri
    K-edge anomalous SAXS for protein solution structure modeling
    Acta Crystallographica Section D Structural Biology , 78 , 2 , 204-211 (2022)
    DOI: 10.1107/s205979832101247x
    B01:   B01 Nobutaka Shimizu  
  40. Kiichi Hirazawa, Michihiro Tateyama, Yoshihiro Kubo, Takushi Shimomura,
    Phosphoinositide regulates dynamic movement of the S4 voltage sensor in the second repeat in two-pore channel 3
    J Biol Chem. , 297 , 6 , 101425 (2021)
    DOI: 10.1016/j.jbc.2021.101425
    A01:2020   A01 Takushi Shimomura  
  41. Pan D, Oyama R, Sato T, Nakane T, Mizunuma R, Matsuoka K, Joti Y, Tono K, Nango E, Iwata S, Nakatsu T and *Kato H.
    Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX
    IUCrJ. , 9 , 1 (2021)
    DOI: https://doi.org/10.1107/S2052252521011611
    プレスリリース: https://www.kyoto-u.ac.jp/ja/research-news/2021-12-23
    A01:  B01:   A01 So Iwata  A01 Toru Nakatsu  B01 Eriko Nango  
  42. *Katayama K, Suzuki K, Suno R, Kise R, Tsujimoto H, Iwata S, Inoue A, Kobayashi T & *Kandori H.
    Vibrational spectroscopy analysis of ligand efficacy in human M2 muscarinic acetylcholine receptor (M2R)
    Communications Biology , 4 , 1321 (2021)
    DOI: https://doi.org/10.1038/s42003-021-02836-1
    プレスリリース: https://www.nitech.ac.jp/news/press/2021/9297.html
    A01:  A01:2020   A01 So Iwata  A01 Kota Katayama  
  43. Shinya Hanashima, Takanori Nakane, *Eiichi Mizohata
    Heavy Atom Detergent/Lipid Combined X-ray Crystallography for Elucidating Structure-function Relationships of Membrane Proteins
    Membranes , 11 , 11 , 823 (2021)
    DOI: 10.3390/membranes11110823
    A01:   A01 Eiichi Mizohata  
  44. H. Nakai, T. Takemura, J. Ono, Y. Nishimura
    Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin using Realistic Models
    J. Phys. Chem. B , 125 , 39 , 10947–10963 (2021)
    DOI: 10.1021/acs.jpcb.1c06231
    C01:2020   C01 Junichi Ono  
  45. 1. *Murakaw T, Suzuki M, Arima T, Sugahara M, Tanaka T, Tanaka R, Iwata S, Nango E, Tono K, Hayashi H, Fukui K, Yano T, Tanizawah K and *Okajima T.
    Microcrystal preparation for serial femtosecond X-ray crystallography of bacterial copper amine oxidase
    Acta Crystallographica Section F. , 77 (2021)
    DOI: https://doi.org/10.1107/S2053230X21008967
    A01:  B01:  A01:2020   A01 So Iwata  B01 Eriko Nango  A01 Takeshi Murakawa  
  46. 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:   C01 Osamu Miyashita  
  47. 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
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  48. Dmitry Ghilarov, Satomi Inaba-Inoue, Piotr Stepien, Feng Qu, Elizabeth Michalczyk, Zuzanna Pakosz, Norimichi Nomura, Satoshi Ogasawara, Graham Charles Walker, Sylvie Rebuffat, So Iwata, Jonathan Gardiner Heddle, Konstantinos Beis
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    Science Advances , 7 , 37 , abj5363 (2021)
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    A01:   A01 So Iwata  A01 Norimichi Nomura  
  49. Hiroyuki H. Okamoto, Hirotake Miyauchi, Asuka Inoue, Francesco Raimondi, Hirokazu Tsujimoto, Tsukasa Kusakizako, Wataru Shihoya, Keitaro Yamashita, Ryoji Suno, Norimichi Nomura, Takuya Kobayashi, So Iwata, Tomohiro Nishizawa, Osamu Nureki
    Cryo-EM structure of the human MT1–Gi signaling complex
    Nature Structural & Molecular Biology , 28 (2021)
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  50. Shingo Nojima, Yoko Fujita, Kanako Terakado Kimura, Norimichi Nomura, Ryoji Suno, Kazushi Morimoto, Masaki Yamamoto, Takeshi Noda, So Iwata, Hideki Shigematsu, Takuya Kobayashi
    Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein
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    DOI: 10.1016/j.str.2020.11.007
    A01:  B01:   A01 So Iwata  A01 Norimichi Nomura  B01 Masaki Yamamoto  
  51. Stephanie L. Neville, Jennie Sjöhamn, Jacinta A. Watts, Hugo MacDermott-Opeskin, Stephen J. Fairweather, Katherine Ganio, Alex Carey Hulyer, Aaron P. McGrath, Andrew J. Hayes, Tess R. Malcolm, Mark R. Davies, Norimichi Nomura, So Iwata, Megan L. O’Mara, Megan J. Maher, Christopher A. McDevitt
    The structural basis of bacterial manganese import
    Science Advances , 7 , 32 , eabg3980 (2021)
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    A01:   A01 So Iwata  A01 Norimichi Nomura  
  52. Fujiyama K, Kato N, Re S, Kinugasa K, Watanabe K, Takita R, Nogawa T, Hino T, Osada H, Sugita Y, Takahashi S, Nagano S.
    Molecular basis for two stereoselective Diels-Alderases that produce decalin skeletons.
    Angew Chem Int Ed. (2021)
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  53. 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
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    C01:   C01 Osamu Miyashita  
  54. Demura K, Kusakizako T, Shihoya W, Hiraizumi M, Nomura K, Shimada H, Yamashita K, Nishizawa T, Taruno A, Nureki O.
    Cryo-EM structures of calcium homeostasis modulator channels in diverse oligomeric assemblies
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    A01:  A01:2020   A01 Tsukasa Kusakizako  A01 Wataru Shihoya  
  56. 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
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  57. Tatsuki Tanaka, Manish Singh, Wataru Shihoya, Keitaro Yamashita, Hideki Kandori, Osamu Nureki
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    Biochem Biophys Res Commun , 533 , 3 , 262-267 (2020)
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    Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping
    Proceedings of the National Academy of Sciences of the United States of America , 118 , 14 , e2016328118 (2021)
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    Unique Electronic Structures of the Highly Ruffled Hemes in Heme-Degrading Enzymes of Staphylococcus aureus, IsdG and IsdI, by Resonance Raman and Electron Paramagnetic Resonance Spectroscopies.
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    The structure of MgtE in the absence of magnesium provides new insights into channel gating
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    A01:   A01 So Iwata  A01 Norimichi Nomura  
  61. Matoba K, Kotani T, Tsutsumi A, Tsuji T, Mori T, Noshiro D, Sugita Y, Nomura N, Iwata S, Ohsumi Y, Fujimoto T, Nakatogawa H, Kikkawa M, Noda NN
    Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion
    Nature Structural & Molecular Biology , 27 , 1185-1193 (2020)
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    A01:   A01 So Iwata  A01 Norimichi Nomura  
  62. Umeda R, Satouh Y, Takemoto M, Nakada-Nakura Y, Liu K, Yokoyama T, Shirouzu M, Iwata S, Nomura N, Sato K, Ikawa M, Nishizawa T, Nureki O
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    Nature Communications , 11 , 1606 (2020)
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    A01:   A01 So Iwata  A01 Norimichi Nomura  
  63. Asada H, Inoue A, Ngako Kadji FM, Hirata K, Shiimura Y, Im D, Shimamura T, Nomura N, Iwanari H, Hamakubo T, Kusano-Arai O, Hisano H, Uemura T, Suno C, Aoki J and Iwata S
    The crystal structure of angiotensin II type 2 receptor with endogenous peptide hormone
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    A01:   A01 So Iwata  A01 Norimichi Nomura  
  64. Kinjo T, Terai K, Horita S, Nomura N, Sumiyama K, Togashi K, Iwata S and Matsuda M.
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    Nature Methods , 16 , 1029-1036 (2019)
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    A01:   A01 So Iwata  A01 Norimichi Nomura  
  65. Ichiro Tanaka, Ryota Nishinomiya, Ryosuke Goto, Shun Shimazaki, Toshiyuki Chatake
    Recent Structural Insights on the Mechanism of Lysozyme Hydrolysis
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    Structure of the dopamine D2 receptor in complex with the antipsychotic drug spiperone
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    プレスリリース: https://www.yokohama-cu.ac.jp/news/2019/202002paku_SA.html
    A01:   A01 Sam-Yong Park  
  95. Katayama T, Northey T, Gawelda W, Milne CJ, Vankó G, Lima FA, Bohinc R, Németh Z, Nozawa S, Sato T, Khakhulin D, Szlachetko J, Togashi T, Owada S, Adachi SI, Bressler C, Yabashi M, Penfold TJ
    Tracking multiple components of a nuclear wavepacket in photexcited Cu(I)-phenanthroline complex using ultrafast X-ray spectroscopy
    Nat. Commun. , 10 (2019)
    DOI: 10.1038/s41467-019-11499-w
    B01:   B01 Sigeki Owada  B01 Shinichi Adachi  B01 Tetsuo Katayama  
  96. Katayama T, Nozawa S, Umena Y, Lee S, Togashi T, Owada S, Yabashi M.
    A versatile experimental system for tracking ultrafast chemical reactions with X-ray free-electron lasers
    Struct. Dyn , 6 , 2019 (2019)
    DOI: 10.1063/1.5111795
    A01:  B01:   A01 Yasufumi Umena  B01 Sigeki Owada  B01 Tetsuo Katayama  

書籍Books

  1. 津本浩平, 前仲勝実（編者）、分担著者
    創薬研究のための相互作用解析パーフェクト : 低中分子・抗体創薬におけるスクリーニング戦略と実例、in silico解析、一歩進んだ分析技術まで
    羊土社 page: 313-322 (2021)
    B01:   B01 Nobutaka Shimizu  
  2. Nomura N, Nomura Y, Sato Y and Iwata S
    Methods in Molecular Biology, Vol. 2247 “Multiprotein Complexes"
    Springer page: 77-103 (2021)
    A01:   A01 So Iwata  A01 Norimichi Nomura  
  3. Nomura N, Nomura Y, Sato Y and Iwata S
    Methods in Enzymology, Vol. 629, "Tumor Immunology and Immunotherapy – Molecular Methods" (Edited by Lorenzo Galluzzi, Nils-Petter Rudqvist)
    Academic Press page: 383-399 (2019)
    A01:   A01 So Iwata  A01 Norimichi Nomura  
  4. Raymond G. Sierra, Uwe Weierstall, Dominik Oberthuer, Michihiro Sugahara, Eriko Nango, So Iwata and Alke Meents.
    X-ray Free Electron Lasers - A Revolution in Structural Biology.
    Springer page: 109-184 (2019)
    A01:  B01:   A01 So Iwata  B01 Eriko Nango  
  5. 山下恵太郎、溝端栄一
    膜タンパク質工学ハンドブック 『X線結晶解析による新規構造の解明』
    (株)エヌ・ティー・エス page: 27-33 (2020)
    A01:   A01 Keitaro Yamashita  A01 Eiichi Mizohata  
  6. 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:  C01:   A01 Eiichi Mizohata  C01 Minoru Kubo  

学会発表Presentations, Lectures

  1. Nobutaka Shimizu
    Structural state estimation of biological macromolecules in solution using BioSAXS
    蛋白研セミナー：Frontier of Dynamic Structural Biology , ( 2022 , 10 )
    B01:   B01 Nobutaka Shimizu  
  2. Nobutaka Shimizu, Keiko Yatabe, Masatsuyo Takahashi, Yasuko Nagatani
    Photon FactoryのBioSAXS測定解析システムの現状
    第36回日本放射光学会年会・放射光科学合同シンポジウム, ( 2023 , 1 )
    B01:   B01 Nobutaka Shimizu  
  3. Nobutaka Shimizu, Kento Yonezawa, Yasuko Nagatani, Keiko Yatabe, Masatsuyo Takahashi
    BioSAXS measurement and analysis system at the Photon Factory
    Asia Oceania International Conference on Synchrotron Radiation Instruments 2022, ( 2022 , 11 )
    B01:   B01 Nobutaka Shimizu  
  4. Nobutaka Shimizu, Hideki Takagi, Yasuko Nagatani, Takeharu Mori, Keiko Yatabe, Masatsuyo Takahashi, Noriyuki Igarashi
    Upgrade of BioSAXS measurement system at the Photon Factory
    第60回日本生物物理学会年会, ( 2022 , 9 )
    B01:   B01 Nobutaka Shimizu  
  5. チャン フ ズイ, 畑　宏明,中矢　光, 北尾彰朗
    Benchmarking the free energy calculation of PaCS-MD/MSM
    第21回日本蛋白質科学会年会, ( 2021 , 6 )
    C01:2022  C01:2020   C01 Akio Kitao  
  6. 平悠太、Duy Tran、北尾彰朗
    DNA binding mechanisms of the p53 C-terminal domain elucidated by MD simulation
    第58回日本生物物理学会年会, ( 2020 , 9 )
    C01:2022  C01:2020   C01 Akio Kitao  
  7. Sobeh Mohamed Marzouk、北尾彰朗
    Investigating the dissociation process of DBD-p53/DNA complex by PaCS-MD and MSM
    第58回日本生物物理学会年会, ( 2020 , 9 )
    C01:2022  C01:2020   C01 Akio Kitao  
  8. 宮澤佳希、Phuoc Duy Tran、竹村和浩、北尾彰朗
    PaCS-MD/MSM を用いたタンパク質複合体の速度定数評価(Kinetic rate evaluation for protein complexes by PaCS-MD/MSM)
    第58回日本生物物理学会年会, ( 2020 , 9 )
    C01:2022  C01:2020   C01 Akio Kitao  
  9. 竹村和浩、北尾彰朗
    Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock
    第58回日本生物物理学会年会, ( 2020 , 9 )
    C01:2022  C01:2020   C01 Akio Kitao  
  10. 宮澤佳希、Duy Phuoc Tran、竹村和浩、北尾彰朗
    Protein-protein complex dissociation simulated by Parallel Cascade Selection Molecular Dynamics
    第20回日本蛋白質科学会年会, ( 2020 , 7 )
    C01:2022  C01:2020   C01 Akio Kitao  
  11. Tran P. Duy、Akio Kitao
    Simulating the association/dissociation process of flexible protein complexes
    第20回日本蛋白質科学会年会, ( 2020 , 7 )
    C01:2022  C01:2020   C01 Akio Kitao  
  12. 竹村和浩、北尾彰朗
    Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock
    第20回日本蛋白質科学会年会, ( 2020 , 7 )
    C01:2022  C01:2020   C01 Akio Kitao  
  13. Wijaya Tegar Nurwahyu、北尾彰朗
    Dynamics of Close-Open State of Candida antarctica Lipase B Obtained by Parallel Cascade Molecular Dynamics Simulation and The Markov State Model
    第10回日本生物物理学会関東支部会, ( 2021 , 3 )
    C01:2022  C01:2020   C01 Akio Kitao  
  14. 溝端栄一
    銅含有亜硝酸還元酵素の動的結晶構造解析
    第93回 日本生化学会大会, ( 2020 , 9 )
    A01:   A01 Eiichi Mizohata  
  15. Eiichi Mizohata
    Damage-free protein observation and structure determination using X-ray free electron laser
    Pacifichem2020, ( 2021 , 12 )
    A01:   A01 Eiichi Mizohata  
  16. Kento Yonezawa, Masatuyo Takahashi, Keishi Oyama, Keiko Yatabe, Yasuko Nagatani, Nobutaka Shimizu
    Development of software for automatic processing of matrix data measured with SEC-SAXS/UV-Vis. spectroscopy
    第59回日本生物物理学会年会, ( 2021 , 11 )
    B01:   B01 Nobutaka Shimizu  
  17. N. Shimizu, H. Takagi, Y. Nagatani, K. Yonezawa, T. Mori, K. Yatabe, M. Takahashi, K. Oyama, N. Igarashi
    Small-angle X-ray scattering beamlines at the photon factory
    IUCr 2021 - XXV General Assembly and Congress of the International Union of Crystallography, ( 2021 , 8 )
    B01:   B01 Nobutaka Shimizu  
  18. 清水伸隆、高木秀彰、永谷康子、米澤健人、大田浩正、森丈晴、 谷田部景子、高橋正剛、西條慎也、鈴木文俊、羽方望、五十嵐教之
    Photon Factory の⼩⾓散乱ビームラインの現状
    第34回日本放射光学会年会・放射光科学合同シンポジウム, ( 2021 , 1 )
    B01:   B01 Nobutaka Shimizu  
  19. Kento Yonezawa, Ayako Furukawa, Naruhiko Adachi, Toshiya Senda, Nobutaka Shimizu, Yoshifumi Nishimura
    Recent hybrid methods approach utilizing Biological Small Angle X-ray Scattering at the Photon Factory
    第58回日本生物物理学会年会, ( 2020 , 9 )
    B01:   B01 Nobutaka Shimizu  
  20. Nobutaka Shimizu, Kento Yonezawa, Masatsuyo Takahashi, Keiko Yatabe, Yasuko Nagatani
    Current Status of BioSAXS at the Photon Factory
    第58回日本生物物理学会年会, ( 2020 , 9 )
    B01:   B01 Nobutaka Shimizu  
  21. K. Yonezawa, M. Takahashi, K. Yatabe, Y. Nagatani, Y. Hayashi, S. Amano, H. Kamikubo, N. Shimizu
    Recent Progress Of BioSAXS Equipment For Complex Molecular Systems At The Photon Factory
    第20回日本タンパク質科学会年会, ( 2020 , 7 )
    B01:   B01 Nobutaka Shimizu  
  22. 清水伸隆
    SEC-SAXS による分子間相互作用測定解析システム
    第33回日本放射光学会年会・放射光科学合同シンポジウム, ( 2020 , 1 )
    B01:   B01 Nobutaka Shimizu  
  23. 米澤健人、林有吾、吉田桂人、天野真治、岡部龍二、清水伸隆、上久保裕生
    連続滴定 X 線溶液散乱測定を利用した分子複合系における多成分平衡状態の解析
    第33回日本放射光学会年会・放射光科学合同シンポジウム, ( 2020 , 1 )
    B01:   B01 Nobutaka Shimizu  
  24. Shimizu, Nobutaka; Yonezawa, Kento; Takahashi, Masatuyo; Yatabe, Keiko, Nagatani, Yasuko
    BioSAXS experiment at the Photon Factory
    International Symposium on Diffraction Structural BIology 2019, ( 2019 , 10 )
    B01:   B01 Nobutaka Shimizu  
  25. Nobutaka Shimizu, Kento Yonezawa, Masatsuyo Takahashi, Keiko Yatabe, Yasuko Nagatani
    Progress of Biological Small-Angle X-ray Scattering at the Photon Factory
    日本生物物理学会, ( 2019 , 9 )
    B01:   B01 Nobutaka Shimizu  
  26. 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:   C01 Minoru Kubo  
  27. 末宗周憲、日野智也、永野真吾
    アナモックス菌のラダラン脂質生合成の全容解明に向けた研究
    第3回生合成リデザイン若手シンポジウム, ( 2019 , 8 )
    A01:   A01 Shingo Nagano  
  28. 上垣哲心、末宗周憲、日野智也、永野真吾
    ラダラン脂質生合成アシルACP中間体の探索に向けた抗ACP抗体の作製
    第92回日本生化学会大会, ( 2019 , 9 )
    A01:   A01 Shingo Nagano  
  29. 安田早希、藤山敬介、日野智也、水谷正治、永野真吾
    トマチン16位水酸化酵素のX線結晶構造解析
    令和元年度結晶学会, ( 2019 , 11 )
    A01:   A01 Shingo Nagano  
  30. 藤山 敬介, 畑田 珠希, 日野 智也, 水谷 正治, 永野 真吾
    結晶構造に基づいたCYP90B1によるステロールC-22位水酸化の立体選択性の改変
    植物化学調節学会第54回大会, ( 2019 , 11 )
    A01:   A01 Shingo Nagano  
  31. 清中　茂樹
    New chemogenetic approaches for artificially controlling neurotransmitter receptor function in neuronal system
    10th RSC-CSJ joint symposium -Chemistry for complex biological systems-, ( 2019 , 9 )
    A01:   A01 Shigeki Kiyonaka  
  32. 清中　茂樹
    グルタミン酸受容体の精密動態を明らかにするためのケミカルラベル化法
    第92回日本生化学会大会 , ( 2019 , 9 )
    A01:   A01 Shigeki Kiyonaka  
  33. 清中　茂樹
    神経伝達物質受容体機能を解き明かすためのケミカルバイオロジー新技術
    第72回日本薬理学会西南部会（次世代薬理学セミナー）, ( 2019 , 11 )
    A01:   A01 Shigeki Kiyonaka  
  34. 清中　茂樹
    Coordination chemogenetics, a new technique for allosteric regulation of membrane receptors
    The 50th NIPS International Symposium “MIRACLES” in Caridiovasucular Physology, ( 2019 , 12 )
    A01:   A01 Shigeki Kiyonaka  
  35. 溝端栄一
    X線自由電子レーザーを応用したタンパク質の動的結晶構造解析
    日本プロテオーム学会2019年大会 第70回日本電気泳動学会総会, ( 2019 , 7 )
    A01:   A01 Eiichi Mizohata  
  36. Osamu Miyashita
    Hybrid Approach for Structural Biology: Simulation and Experimental Data
    CBI Society Meeting, ( 2019 , 10 )
    C01:   C01 Osamu Miyashita