研究成果

Results list研究成果一覧

Publication year発行年

Categoryカテゴリー

Type班タイプ

Member研究者名

Keywordタイトルキーワード

謝辞の記載についてAcknowledgement remarks

雑誌論文Papers

*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:計画研究 B01:計画研究 A01 岩田　想 A01 別所　義隆 B01 南後　恵理子 B01 大和田　成起
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:計画研究 B01 足立　伸一 B01 片山　哲夫
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01:計画研究 A01 岩田　想 A01 野村　紀通 B01 山本　雅貴
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
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01:計画研究 A01 岩田　想 A01 中津　亨 B01 南後　恵理子
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:計画研究 B01:計画研究 A01:2020年公募班 A01 岩田　想 B01 南後　恵理子 A01 村川　武志
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
Structure , 29 , 3 , 252-260 (2021)
DOI: 10.1016/j.str.2020.11.007
A01:計画研究 B01:計画研究 A01 岩田　想 A01 野村　紀通 B01 山本　雅貴
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
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
Im D, Inoue A, Fujiwara T, Nakane T, Yamanaka Y, Uemura T, Mori C, Shiimura Y, Kimura KT, Asada H, Nomura N, Tanaka T, Yamashita A, Nango E, Tono K, Kadji FMN, Aoki J, Iwata S and Shimamura T.
Structure of the dopamine D2 receptor in complex with the antipsychotic drug spiperone
Nat Commun. , 11 , 1 , 6442 (2020)
DOI: 10.1038/s41467-020-20221-0
プレスリリース: https://www.kyoto-u.ac.jp/ja/research-news/2020-12-24-2
A01:計画研究 B01:計画研究 A01 岩田　想 A01 野村　紀通 B01 南後　恵理子
Jong Goo Kim, Shunsuke Nozawa, Hanui Kim, Eun Hyuk Choi, Tokushi Sato, Tae Wu Kim, Kyung Hwan Kim, Hosung Ki, Jungmin Kim, Minseo Choi, Yunbeom Lee, Jun Heo, Key Young Oang, Kouhei Ichiyanagi, Ryo Fukaya, Jae Hyuk Lee, Jaeku Park, Intae Eom, Sae Hwan Chun, Sunam Kim, Minseok Kim, Tetsuo Katayama, Tadashi Togashi, Sigeki Owada, Makina Yabashi, Sang Jin Lee, Seonggon Lee, Chi Woo Ahn, Doo-Sik Ahn, Jiwon Moon, Seungjoo Choi, Joonghan Kim, Taiha Joo, Jeongho Kim, Shin-ichi Adachi, and Hyotcherl Ihee.
Mapping the emergence of molecular vibrations mediating bond formation
Nature , 582 , 520–524 (2020)
DOI: 10.1038/s41586-020-2417-3
プレスリリース: https://www.kek.jp/ja/newsroom/2020/06/25/1005/
B01:計画研究 B01 大和田　成起 B01 足立　伸一 B01 片山　哲夫
C. Wickstrand , G. Katona , T. Nakane, P. Nogly , J. Standfuss , E. Nango and R. Neutze.
A tool for visualizing protein motions in time-resolved crystallography
Struct Dyn. , 7 , 024701 (2020)
DOI: https://doi.org/10.1063/1.5126921
B01:計画研究 B01 南後　恵理子
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
M. Hada, K. Miyata, S. Ohmura, Y. Arashida, K. Ichiyanagi, I. Katayama, T. Suzuki, W. Chen, S. Mizote S, T. Sawa, T. Yokoya, T. Seki, J. Matsuo, T. Tokunaga, C. Itoh, K. Tsuruta, R. Fukaya, S. Nozawa, S. Adachi, J. Takeda, K. Onda, S. Koshihara, Y. Hayashi, and Y. Nishina
Selective Reduction Mechanism of Graphene Oxide Driven by the Photon Mode versus the Thermal Mode
ACS NANO , 13 , (9) , 10103-10112 (2019)
DOI: 10.1021/acsnano.9b03060
B01:計画研究 B01 足立　伸一
A. Suzuki, K. Aratsu, S. Datta, N. Shimizu, H. Takagi, R. Haruki, S. Adachi, M. Hollamby, F. Silly and S. Yagai
Topological Impact on the Kinetic Stability of Supramolecular Polymers
J. Am. Chem. Soc. , 141 , (33) , 13196-13202 (2019)
DOI: 10.1021/jacs.9b06029
B01:計画研究 B01 足立　伸一
T. Ishizuka, T. Kogawa, M. Makino, Y. Shiota, K. Ohara, H. Kotani, S. Nozawa, S. Adachi, K. Yamaguchi, K. Yoshizawa and T. Kojima
Formation of a Ruthenium(V)-Imido Complex and the Reactivity in Substrate Oxidation in Water through the Nitrogen Non-Rebound Mechanism
Inorg. Chem. , 58 , (19) , 12815-12824 (2019)
DOI: 10.1021/acs.inorgchem.9b01781
B01:計画研究 B01 足立　伸一
A. Koide, Y. Uemura, D. Kido, Y. Wakisaka, S. Takakusagi, B. Ohtani, Y. Niwa, S. Nozawa, K. Ichiyanagi, R. Fukaya, S. Adachi, T. Katayama, T. Togashi, S. Owada, M. Yabashi, Y. Yamamoto, M. Katayama, K. Hatada, T. Yokoyama, and K. Asakura
Photoinduced anisotropic distortion as the electron trapping site of tungsten trioxide by ultrafast W L1-edge X-ray absorption spectroscopy with full potential multiple scattering calculations
Phys. Chem. Chem. Phys. , 22 , (5) , 2615-2621 (2020)
DOI: 10.1039/C9CP01332F
B01:計画研究 B01 足立　伸一 B01 片山　哲夫
K. Aratsu, R. Takeya, B. R. Pauw, M. J. Hollamby, Y. Kitamoto, N. Shimizu, H. Takagi, R. Haruki, S. Adachi, and S. Yagai
Supramolecular copolymerization driven by integrative self-sorting of hydrogen-bonded rosettes
Nature Comm. , 11 , (1)1623 (2020)
DOI: 10.1038/s41467-020-15422-6
プレスリリース: https://www.kek.jp/ja/newsroom/attic/PR20200331.pdf
B01:計画研究 B01 足立　伸一
Y. Kitamoto, Z. Pan, D. D. Prabhu, A. Isobe, T. Ohba, N. Shimizu, H. Takagi, R. Haruki, S. Adachi and S. Yagai
One-shot preparation of topologically chimeric nanofibers via a gradient supramolecular copolymerization
Nature Comm. , 10 , (1)4578 (2019)
DOI: 10.1038/s41467-019-12654-z
B01:計画研究 B01 足立　伸一
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:計画研究 B01 大和田　成起 B01 足立　伸一 B01 片山　哲夫
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:計画研究 B01:計画研究 A01 梅名　泰史 B01 大和田　成起 B01 片山　哲夫

書籍Books

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:計画研究 B01 清水　伸隆
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:計画研究 B01:計画研究 A01 岩田　想 B01 南後　恵理子

学会発表Presentations, Lectures

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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆
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:計画研究 B01 清水　伸隆