2023年
Multimodal action of KRP203 on phosphoinositide kinases in vitro and in cells.
Yoshiki Ikeda a b, Mindy I. Davis c, Kazutaka Sumita a d, Yuxiang Zheng e, Satoshi Kofuji a f, Mika Sasaki a, Yoshihisa Hirota a g, Rajan Pragani c, Min Shen c, Matthew B. Boxer c, Koh Takeuchi h, Toshiya Senda i j k, Anton Simeonov c, Atsuo T. Sasaki
Biochemical and Biophysical Research Communications Volume 679, Pages 116-121, 30 October 2023
Stromal Interaction Molecule 1 Maintains β-Cell Identity and Function in Female Mice Through Preservation of G-Protein–Coupled Estrogen Receptor 1 Signaling.
Paul Sohn, Madeline R. McLaughlin, Preethi Krishnan, Wenting Wu, Marjan Slak Rupnik, Akira Takasu, Toshiya Senda, Chih-Chun Lee, Tatsuyoshi Kono, Carmella Evans-Molina
Diabetes Volume 72, Issue 10 October 2023
Identification and characterization of endo-α-, exo-α-, and exo-β-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria.
Michiko Shimokawa, Akihiro Ishiwata, Toma Kashima, Chiho Nakashima, Jiaman Li, Riku Fukushima, Naomi Sawai, Miku Nakamori, Yuuki Tanaka, Azusa Kudo, Sae Morikami, Nao Iwanaga, Genki Akai, Nobutaka Shimizu, Takatoshi Arakawa, Chihaya Yamada, Kanefumi Kitahara, Katsunori Tanaka, Yukishige Ito, Shinya Fushinobu & Kiyotaka Fujita
Nature Communications 9 September 2023
Crystal Structure Analysis of SH2 Domains in Complex with Phosphotyrosine Peptides.
Miki Senda & Toshiya Senda
Methods in molecular biology (MIMB) volume 2705 06 September 2023
Structural bases for the Charcot-Marie-Tooth disease induced by single amino acid substitutions of myelin protein zero.
Masayoshi Sakakura, Mikio Tanabe, Masaki Mori, Hideo Takahashi, Kazuhiro Mio
Structure September 11, 2023
The two-step cargo recognition mechanism of heterotrimeric kinesin.
Xuguang Jiang, Tadayuki Ogawa, Kento Yonezawa, Nobutaka Shimizu, Sotaro Ichinose, Takayuki Uchihashi, Wataru Nagaike, Toshio Moriya, Naruhiko Adachi, Masato Kawasaki, Naoshi Dohmae, Toshiya Senda, Nobutaka Hirokawa
EMBO Reports (2023)e56864 14 August 2023
Anti-nanodisc antibodies specifically capture nanodiscs and facilitate molecular interaction kinetics studies for membrane protein.
Fuhito Nakagawa, Marin Kikkawa, Sisi Chen,Yasuomi Miyashita ,Norie Hamaguchi-Suzuki, Minami Shibuya, Soichi Yamashita, Lisa Nagase, Satoshi Yasuda, Mitsunori Shiroishi, Toshiya Senda, Keisuke Ito, Takeshi Murata, Satoshi Ogasawara
Scientific reports 19 July 2023
Design of allosteric sites into rotary motor V1-ATPase by restoring lost function of pseudo-active sites.
Takahiro Kosugi, Tatsuya Iida, Mikio Tanabe, Ryota Iino & Nobuyasu Koga
Nature Chemistry 06 July 2023
X-ray and Electron Diffraction Observations of Steric Zipper Interactions in Metal-Induced Peptide Cross-β Nanostructures.
Eisuke Tsunekawa, Yusuke Otsubo, Yusuke Yamada, Akihito Ikeda, Naruhiko Adachi, Masato Kawasaki, Akira Takasu, Shinji Aramaki, Toshiya Senda, Sota Sato, Satoshi Yoshida, Makoto Fujita, and Tomohisa Sawada
J. Am. Chem. Soc. 2023, 145, 29, 16160–16165 July 12, 2023
X-Ray Conformation and Structure–Activity Relationships of MA026, a Reversible Tight Junction Opener.
Minagi Mukaiyama, Chihiro Uchiyama, Akane Fukuda, Yoshiki Nakazawa, Yuka Kuramochi, Yudai Shibata, Sho Konno, Kyohei Muguruma, Naohiro Matsugaki, Tomo Asari, Kazuyoshi Ogawa, Akihiro Taguchi, Kentaro Takayama, Atsuhiko Taniguchi, Yoko Nagumo, Toshiya Senda, Yoshio Hayashi, and Takeo Usui
J. Med. Chem. 2023, 66, 13, 8717–8724 June 23, 2023
Targeting transglutaminase 2 mediated exostosin glycosyltransferase 1 signaling in liver cancer stem cells with acyclic retinoid.
Qin, XY., Furutani, Y., Yonezawa, K., Shimizu, N., Kato-Muramatsu, M., Shiriuzu, M., Xu, Y., Yamano, Y., Wada, A., Gailhouste, L., Shresttha, R., Takahashi, M., Keillor, J. W., Su, T., Yu,
Cell Death Dis. 14 358 13 June 2023
Effect of Alkali Metal Cations on the Unilamellar Vesicle of a Squalene Bearing 18-Crown-6.
Tran Ngoc Linh, Takashi Arimura*, Ken-Ichi Tominaga, Hiroko Isoda, Masato Kawasaki, and Naruhiko Adachi
ACS Omega. 8, 12, 11583–11587 March 17, 2023
Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ.
Koh Takeuchi, Miki Senda, Yoshiki Ikeda, Koji Okuwaki, Kaori Fukuzawa, So Nakagawa, Mika Sasaki, Atsuo T. Sasaki, Toshiya Senda
Febs J. 01 March 2023
Structural basis underlying the synergism of NADase and SLO during group A Streptococcus infection.
Wei-Jiun Tsai, Yi-Hsin Lai, Yong-An Shi, Michal Hammel, Anthony P. Duff, Andrew E. Whitten, Karyn L. Wilde, Chun-Ming Wu, Robert Knott, U-Ser Jeng, Chia-Yu Kang, Chih-Yu Hsu, Jian-Li Wu, Pei-Jane Tsai, Chuan Chiang-Ni, Jiunn-Jong Wu, Yee-Shin Lin, Ching-Chuan Liu, Toshiya Senda & Shuying Wang
Commun Biology. 6 124 31 Jan. 2023
Uphill energy transfer mechanism for photosynthesis in an Antarctic alga.
Makiko Kosugi, Masato Kawasaki, Yutaka Shibata, Kojiro Hara, Shinichi Takaichi, Toshio Moriya, Naruhiko Adachi, Yasuhiro Kamei, Yasuhiro Kashino, Sakae Kudoh, Hiroyuki Koike & Toshiya Senda
Nature Communications 15 Feb. 2023
Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions.
Naoya Ohara, Norifumi Kawakami, Ryoichi Arai, Naruhiko Adachi, Toshio Moriya, Masato Kawasaki, and Kenji Miyamoto
J. Am. Chem. Soc. 2023, 145, 1, 216–223
MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV–visible spectroscopy combined with size-exclusion chromatography.
Kento Yonezawa, Masatsuyo Takahashi, Keiko Yatabe, Yasuko Nagatani, Nobutaka Shimizu
Biophys. Physicobiol 2023 #20 e200001
2022
Structural basis for activation of DNMT1.
Amika Kikuchi, Hiroki Onoda, Kosuke Yamaguchi, Satomi Kori, Shun Matsuzawa, Yoshie Chiba, Shota Tanimoto, Sae Yoshimi, Hiroki Sato, Atsushi Yamagata, Mikako Shirouzu, Naruhiko Adachi, Jafar Sharif, Haruhiko Koseki, Atsuya Nishiyama, Makoto Nakanishi, Pierre-Antoine Defossez & Kyohei Arita
Nature Communications Article number: 7130 21 November 2022
Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase.
Takuya Miyakawa, Jian Yang, Masato Kawasaki, Naruhiko Adachi, Ayumu Fujii, Yumiko Miyauchi, Tomonari Muramatsu, Toshio Moriya, Toshiya Senda, Masaru Tanokura
Nature Communications Article number: 5097 30 August 2022
Core fucose-specific Pholiota squarrosa lectin (PhoSL) as a potent broad-spectrum inhibitor of SARS-CoV-2 infection.
Kazuhiko Yamasaki, Naruhiko Adachi, Mya Myat Ngwe Tun, Akihito Ikeda, Toshio Moriya, Masato Kawasaki, Tomoko Yamasaki, Tomomi Kubota, Izuru Nagashima, Hiroki Shimizu, Hiroaki Tateno, Kouichi Morita
The FEBS Journal 25 August 2022
Ligand Recognition by the Lipid Transfer Domain of Human OSBP Is Important for Enterovirus Replication.
Jun Kobayashi, Minetaro Arita*, Shota Sakai, Hirotatsu Kojima, Miki Senda, Toshiya Senda, Kentaro Hanada, and Ryuichi Kato
ACS Infectious Diseases 1161–1170 6 Aug 2022
Molecular Tension Probe for In Vitro Bioassays.
Sung-Bae Kim, Rika Fujii, Simon Miller & Mikio Tanabe
Methods in Molecular Biology 13 July 2022
Serial crystallography with multi-stage merging of thousands of images.
Alexei S. Soares, Yusuke Yamada, Jean Jakoncic, Sean McSweeney, Robert M. Sweet, John Skinner, James Foadi, Martin R. Fuchs, Dieter K. Schneider, Wuxian Shi, Babak Andi, Lawrence C. Andrews
, Herbert J. Bernstein.
Acta Crystallographica. Section F, Structural Biology Communications Volume 78 Part 7 2022 July
A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin.
Miho Watanabe-Takahashi, Miki Senda, Ryunosuke Yoshino, Masahiro Hibino, Shinichiro Hama, Tohru Terada, Kentaro Shimizu, Toshiya Senda & Kiyotaka Nishikawa.
Scientific Reports 06 July 2022
Chemical and Chemo-Enzymatic Syntheses of Glycans Containing Ribitol Phosphate Scaffolding of Matriglycan.
Jun-Ichi Tamura, Takahiro Tamura, Shunsuke Hoshino, Rieko Imae, Ryuichi Kato, Mizuki Yokono, Mao Nagase, Shiho Ohno, Noriyoshi Manabe, Yoshiki Yamaguchi, Hiroshi Manya, and Tamao Endo*
ACS chemical biology 2022 17, 6, 1513–1523 June 6, 2022
The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity.
Koh Takeuchi, Yoshiki Ikeda, Miki Senda, Ayaka Harada, Koji Okuwaki, Kaori Fukuzawa, So Nakagawa, Hong Yang Yu, Lisa Nagase, Misaki Imai, Mika Sasaki , Yu-Hua Lo, Doshun Ito, Natsuki Osaka, Yuki Fujii , Atsuo T Sasaki, Toshiya Senda
Structure 2022 Jun 2;30(6):886-899
Discovery of non-squalene triterpenes.
Hui Tao, Lukas Lauterbach, Guangkai Bian, Rong Chen, Anwei Hou, Takahiro Mori, Shu Cheng, Ben Hu, Li Lu, Xin Mu, Min Li, Naruhiko Adachi, Masato Kawasaki, Toshio Moriya, Toshiya Senda, Xinghuan Wang, Zixin Deng, Ikuro Abe, Jeroen S. Dickschat, Tiangang Liu.
Nature volume 606, pages414–419 01 June 2022
Exploration and structure-based engineering of alkenal double bond reductases catalyzing the Cαsingle bondCβ double bond reduction of coniferaldehyde.
Naofumi Kamimura,Shingo Watanabe,Keisuke Sugimoto, MikiSenda, Takuma Araki, Hong Yang Yu, Shojiro Hishiyama, Shinya Kajita, Toshiya Senda, Eiji Masai.
New Biotechnology Volume 68, 25 May 2022, Pages 57-67
Structural basis of the strict specificity of a bacterial GH31 α-1,3-glucosidase for nigerooligosaccharides.
Marina Ikegaya, Toshio Moriya, Naruhiko Adachi, Masato Kawasaki, Enoch Y Park, Takatsugu Miyazaki
Journal of Biological Chemistry Volume 298, Issue 5, May 2022, 101827
Ca2+-induced structural changes and intramolecular interactions in N-terminal region of diacylglycerol kinase alpha.
Takahashi, D., Yonezawa, K., Okizaki, Y., Caaveiro, J. M. M., Ueda, T., Shimada, A., Sakane, F. and Shimizu, N.
Protein Science 31, e4365 .
K-edge anomalous SAXS for protein solution structure modeling.
Virk, K., Yonezawa, K., Choukate, K., Singh, L., Shimizu, N. and Chaudhuri, B.
Acta Crystallographica Section D 78, 204-211 .
A crystal-processing machine using a deep-ultraviolet laser: application to long-wavelength native SAD experiments.
Yoshiaki Kawano, Masahide Hikita, Naohiro Matsugaki, Masaki Yamamoto and Toshiya Sendab
Acta Crystallographica Section F Structural Biology Communications Vol.78 Part2 P88-95 February 2022
Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti.
Kazue Inaba, Kana Ebihara, Miki Senda, Ryunosuke Yoshino, Chisako Sakuma, Kotaro Koiwai, Daisuke Takaya, Chiduru Watanabe, Akira Watanabe, Yusuke Kawashima, Kaori Fukuzawa, Riyo Imamura, Hirotatsu Kojima, Takayoshi Okabe, Nozomi Uemura, Shinji Kasai, Hirotaka Kanuka, Takashi Nishimura, Kodai Watanabe, Hideshi Inoue, Yuuta Fujikawa, Teruki Honma, Takatsugu Hirokawa, Toshiya Senda, Ryusuke Niwa.
BMC Biology vol.20 #43. 2022 Feb 17.
2021
Non-conventional octameric structure of C-phycocyanin.
Takuo MInato, Takamasa Teramoto, Naruhiko Adachi, Nguyen Khac Hung, Kaho Yamada, Masato Kawasaki, Masato Akutsu, Toshio Moriya, Toshiya Senda, Seiji Ogo, Yoshimitsu Kakuta*, Ki-Seok Yoon*
Communications Biology , 02 November 2021.
C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes.
Takahiro Mori, Takuto Kumano, Haibing He, Satomi Watanabe, Miki Senda, Toshio Moriya, Naruhiko Adachi, Sanae Hori, Yuzu Terashita, Masato Kawasaki, Yoshiteru Hashimoto, Takayoshi Awakawa, Toshiya Senda*, Ikuro Abe*, Michihiko Kobayashi*
Nature Communicaions , 02 November 2021.
FAD-dependent C-glycoside-metabolizing Enzymes in Microorganisms: Screening, Characterization and Crystal Structure Analysis.(in press)
Takuto Kumano, Sanae Hori, Satomi Watanabe, Yuzu Terashita, Hong Yang Yu, Yoshiteru Hashimoto, Toshiya Senda, Miki Senda*, Michihiko Kobayashi*
Proc. Natl. Acad. Sci. USA, 2021.
Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S-transferase Noppera-bo.
Koiwai, K., Morohashi, K., Inaba, K., Ebihara, K., Kojima, H., Okabe, T., Yoshino, R., Hirokawa, T., Nampo, T., Fujikawa, Y., Inoue, H., Yumoto, F., Senda, T., Niwa, R.*
J. Pepstic Sci. 2021, Vo.46, Issue 1, Pages 75-87
Characterization of a novel type of carbonic anhydrase that acts without metal cofactors.
Hirakawa, Y.*, Senda, M., Fukuda, K., Yu, H.Y., Ishida, M., Taira, M., Kinbara, K., Senda, T.*
BMC Biology. 2021, 9, 105
Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis.
Teramoto, T.*, Koyasu, T., Adachi, N., Kawasaki, M., Moriya, T., NUmata, T., Senda, T., Kakuta, Y.*
J. Biol. Chem. September 2021, Vol.297, Issue 3, 101028
Structural insight into host plasma membrane association and assembly of HIV1 matrix protein.
Ciftci, H., Tateishi, H., Koiwai, K., Koga, R., Anraku, K., Monde, K., Dağ, C., Destan, E., Yuksel, B., Ayan, E., Yildirim, G., Yigin, M., Ertem, F. B., Shafiei, A., Guven, O., Besler S. O., Sierra R. G., Yoon, C. H., Su, Z., Liangm M., Acar, B., Haliloglu, T., Otsuka, M., Yumoto, F., Fujita, M.*, Senda, T.*, DeMirci, H.*
Scientific Reports. 2021, 11, 15819
2.85 and 2.99 Å resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.
Adachi, N., Yamaguchi, T., Moriya, T., Kawasaki, M., Koiwai, K., Shinoda, A., Yamada, Y., Yumoto, F., Kohzuma, T.*, Senda, T.*
Journal of Structural Biology. 2021, 213, 107768
Divergent Mechanisms Activating RAS and Small GTPases Through Post-translational Modification.
Osaka, N., Hirota, Y., Ito, D., Ikeda, Y., Kamata, R., Fujii, Y., Chirasani, V. R., Campbell S. L., Takeuchi, K., Senda, T., Sasaki, A. T.* .
Front. Mol. Biosci. 2021, 8, 707439
3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents.
Konno, S., Kobayashi, K., Senda, M., Funai, Y., Seki, Y., Tamai, I., Schäkel, L., Sakata, K., Pillaiyar, T., Taguchi, A., Taniguchi, A., Gütschow, M., Müller, C. E., Takeuchi, K., Hirohama, M., Kawaguchi, A., Kojima, M., Senda, T., Shirasaka, Y., Kamitani, W., Hayashi, Y*.
J. Med. Chem. July, 2021
An antibiotic-resistance conferring mutation in a neisserial porin: Structure, ion flux, and ampicillin binding.
Bartsch A, Ives CM, Kattner C, Pein F, Diehn M, Tanabe M, Munk A, Zachariae U, Steinem C and Llabrés S.
BBA Biomembr. Jun.2021 Volume 1863, Issue 6, 183601
Structures and General Transport Mechanisms by the Major Facilitator Superfamily (MFS).
Drew D, North AR, Nagarathinam K, Tanabe M.
Chem. Rev. 2021, 121, 5289-5335
Identification of a peptide motif that potently inhibits two functionally distinct subunits of Shiga toxin.
Watanabe-Takahashi, M., Tamada, M., Senda, M., Hibino, M., Shimizu, E., Okuta A., Miyazawa A., Senda, T., Nishikawa, K.
Commun. Biol. May 2021 # 538
Structural and functional analyses of the tridomain-nonribosomal peptide synthetase FmoA3 for 4-methyloxazoline ring formation.
Katsuyama Y, Sone K, Harada A, Kawai S, Urano N, Adachi N, Moriya T, Kawasaki M, Shin-Ya K, Senda T, Ohnishi Y.
Angew Chem Int Ed Engl March 2021
Crystal structure of the full‐length LysR‐type transcription regulator CbnR in complex with promoter DNA.
Giannopoulou, E., Senda, M., Koentjoro, M. P., Adachi, N.Ogawa, N. & Senda, T.
FEBS Journal Feb 2021.
A fully automated crystallization apparatus for small protein quantities.
Kato R, Hiraki M, Yamada Y, Tanabe M, and Senda T.
Acta Cryst. F. January 2021, Volume 77, Part 1, P29-36
Cryo-EM Structure of K +-Bound hERG Channel Complexed with the Blocker Astemizole.
Asai T, Adachi N, Moriya T, Oki H, Maru T, Kawasaki M, Suzuki K, Chen S, Ishii R, Yonemori K, Igaki S, Yasuda S, Ogasawara S, Senda T, Murata T.
Structure March 2021, Volume 29, Issue 3, P203-212
2020
Impact and relevance of alchol dehydrogenase enantioselectivities on biotechnogokical applications.
Koesoema, A. A., Standley, D. M., Senda, T and Matsuda, T.
Appl. Microbiol. Biotechnol. 2020,104(7):2897-2909.
An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo.
Koiwai, K., Inaba, K., Morohashi, K., Nnya, S., Arai, R., Kojima, H., Okabe, T., Fujikawa, Y., Inoue, H., Yoshino, R., Hirokawa, T., Kato, K., Fukuzawa, K., Shimada-Niwa, Y., Nakamura, A., Yumoto, F., Senda, T. and Niwa, R..
J. Biol. Chem. Volume 295, Issue 20, 15 May 2020, Pages 7154-7167
Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure.
Toma-Fukai, S., Hibi, R., Naganuma, T., Sakai, M., Saijo, S., Shimizu, N., Matsumoto, M. and Shimizu, T.
J. Biol. Chem. 2020 Oct 23;295(43):14630-14639
クライオ電子顕微鏡単粒子解析への深層学習 AI 技術の応用の現状と展望.
Toshio Moriya 守屋俊夫
顕微鏡 55(3):114-119
De Novo Design of Allosteric Control into Rotary Motor V1-ATPase by Restoring Lost Function.
Takahiro Kosugi, Tatsuya Iida, Mikio Tanabe, Ryota Iino, Nobuyasu Koga.
BioRxiv September 09, 2020
Size matters: optimal mask diameter and box size for single-particle cryogenic electron microscopy.
Moriya T, Adachi N, Kawasaki M, Yamada Y, Shinoda A, Koiwai K, Yumoto F, Senda T.
BioRxiv August 24, 2020.
A crystal-mounting platform has been developed for native SAD phasing. This platform includes a newly designed solution-free tool and an automatic freezing–extracting robot for use at synchrotron facilities.
Jian Yu, Akira Shinoda, Koji Kato, Isao Tanaka and Min Yao.
Acta Cryst. Volume 76, Part 10, Pages 938-945
The measles virus V protein binding site to STAT2 overlaps with that of IRF9.
Nagano, Y., Sugiyama, A., Kimoto, M., Wakahara, T., Noguchi, Y., Jiang, X.,Saijo, S., Shimizu, N. , Yabuno, N., Yao, M., Gooley, P. R., Moseley, G .W., Tadokoro, T., Maenaka, K. and Ose, T.
Journal of Virology 2020 Jun
200 kV単粒子クライオ電子顕微鏡による小さいタンパク質の三次元構造再構築におけるボックスサイズと粒子マスク直径の決定方法.
Toshio Moriya 守屋俊夫
顕微鏡 55(1):37-42
Impact and relevance of alchol dehydrogenase enantioselectivities on biotechnogokical applications.
Koesoema, A. A., Standley, D. M., Senda, T and Matsuda, T.*
Appl. Microbiol. Biotechnol, Feb 2020 104, 2897-2909.
Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii.
Yuta Sato, Takashi Yabuki, Naruhiko Adachi, Toshio Moriya, Takatoshi Arakawa, Masato Kawasaki, Chihaya Yamada, Toshiya Senda, Shinya Fushinobu, Takayoshi Wakagi.
Journal of Structural Biology Volume 4, 2020, 100030
Structural analysis reveals TLR7 dynamics underlying antagonism.
Tojo, S., Zhang, Z., Matsui, H., Tahara, M., Ikeguchi, M., Kochi, M., Kamada, M., Sigematsu, H., Tsutsumi, A., Adachi, N., Shibata, T., Yamamoto, M., Kikkawa, M., Seda, T., Isobe, Y., Ohto, U. and Shimizu, T .
Nat. Commun. 2020 11, 5204
FAM3B/PANDER-Like Carbohydrate-Binding Domain in a Glycosyltransferase, POMGNT1.
Hiroshi Manya, Naoyuki Kuwabara, Ryuichi Kato, and Tamao Endo.
Lectin Purification and Analysis 2020 vol. 2132 609-619
MFS型多剤排出トランスポーターMdfAの薬剤輸送に伴う構造変化のメカニズム.
Mikio Tanabe 田辺 幹雄
ファルマシア 2020 56巻 6号 509-513
Short-Distance Intermolecular Correlations of Mono- and Disaccharides in Condensed Solutions: Bulky Character of Trehalose.
Hirai, M., Ajito, S., Iwase, T., Wen, D., Igarashi, N. and Shimizu, N.
ACS Omega 2020 10815-10825
ゲル濾過クロマトグラフィーと組み合わせたタンパク質X線溶液散乱解析技術.
Kento Yonezawa, Nobutaka Shimuzu. 米澤 健人, 清水 伸隆.
生物物理 2020 180 -184
Crystal structures of fukutin-related protein (FKRP), a ribitol-phosphate transferase related to muscular dystrophy.
Naoyuki Kuwabara, Rieko Imae, Hiroshi Manya, Tomohiro Tanaka, Mamoru Mizuno, Hiroki Tsumoto, Motoi Kanagawa, Kazuhiro Kobayashi, Tatsushi Toda, Toshiya Senda, Tamao Endo, Ryuichi Kato.
Nature Communication 2020 11,303
How Does a Microbial Rhodopsin RxR Realize Its Exceptionally High Thermostability with the Proton-Pumping Function Being Retained?
Tomohiko Hayashi, Satoshi Yasuda, Kano Suzuki, Tomoki Akiyama, Kanae Kanehara, Keiichi Kojima, Mikio Tanabe, Ryuichi Kato, Toshiya Senda, Yuki Sudo,Takeshi Murata, Masahiro Kinoshita.
J. Phys. Chem. B 2020 124, 990-1000
Snapshots of PLP-substrate and PLP-product external aldimines as intermediates in two types of cysteine desulfurase enzymes.
Ryosuke Nakamura, Masahide Hikita, Shoko Ogawa, Yasuhiro Takahashi and Takashi Fujishiro.
The FEBS Journal 2020 Vol.287 No.6 p1138-1154
Optimal Mutant Model of Human S100A3 Protein Citrullinated at Arg51 by Peptidylarginine Deiminase Type III and Its Solution Structural Properties.
Ite, K., Yonezawa, K., Kitanishi, K., Shimizu, N. and Ueno, M.
ACS Omega 2020 5, 4032-4042
X線結晶構造解析-技術革新- 山田悠介,千田俊哉
クライオ電子顕微鏡を使いたいと思ったら 安達成彦,千田俊哉
実験医学増刊 イメージング時代の構造生命科学 2020 Vol.38 No.5
長波長X線を利用したタンパク質結晶構造解析
松垣直宏, 山田悠介, 引田理英, 平木雅彦, 千田美紀, 千田俊哉.
日本結晶学会誌 2020 62, 56-61
2019
Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction.
Koesoema, A., Sugiyama, Y., Sriwong, K. T. Xu, Z., Verina, S. Standley, D. M., Senda, M., Senda, T. & Matsuda, T.
Applied Microbiology and Biotechnology 2019 103, 9529
Structural basis for highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain.
Koesoema, A., Sugiyama, Y., Xu, Z., Standley, D. M., Senda, M., Senda, T. & Matsuda, T.
Applied Microbiology and Biotechnology 2019 103, 9543
SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM.
Thorsten Wagner, Felipe Merino, Markus Stabrin, Toshio Moriya, Claudia Antoni, Amir Apelbaum, Philine Hagel, Oleg Sitsel, Tobias Raisch, Daniel Prumbaum, Dennis Quentin, Daniel Roderer, Sebastian Tacke, Birte Siebolds, Evelyn Schubert, Tanvir R Shaikh, Pascal Lill, Christos Gatsogiannis, Stefan Raunser.
Communications Biology. 2019 75, 4941-4952
Effects of Loading Amount of Plasticizers on Improved Crystallization of Poly (L-lactic acid).
Diep, P, T, N., Takagi, H., Shimizu, N., Igarashi, N., Sasaki, S. and Sakurai, S.
J. Fiber Sci. Technol. 2019 Vol.75 8 99-111
Improvement of Production and Isolation of Human Neuraminidase-1 in Cellulo Crystals.
Kotaro Koiwai, Jun Tsukimoto, Tetsuya Higashi, Fumitaka Mafuné, Ken Miyajima, Takanori Nakane, Naohiro Matsugaki, Ryuichi Kato, Serena Sirigu, Arjen Jakobi, Matthias Wilmanns, Michihiro Sugahara, Tomoyuki Tanaka, Kensuke Tono, Yasumasa Joti, Makina Yabashi, Osamu Nureki, Eiichi Mizohata, Toru Nakatsu, Eriko Nango, So Iwata, Leonard M. G. Chavas, Toshiya Senda, Kohji Itoh, Fumiaki Yumoto.
Bio Materials 2019 2 (11), 4941–4952
Structural Evolution in Isothermal Crystallization Process of Poly(L-lactic acid) Enhanced by Silk Fibroin Nano-Disc.
Pandey, A. K., Katiyar, V., Takagi, H., Shimizu, N., Igarashi, N., Sasaki, S. and Sakurai, S.
Materials 2019 12, 1872
One-shot preparation of topologically chimeric nanofibers via a gradient supramolecular copolymerization.
Kitamoto, Y., Pan, Z., Prabhu, D. D., Isobe, A., Ohba, T., Shimizu, N., Takagi, H., Haruki, R., Adachi, S. and Yagai, S.
Nature Communication 2019 10, 4578
Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.
Hirata, A., Okada, K., Yoshii, K., Shiraishi, H., Saijo, S., Yonezawa, K., Shimizu, N. and Hori, H.
Nucleic Acids Research 2019 47, 10942-10955
Glycoscience: Basic Science to Applications (ed. by N.Taniguchi et al.).
Structural Analysis of Sugar Related Proteins
Ryuichi Kato.
Springer 2019 46-47
Anti-Tumor Potential of IMP Dehydrogenase Inhibitors: A Century-Long Story.
Rand Naffouje, Punita Grover, Hongyang Yu, Arun Sendilnathan, Kara Wolfe, Naznin Majd, Eric Smith, Koh Takeuchi, Toshiya Senda, Satoshi Kofuji, Atsuo Sasaki.
Cancers 2019 11(9), 1346
Topological Impact on the Kinetic Stability of Supramolecular Polymers.
Suzuki, A., Aratsu, K., Datta, S., Shimizu, N., Takagi, H., Haruki, R., Adachi, S., Hollamby, M., Silly, F. and Yagai, S.
J. Am. Chem. Soc. 2019 141, 13196-13202
レクチンの複数の糖結合部位の親和性解析-セレン糖鎖とX線結晶構造解析
加藤龍一
医学のあゆみ 2019 269, 757-760
Effects of drying temperature in solution coating process on microphase-separated structures in coated layers of pressure-sensitive adhesive composed of di- and triblock copolymer blends as revealed by small-angle X-ray scattering.
Doi, T., Takagi, H., Shimizu, N., Igarashi, N. and Sakurai, S.
Polymer 2019 170, 211-221
Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.
Miyamoto, T., Hayashi, Y., Yoshida, K., Watanabe, H., Uchihashi, T., Yonezawa, K., Shimizu, N., Kamikubo, H. and Hirota, S.
ACS Synthetic Biology 2019 8, 1112-1120
Structure of Ultrafine Bubbles and Their Effects on Protein and Lipid Membrane Structures Studied by Small- and Wide-Angle X-ray Scattering.
Hirai, M., Ajito, S., Takahashi, K., Iwasa, T., Li, X., Wen, D., Kawai-Hirai, R., Ohta, N., Igarashi, N. and Shimizu, N.
J. Phys. Chem. B 2019 123, 3421-3429
High-resolution experimental and computational electrophysiology reveals weak β-lactam binding events in the porin PorB.
Bartsch A, Llabrés S, Pein F, Kattner C, Schön M, Diehn M, Tanabe M, Munk A, Zachariae U, Steinem C.
Scientific Reports 2019 9, 1264
Long-wavelength native-SAD phasing: opportunities and challenges.
Basu S, Olieric V, Leonarski F, Matsugaki N, Kawano Y, Takashi T, Huang CY, Yamada Y, Vera L, Olieric N, Basquin J, Wojdyla JA, Bunk O, Diederichs K, Yamamoto M, Wang M.
IUCr Journal 2019 6, 373–386
Hyperbolic Pressure-Temperature Phase Diagram of the Zinc-Finger Protein apoKti11 Detected by NMR Spectroscopy.
Klamt A, Nagarathinam K, Tanabe M, Kumar A, Balbach J.
J. Phys. Chem. B 2019 6, 373–386
Effects of a special diluent as an agent of improving the crystallizability of poly(L-lactic acid).
Diep, P, T, N., Mochizuki, M., Doi, M., Takagi, H., Shimizu, N., Igarashi, N., Sasaki, S. and Sakurai, S.
J. Phys. Chem. B 2019, 123, 4, 792–801
Purification and functional characterization of tomato mosaic virus130K protein expressed in silkworm pupae using a baculovirus vector.
Kobayashi, C., Kato, M., Nagaya, H., Shimizu, N., Ishibashi, K., Ishikawa, M. and Katoh, E.
Protein Expr. Purif. 2019 154, 85-90
Software for serial data analysis measured by SEC-SAXS/UV-Vis spectroscopy.
Yonezawa, K., Takahashi, M., Yatabe, K., Nagatani, Y. and Shimizu, N.
AIP Conf. Proc. 2019 2054, 060082
New high-brilliance small angle x-ray scattering beamline, BL-15A2 at the photon factory.
Takagi, H., Igarashi, N., Nagatani, Y., Ohta, H., Mori, T., Kosuge, T. and Shimizu, N.
AIP Conf. Proc. 2019 2054, 060038
Further developments of the tender x-ray diffractometer at BL-15A2 of the photon factory.
Igarashi, N., Takagi, H., Ohta, H., Mori, T., Tomita, S., Nagatani, Y., Kosuge, T., Okuda, H. and Shimizu, N.
AIP Conf. Proc. 2019 2054, 060043
BL-10C, the small-angle x-ray scattering beamline at the photon factory.
Shimizu, N., Mori, T., Nagatani, Y., Ohta, H., Saijo, S., Takagi, H., Takahashi, M., Yatabe, K., Kosuge, T. and Igarashi, N.
AIP Conf. Proc. 2019 2054, 060041
RFID tag system for sample tracking at structural biology beamlines.
Masahiko Hiraki, Naohiro Matsugaki, Yusuke Yamada, Masahide Hikita, Masashi Yamanaka, and Toshiya Senda.
AIP Conf. Proc. 2019 2054, 060074
High spatial resolution small angle X-ray scattering experiments using SOPHIAS detector.
Takagi, H., Hashimoto, R., Igarashi, N., Yamamoto, K., Kishimoto, S.
Nucl. Instrum. Methods Phys. Res. A 2019 924 417-421
2018
Restoration of Myoglobin Native Fold from Its Initial State of Amyloid Formation by Trehalose.
Hirai, M., Ajito, S., Iwase, H., Takata, SI., Ohta, N., Igarashi, N. and Shimizu, N.
J. Phys. Chem. B 2018 122, 11962-11968
Application of the SOPHIAS Detector to Synchrotron Radiation X-Ray Experiments.
Hashimoto, R., Igarashi, N., Kumai, R., Takagi, H., Kishimoto, S., Kudo, T. and Hatsui, T.
Springer Proc. in Phys. 2018 213, 263-266
Outward open conformation of a Major Facilitator Superfamily multidrug/H+ antiporter provides insights into switching mechanism.
Nagarathinam K, Nakada-Nakura Y, Parthier C, Terada T, Juge N, Jaenecke F, Liu K, Hotta Y, Miyaji T, Omote H, Iwata S, Nomura N, Stubbs MT. & Tanabe M.
Nature Communications 2018 9, 4005
Structural and Computational Bases for Dramatic Skeletal Rearrangement in Anditomin Biosynthesis.
Nakashima Y, Mitsuhashi T, Matsuda Y, Senda M, Sato H, Yamazaki M, Uchiyama M, Senda T, Abe I.
J. Am. Chem. Soc. 2018 140, 9743-9750
Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit.
Ray-Gallet D, Ricketts MD, Sato Y, Gupta K, Boyarchuk E, Senda T, Marmorstein R, Almouzni G.
Nature commuinications 2018 9, 3103
Structure of MHC class I-like MILL2 reveals heparan-sulfate binding and interdomain flexibility.
Kajikawa, M., Ose, T., Fukunaga, Y., Okabe, Y., Matsumoto, N., Yonezawa, K., Shimizu, N., Kollnberger, S., Kasahara, M. and Maenaka, K.
Nature Communication 2018 9 4330
Preferential Intercalation of Human Amyloid-β Peptide into Interbilayer Region of Lipid-Raft Membrane in Macromolecular Crowding Environment.
Hirai, M., Ajito, S., Sato, S., Ohta, N., Igarashi, N. and Shimizu, N..
The Journal of Physical Chemistry B 2018 122 9482-9489
Self-folding of supramolecular polymers into bioinspired topology.
Prabhu, D. D., Aratsu, K., Kitamoto, Y., Ouchi, H., Ohba, T., Hollamby, M. J., Shimizu, N., Takagi, H., Haruki, R., Adachi, S. and Yagai, S.
Science Advances Apr 2018 eaat8466
Grain coarsening on the free surface and in the thickness direction of a sphere-forming triblock copolymer film.
Bayomi, R.A.H., Honda, K., Wataoka, I., Takagi, H., Shimizu, N., Igarashi, N., Sasaki, S., Sakurai, S.
Polymer Journal 2018 50 1029-1042
Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition.
Hirai, M., Ajito, S., Sugiyama, M., Iwase, H., Takata, S., Shimizu, N.,Igarashi, N., Martel, A. and Porcar, L.
Biophysical Journal July 2018 Volume 115 Issue 2 313-327
Compact Seahorse-Shaped T Cell-Activating Antibody for Cancer Therapy.
Fujii, H., Tanaka, Y., Nakazawa, H., Sugiyama, A., Manabe, N., Shinoda, A., Shimizu, N., Hattori, T., Hosokawa, K., Sujino, T., Ito, T., Niide, T., Asano, R., Kumagai, I. and Umetsu, M.
Advanced Therapeutics July 2018 Volume 1 Issue 3 1700031
Structural analyses of sphere- and cylinder-forming triblock copolymer thin films near the free surface by atomic force microscopy, X-ray photoelectron spectroscopy, and grazing-incidence small-angle X-ray scattering.
Bayomi, R. A. H., Aoki, T., Shimojima, T., Takagi, H., Shimizu, N., Igarashi, N., Sasaki, S. and Sakurai, S.
Polymer July 2018 Volume 147 202-212
Synchrotron SAXS Studies on Lattice Structure of Spherical Micelles in Binary Mixtures of Block Copolymers and Homopolymers.
Takagi, H., Hashimoto, R., Igarashi, N., Kishimoto, S. and Yamamoto, K.
Journal of Fiber Science and Technology 2018 Volume 74 Issue 1 , 10-16
LysRタイプ転写調節因子CbnRのDNA結合ドメインとDNAとの複合体構造
千田美紀、安達成彦、Maharani Pertiwi Koentjoro, 小川直人、千田俊哉
日本結晶学会誌 2018 60, 135-141
Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination.
Katsuyama Y., Sato, Y., Sugai, Y., Higashiyama, Y., Senda, M., Senda, T., Ohnishi, Y.
The FEBS Journal(2018)285, 1540-1555
Protective action of trehalose and glucose on protein hydration shell clarified by using X-ray and neutron scattering.
Ajito, S., Hirai, M., Iwase, H., Shimizu, N., Igarashi, N. and Ohta, N.
Physica B: Condensed Matter(2018)In Press
キノコ由来ガレクチンACGの糖認識メカニズム
平林 淳, 胡 丹, 舘野 浩章, 桑原 直之, 加藤 龍一, 八木 史郎
Trends in Glycoscience and Glycotechnology(2018).30, SJ33-46
Carbohydrate Recognition Mechanism of the Mushroom Galectin ACG
Jun Hirabayashi, Dan Hu, Hiroaki Tateno, Naoyuki Kuwabara, Ryuichi Kato, Fumio Yagi
Trends in Glycoscience and Glycotechnology(2018).30, SE75-88
Crystal structure of the DNA–binding domain of the LysR–type transcriptional regulator CbnR in complex with a DNA fragment of the recognition binding site in the promoter region
Koentjoro, M.P., Adachi, N., Senda, M., Ogawa, N. and Senda, T.
FEBS Journal(2018).2018.1.11 Epub
Structure, function and engineering of multifunctional non-heme iron dependent oxygenases in fungal meroterpenoid biosynthesis
Y. Nakashima, T. Mori, H. Nakamura, T. Awakawa, S. Hoshino, M. Senda, T. Senda, I. Abe
Nature Communications(2017).9,104
Macromolecular crowding effect on protein structure and hydration clarified by using X-ray and neutron scattering.
Hirai, M., Ajito, S., Sugiyama, M., Iwase, H., Takata, S., Shimizu, N., Igarashi, N., Martel, A. and Porcar, L.
Phys. B Condens. Matter., in press.
Solution scattering approaches to dynamical ordering in biomolecular systems.
Bernadó, P., Shimizu, N., Zaccai, G., Kamikubo, H. and Sugiyama, M.
BBA - General Subjects, 1862, 253(2018).
2017
Anaerobic crystallization of proteins
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Biophysical Reviews(2017).
Generation of Conformation-Specific Antibody Fragments for Crystallization of the Multidrug Resistance Transporter MdfA.
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Methods in Molecular Biology(2017).1700, 97-109.
Leading role of TBP in the establishment of complexity in eukaryotic transcription initiation systems.
Kawakami, E., Adachi, N., Senda, T. & Horikoshi, M.
Cell Rep. 21, 3941-3956 (2017).
Generation of Conformation-Specific Antibody Fragments for Crystallization of the Multidrug Resistance Transporter MdfA.
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Methods Mol. Biol. 1700, 97-109 (2018).
Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography.
Yamashita K,Kuwabara N,Nakane T,Murai T, Mizohata E,Sugahara M,Pan D,Masuda T, Suzuki M, Sato T, Kodan A,Yamaguchi T, Nango E, Tanaka T,Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Manya H, Endo T, Kato R, Senda T, Kato H, Iwata S, Ago H, Yamamoto M, Yumoto F and Nakatsu T.
IUCrJ 4, 1-9 (2017).
Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl Group-Substituted Heme Cofactor.
Kanai Y, Harada A, Shibata T, Nishimura R, Namiki K, Watanabe M, Nakamura S, Yumoto F, Senda T, Suzuki A, Neya S, Yamamoto Y.
Biochemistry doi: 10.1021/acs.biochem.7b00457 (2017).
POMGnT1の構造解析による筋ジストロフィー疾患発症機序解明
桑原 直之, 加藤 龍一, 萬谷 博, 遠藤 玉夫
日本結晶学会誌 59, 114-120 (2017).
X-ray structure of a protease-resistant mutant form of human galectin-9 having two carbohydrate recognition domains with a metal-binding site.
Yoshida H, Nishi N, Wada K, Nakamura T, Hirashima M, Kuwabara N, Kato R, Kamitori S.
Biochem Biophys Res Commun. 490, 1287-1293 (2017).
The multidrug-resistance transporter MdfA from Escherichia coli : crystallization and X-ray diffraction analysis
Kumar Nagarathinam, Frank Jaenecke, Yoshiko Nakada-Nakura, Yunhon Hotta, Kehong Liu, So Iwata, Milton T. Stubbs, Norimichi Nomura and Mikio Tanabe
Acta Cryst. F73, 423–430 (2017).
The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6.
Harada A, Kamimura N, Takeuchi K, Yu HY, Masai E, Senda T.
FEBS J. 2017 Jun;284(12):1855-1867.
The First Crystal Structure of a Family 129 Glycoside Hydrolase from a Probiotic Bacterium Reveals Critical Residues and Metal Co-factors.
Sato M, Liebschner D, Yamada Y, Matsugaki N, Arakawa T, Wills SS, Hattie M, Stubbs KA, Ito T, Senda T, Ashida H, Fushinobu S.
J. Biol. Chem. 292, 12126-12138 (2017)
3D structural analysis of protein O-mannosyl kinase, POMK, a causative gene product of dystroglycanopathy.
Nagae M, Mishra SK, Neyazaki M, Oi R, Ikeda A, Matsugaki N, Akashi S, Manya H, Mizuno M, Yagi H, Kato K, Senda T, Endo T, Nogi T, Yamaguchi Y.
Genes Cells. 2017 Apr;22(4):348-359.
Crystallographic analysis of murine p24γ2 Golgi dynamics domain.
Nagae M, Liebschner D, Yamada Y, Morita-Matsumoto K, Matsugaki N, Senda T, Fujita M, Kinoshita T, Yamaguchi Y.
Proteins. 2017 Apr;85(4):764-770.
Improved method for soluble expression and rapid purification of yeast
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Adachi, N., Aizawa, K., Kratzer, Y., Saijo, S., Shimizu, N. & Senda ,T.
Protein Expr. Purif. 133, 50-56 (2017).
2016
Six independent fucose-binding sites in the crystal structure of Aspergillus oryzae lectin.
Makyio H, Shimabukuro J, Suzuki T, Imamura A, Ishida H, Kiso M, Ando H Kato R.
Biochem Biophys Res Commun. 2016 Aug 26;477(3):477-82.
Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of α-dystroglycan.
Naoyuki Kuwabara, Hiroshi Manya, Takeyuki Yamada, Hiroaki Tateno, Motoi Kanagawa, Kazuhiro Kobayashi, Keiko Akasaka-Manya, Yuriko Hirose, Mamoru Mizuno, Mitsunori Ikeguchi, Tatsushi Toda, Jun Hirabayashi, Toshiya Senda, Tamao Endo, and Ryuichi Kato
Proceedings of the National Academy of Sciences USA. Aug 16, 2016, vol. 113 no. 33, 9280–9285,
Development of sample exchange robot PAM-HC for beamline BL-1A at the photon factory.
Hiraki, M., Matsugaki, N., Yamada, Y. & Senda, T.
AIP Conf. Proc. 1741, 030029 (2016).
Newly designed double surface bimorph mirror for BL-15A of the photon factory.
Igarashi, N., Nitani, H., Takeichi, Y., Niwa, Y., Abe, H., Kimura, M., Mori, T., Nagatani, Y., Kosuge, T., Kamijo, A., Koyama, A., Ohta, H. & Shimizu, N.
AIP Conf. Proc. 1741, 040021 (2016).
In-situ data collection at the photon factory macromolecular crystallography beamlines.
Yamada, Y., Hiraki, M., Matsugaki, N., Kato, R. & Senda, T.
AIP Conf. Proc. 1741, 050023 (2016).
Upgrade of small angle x-ray scattering beamline BL-6A at the photon factory.
Takagi, H., Igarashi, N., Mori, T., Saijo, S., Ohta, H., Nagatani, Y., Kosuge, T. & Shimizu, N.
AIP Conf. Proc. 1741, 030018 (2016).
Test results of a counting type SOI device for a new x-ray area detector.
Hashimoto, R., Arai, Y., Igarashi, N., Kumai, R., Miyoshi, T. & Kishimoto, S.
AIP Conf. Proc. 1741, 040031 (2016).
Software development for analysis of small-angle x-ray scattering data.
Shimizu, N., Yatabe, K., Nagatani, Y., Saijyo, S., Kosuge, T. & Igarashi,N.
AIP Conf. Proc. 1741, 050017 (2016).
On the influence of crystal size and wavelength on native SAD phasing.
Liebschner, D., Yamada, Y., Matsugaki, N., Senda, M. & Senda, T.
Acta Crystallogr. D Biol. Crystallogr. 72, 728-741 (2016).
Uncovering ancient transcription systems with a novel evolutionary indicator.
Adachi, N., Senda, T. & Horikoshi, M.
Sci. Rep. 6, 27922 (2016).
A conserved island of BAG6/Scythe is related to ubiquitin domains and participates in short hydrophobicity recognition.
Tanaka, H., Takahashi, T., Xie, Y., Minami, R., Yanagi, Y., Hayashishita, M., Suzuki, R., Yokota, N., Shimada, M., Mizushima, T., Kuwabara, N., Kato, R. & Kawahara, H.
FEBS J. 283, 662-677 (2016).
Classification and Comparison of Fucose-Binding Lectins Based on Their Structures
Makyio, H. & Kato, R.
Trends Glycosci. Glycotechnol. 28, E25–E37 (2016).
立体構造に基づいたフコースを結合するレクチンの比較と分類
牧尾 尚能, 加藤 龍一
Trends Glycosci. Glycotechnol. 28, J25–J38 (2016).
Use of multiple cryoprotectants to improve diffraction quality from protein crystals.
Senda, M., Hayashi, T., Hatakeyama, M., Takeuchi, K., Sasaki, A.T., Senda, T.
Crystal Growth & Design. 16, 1565–1571 (2016).
A novel method of preparing the monoform structure of catalytic antibody light chain.
Hifumi, E., Matsumoto, S., Nakashima, H., Itonaga, S., Arakawa, M., Katayama, Y., Kato, R. & Uda, T.
FASEB J. 30, 895-908 (2016).
The Lipid Kinase PI5P4Kβ Is an Intracellular GTP Sensor for Metabolism and Tumorigenesis.
Sumita, K., Lo, Y.H., Takeuchi, K., Senda, M., Kofuji, S., Ikeda, Y., Terakawa, J., Sasaki, M., Yoshino, H., Majd, N., Zheng, Y., Kahoud, E.R., Yokota, T., Emerling, B.M., Asara, J.M., Ishida, T., Locasale, J.W., Daikoku, T., Anastasiou, D., Senda, T. & Sasaki A.T.
Mol. Cell 61, 187-198 (2016).
2015
Dramatic increase in SHP2 binding activity of Helicobacter pylori Western CagA by EPIYA-C duplication: its implications in gastric carcinogenesis.
Nagase, L., Hayashi, T., Senda, T. & Hatakeyama, M.
Sci. Rep. 5, 15749 (2015).
POMGNT1 is glycosylated by mucin-type O-glycans.
Xin, X., Akasaka-Manya, K., Manya, H., Furukawa, J., Kuwahara, N., Okada, K., Tsumoto, H., Higashi, N., Kato, R., Shinohara, Y., Irimura, T. & Endo, T.
Biol. Pharm. Bull. 38, 1389–1394 (2015).
Structure of a BAG6 (Bcl-2-associated Athanogene 6)-Ubl4a (Ubiquitin-like Protein 4a) Complex Reveals a Novel Binding Interface That Functions in Tail-anchored Protein Biogenesis.
Kuwabara, N., Minami, R., Yokota, N., Matsumoto, H., Senda, T., Kawahara, H. & Kato, R.
J. Biol. Chem. 290, 9387-9398 (2015).
セレン含有糖鎖を用いた糖鎖結合タンパク質の位相決定法
牧尾尚能、加藤龍一
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X-ray Crystallography of Sugar Related Proteins
Makyio, H. & Kato, R.
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2014
Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6.
Sugimoto, K., Senda, M., Kasai, D., Masai, E., Fukuda, M. & Senda, T.
PLoS One 9, e92249 (2014).
Expanded potential of seleno-carbohydrates as a molecular tool for X-ray structural determination of a carbohydrate-protein complex with single/multi-wavelength anomalous dispersion phasing.
Suzuki, T., Makyio, H., Ando, H., Komura, N., Menjo, M., Yamada, Y., Imamura, A., Ishida, H., Wakatsuki, S., Kato, R. & Kiso, M.
Bioorg. Med. Chem. 22, 2090-2101 (2014).
Mechanism underlying IKK activation mediated by the linear ubiquitin chain assembly complex (LUBAC).
Fujita, H., Rahighi, S., Akita, M., Kato, R., Sasaki, Y., Wakatsuki, S. & Iwai, K.
Mol. Cell. Biol. 34, 1322-1335 (2014).
Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism.
Suzuki, H., Tabata, K., Morita, E., Kawasaki, M., Kato, R., Dobson, R.C., Yoshimori, T. & Wakatsuki, S.
Structure 22, 47-58 (2014).
A New Structure Determination Method of Lectins, Using a Selenium-containing Sugar Ligand.
Makyio, H. & Kato, R.
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2013
Conformational change of a unique sequence in a fungal galectin from Agrocybe cylindracea controls glycan ligand-binding specificity.
Kuwabara, N., Hu, D., Tateno, H., Makyio, H., Hirabayashi, J. & Kato, R.
FEBS Lett. 587, 3620-3625 (2013).
Improvement of an Automated Protein Crystal Exchange System PAM for High-throughput Data Collection.
Hiraki, M., Yamada, Y., Chavas, L.M., Wakatsuki, S. & Matsugaki, N.
J. Synchrotron Radiat. 20, 890-893 (2013).
Improvements toward highly accurate diffraction experiments at the macromolecular micro-crystallography beamline BL-17A.
Yamada, Y., Chavas, L.M., Igarashi, N., Hiraki, M., Wakatsuki, S. & Matsugaki, N.
J. Synchrotron Radiat. 20, 938-942 (2013).
New methodologies at PF AR-NW12A: the implementation of high-pressure macromolecular crystallography.
Chavas, L.M., Nagae, T., Yamada, H., Watanabe, N., Yamada, Y., Hiraki, M. & Matsugaki, N.
J. Synchrotron Radiat. 20, 838-842 (2013).
Structural basis for phosphorylation-triggered autophagic clearance of Salmonella.
Rogov, V.V., Suzuki, H., Fiskin, E., Wild, P., Kniss, A., Rozenknop, A., Kato, R., Kawasaki, M., McEwan, D.G., Löhr, F., Güntert, P., Dikic, I., Wakatsuki, S. & Dötsch, V.
Biochem. J. 454, 459-466 (2013).
Structural basis of preferential binding of fucose-containing saccharide by the Caenorhabditis elegans galectin LEC-6.
Makyio, H., Takeuchi, T., Tamura, M., Nishiyama, K., Takahashi, H., Natsugari, H., Arata, Y., Kasai, K., Yamada, Y., Wakatsuki, S. & Kato, R.
Glycobiology 23, 797-805 (2013).
Direct metal recognition by guanine nucleotide exchange factor in the initial step of exchange reaction.
Uejima, T., Ihara, K., Sunada, M., Kawasaki, M., Ueda, T., Kato, R., Nakano, A. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 69, 345-351 (2013).
Data Management System at the Photon Factory Macromolecular Crystallography Beamline
Yamada, Y., Matsugaki, N., Chavas, L.M., Hiraki, M., Igarashi, N. & Wakatsuki, S.
J. Phys.: Conf. Ser. 425, 012017 (2013).
Current status and future prospects of an automated sample exchange system PAM for protein crystallography
Hiraki, M., Yamada, Y., Chavas, L.M., Matsugaki, N., Igarashi, N. & Wakatsuki, S.
J. Phys.: Conf. Ser. 425, 012014 (2013).
10 years of protein crystallography at AR-NW12A beamline
Chavas, L.M., Matsugaki, N., Yamada, Y., Hiraki, M., Igarashi, N., Suzuki, M. & Wakatsuki, S.
J. Phys.: Conf. Ser. 425 012008 (2013).
2012
Structural basis for membrane binding specificity of the Bin/Amphiphysin/Rvs(BAR) domain of Arfaptin-2 determined by Arl1 GTPase.
Nakamura, K., Man, Z., Xie, Y., Hanai, A., Makyio, H., Kawasaki, M., Kato, R., Shin, H.W., Nakayama, K. & Wakatsuki, S.
J. Biol. Chem. 287, 25478-25489 (2012).
Beamline AR-NW12A: high-throughput beamline for macromolecular crystallography at the Photon Factory
Chavas, L.M., Matsugaki, N., Yamada, Y., Hiraki, M., Igarashi, N., Suzuki, M. & Wakatsuki S.
J. Synchrotron Radiat. 19, 450-454 (2012).
S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS
Ru, H., Zhao, L., Ding, W., Jiao, L., Shaw, N., Liang, W., Zhang, L., Hung, L, Matsugaki, N., Wakatsuki, S. & Liu, Z.
Acta Crystallogr. D Biol. Crystallogr. 68, 521-530 (2012).
Structural basis for Arf6-MKLP1 complex formation on the Flemming body responsible for cytokinesis
Makyio, H., Ohgi, M., Takei, T., Takahashi, S., Takatsu, H., Katoh, Y., Hanai, A., Ueda, T., Kanaho, Y., Xie, Y., Shin, H.W., Kamikubo, H., Kataoka, M., Kawasaki, M., Kato, R., Wakatsuki, S. & Nakayama, K.
EMBO J. 31, 2590-2603 (2012).
High-pressure-induced water penetration into 3-isopropylmalage dehydrogenase
Nagae, T., Kawamura, T., Chavas, L.M.G., Niwa, K., Hasegawa, M., Kato, C. & Watanabe, N.
Acta Crystallogr. D Biol. Crystallogr. 68, 300-309 (2012).
Structural basis of the strict phospholipid binding specificity of the pleckstrin homology domain of human evectin-2
Okazaki, S., Kato, R., Uchida, Y., Taguchi, T., Arai, H. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 68, 117-123 (2012).
Structure of a compact conformation of linear diubiquitin
Rohaim, A., Kawasaki, M., Kato, R., Dikic, I. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 68, 102-108 (2012).
PF構造生物学ビームラインにおける全自動回折データセット収集/処理システムの開発
山田悠介、平木雅彦、松垣直宏、Leonard M. G. Chavas、五十嵐教之、若槻壮市
日本結晶学会誌 Vol. 54, No.6 359-363 (2012).
ヒト由来Evectin-2のリン脂質結合特異性についての構造学的洞察
岡崎誠司、加藤龍一、若槻壮市、内田安則、田口友彦、新井洋由
日本結晶学会誌 Vol. 54, No.2 101-106 (2012).
2011
Intracellular phosphatidylserine is essential for retrograde membrane traffic through endosomes
Uchida, Y., Hasegawa, J., Chinnapen, D., Inoue, T., Okazaki, S., Kato, R., Wakatsuki, S., Misaki, R., Koike, M., Uchiyama, Y., Iemura, S., Natsume, T., Kuwahara, R., Nakagawa, T., Nishikawa, K., Mukai, K., Miyoshi, E., Taniguchi, N., Sheff, D., Lencer, W.I., Taguchi, T. & Arai, H.
Proc. Natl. Acad. Sci. USA 108, 15846-15851 (2011).
UV LED lighting for automated crystal centring
Chavas, L.M., Yamada, Y., Hiraki, M., Igarashi, N., Matsugaki, N. & Wakatsuki, S.
J. Synchrotron Radiat. 18, 11-15 (2011).
Improved Inactivation Effect of Bacteria: Fabrication of Mesoporous Anatase
Films with Fine Ag Nanoparticles Prepared by Coaxial Vacuum Arc Deposition
Oveisi, H., Rahighi, S., Jiang, X., Agawa, Y., Beitollahi, A., Wakatsuki, S. & Yamauchi, Y.
Chem. Lett. 40, 420-422 (2011).
Selective binding of linear ubiquitin chains to NEMO in NF-kB activation
Ikeda, F., Rahighi, S., Wakatsuki, S. & Dikic, I.
Adv. Exp. Med. Biol. 691, 107-114 (2011).
2010
GDP-bound and nucleotide-free intermediates of the guanine nucleotideexchange in the Rab5/Vps9 system
Uejima, T., Ihara, K., Goh, T., Ito, E., Sunada, M., Ueda, T., Nakano, A. & Wakatsuki, S.
J. Biol. Chem. 285, 36689-36697 (2010).
Crystallization of small proteins assisted by green fluorescent protein
Suzuki, N., Hiraki, M., Yamada, Y., Matsugaki, N., Igarashi, N., Kato, R., Dikic, I., Drew, D., Iwata, S., Wakatsuki, S. & Kawasaki, M.
Acta Crystallogr. D Biol. Crystallogr. 66, 1059-1066 (2010).
Crystal structure of cyclic Lys48-linked tetraubiquitin
Satoh, T., Sakata, E., Yamamoto, S., Yamaguchi, Y., Sumiyoshi, A., Wakatsuki, S. & Kato, K.
Biochem. Biophys. Res. Commun. 400, 329-333 (2010).
Unusual antibacterial property of mesoporous titania films: drastic improvement by controlling surface area and crystallinity
Oveisi, H., Rahighi, S., Jiang, X., Nemoto, Y., Beitollahi, A., Wakatsuki, S. & Yamauchi, Y.
Chem. Asian J. 5, 1978-1983 (2010).
Molecular basis for defect in Alix-binding by alternatively spliced isoform of ALG-2 (ALG-2DeltaGF122) and structural roles of F122 intarget recognition
Inuzuka, T., Suzuki, H., Kawasaki, M., Shibata, H., Wakatsuki, S. & Maki, M.
BMC Struct. Biol. 10, 25 (2010).
GMF is an evolutionarily developed ADF/cofilin-super family protein involved in the Arp2/3 complex-mediated organization of the actin cytoskeleton
Nakano, K., Kuwayama, H., Kawasaki, M., Numata, O. & Takaine, M.
Cytoskeleton 67, 373-382 (2010).
Complexity in influenza virus targeted drug design: interaction with human sialidases
Chavas, L.M., Kato, R., Suzuki, N., von Itzstein, M., Mann, M.C., Thomson, R.J., Dyason, J.C., McKimm-Breschkin, J., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E. & Wakatsuki, S.
J. Med. Chem. 53, 2998-3002 (2010).
Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer
Kudo, N., Kumagai, K., Matsubara, R., Kobayashi, S., Hanada, K., Wakatsuki, S. & Kato, R.
J. Mol. Biol. 396, 245-251 (2010).
Crystal Structure of UbcH5b-Ubiquitin Intermediate: Insight into the Formation of the Self-Assembled E2-Ub Conjugates
Sakata, E., Satoh, T., Yamamoto, S., Yamaguchi, Y., Yagi-Utsumi, M., Kurimoto, E., Tanaka, K., Wakatsuki, S. & Kato, K.
Structure 18, 138-147 (2010).
「-リボソーム構造解析の先駆者- アダ・ヨナット教授に聞く」
聞き手:若槻壮市
現代化学 2010年10月号 No.475 2010.9.18発刊 0348710
ターゲットタンパク研究プログラムで目指すX線構造解析の高度化:フォトンファクトリーにおける技術開発
若槻壮市、山田悠介、Leonard M.G. Chavas、五十嵐教之、川崎政人、加藤龍一、平木雅彦、松垣直宏
薬学雑誌 Vol.130, No.5 631-640 (2010).
ターゲットタンパク研究プログラムの目指す放射光構造生物学
平田邦生, 山本雅貴, 松垣直宏, 若槻壮市
日本結晶学会誌 Vol. 52, No.1 43-47 (2010).
「入門 構造生物学 -放射光X線と中性子で最新の生命現象を読み解く-」
加藤龍一、山田悠介、平木雅彦、松垣直宏、五十嵐教之、川崎政人 他著
高エネルギー加速器研究機構 構造生物学研究センター 編 加藤龍一 編集
共立出版 2010.4.25発刊 ISBN978-4-320-05704-3
2009
AR-NE3A, a New Macromolecular Crystallography Beamline for Pharmaceutical Applications at the Photon Factory
Yamada, Y., Hiraki, M., Sasajima, K., Matsugaki, N., Igarashi, N., Amano, Y., Warizaya, M., Sakashita, H., Kikuchi, T., Mori, T., Toyoshima, A., Kishimoto, S. & Wakatsuki, S.
AIP Conf. Proc. 1234, 415-418 (2009).
Fully Automated Data Collection Using PAM and the Development of PAM/SPACE Reversible Cassettes
Hiraki, M., Watanabe, S., Chavas, L.M.G., Yamada, Y., Matsugaki, N., Igarashi, N., Wakatsuki, S., Fujihashi, M., Miki, K., Baba, S., Ueno, G., Yamamoto, M., Suzuki, M., Nakagawa, A., Watanabe, N. & Tanaka, I.
AIP Conf. Proc. 1234, 673-676 (2009).
Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation
Rahighi, S., Ikeda, F., Kawasaki, M., Akutsu, M., Suzuki, N., Kato, R., Kensche, T., Uejima, T., Bloor, S., Komander, D., Randow, F., Wakatsuki, S. & Dikic, I.
Cell 136, 1098-1109 (2009).
Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain
Nagae, M., Nishi, N., Murata, T., Usui, T., Nakamura, T., Wakatsuki, S. & Kato, R.
Glycobiology 19, 112-117 (2009).
高難度蛋白質をターゲットとした放射光X線結晶構造解析技術の開発
若槻壮市、山本雅貴、田中勲、三木邦夫、中川敦史 他著
長野哲雄、若槻壮市、高木淳一、古谷利夫 編
「融合発展する構造生物学とケミカルバイオロジーの最前線」共立出版 (2009).
NEMOによる直鎖状ユビキチン鎖の特異的認識はNF-κB活性化に重要である
池田史代、Simin Rahighi、若槻壮市、川崎政人
実験医学 Vol.27, No.14, 2240-2243 (2009).
エフェクタータンパク質群によるRab27取り込みへの構造的知見
レオナルド シャバス、伊原健太郎、川崎政人、若槻壮市
日本結晶学会誌 Vol. 51, No.6 334-339 (2009).
The mechanism of Ca2+-dependent recognition of Alix by ALG-2: insights from X-ray crystal structures
Suzuki H, Kawasaki M, Inuzuka T, Okumura M, Kakiuchi T, Shibata H, Wakatsuki S, Maki M
Biochem. Soc. Trans. 37, 190-194 (2009).
2008
Nucleotide-Dependent Conformational Changes and Assembly of the AAA ATPase SKD1/VPS4B
Inoue, M., Kamikubo, H., Kataoka, M., Kato, R., Yoshimori, T., Wakatsuki, S. & Kawasaki, M.
Traffic 9, 2180-2189 (2008).
Crystallization and X-ray diffraction analysis of N-terminally truncated human ALG-2
Suzuki, H., Kawasaki, M., Kakiuchi, T., Shibata, H., Wakatsuki, S. & Maki, M.
Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64, 974-977 (2008).
1,2-alpha-l-Fucosynthase: A glycosynthase derived from an inverting alpha-glycosidase with an unusual reaction mechanism
Wada, J., Honda, Y., Nagae, M., Kato, R., Wakatsuki, S., Katayama, T., Taniguchi, H., Kumagai, H., Kitaoka, M. & Yamamoto, K.
FEBS Lett. 582, 3739-3743 (2008).
Structural basis for Ca2+ -dependent formation of ALG-2/Alix peptide complex: Ca2+/EF3-driven arginine switch mechanism
Suzuki, H., Kawasaki, M., Inuzuka, T., Okumura, M., Kakiuchi, T., Shibata, H., Wakatsuki, S. & Maki, M.
Structure 16, 1562-1573 (2008).
Elucidation of Rab27 Recruitment by Its Effectors: Structure of Rab27a Bound to Exophilin4/Slp2-a
Chavas, L.M.G., Ihara, K., Kawasaki, M., Torii, S., Uejima, T., Kato, R., Izumi, T. & Wakatsuki, S.
Structure 16, 1468-1477 (2008).
Purification, crystallization and preliminary X-ray crystallographic analysis of Rab27a GTPase in complex with exophilin4/Slp2-a effector
Chavas L.M., Ihara, K., Kawasaki, M., Kato, R., Izumi, T. & Wakatsuki, S.
Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64, 599-601 (2008).
Structural basis for tropomyosin overlap in thin (actin) filaments and the generation of a molecular swivel by troponin-T
Murakami, K., Stewart, M., Nozawa, K., Tomii, K., Kudou, N., Igarashi, N., Shirakihara, Y., Wakatsuki, S., Yasunaga, T. & Wakabayashi, T.
Proc. Natl. Acad. Sci. USA 105, 7200-7205 (2008).
Miranda cargo-binding domain forms an elongated coiled-coil homodimer in solution: implications for asymmetric cell division in Drosophila
Yousef, M.S., Kamikubo, H., Kataoka, M., Kato, R. & Wakatsuki, S.
Protein Sci. 17, 908-917 (2008).
Development of an X-ray HARP-FEA detector system for high-throughput protein crystallography
Miyoshi, T., Igarashi, N., Matsugaki, N., Yamada, Y., Hirano, K., Hyodo, K., Tanioka, K., Egami, N., Namba, M., Kubota, M., Kawai, T. & Wakatsuki, S.
J. Synchrotron Radiat. 15, 281-284 (2008).
X-ray beam stabilization at BL-17A, the protein microcrystallography beamline of the Photon Factory
Igarashi, N., Ikuta, K., Miyoshi, T., Matsugaki, N., Yamada, Y., Yousef, M.S. & Wakatsuki, S.
J. Synchrotron Radiat. 15, 292-295 (2008).
Implementation of remote monitoring and diffraction evaluation systems at the Photon Factory macromolecular crystallography beamlines
Yamada, Y., Honda, N., Matsugaki, N., Igarashi, N., Hiraki, M. & Wakatsuki, S.
J. Synchrotron Radiat. 15, 296-299 (2008).
High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlines
Hiraki, M., Watanabe, S., Honda, N., Yamada, Y., Matsugaki, N., Igarashi, N., Gaponov, Y. & Wakatsuki, S.
J. Synchrotron Radiat. 15, 300-303 (2008).
Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide
Kudo, N., Kumagai, K., Tomishige, N., Yamaji, T., Wakatsuki, S., Nishijima, M., Hanada, K. & Kato, R.
Proc. Natl. Acad. Sci. USA 105, 488-493 (2008).
Structural Analysis of the Human Galectin-9 N-terminal Carbohydrate Recognition Domain Reveals Unexpected Properties that Differ from the Mouse Orthologue
Nagae, M., Nishi, N., Nakamura-Tsuruta, S., Hirabayashi, J., Wakatsuki, S. & Kato, R.
J. Mol. Biol. 375, 119-135 (2008).
Biophysical methods: structure, function and dynamics studies of macromolecular assemblies using electrons, lasers, neutrons and X-rays
Hasnain, S.S. & Wakatsuki, S.
Curr. Opin. Struct. Biol. 18, 577-580 (2008).
蛋白質X線結晶構造解析ー放射光を利用した回折実験
五十嵐教之
蛋白質科学会アーカイブ, 200
糖鎖情報の独自性と普遍性「糖鎖-ガレクチン蛋白質間の相互作用の分子機構」
加藤龍一、長江雅倫、若槻壮市
蛋白質核酸酵素 Vol. 53 No. 12 1670-1675 (2008).
特集タンパク3000プロジェクトの産んだもの、第Ⅰ部、成果とインパクト:個別的解析拠点の研究成果、「翻訳後修飾と輸送、真核生物における構造機能生物学」
若槻壮市・加藤龍一・川崎政人・五十嵐教之・平木雅彦
蛋白質核酸酵素 Vol. 53 No. 5 628-631 (2008).
ビフィズス菌由来AfcAフコシダーゼ触媒ドメインの立体構造解析
長江雅倫、土屋敦子、山本憲二、片山高嶺、若槻壮市、加藤龍一
日本結晶学会誌 Vol. 50, No.2 138-143 (2008).
2007
Design and Construction of the High-speed Network Connecting All the Protein Crystallography Beam Lines at the Photon Factory
Matsugaki, N., Yamada, Y., Igarashi, N. & Wakatsuki, S.
AIP Conf. Proc. 879, 1936-1939 (2007).
Automated Sample Exchange Robots for the Structural Biology Beam Lines at the Photon Factory
Hiraki, M., Watanabe, S., Yamada, Y., Matsugaki, N., Igarashi, N., Gaponov, Y. & Wakatsuki, S.
AIP Conf. Proc. 879, 1924-1927 (2007).
Development of Control Applications for High-Throughput Protein Crystallography Experiments
Gaponov, Y.A., Matsugaki, N., Honda, N., Sasajima, K., Igarashi, N., Hiraki, M., Yamada, Y. & Wakatsuki, S.
AIP Conf. Proc. 879, 1932-1935 (2007).
BL-17A, A New Protein Micro-Crystallography Beam Line of the Photon Factory
Igarashi, N., Matsugaki, N., Yamada, Y., Hiraki, M., Koyama, A., Hirano, K., Miyoshi, T. & Wakatsuki, S.
AIP Conf. Proc., 879, 812-815 (2007).
Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts
Das, M., Kobayashi, M., Yamada, Y., Sreeramulu, S., Ramakrishnan, C., Wakatsuki, S., Kato, R. & Varadarajan, R.
J. Mol. Biol. 372, 1278-1292 (2007).
Structural Basis for Recognition of High Mannose Type Glycoproteins by Mammalian Transport Lectin VIP36
Satoh, T., Cowieson, N.P., Hakamata, W., Ideo, H., Fukushima, K., Kurihara, M., Kato, R., Yamashita, K. & Wakatsuki, S.
J. Biol. Chem. 282, 28246-28255 (2007).
Structure of the small GTPase Rab27b shows an unexpected swapped dimer
Chavas, L.M., Torii, S., Kamikubo, H., Kawasaki, M., Ihara, K., Kato, R., Kataoka, M., Izumi, T. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 63, 769-779 (2007).
Molecular Basis for Autoregulatory Interaction Between GAE Domain and Hinge Region of GGA1
Inoue, M., Shiba, T., Ihara, K., Yamada, Y., Hirano, S., Kamikubo, H., Kataoka, M., Kawasaki, M., Kato, R., Nakayama, K. & Wakatsuki, S.
Traffic 8, 904-913 (2007).
Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
Nagae, M., Tsuchiya, A., Katayama, T., Yamamoto, K., Wakatsuki, S. & Kato, R.
J. Biol. Chem. 282, 18497-18509 (2007).
X-ray phase imaging of biological soft tissue using a direct-sensing x-ray HARP tube camera
Hirano, K., Miyoshi, T., Igarashi, N., Takeda, T., Wu, J., Lwin, T.T., Kubota, M., Egami, N., Tanioka, K., Kawai, T. & Wakatsuki, S.
Phys. Med. Biol. 52, 2545-2552 (2007).
フォトンファクトリー構造生物ビームラインにおける自動化に向けた取り組み
五十嵐教之, 平木雅彦, 松垣直宏, 山田悠介, 若槻壮市
日本結晶学会誌 Vol. 49, No.6 359-363 (2007).
FIP3による低分子量GTPase Rab11の認識機構の研究
志波智生、古賀裕士、申 惠媛、中山和久、川崎政人、加藤龍一、若槻壮市
日本結晶学会誌 Vol. 49, No.4 231-237 (2007).
小特集 結晶評価技術の新展開、解説、「蛋白質結晶評価技術の新展開」
平木雅彦、五十嵐教之、加藤龍一、山田悠介、松垣直宏、川崎政人、若槻壮市
日本結晶成長学会誌 Vol. 34 No. 3 131-138 (2007).
2006
Structural basis of ubiquitin recognition by mammalian Eap45 GLUE domain
Hirano, S., Suzuki, N., Slagsvold, T., Kawasaki, M., Trambaiolo, D., Kato, R., Stenmark, H. & Wakatsuki, S.
Nat. Struct. Mol. Biol. 13, 1031-1032 (2006).
Monoubiquitylation of GGA3 by hVPS18 regulates its ubiquitin-binding ability
Yogosawa, S., Kawasaki, M., Wakatsuki, S., Kominami, E., Shiba, Y., Nakayama, K., Kohsaka, S. & Akazawa, C.
Biochem. Biophys. Res. Commun. 350, 82-90 (2006).
Crystal structure of the galectin-9 N-terminal carbohydrate recognition domain from Mus musculus reveals the basic mechanism of carbohydrate recognition
Nagae, M., Nishi, N., Murata, T., Usui, T., Nakamura, T., Wakatsuki, S. & Kato, R.
J. Biol. Chem. 281, 35884-35893 (2006).
Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope
Shiba, T., Kakuda, S., Ishiguro, M., Morita, I., Oka, S., Kawasaki, T., Wakatsuki, S. & Kato, R.
Proteins 65, 499-508 (2006).
Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1
Shiba, T., Koga, H., Shin, H.W., Kawasaki, M., Kato, R., Nakayama, K. & Wakatsuki, S.
Proc. Natl. Acad. Sci. USA 103, 15416-15421 (2006).
Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses
Hiraki, M., Kato, R., Nagai, M., Satoh, T., Hirano, S., Ihara, K., Kudo, N., Nagae, M., Kobayashi, M., Inoue, M., Uejima, T., Oda, S., Chavas, L.M., Akutsu, M., Yamada, Y., Kawasaki, M., Matsugaki, N., Igarashi, N., Suzuki, M. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 62, 1058-165 (2006).
Structural Basis of Carbohydrate Transfer Activity by Human UDP-GalNAc: Polypeptide alpha-N-Acetylgalactosaminyltransferase (pp-GalNAc-T10)
Kubota, T., Shiba, T., Sugioka, S., Furukawa, S., Sawaki, H., Kato, R., Wakatsuki, S. & Narimatsu, H.
J. Mol. Biol. 359, 708-727 (2006).
Structures of carbohydrate recognition domain of Ca2+ -independent cargo receptors Emp46p and Emp47p
Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Yamada, Y., Igarashi, N., Kato, R., Nakano, A. & Wakatsuki, S.
J. Biol. Chem. 281, 10410-10419 (2006).
Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting
Hirano, S., Kawasaki, M., Ura, H., Kato, R., Raiborg, C., Stenmark, H. & Wakatsuki, S.
Nat. Struct. Mol. Biol. 13, 272-277 (2006).
2005
Structural basis for transcription inhibition by tagetitoxin
Vassylyev, D.G., Svetlov, V., Vassylyeva, M.N., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S. & Artsimovitch, I.
Nat. Struct. Mol. Biol. 12, 1086-1093 (2005).
Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain
Akutsu, M., Kawasaki, M., Katoh, Y., Shiba, T., Yamaguchi, Y., Kato, R., Kato, K., Nakayama, K. & Wakatsuki, S.
FEBS Lett. 579, 5385-5391.
Structural basis of transcription inhibition by antibiotic streptolydigin
Temiakov, D., Zenkin, N., Vassylyeva, M.N., Perederina, A., Tahirov, T.H., Kashkina, E., Savkina, M., Zorov, S., Nikiforov, V., Igarashi, N., Matsugaki, N., Wakatsuki, S., Severinov, K. & Vassylyev, D.G.
Mol. Cell. 19, 655-666 (2005).
Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins
Artsimovitch, I., Vassylyeva, M.N., Svetlov, D., Svetlov, V., Perederina, A., Igarashi, N., Matsugaki, N., Wakatsuki, S., Tahirov, T.H. & Vassylyev, D.G.
Cell 122, 351-363 (2005).
Structure of the ectodomain of Drosophila peptidoglycan-recognition protein LCa suggests a molecular mechanism for pattern recognition
Chang, C.I., Ihara, K., Chelliah, Y., Mengin-Lecreulx, D., Wakatsuki, S. & Deisenhofer, J.
Proc. Natl. Acad. Sci. USA 102, 10279-10284 (2005).
Molecular mechanism of ubiquitin recognition by GGA3 GAT domain
Kawasaki, M., Shiba, T., Shiba, Y., Yamaguchi, Y., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Kato, K., Nakayama, K. & Wakatsuki, S.
Genes Cells 10, 639-654 (2005).
Structure determination of GGA-GAE and gamma1-ear in complex with peptides: crystallization of low-affinity complexes in membrane traffic
Yamada, Y., Inoue, M., Shiba, T., Kawasaki, M., Kato, R., Nakayama, K. & Wakatsuki, S.
Acta Crystallogr. D Biol. Crystallogr. 61, 731-736 (2005).
Eap45 in mammalian ESCRT-II binds ubiquitin via a phosphoinositide-interacting GLUE domain
Slagsvold, T., Aasland, R., Hirano, S., Bache, K.G., Raiborg, C., Trambaiolo, D., Wakatsuki, S. & Stenmark, H.
J. Biol. Chem. 280, 19600-19606 (2005).
Crystal structure of the human cytosolic sialidase Neu2. Evidence for the dynamic nature of substrate recognition
Chavas, L.M., Tringali, C., Fusi, P., Venerando, B., Tettamanti, G., Kato, R., Monti, E. & Wakatsuki, S.
J. Biol. Chem. 280, 469-475 (2005).
Membrane recruitment of effector proteins by Arf and Rab GTPases
Kawasaki, M., Nakayama, K. & Wakatsuki, S.
Curr. Opin. Struct. Biol. 15, 681-689 (2005).
入門講座、こんなことができる放射光(10)、「構造プロテオミクス科学時代の放射光結晶学」
若槻壮市
日本結晶学会誌 Vol. 47, No.6 380-389 (2005).
総説、「GGA-メンブレン・トラフィックを調節する新規のクラスリンアダプターの構想と機能-」
中山和久、若槻壮市
生化学 第77巻 第11号 1367-1381 (2005).
みにれびゅう、「HNK-1糖鎖の生合成に必須な糖転移酵素GlcAT-Pのユニークな糖鎖基質認識機構」
志波智生、角田品子、岡昌吾、石黒正路、川嵜敏祐、若槻壮市、加藤龍一
生化学 第77巻 第2号 153-158 (2005).
特集構造ゲノムプロジェクトの進展、「蛋白質X線結晶構造解析手法の成熟」
若槻壮市、加藤龍一、五十嵐教之、川崎政人、松垣直宏、平木雅彦、山田悠介
蛋白質核酸酵素 Vol. 50 No. 7 846-852 (2005).
2004
Insights into the phosphoregulation of beta-secretase sorting signal by the VHS domain of GGA1
Shiba, T., Kametaka, S., Kawasaki, M., Shibata, M., Waguri, S., Uchiyama, Y. & Wakatsuki, S.
Traffic 5, 437-448 (2004).
Structural basis for acceptor substrate recognition of a human glucuronyltransferase, GlcAT-P, an enzyme critical in the biosynthesis of the carbohydrate epitope HNK-1
Kakuda, S., Shiba, T., Ishiguro, M., Tagawa, H., Oka, S., Kajihara, Y., Kawasaki, T., Wakatsuki, S. & Kato, R.
J. Biol. Chem. 279, 22693-22703 (2004).
GAT (GGA and Tom1) domain responsible for ubiquitin binding and ubiquitination
Shiba, Y., Katoh, Y., Shiba, T., Yoshino, K., Takatsu, H., Kobayashi, H., Shin, H.W., Wakatsuki, S. & Nakayama, K.
J. Biol. Chem. 279, 7105-7111 (2004).
Secure UNIX socket-based controlling system for high-throughput protein crystallography experiments
Gaponov, Y., Igarashi, N., Hiraki, M., Sasajima, K., Matsugaki, N., Suzuki, M., Kosuge, T. & Wakatsuki, S.
J. Synchrotron Radiat. 11, 17-20 (2004).
ゲノミクス・プロテオミクスの新展開 生物情報の解析と応用 「X線結晶構造解析 タンパク質結晶X線回折実験における自動化」
若槻壮市、平木雅彦、Yurii Gaponov、松垣直宏、五十嵐教之、鈴木守
第2編 618-622、NTS inc. 今中忠行京都大学大学院工学研究科教授監修、2004.4.5発刊。ISBN4-86043-049-2
ゲノミクス・プロテオミクスの新展開 生物情報の解析と応用 「X線結晶構造解析 タンパク質結晶構造解析ビームライン(Photon Factory)」
鈴木守、五十嵐教之、松垣直宏、若槻壮市
第2編 612-617、NTS inc. 今中忠行京都大学大学院工学研究科教授監修、2004.4.5発刊。ISBN4-86043-049-2
「タンパク質の成熟:糖鎖修飾と輸送」
若槻壮市
2004第18回「大学と科学」公開シンポジウム講演収録集 タンパク質のかたちから生命のなぞを解く。生物マシーナリー構造生物学の最前線, 51-65 (2004).
2003
Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport
Shiba, T., Kawasaki, M., Takatsu, H., Nogi, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Nakayama, K. & Wakatsuki, S.
Nat. Struct. Biol. 10, 386-393 (2003).
The structure and function of GGAs, the traffic controllers at the TGN sorting crossroads
Nakayama, K. & Wakatsuki, S.
Cell Struct. Funct. 28, 431-442 (2003).
2002
Structural basis for the accessory protein recruitment by the gamma-adaptin ear domain
Nogi, T., Shiba, Y., Kawasaki, M., Shiba, T., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Takatsu, H., Nakayama, K. & Wakatsuki, S.
Nat. Struct. Biol. 9, 527-531 (2002).
Structural basis for recognition of acidic-cluster dileucine sequence by GGA1
Shiba, T., Takatsu, H., Nogi, T., Matsugaki, N., Kawasaki, M., Igarashi, N., Suzuki, M., Kato, R., Earnest, T., Nakayama, K. & Wakatsuki, S.
Nature 415, 937-941 (2002).