Department of Structural Biology

122  articles.  
* There may be some overlapped articles listed due to the difference of format.

  1. Imai D, Numoto N, Tokiwa H, Kakuta H, Ito N: Structural basis for the full and partial agonist activities of retinoid X receptor α ligands with an iso-butoxy and an isopropyl group. Biochemical and biophysical research communications. 2024.08; 734 150617. ( PubMed , DOI )

  2. Yoshida M, Hanazono Y, Numoto N, Nagao S, Yabuno S, Kitagawa Y, Sekiguchi H, Ito N, Azuma T, Oda M: Affinity-matured antibody with a disulfide bond in H-CDR3 loop. Archives of biochemistry and biophysics. 2024.06; 758 110068. ( PubMed , DOI )

  3. Akatsu C, Tsuneshige T, Numoto N, Long W, Uchiumi T, Kaneko Y, Asano M, Ito N, Tsubata T: CD72 is an inhibitory pattern recognition receptor that recognizes ribosomes and suppresses production of anti-ribosome autoantibody. Journal of autoimmunity. 2024.05; 146 103245. ( PubMed , DOI )

  4. Omori S, Hanazono Y, Nishi H, Kinoshita K: The role of the STAS domain in SLC26A9 for chloride ion transporter function. Biophysical journal. 2024.05; 123 (12): 1751-1762. ( PubMed , DOI )

  5. Yuki S Tateishi, Tamasa Araki, Satoru Kawai, Shuhei Koide, Yuko Umeki, Takashi Imai, Yumiko Saito-Nakano, Masaki Kikuchi, Atsushi Iwama, Hajime Hisaeda, Cevayir Coban, Takeshi Annoura: Histone H3.3 variant plays a critical role on zygote-to-oocyst development in malaria parasites. Parasitology International. 2024.01; ( PubMed , DOI )

  1. Masaki Kikuchi, Shohei Takase, Tsuyoshi Konuma, Kota Noritsugu, Saaya Sekine, Takahisa Ikegami, Akihiro Ito, Takashi Umehara: GAS41 promotes H2A.Z deposition through recognition of the N terminus of histone H3 by the YEATS domain. Proceedings of the National Academy of Sciences of the United States of America. 2023.10; 120 (43): e2304103120. ( PubMed , DOI )

  2. Bekker GJ, Numoto N, Kawasaki M, Hayashi T, Yabuno S, Kozono Y, Shimizu T, Kozono H, Ito N, Oda M, Kamiya N: Elucidation of binding mechanism, affinity and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02. Protein Science. 2023.09; 32 (10): e4775. ( PubMed , DOI )

  3. Yuya Hanazono, Yu Hirano, Taro Tamada, Kunio Miki: Description of peptide bond planarity from high-resolution neutron crystallography Biophysics and Physicobiology. 2023.09; 20 (3): e200035.

  4. Masaki Kikuchi, Satoshi Morita, Masatoshi Wakamori, Shin Sato, Tomomi Uchikubo-Kamo, Takehiro Suzuki, Naoshi Dohmae, Mikako Shirouzu, Takashi Umehara: Epigenetic mechanisms to propagate histone acetylation by p300/CBP. Nature communications. 2023.07; 14 (1): 4103. ( PubMed , DOI )

  5. Nan Liu, Tsuyoshi Konuma, Rajal Sharma, Deyu Wang, Nan Zhao, Lingling Cao, Ying Ju, Di Liu, Shuai Wang, Almudena Bosch, Yifei Sun, Siwei Zhang, Donglei Ji, Satoru Nagatoishi, Noa Suzuki, Masaki Kikuchi, Masatoshi Wakamori, Chengcheng Zhao, Chunyan Ren, Thomas Jiachi Zhou, Yaoyao Xu, Jamel Meslamani, Shibo Fu, Takashi Umehara, Kouhei Tsumoto, Satoko Akashi, Lei Zeng, Robert G Roeder, Martin J Walsh, Qiang Zhang, Ming-Ming Zhou: Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin. Molecular cell. 2023.07; 83 (13): 2206-2221. ( PubMed , DOI )

  1. Hall D, Basu G, Ito N: Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday. Biophysical reviews. 2022.12; 14 (6): 1211-1222. ( PubMed , DOI )

  2. Masaki Kikuchi, Satoshi Morita, Mie Goto, Masatoshi Wakamori, Kazushige Katsura, Kazuharu Hanada, Mikako Shirouzu, Takashi Umehara: Elucidation of binding preferences of YEATS domains to site-specific acetylated nucleosome core particles. The Journal of biological chemistry. 2022.08; 298 (8): 102164. ( PubMed , DOI )

  3. Hanazono Yuya, Hirano Yu, Takeda Kazuki, Kusaka Katsuhiro, Tamada Taro, Miki Kunio: Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis SCIENCE ADVANCES. 2022.05; 8 (20): eabn2276. ( PubMed , DOI )

  4. Nobutaka Numoto, Seiko Onoda, Yoshiaki Kawano, Hideo Okumura, Seiki Baba, Yoshihiro Fukumori, Kunio Miki, Nobutoshi Ito: Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. Biophys Physicobiol. 2022.05; 19 1-10. ( PubMed , DOI )

  5. Basu G, Hall D, Ito N: Special Issue call: Computational biophysics and structural biology of proteins-A Special Issue in honor of Prof. Haruki Nakamura's 70th birthday. Biophysical reviews. 2022.02; 14 (1): 21-22. ( PubMed , DOI )

  6. Oda Masayuki, Sano Tomoki, Kamatari Yuji O., Abe Yoshito, Ikura Teikichi, Ito Nobutoshi: Structural Analysis of Hen Egg Lysozyme Refolded after Denaturation at Acidic pH PROTEIN JOURNAL. 2022.02; 41 (1): 71-78. ( PubMed , DOI )

  7. Miyazaki Y, Kikuchi M, Umezawa K, Descamps A, Nakamura D, Furuie G, Sumida T, Saito K, Kimura N, Niwa T, Sumida Y, Umehara T, Hosoya T, Kii I: Structure-activity relationship for the folding intermediate-selective inhibition of DYRK1A. Eur J Med Chem. 2022.01; 227 113948. ( PubMed , DOI )

  8. Fujioka Toshifumi, Numoto Nobutaka, Akama Hiroyuki, Shilpa Kola, Oka Michiko, Roy Prodip K., Krishna Yarkali, Ito Nobutoshi, Baker David, Oda Masayuki, Tanaka Fujie: Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions CHEMBIOCHEM. 2022.01; 23 (2): e202100435. ( PubMed , DOI )

  9. Yoshihara Ayana, Kawasaki Haru, Masuno Hiroyuki, Takada Koki, Numoto Nobutaka, Ito Nobutoshi, Hirata Naoya, Kanda Yasunari, Ishizawa Michiyasu, Makishima Makoto, Kagechika Hiroyuki, Tanatani Aya: Lithocholic Acid Amides as Potent Vitamin D Receptor Agonists BIOMOLECULES. 2022.01; 12 (1): ( PubMed , DOI )

  10. Numoto Nobutaka, Onoda Seiko, Kawano Yoshiaki, Okumura Hideo, Baba Seiki, Fukumori Yoshihiro, Miki Kunio, Ito Nobutoshi: 400kDa V2ヘモグロビンの酸素解離中間体の構造は蛋白質アロステリーの粗スナップショットを提供する(Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery) Biophysics and Physicobiology. 2022; 19 e190019_1-e190019_10. ( ichushi )

  1. Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, GiełdoŃ A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Ślusarz R, Wesołowski PA, ZiĘba K, Del Carpio Muñoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Honorato RV, Jandova Z, Jiménez-García B, Koukos PI, Van Keulen S, Van Noort CW, Réau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodríguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, DapkŪnas J, Olechnovič K, Venclovas Č, Duan R, Qiu L, Zhang S, Zou X, Wodak SJ: Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins. 2021.12; 89 (12): 1800-1823. ( PubMed , DOI )

  2. Tanaka H, Kondo K, Fujita K, Homma H, Tagawa K, Jin X, Jin M, Yoshioka Y, Takayama S, Masuda H, Tokuyama R, Nakazaki Y, Saito T, Saido T, Murayama S, Ikura T, Ito N, Yamamori Y, Tomii K, Bianchi ME, Okazawa H: HMGB1 signaling phosphorylates Ku70 and impairs DNA damage repair in Alzheimer's disease pathology. Commun Biol. 2021.10; 4 (1): 1175. ( PubMed , DOI )

  3. Kondo K, Ikura T, Tanaka H, Fujita K, Takayama S, Yoshioka Y, Tagawa K, Homma H, Liu S, Kawasaki R, Huang Y, Ito N, Tate SI, Okazawa H: Hepta-Histidine Inhibits Tau Aggregation. ACS Chem Neurosci. 2021.08; 12 (16): 3015-3027. ( PubMed , DOI )

  4. Yosuke Inoue, Yuya Hanazono, Kentaro Noi, Akihiro Kawamoto, Masato Kimatsuka, Ryuhei Harada, Kazuki Takeda, Ryoichi Kita, Natsuki Iwamasa, Kyoka Shibata, Keiichi Noguchi, Yasuteru Shigeta, Keiichi Namba, Teru Ogura, Kunio Miki, Kyosuke Shinohara, Masafumi Yohda: Split conformation of Chaetomium thermophilum Hsp104 disaggregase. Structure. 2021.07; 29 (7): 721-730. ( PubMed , DOI )

  5. Hiroki Kitagawa, Masaki Kikuchi, Shin Sato, Hisami Watanabe, Naoki Umezawa, Maiko Kato, Yosuke Hisamatsu, Takashi Umehara, Tsunehiko Higuchi: Structure-Based Identification of Potent Lysine-Specific Demethylase 1 Inhibitor Peptides and Temporary Cyclization to Enhance Proteolytic Stability and Cell Growth-Inhibitory Activity. Journal of medicinal chemistry. 2021.03; 64 (7): 3707-3719. ( PubMed , DOI )

  6. Erna Davydova, Tadahiro Shimazu, Maren Kirstin Schuhmacher, Magnus E Jakobsson, Hanneke L D M Willemen, Tongri Liu, Anders Moen, Angela Y Y Ho, Jędrzej Małecki, Lisa Schroer, Rita Pinto, Takehiro Suzuki, Ida A Grønsberg, Yoshihiro Sohtome, Mai Akakabe, Sara Weirich, Masaki Kikuchi, Jesper V Olsen, Naoshi Dohmae, Takashi Umehara, Mikiko Sodeoka, Valentina Siino, Michael A McDonough, Niels Eijkelkamp, Christopher J Schofield, Albert Jeltsch, Yoichi Shinkai, Pål Ø Falnes: The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes. Nature communications. 2021.02; 12 (1): 891. ( PubMed , DOI )

  7. Senga Akane, Numoto Nobutaka, Yamashita Mitsuaki, Iida Akira, Ito Nobutoshi, Kawai Fusako, Oda Masayuki: Multiple structural states of Ca2+-regulated PET hydrolase, Cut190, and its correlation with activity and stability The Journal of Biochemistry. 2021.02; 169 (2): 207-213. ( ichushi )

  8. Alborzian Deh Sheikh A, Gomaa S, Li X, Routledge M, Saigoh K, Numoto N, Angata T, Hitomi Y, Takematsu H, Tsuiji M, Ito N, Kusunoki S, Tsubata T: A Guillain-Barré syndrome-associated SIGLEC10 rare variant impairs its recognition of gangliosides. Journal of autoimmunity. 2021.01; 116 102571. ( PubMed , DOI )

  1. Iiyama M, Numoto N, Ogawa S, Kuroda M, Morii H, Abe R, Ito N, Oda M: Molecular interactions of the CTLA-4 cytoplasmic region with the phosphoinositide 3-kinase SH2 domains. Molecular immunology. 2020.12; 131 51-59. ( PubMed , DOI )

  2. Emori Miho, Numoto Nobutaka, Senga Akane, Bekker Gert-Jan, Kamiya Narutoshi, Kobayashi Yuma, Ito Nobutoshi, Kawai Fusako, Oda Masayuki: Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. 2020.12; 89 (5): 502-511. ( PubMed , DOI )

  3. Sasaki H, Masuno H, Kawasaki H, Yoshihara A, Numoto N, Ito N, Ishida H, Yamamoto K, Hirata N, Kanda Y, Kawachi E, Kagechika H, Tanatani A: Lithocholic Acid Derivatives as Potent Vitamin D Receptor Agonists. Journal of medicinal chemistry. 2020.12; 64 (1): 516-526. ( PubMed , DOI )

  4. Senga A, Numoto N, Yamashita M, Iida A, Ito N, Kawai F, Oda M: Multiple structural states of Ca2+ regulated PET hydrolase, Cut190, and its correlation with activity and stability. Journal of biochemistry. 2020.09; 169 (2): 207-213. ( PubMed , DOI )

  5. Helen D Wu, Masaki Kikuchi, Onur Dagliyan, Adam K Aragaki, Hideki Nakamura, Nikolay V Dokholyan, Takashi Umehara, Takanari Inoue: Rational design and implementation of a chemically inducible heterotrimerization system. Nature methods. 2020.09; 17 (9): 928-936. ( PubMed , DOI )

  6. Ikura Teikichi, Ito Nobutoshi: Pin1の変異体C113AとC113Sの構造解析(Structural analysis of Pin1 mutants C113A And C113S) 生物物理. 2020.08; 60 (Suppl.1-2): S144. ( ichushi )

  7. Yuya Hanazono, Kazuki Takeda, Kunio Miki: Characterization of perdeuterated high-potential iron-sulfur protein with high-resolution X-ray crystallography. Proteins. 2020.02; 88 (2): 251-259. ( PubMed , DOI )

  1. Yang Tai, Kiyofumi Takaba, Yuya Hanazono, Hoang Anh Dao, Kunio Miki, Kazuki Takeda: X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-ångström resolutions. Acta Crystallogr D Struct Biol. 2019.12; 75 (12): 1096-1106. ( PubMed , DOI )

  2. Nishiguchi A, Numoto N, Ito N, Azuma T, Oda M: Three-dimensional structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain. Molecular immunology. 2019.10; 114 545-552. ( PubMed , DOI )

  3. Numoto Nobutaka, Fukumori Yoshihiro, Miki Kunio, Ito Nobutoshi: 巨大ヘモグロビンのアロステリック中間体の時分割構造解析(Time-resolved structure analysis of allosteric intermediate of the giant hemoglobin) 生物物理. 2019.08; 59 (Suppl.1-2): S245. ( ichushi )

  4. Yasukochi Shotaro, Numoto Nobutaka, Hori Kiminori, Tenno Natsuko, Tenno Takeshi, Ito Nobutoshi, Hiroaki Hidekazu: ヒトDishevelled1 PDZドメインと阻害剤の共結晶構造解析(Crystal structure of human Dishevelled1 PDZ with its inhibitor) 生物物理. 2019.08; 59 (Suppl.1-2): S240. ( ichushi )

  5. Masuno Hiroyuki, Kazui Yuko, Tanatani Aya, Fujii Shinya, Kawachi Emiko, Ikura Teikichi, Ito Nobutoshi, Yamamoto Keiko, Kagechika Hiroyuki: Development of novel lithocholic acid derivatives as vitamin D receptor agonists BIOORGANIC & MEDICINAL CHEMISTRY. 2019.08; 27 (16): 3674-3681. ( PubMed , DOI )

  6. Kiyofumi Takaba, Yang Tai, Haruhiko Eki, Hoang-Anh Dao, Yuya Hanazono, Kazuya Hasegawa, Kunio Miki, Kazuki Takeda: Subatomic resolution X-ray structures of green fluorescent protein. IUCrJ. 2019.05; 6 (3): 387-400. ( PubMed , DOI )

  7. Nakayama S, Shimonaka S, Elahi M, Nishioka K, Oji Y, Matsumoto SE, Li Y, Yoshino H, Mogushi K, Hatano T, Sato T, Ikura T, Ito N, Motoi Y, Hattori N: Tau aggregation and seeding analyses of two novel MAPT variants found in patients with motor neuron disease and progressive parkinsonism. Neurobiology of aging. 2019.03; 84 240.e13-240.e22. ( PubMed , DOI )

  8. Yurina Miyashita, Nobutaka Numoto, Sundaram Arulmozhiraja, Shogo Nakano, Naoya Matsuo, Kanade Shimizu, Osamu Shibahara, Michiko Fujihara, Hiroki Kakuta, Sohei Ito, Teikichi Ikura, Nobutoshi Ito, Hiroaki Tokiwa: Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor α (RXRα). FEBS Lett.. 2019.01; 593 (2): 242-250. ( PubMed , DOI )

  9. Ikura T, Yonezawa Y, Ito N: Mutational effects of Cys113 on structural dynamics of Pin1. Biophysics and physicobiology. 2019; 16 452-465. ( PubMed , DOI )

  10. Hosoe Y, Numoto N, Inaba S, Ogawa S, Morii H, Abe R, Ito N, Oda M: Structural and functional properties of Grb2 SH2 dimer in CD28 binding. Biophysics and physicobiology. 2019; 16 80-88. ( PubMed , DOI )

  1. Rocio Otero, Michiyasu Ishizawa, Nobutaka Numoto, Teikichi Ikura, Nobutoshi Ito, Hiroaki Tokiwa, Antonio Mouriño, Makoto Makishima, Sachiko Yamada: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex. J. Med. Chem.. 2018.08; 61 (15): 6658-6673. ( PubMed , DOI )

  2. Teikichi Ikura, Naoya Tochio, Ryosuke Kawasaki, Mizuki Matsuzaki, Akihiro Narita, Mahito Kikumoto, Naoko Utsunomiya-Tate, Shin-Ichi Tate, Nobutoshi Ito: The trans isomer of Tau peptide is prone to aggregate, and the WW domain of Pin1 drastically decreases its aggregation. FEBS Lett.. 2018.08; 592 (18): 3082-3091. ( PubMed , DOI )

  3. Nobutaka Numoto, Narutoshi Kamiya, Gert-Jan Bekker, Yuri Yamagami, Satomi Inaba, Kentaro Ishii, Susumu Uchiyama, Fusako Kawai, Nobutoshi Ito, Masayuki Oda: Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle. Biochemistry. 2018.08; 57 (36): 5289-5300. ( PubMed , DOI )

  4. Yuya Hanazono, Kazuki Takeda, Kunio Miki: Co-translational folding of α-helical proteins: structural studies of intermediate-length variants of the λ repressor. FEBS Open Bio. 2018.08; 8 (8): 1312-1321. ( PubMed , DOI )

  5. Naoki Miyamoto, Miho Yoshimura, Yuji Okubo, Kayo Suzuki-Nagata, Takeshi Tsumuraya, Nobutoshi Ito, Ikuo Fujii: Structural basis of the broad substrate tolerance of the antibody 7B9-catalyzed hydrolysis of p-nitrobenzyl esters. Bioorg. Med. Chem.. 2018.05; 26 (8): 1412-1417. ( PubMed , DOI )

  6. Naoko Matsubara, Akihiro Imamura, Tatsuya Yonemizu, Chizuru Akatsu, Hongrui Yang, Akiharu Ueki, Natsuki Watanabe, Hajjaj Abdu-Allah, Nobutaka Numoto, Hiromu Takematsu, Shinobu Kitazume, Thomas F Tedder, Jamey D Marth, Nobutoshi Ito, Hiromune Ando, Hideharu Ishida, Makoto Kiso, Takeshi Tsubata: CD22-Binding Synthetic Sialosides Regulate B Lymphocyte Proliferation Through CD22 Ligand-Dependent and Independent Pathways, and Enhance Antibody Production in Mice. Front Immunol. 2018.04; 9 820. ( PubMed , DOI )

  7. Naoki Umezawa, Kasumi Tsuji, Shin Sato, Masaki Kikuchi, Hisami Watanabe, Yuhei Horai, Masashi Yamaguchi, Yosuke Hisamatsu, Takashi Umehara, Tsunehiko Higuchi: Inhibition of FAD-dependent lysine-specific demethylases by chiral polyamine analogues. RSC Advances. 2018; 8 (64): 36895. ( DOI )

  8. Tsusaka T, Kikuchi M, Shimazu T, Suzuki T, Sohtome Y, Akakabe M, Sodeoka M, Dohmae N, Umehara T, Shinkai Y: Tri-methylation of ATF7IP by G9a/GLP recruits the chromodomain protein MPP8. Epigenetics Chromatin. 2018; 11 (1): 56. ( PubMed , DOI )

  1. Yuta Shinohara, Yohei M. Koyama, Maki Ukai-Tadenuma, Takatsugu Hirokawa, Masaki Kikuchi, Rikuhiro G. Yamada, Hideki Ukai, Hiroshi Fujishima, Takashi Umehara, Kazuki Tainaka, Hiroki R. Ueda: Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock. Molecular cell. 2017.09; 67 (5): 783-798. ( DOI )

  2. Ikura Teikichi, Ito Nobutoshi: タウタンパク質に対するPin1由来のプロテアーゼの活性の定量的評価(Quantitative evaluation of activity of a protease derived from Pin1 for tau protein) 生物物理. 2017.08; 57 (Suppl.1-2): S315. ( ichushi )

  3. Numoto Nobutaka, Akatsu Chizuru, Shinagawa Kenro, Tsubata Takeshi, Ito Nobutoshi: B細胞抑制性因子CD72の分子表面電荷分布によるリガンド結合制御機構(Charge distribution regulates the ligand-binding affinity of B cell inhibitory receptor CD72) 生物物理. 2017.08; 57 (Suppl.1-2): S276. ( ichushi )

  4. Nagano-Shoji M, Hamamoto Y, Mizuno Y, Yamada A, Kikuchi M, Shirouzu M, Umehara T, Yoshida M, Nishiyama M, Kosono S: Characterization of lysine acetylation of a phosphoenolpyruvate carboxylase involved in glutamate overproduction in Corynebacterium glutamicum. Molecular Microbiology. 2017.05;

  5. Yuichi Amano, Masaki Kikuchi, Shin Sato, Shigeyuki Yokoyama, Takashi Umehara, Naoki Umezawa, Tsunehiko Higuchi: Development and crystallographic evaluation of histone H3 peptide with N-terminal serine substitution as a potent inhibitor of lysine-specific demethylase 1. Bioorganic & Medicinal Chemistry. 2017.05; 25 (9): 2617-2624. ( DOI )

  6. Hiraku Ohno, Kazuki Takeda, Satomi Niwa, Tomotaka Tsujinaka, Yuya Hanazono, Yu Hirano, Kunio Miki: Crystallographic characterization of the high-potential iron-sulfur protein in the oxidized state at 0.8 Å resolution. PLoS One. 2017.05; 12 (5): e0178183. ( PubMed , DOI )

  7. Satomi Inaba, Nobutaka Numoto, Shuhei Ogawa, Hisayuki Morii, Teikichi Ikura, Ryo Abe, Nobutoshi Ito, Masayuki Oda: Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins. J. Biol. Chem.. 2017.01; 292 (3): 1052-1060. ( PubMed , DOI )

  8. Kulkarni Manjiri R., Islam Monirul, Numoto Nobutaka, Elahi Montasir, Ito Nobutoshi, Kuroda Yutaka: Crystallographic studies of sero-specific Dengue ED3 immune response ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES. 2017; 73 A404. ( DOI )

  9. Kulkarni Manjiri Ravindra, Islam Monirul, Numoto Nobutaka, Ito Nobutoshi, Kuroda Yutaka: Crystal structures of dengue virus protein revealed ED3 sero-specificity ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES. 2017; 73 C394. ( DOI )

  1. Chizuru Akatsu, Kenro Shinagawa, Nobutaka Numoto, Zhihong Liu, Ayse Konuskan Ucar, Mohammad Aslam, Shirly Phoon, Takahiro Adachi, Koji Furukawa, Nobutoshi Ito, Takeshi Tsubata: CD72 negatively regulates B lymphocyte responses to the lupus-related endogenous toll-like receptor 7 ligand Sm/RNP. J. Exp. Med.. 2016.11; 213 (12): 2691-2706. ( PubMed , DOI )

  2. Yuya Hanazono, Kazuki Takeda, Kunio Miki: Structural studies of the N-terminal fragments of the WW domain: Insights into co-translational folding of a beta-sheet protein. Sci Rep. 2016.10; 6 34654. ( PubMed , DOI )

  3. Tomomi Imamura, Kyota Fujita, Kazuhiko Tagawa, Teikichi Ikura, Xigui Chen, Hidenori Homma, Takuya Tamura, Ying Mao, Juliana Bosso Taniguchi, Kazumi Motoki, Makoto Nakabayashi, Nobutoshi Ito, Kazunori Yamada, Kentaro Tomii, Hideyuki Okano, Julia Kaye, Steven Finkbeiner, Hitoshi Okazawa: Identification of hepta-histidine as a candidate drug for Huntington's disease by in silico-in vitro- in vivo-integrated screens of chemical libraries. Sci Rep. 2016.09; 6 33861. ( PubMed , DOI )

  4. Yuya Hanazono, Kazuki Takeda, Kunio Miki: Characterization of the Nqo5 subunit of bacterial complex I in the isolated state. FEBS Open Bio. 2016.06; 6 (7): 687-695. ( PubMed , DOI )

  5. Manjiri R Kulkarni, Nobutaka Numoto, Nobutoshi Ito, Yutaka Kuroda: Modeling and experimental assessment of a buried Leu-Ile mutation in dengue envelope domain III. Biochem. Biophys. Res. Commun.. 2016.02; 471 (1): 163-168. ( PubMed , DOI )

  6. Yuya Hanazono, Kazuki Takeda, Satomi Niwa, Masahito Hibi, Naoya Takahashi, Tamotsu Kanai, Haruyuki Atomi, Kunio Miki: Crystal structures of chitin binding domains of chitinase from Thermococcus kodakarensis KOD1. FEBS Lett. 2016.01; 590 (2): 298-304. ( PubMed , DOI )

  7. Teikichi Ikura, Nobutoshi Ito: Crystal Structure of the Vitamin D Receptor Ligand-Binding Domain with Lithocholic Acids. Vitam. Horm.. 2016; 100 117-136. ( PubMed , DOI )

  8. Isao Kii, Yuto Sumida, Toshiyasu Goto, Rie Sonamoto, Yukiko Okuno, Suguru Yoshida, Tomoe Kato-Sumida, Yuka Koike, Minako Abe, Yosuke Nonaka, Teikichi Ikura, Nobutoshi Ito, Hiroshi Shibuya, Takamitsu Hosoya, Masatoshi Hagiwara: Selective inhibition of the kinase DYRK1A by targeting its folding process. Nat Commun. 2016; 7 11391. ( PubMed , DOI )

  1. Yusuke Watarai, Michiyasu Ishizawa, Teikichi Ikura, Flavia C M Zacconi, Shigeyuki Uno, Nobutoshi Ito, Antonio Mouriño, Hiroaki Tokiwa, Makoto Makishima, Sachiko Yamada: Synthesis, Biological Activities, and X-ray Crystal Structural Analysis of 25-Hydroxy-25(or 26)-adamantyl-17-[20(22),23-diynyl]-21-norvitamin D Compounds. J. Med. Chem.. 2015.12; 58 (24): 9510-9521. ( PubMed , DOI )

  2. Yasuaki Anami, Yuta Sakamaki, Toshimasa Itoh, Yuka Inaba, Makoto Nakabayashi, Teikichi Ikura, Nobutoshi Ito, Keiko Yamamoto: Fine tuning of agonistic/antagonistic activity for vitamin D receptor by 22-alkyl chain length of ligands: 22S-Hexyl compound unexpectedly restored agonistic activity. Bioorg. Med. Chem.. 2015.11; 23 (22): 7274-7281. ( PubMed , DOI )

  3. Manjiri R Kulkarni, Monirul M Islam, Nobutaka Numoto, Montasir Elahi, Mamunur R Mahib, Nobutoshi Ito, Yutaka Kuroda: Structural and biophysical analysis of sero-specific immune responses using epitope grafted Dengue ED3 mutants. Biochim. Biophys. Acta. 2015.10; 1854 (10 Pt A): 1438-1443. ( PubMed , DOI )

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  2. Kudo Takeru, Ishizawa Michiyasu, Maekawa Kazuki, Nakabayashi Makoto, Watarai Yusuke, Uchida Hikaru, Tokiwa Hiroaki, Ikura Teikichi, Ito Nobutoshi, Makishima Makoto, Yamada Sachiko: Combination of triple bond and adamantane ring on the vitamin D side chain produced partial agonists for vitamin D receptor. J Med Chem. 2014.05; 57 (10): 4073-4087. ( PubMed , DOI )

  1. Ikura Teikichi, Ito Nobutoshi: Peptidyl-prolyl isomerase activity of FK506 binding protein 12 prevents tau peptide from aggregating. Protein Eng Des Sel. 2013.09; 26 (9): 539-546. ( PubMed , DOI )

  2. Nakabayashi Makoto, Tsukahara Yoshito, Iwasaki-Miyamoto Yukiko, Mihori-Shimazaki Mika, Yamada Sachiko, Inaba Satomi, Oda Masayuki, Shimizu Masato, Makishima Makoto, Tokiwa Hiroaki, Ikura Teikichi, Ito Nobutoshi: Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands. J Med Chem. 2013.09; 56 (17): 6745-6760. ( PubMed , DOI )

  3. Higo K, Ikura T, Oda M, Morii H, Takahashi J, Abe R, Ito N: High resolution crystal structure of the Grb2 SH2 domain with a phosphopeptide derived from CD28 PLoS One. 2013.08; 8 (9): e74482. ( DOI )

  4. Masaki Kikuchi, Shinichiro Iwabuchi, Tatsuhiko Kikkou, Keiichi Noguchi, Masafumi Odaka, Masafumi Yohda, Masaaki Kawata, Chikara Sato, Osamu Matsumoto: Expression, purification, crystallization and preliminary crystallographic analysis of hepatitis B virus core protein dimerized via a peptide linker containing an EGFP insertion. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013.08; 69 (Pt 8): 942-945. ( PubMed , DOI )

  5. Masuno Hiroyuki, Ikura Teikichi, Morizono Daisuke, Orita Isamu, Yamada Sachiko, Shimizu Masato, Ito Nobutoshi: Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives. J Lipid Res. 2013.08; 54 (8): 2206-2213. ( PubMed , DOI )

  6. Masaki Kikuchi, Shinichiro Iwabuchi, Tatsuhiko Kikkou, Keiichi Noguchi, Masafumi Odaka, Masafumi Yohda, Masaaki Kawata, Chikara Sato, Osamu Matsumoto: Expression, purification, crystallization and preliminary X-ray crystallographic studies of hepatitis B virus core fusion protein corresponding to octahedral particles. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013.02; 69 (Pt 2): 165-169. ( PubMed , DOI )

  7. Yuya Hanazono, Kazuki Takeda, Toshihiko Oka, Tetsuya Abe, Taichi Tomonari, Nobuhiko Akiyama, Yoshiki Aikawa, Masafumi Yohda, Kunio Miki: Nonequivalence observed for the 16-meric structure of a small heat shock protein, SpHsp16.0, from Schizosaccharomyces pombe. Structure. 2013.02; 21 (2): 220-228. ( PubMed , DOI )

  8. Higo Kunitake, Ikura Teikichi, Oda Masayuki, Morii Hisayuki, Takahashi Jun, Abe Ryo, Ito Nobutoshi: High resolution crystal structure of the Grb2 SH2 domain with a phosphopeptide derived from CD28. PLoS One. 2013; 8 (9): e74482. ( PubMed , DOI )

  1. Yuya Hanazono, Kazuki Takeda, Masafumi Yohda, Kunio Miki: Structural studies on the oligomeric transition of a small heat shock protein, StHsp14.0. J Mol Biol. 2012.09; 422 (1): 100-108. ( PubMed , DOI )

  2. Yoshimoto Nobuko, Sakamaki Yuta, Haeta Minoru, Kato Akira, Inaba Yuka, Itoh Toshimasa, Nakabayashi Makoto, Ito Nobutoshi, Yamamoto Keiko: Butyl pocket formation in the vitamin D receptor strongly affects the agonistic or antagonistic behavior of ligands. J Med Chem. 2012.05; 55 (9): 4373-4381. ( PubMed , DOI )

  3. Nomura W, Masuda A, Ohba K, Urabe A, Ito N, Ryo A, Yamamoto N, Tamamura H: Effects of DNA binding of the zinc finger and linkers for domain fusion on the catalytic activity of sequence-specific chimeric recombinases determined by a facile fluorescent system. Biochemistry. 2012.02; 51 (7): 1510-1517. ( PubMed , DOI )

  4. Tamashiro Tomonari, Tanabe Yoichi, Ikura Teikichi, Ito Nobutoshi, Oda Masayuki: Critical roles of Asp270 and Trp273 in the alpha-repeat of the carbohydrate-binding module of endo-1,3-beta-glucanase for laminarin-binding avidity. Glycoconj J. 2012.01; 29 (1): 77-85. ( PubMed , DOI )

  1. Fujii Shinya, Masuno Hiroyuki, Taoda Yoshiyuki, Kano Atsushi, Wongmayura Angsuma, Nakabayashi Makoto, Ito Nobutoshi, Shimizu Masato, Kawachi Emiko, Hirano Tomoya, Endo Yasuyuki, Tanatani Aya, Kagechika Hiroyuki: Boron cluster-based development of potent nonsecosteroidal vitamin D receptor ligands: direct observation of hydrophobic interaction between protein surface and carborane. J Am Chem Soc. 2011.12; 133 (51): 20933-20941. ( PubMed , DOI )

  2. Nomura W, Ohashi N, Okuda Y, Narumi T, Ikura T, Ito N, Tamamura H: Fluorescence-quenching screening of protein kinase C ligands with an environmentally sensitive fluorophore. Bioconjug Chem. 2011.05; 22 (5): 923-930. ( PubMed , DOI )

  3. Kazuki Takeda, Takuro Hayashi, Tetsuya Abe, Yu Hirano, Yuya Hanazono, Masafumi Yohda, Kunio Miki: Dimer structure and conformational variability in the N-terminal region of an archaeal small heat shock protein, StHsp14.0. J Struct Biol. 2011.04; 174 (1): 92-99. ( PubMed , DOI )

  1. Ogawa Y., Nonaka Y., Goto T., Ohnishi E., Hiramatsu T., Kii I., Yoshida M., Ikura T., Onogi H., Shibuya H., Hosoya T., Ito N., Hagiwara M.: Development of a novel selective inhibitor of the Downsyndrome-related kinase Dyrk1A. Nat. Commun.. 2010.10; ( PubMed , DOI )

  2. Inaba Yuka, Nakabayashi Makoto, Itoh Toshimasa, Yoshimoto Nobuko, Ikura Teikichi, Ito Nobutoshi, Shimizu Masato, Yamamoto Keiko: 22S-butyl-1alpha,24R-dihydroxyvitamin D3: recovery of vitamin D receptor agonistic activity. J Steroid Biochem Mol Biol. 2010.07; 121 (1-2): 146-150. ( PubMed , DOI )

  1. Inaba Y, Yoshimoto N, Sakamaki Y, Nakabayashi M, Ikura T, Tamamura H, Ito N, Shimizu M, Yamamoto K: A New Class of Vitamin D Analogues that Induce Structural Rearrangement of the Ligand-Binding Pocket of the Receptor. J Med Chem. 2009.02; ( PubMed , DOI )

  1. Nakabayashi Makoto, Yamada Sachiko, Yoshimoto Nobuko, Tanaka Takashi, Igarashi Miharu, Ikura Teikichi, Ito Nobutoshi, Makishima Makoto, Tokiwa Hiroaki, DeLuca Hector F, Shimizu Masato: Crystal structures of rat vitamin D receptor bound to adamantyl vitamin D analogs: structural basis for vitamin D receptor antagonism and partial agonism. J Med Chem. 2008.09; 51 (17): 5320-5329. ( PubMed , DOI )

  2. Shimizu Masato, Miyamoto Yukiko, Takaku Hajime, Matsuo Mayumi, Nakabayashi Makoto, Masuno Hiroyuki, Udagawa Nobuyuki, DeLuca Hector F, Ikura Teikichi, Ito Nobutoshi: 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation, and crystal structure. Bioorg Med Chem. 2008.07; 16 (14): 6949-6964. ( PubMed , DOI )

  3. Urakubo Yoshiaki, Ikura Teikichi, Ito Nobutoshi: Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation. Protein Sci. 2008.06; 17 (6): 1055-1065. ( PubMed , DOI )

  4. Ikura Teikichi, Kinoshita Kengo, Ito Nobutoshi: A cavity with an appropriate size is the basis of the PPIase activity. Protein Eng Des Sel. 2008.02; 21 (2): 83-89. ( PubMed , DOI )

  1. Ikura Teikichi, Ito Nobutoshi: Requirements for peptidyl-prolyl isomerization activity: a comprehensive mutational analysis of the substrate-binding cavity of FK506-binding protein 12. Protein Sci. 2007.12; 16 (12): 2618-2625. ( PubMed , DOI )

  2. Oda Masayuki, Ito Nobutoshi, Tsumuraya Takeshi, Suzuki Kayo, Sakakura Masayoshi, Fujii Ikuo: Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis. J Mol Biol. 2007.05; 369 (1): 198-209. ( PubMed , DOI )

  1. Tsuchiya Yuko, Kinoshita Kengo, Ito Nobutoshi, Nakamura Haruki: PreBI: prediction of biological interfaces of proteins in crystals. Nucleic Acids Res. 2006.07; 34 (Web Server issue): W320-W324. ( PubMed , DOI )

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  1. Yuya Hanazono: Revisiting the Peptide Bond Planarity by High-resolution Neutron Crystallography SEIBUTSU BUTSURI. 2023.08; 63 (4): 205-206.

  1. Hanazono Yuya, Hirano Yu, Tamada Taro, Miki Kunio: New Description of the Peptide Bond in Proteins Revealed by High-Resolution Neutron Crystallography Journal of the Crystallographic Society of Japan. 2022.08; 64 (3):

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