研究業績 Publications
-
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., 32, e4775. (2023).
Hanazono Y, Hirano Y, Tamada T, Miki K., "Description of peptide bond planarity from high-resolution neutron crystallography." Biophys Physicobiol., 20, e200035. (2023).
Akiko Kamegawa, Shota Suzuki, Hiroshi Suzuki, Kouki Nishikawa, Nobutaka Numoto, Yoshinori Fujiyoshi., "Structural analysis of the water channel AQP2 by single-particle cryo-EM." J Struct Biol., 215, 107984 (2023).
Daisuke Kozai, Nobutaka Numoto, Kouki Nishikawa, Akiko Kamegawa, Shohei Kawasaki, Yoko Hiroaki, Katsumasa Irie, Atsunori Oshima, Hiroyuki Hanzawa, Kousei Shimada, Yutaka Kitano, Yoshinori Fujiyoshi., "Recognition Mechanism of a Novel Gabapentinoid Drug, Mirogabalin, for Recombinant Human α2δ1, a Voltage-Gated Calcium Channel Subunit" J Mol Biol., 435, 168049 (2023).
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., 14, 1211-1222. (2022).
Hanazono Y, Hirano Y, Takeda K, Kusaka K, Tamada T, Miki K., "Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis." Sci Adv., 8, eabn2276. (2022).
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., 19, 1-10. (2022).
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., 41, 71-78. (2022).
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., 14, 21-22. (2022).
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., 23, e202100435. (2022).
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., 12, 130. (2022).
Numoto Nobutaka, Onoda Seiko, Kawano Yoshiaki, Okumura Hideo, Baba Seiki, Fukumori Yoshihiro, Miki Kunio, Ito Nobutoshi., "Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery" Biophysics and Physicobiology., 19, e190019_1-e190019_10. (2022).
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." Communications biology., 4, 1175. (2021).
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 chemical neuroscience., 12, 3015-3027. (2021).
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., 169, 207-213. (2021).
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., 116, 102571. (2021).
Oda M, Numoto N, Bekker GJ, Kamiya N, Kawai F., "Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization." Methods Enzymol., 648, 159-185. (2021).
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., 64, 516-526. (2020).
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., 89, 502-511. (2020).
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., 131, 51-59. (2020).
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., 169, 207-213. (2020).
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., 114, 545-552. (2019).
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., 27, 3674-3681. (2019).
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., 84, 240.e13-240.e22. (2019).
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., 593, 242-250. (2019).
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., 16, 80-88. (2019).
Ikura T, Yonezawa Y, Ito N., "Mutational effects of Cys113 on structural dynamics of Pin1." Biophysics and physicobiology., 16, 452-465. (2019).
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., 61, 6658-6673. (2018).
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., 57, 5289-5300. (2018).
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., 592, 3082−3091 (2018).
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., 26, 1412–1417 (2018).
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 and 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., 9, 820 (2018).
Rocio Otero, Michiyasu Ishizawa, Nobutaka Numoto, Teikichi Ikura, Nobutoshi Ito, Hiroaki Tokiwa, Antonio Mouriño, Makoto Makishima, and Sachiko Yamada. “25S-Adamantyl-23-yne-26,27-dinor-1α,25-dihydroxyvitamin D3: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex” J. Med. Chem., 61, 6658–6673 (2018)
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., 592, 3082–3091 (2018)
Nobutaka Numoto, Narutoshi Kamiya, Gert-Jan Bekker, Yuri Yamagami, Satomi Inaba, Kentaro Ishii, Susumu Uchiyama, Fusako Kawai, Nobutoshi Ito, and 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, 57, 5289–5300 (2018)
Satomi Inaba, Nobutaka Numoto, Shuhei Ogawa, Hisayuki Morii, Teikichi Ikura, Ryo Abe, Nobutoshi Ito and 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., 292, 1052–1060 (2017)
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., 471, 163–168 (2016)
Isao Kii, Yuto Sumida, Toshiyasu Goto, Rie Sonamoto, Yukiko Okuno, Suguru Yoshida, Tomoe Kato, Yuka Koike, Minako Abe, Yosuke Nonaka, Teikichi Ikura, Nobutoshi Ito, Hiroshi Shibuya, Takamitsu Hosoya, and Masatoshi Hagiwara. “Selective inhibition of the kinase DYRK1A by targeting its folding process” Nature Commun., 7, 11391 (2016)
Ikura, T. & Ito, N. “Crystal Structure of the Vitamin D Receptor Ligand-Binding Domain with Lithocholic Acids” Vitam. Horm., 100, 117-136 (2016)
Chizuru Akatsu, Kenro Shinagawa, Nobutaka Numoto, Zhihong Liu, Ayse Konuskan Ucar, Mohammad Aslam, Shirly Phoon, Takahiro Adachi, Koji Furukawa, Nobutoshi Ito, and Takeshi Tsubata. “CD72 negatively regulates B lymphocyte responses to the lupus-related endogenous toll-like receptor 7 ligand Sm/RNP” J. Exp. Med., 213, 2691-2706 (2016)
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., 6, 33861 (2016)
Satoshi Morooka, Mitsuteru Hoshina, Isao Kii, Takayoshi Okabe, Hirotatsu Kojima, Naoko Inoue, Yukiko Okuno, Masatsugu Denawa, Suguru Yoshida, Junichi Fukuhara, Kensuke Ninomiya, Teikichi Ikura, Toshio Furuya, Tetsuo Nagano, Kousuke Noda, Susumu Ishida, Takamitsu Hosoya, Nobutoshi Ito, Nagahisa Yoshimura, Masatoshi Hagiwara. “Identification of a dual inhibitor of SRPK1 and CK2 that attenuates pathological angiogenesis of macular degeneration in mice” Molecular Pharmacology, 88, 316-325 (2015).
So Masaki, Isao Kii, Yuto Sumida, Tomoe Kato-Sumida, Yasushi Ogawa, Nobutoshi Ito, Mitsuhiro Nakamura, Rie Sonamoto, Naoyuki Kataoka, Takamitsu Hosoya, Masatoshi Hagiwara. “Design and synthesis of a potent inhibitor of class 1 DYRK kinases as a suppressor of adipogenesis” Bioorganic & Medicinal Chemistry, 23, 4434-4441 (2015).
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 Protein Proteomics, 1854, 1438–1443 (2015)
Yusuke Watarai, Michiyasu Ishizawa, Teikichi Ikura, Flavia C.M. Zacconi, Shigeyuki Uno, Nobutoshi Ito, Antonio Mourińo, Hiroaki Tokiwa, Makoto Makishima, and 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., 58, 9510−9521 (2015)
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., 23, 7274−7281 (2015)
Takeru Kudo, Michiyasu Ishizawa, Kazuki Maekawa, Makoto Nakabayashi, Yusuke Watarai, Hikaru Uchida, Hiroaki Tokiwa, Teikichi Ikura, Nobutoshi Ito, Makoto Makishima, and Sachiko Yamada: Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor. J. Med. Chem., 57 (10), 4073–4087 (2014).
Yamamoto M, Onogi H, Kii I, Yoshida S, Iida K, Sakai H, Abe M, Tsubota T, Ito N, Hosoya T, Hagiwara M. (2014) CDK9 inhibitor FIT-039 prevents replication of multiple DNA viruses. J. Clin. Invest., 124, 3479-3488 (2014).
東京医科歯科大学