Publications
Publications

Publication (Contributions to Science)：

2022

・Photoreaction Pathways of Bacteriorhodopsin and Its D96N Mutant as Revealed by in Situ Photoirradiation Solid-State NMR. Arisu Shigeta, Yuto Otani, Ryota Miyasa, Yoshiteru Makino, Izuru Kawamura, Takashi Okitsu, Akimori Wada, Akira Naito.
Membranes 12(3): 279-279 （2022）

2021

・Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein. Shigeyuki Matsumoto, Haruka Taniguchi-Tamura, Mitsugu Araki, Takashi Kawamura, Ryo Miyamoto, Chiemi Tsuda, Fumi Shima, Takashi Kumasaka, Yasushi Okuno, Tohru Kataoka.
Biochemical and Biophysical Research Communications 565: 85-90 (2021)

・Structure of a retinal chromophore of dark-adapted middle rhodopsin as studied by solid-state nuclear magnetic resonance spectroscopy. Izuru Kawamura, Hayato Seki, Seiya Tajima, Yoshiteru Makino, Arisu Shigeta, Takashi Okitsu, Akimori Wada, Akira Naito, Yuki Sudo
Biophysics and Physicobiology 18: 177-185 (2021)

2020

・31P and 13C solid-state NMR analysis of morphological changes of phospholipid bilayers containing glucagon during fibril formation of glucagon under neutral condition.
Kazumi Haya, Yoshiteru Makino, Akie Kikuchi-Kinoshita, Izuru Kawamura, Akira Naito Biochimica et Biophysica Acta (BBA) - Biomembranes 1862(7): 183290-183290 (2020)

2019

・Phospholipase Cε plays a crucial role in neutrophilic inflammation accompanying acute lung injury through augmentation of CXC chemokine production from alveolar epithelial cells. Kanoko Umezawa, Tatsuya Nagano, Kazuyuki Kobayashi, Ryota Dokuni, Masahiro Katsurada, Masatsugu Yamamoto, Yoko Yoshikawa, Tohru Kataoka, Yoshihiro Nishimura.
Respiratory Research 20(9): 1-12 (2019)

・Photoreaction pathways and photointermediates of retinal-binding photoreceptor proteins as revealed by in situ photoirradiation solid-state NMR spectroscopy. Akira Naito, Yoshiteru Makino, Arisu Shigeta, Izuru Kawamura.
Biophys Rev 11(2): 167-181 （2019）

2018

・Molecular Basis for Allosteric Inhibition of GTP-Bound H-Ras Protein by a Small-Molecule Compound Carrying a Naphthalene Ring. Matsumoto S, Hiraga T, Hayashi Y, Yoshikawa Y, Tsuda C, Araki M, Neya M, Shima F, Kataoka T.
Biochemistry 57(36): 5350-5358 (2018)

・Retinal Configuration of ppR Intermediates Revealed by Photoirradiation Solid-State NMR and DFT. Yoshiteru Makino, Izuru Kawamura, Takashi Okitsu, Akimori Wada, Naoki Kamo, Yuki Sudo, Kazuyoshi Ueda, Akira Naito.
Biophysical Journal 115(1): 72-83 (2018)

2017

・Ras inhibitors display an anti-metastatic effect by downregulation of lysyl oxidase through inhibition of the Ras-PI3K-Akt-HIF-1α pathway. YoshikawaY, TakanoO, KatoI, TakahashiY, ShimaF, KataokaT.
Cancer Lett 410 82-91 (2017)

・Rapgef2, a guanine nucleotide exchange factor for Rapl small GTPases, plays a crucial role in adherence junction (AJ) formation in radial glial cells through ERK-mediated upregulation of the AJ-constituent protein expression. Maged Ibrahim Farag, Yoko Yoshikawa, Kazuhiro Maeta, Tohru Kataoka.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 493(1): 139-145 (2017)

・Photoirradiation and microwave irradiation NMR spectroscopy. Akira Naito, Yoshiteru Makino, Yugo Tasei, Izuru Kawamura.
Experimental Approaches of NMR Spectroscopy: Methodology and Application to Life Science and Materials Science 135-170 (2017)

・Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy. Shota Matsunaga, Yuta Hano, Yuta Saito, Kazuhiro J. Fujimoto, Takashi Kumasaka, Shigeyuki Matsumoto, Tohru Kataoka, Fumi Shima, Shigenori Tanaka.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING 77: 51-63 (2017)

・Structural basis for intramolecular interaction of post-translationally modified H-Ras.GTP prepared by protein ligation.
Haoliang Ke, Shigeyuki Matsumoto, Yosuke Murashima, Haruka Taniguchi-Tamura, Ryo Miyamoto, Yoko Yoshikawa, Chiemi Tsuda, Takashi Kumasaka, Eiichi Mizohata, Hironori Edamatsu, Tohru Kataoka.
FEBS LETTERS 591(16): 2470-2481 (2017)

2016

・Integrin-α10 Dependency Identifies RAC and RICTOR as Therapeutic Targets in High-Grade Myxofibrosarcoma. OkadaT, LeeAY, QinLX, AgaramN, MimaeT, ShenY, O''ConnorR, López-LagoMA, CraigA, MillerML, AgiusP, MolinelliE, SocciND, CragoAM, ShimaF, SanderC, SingerS.
Cancer Discov 6(10): 1148-1165 (2016)

・Molecular Mechanism for Conformational Dynamics of Ras･GTP Elucidated from In-Situ Structural Transition in Crystal.
MatsumotoS, MiyanoN, BabaS, LiaoJ, KawamuraT, TsudaC, TakedaA, YamamotoM, KumasakaT, KataokaT, ShimaF Sci Rep 6: 25931 (2016)

2015

・Characterization of photo-intermediates in the photo-reaction pathways of a bacteriorhodopsin Y185F mutant using in situ photo-irradiation solid-state NMR spectroscopy. Kyosuke Oshima, Arisu Shigeta, Yoshiteru Makino, Izuru Kawamura, Takashi Okitsu, Akimori Wada, Satoru Tuzi, Tatsuo Iwasa, Akira Naito
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES 14(9): 1694-1702 (2015)

・Deletion of Rapgef6, a candidate schizophrenia susceptibility gene, disrupts amygdala function in mice. R. J. Levy, M. Kvajo, Y. Li, E. Tsvetkov, W. Dong, Y. Yoshikawa, T. Kataoka, V. Y. Bolshakov, M. Karayiorgou, J. A. Gogos.
TRANSLATIONAL PSYCHIATRY 5(6) (2015)

2014

・Color-Discriminating Retinal Configurations of Sensory Rhodopsin I by Photo-Irradiation Solid-State NMR Spectroscopy. Hiroki Yomoda, Yoshiteru Makino, Yuya Tomonaga, Tetsurou Hidaka, Izuru Kawamura, Takashi Okitsu, Akimori Wada, Yuki Sudo, Akira Naito.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 53(27): 6960-6964 (2014)

2013

・In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction. Fumi Shima, Yoko Yoshikawa, Min Ye, Mitsugu Araki, Shigeyuki Matsumoto, Jingling Liao, Lizhi Hu, Takeshi Sugimoto, Yuichi Ijiri, Azusa Takeda, Yuko Nishiyama, Chie Sato, Shin Muraoka, Atsuo Tamura, Tsutomu Osoda, Ken-ichiro Tsuda, Tomoya Miyakawa, Hiroaki Fukunishi, Jiro Shimada, Takashi Kumasaka, Masaki Yamamoto, Tohru Kataoka.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 110(20): 8182-8187 (2013)

・Discovery of Small-Molecule Ras Inhibitors that Display Antitumor Activity by Interfering with Ras·GTP-Effector Interaction. Fumi Shima, Yoko Yoshikawa, Shigeyuki Matsumoto, Tohru Kataoka
Enzymes 34: 1-23 (2013)

・Structure-based drug design of small-molecule Ras inhibitors having anti-tumor activity. Shima F, Kataoka T. SPring-8 Research Frontiers 12-13 (2013)

～2012

・Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants. Shin Muraoka, Fumi Shima, Mitsugu Araki, Tomoko Inoue, Akiko Yoshimoto, Yuichi Ijiri, Nobuaki Seki, Atsuo Tamura, Takashi Kumasaka, Masaki Yamamoto, Tohru Kataoka.
FEBS LETTERS 586(12:) 1715-1718 (2012)

・Critical Roles of Interactions among Switch I-preceding Residues and between Switch II and Its Neighboring alpha-Helix in Conformational Dynamics of the GTP-bound Ras Family Small GTPases. Kousuke Matsumoto, Fumi Shima, Shin Muraoka, Mitsugu Araki, Lizhi Hu, Yuichi Ijiri, Rina Hirai, Jingling Liao, Takashi Yoshioka, Takashi Kumasaka, Masaki Yamamoto, Atsuo Tamura, Tohru Kataoka.
JOURNAL OF BIOLOGICAL CHEMISTRY 286(17): 15403-15412 (2011)

・Solution Structure of the State 1 Conformation of GTP-bound H-Ras Protein: Implication for the Role of the Conformational Dynamics in Its Signaling Functions. Mitsugu Araki, Fumi Shima, Yoko Yoshikawa, Shin Muraoka, Yuichi Ijiri, Yuka Nagahara, Tomoya Shirono, Tohru Kataoka, Atsuo Tamura.
J. Biol. Chem 286(45): 39644-39653 (2011)

・Structural Basis for Conformational Dynamics of GTP-bound Ras Protein. Fumi Shima, Yuichi Ijiri, Shin Muraoka, Jingling Liao, Min Ye, Mitsugu Araki, Kousuke Matsumoto, Naoki Yamamoto, Takeshi Sugimoto, Yoko Yoshikawa, Takashi Kumasaka, Masaki Yamamoto, Atsuo Tamura, Tohru Kataoka.
JOURNAL OF BIOLOGICAL CHEMISTRY 285(29): 22696-22705 (2010)

・Biochemical characterization of missense mutations in the Arf/Arl-family small GTPase Arl6 causing Bardet-Biedl syndrome. Tetsuo Kobayashi, Yuji Hori, Nami Ueda, Hiroaki Kajiho, Shin Muraoka, Fumi Shima, Tohru Kataoka, Kenji Kontani, Toshiaki Katada.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 381(3): 439-442 (2009)

・Two conformational states of Ras GTPase exhibit differential GTP-binding kinetics. Jingling Liao, Fumi Shima, Mitsugu Araki, Min Ye, Shin Muraoka, Takeshi Sugimoto, Mei Kawamura, Naoki Yamamoto, Atsuo Tamura, Tohru Kataoka.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 369(2): 327-332 (2008)

・Defective vascular morphogenesis and mid-gestation in mice lacking RA-GEF-1. Ping Wei, Takaya Satoh, Hironori Edamatsu, Atsu Aiba, Tomiyoshi Setsu, Toshio Terashima, Sohei Kitazawa, Kazuki Nakao, Yoko Yoshikawa, Masako Tamada, Tohru Kataoka.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 363(1): 106-112 (2007)

・The M-Ras-RA-GEF-2-Rap1 pathway mediates tumor necrosis factor-alpha- dependent regulation of integrin activation in splenocytes. Yoko Yoshikawa, Takaya Satoh, Takashi Tamura, Ping Wei, Shymaa E. Bilasy, Hironori Edamatsu, Atsu Aiba, Koko Katagiri, Tatsuo Kinashi, Kazuki Nakao, Tohru Kataoka.
MOLECULAR BIOLOGY OF THE CELL 18(8): 2949-2959 (2007)

・Crystal structure of M-Ras reveals a GTP-bound "off" state conformation of Ras family small GTPases. M Ye, F Shima, S Muraoka, JL Liao, H Okamoto, M Yamamoto, A Tamura, N Yagi, T Ueki, T Kataoka.
JOURNAL OF BIOLOGICAL CHEMISTRY 280(35): 31267-31275 (2005)

・Critical role of posttranslational modification of Ras proteins in effector activation. F Shima, T Kataoka SEIKAGAKU 77(6): 519-526 (2005)

・Direct activation of fission yeast adenylyl cyclase by heterotrimeric G protein gpa2. Hideki Ogihara, Fumi Shima, Kana Naito, Tsuyoshi Asato, Ken-Ichi Kariya, Tohru Kataoka.
Kobe Journal of Medical Sciences 50(3-4): 111-121 (2004)

・Critical function of the ras-associating domain as a primary ras-binding site for regulation of Saccharomyces cerevisiae adenylyl cyclase. M Kido, F Shima, T Satoh, T Asato, K Kariya, T Kataoka.
JOURNAL OF BIOLOGICAL CHEMISTRY 277(5): 3117-3123 (2002)

・Role of Raf-1 conserved region 2 in regulation of Ras-dependent Raf-1 activation. H Sendoh, CD Hu, DM Wu, CH Song, Y Yamawaki-Kataoka, J Kotani, T Okada, F Shima, K Kariya, T Kataoka.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 271(3): 596-602 (2000)

・Characterization of a novel Ras-binding protein Ce-FLI-1 comprising leucine-rich repeats and gelsolin-like domains. M Goshima, K Kariya, Y Yamawaki-Kataoka, T Okada, M Shibatohge, F Shima, E Fujimoto, T Kataoka.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 257(1): 111-116 (1999)

・Coiled-coil interaction of N-terminal 36 residues of cyclase-associated protein with adenylyl cyclase is sufficient for its function in Saccharomyces cerevisiae Ras pathway. Yoshimitsu Nishida, Fumi Shima, Hiroyoshi Sen, Yasuhiro Tanaka, Chie Yanagihara, Yuriko Yamawaki-Kataoka, Ken-Ichi Kariya, Tohru Kataoka.
Journal of Biological Chemistry 273(43): 28019-28024 (1998)

・Identification of PLC210, a Caenorhabditis elegans phospholipase C, as a putative effector of Ras. M Shibatohge, K Kariya, YH Liao, CD Hu, Y Watari, M Goshima, F Shima, T Kataoka.
JOURNAL OF BIOLOGICAL CHEMISTRY 273(11): 6218-6222 (1998)

・Effect of association with adenylyl cyclase-associated protein on the interaction of yeast adenylyl cyclase with Ras protein.
Shima F, Yamawaki-Kataoka Y, Yanagihara C, Tamada M, Okada T, Kariya K, Kataoka T. Mol Cell Biol.,17(3):1057-1064 (1997)

・Differential structural requirements for interaction of Ras protein with its distinct downstream effectors.　Akasaka K, Tamada M, Wang F, Kariya K, Shima F, Kikuchi A, Yamamoto M, Shirouzu M, Yokoyama S, Kataoka T. J Biol Chem.
271(10):5353-60. doi: 10.1074/jbc.271.10.5353. PubMed PMID: 8621388. (1996)

Research Support and/or Scholastic Performance:

AMED_Project Promoting Support for Drug Discovery “The iD3 Booster” (2024)

  • Number: DNW19019 (24nk0101530h0006)
  • Project Title: Development of Novel PPI inhibitors as anti-cancer drugs.
  • Role: PI

AMED_Project Promoting Support for Drug Discovery “The iD3 Booster” (2019-2023)

  • Grant Number: DNW19019 (17nk0101309h0003)
  • Project Title: Development of Novel PPI inhibitors as anti-cancer drugs.
  • Role: PI

Translational Research Program, Seeds A (2022)

  • Number: A-180
  • Project Title: Development of novel leukemia therapeutics.
  • Role: PI

JSPS KAKENHI_”Grant-in-Aid for Scientific Research on Innovation Areas” (2022-2023)

  • Grant Number: 22H04752
  • Project Title: Elucidation of cancer signal transduction mechanism using photo-controllable Ras on an atomic scale.
  • Role: PI

JST SCORE University Program Type (2022)

  • Grant Number: 22-201031706
  • Project Title: Development of innovative cancer therapeutic agents based on comprehensive Ras-signaling inhibition.
  • Role: PI

JSPS KAKENHI_Grant-in-Aid for Scientific Research (C) (2022-2024)

  • Grant Number: 22K07191
  • Project Title: Evaluation of drug efficacy and elucidation of the mechanism of action of novel RAS/RAF binding inhibitos in drug-resistant cancer.
  • Role: PI

JSPS KAKENHI_ Grant-in-Aid for Young Scientists (2022-2024)

  • Grant Number: 22K15048
  • Project Title: Allosteric conformational changes of oncogene products Ras on the GTP hydrolysis process.
  • Role: PI

Translational Research program; Strategic Promotion for practical application of Innovative medical Technology (TR-SPRINT). Project for promotion of interdisciplinary collaborative research and developmental initiatives (2020-2021)

  • Number: H-14
  • Project Title: Development of novel Ras-signaling inhibitors.
  • Role: PI

JSPS KAKENHI_”Grant-in-Aid for Scientific Research on Innovation Areas” (2020-2021)

  • Grant Number: 20H05444
  • Project Title: Time-resolved structural analysis of small GTPase Ras signaling transduction by utilizing caged-GTP-coupled Ras protein.

JSPS KAKENHI_Grant-in-Aid for Scientific Research (C) (2019-2021)

  • Grant Number: 19K06525
  • Project Title: Atomic-scale dynamic structural analysis of Ras by SACLA, which provide promising information on designing cancer therapeutic agents.
  • Role: PI

JSPS KAKENHI_ Grant-in-Aid for Young Scientists (2019-2021)

  • Grant Number: 19K16055
  • Project Title: Conformational dynamics of Ras using by SACLA and NMR for the development of anti-cancer drugs.
  • Role: PI

JSPS KAKENHI_Grant-in-Aid for Scientific Research (C) (2018-2020)

  • Grant Number: 18K07230
  • Project Title: Analysis of the mechanism of suppression of bone metastasis of breast cancer by Ras inhibitors
  • Role: PI

AMED_Project Promoting Support for Drug Discovery “The iD3 Booster” (2014-2018)

  • Grant Number: DNW14007 (17nk0101309h0003)
  • Project Title: Screening for novel anti-cancer drugs that block Ras/Raf signals.
  • Role: PI

JSPS KAKENHI_Grant-in-Aid for Japan Society for the Promotion of Research as Research Fellowship(2016-2017)

  • Grant Number: 16J00073
  • Project Title: Retinal – protein interaction of Sensory Rhodopsin Revealed by Photoirradiation Solid-State NMR and DFT.
  • Role: PI

AMED_P-CREATE (2016-2018)

  • Grant Number: 18cm0106212h0003
  • Project Title: Development of selective inhibitors of Ras-effector PLCε that controls cancer microenvironments.
  • Role: Research Collaborator

JSPS KAKENHI_Grant-in-Aid for Scientific Research (B) (2014-2016)

  • Grant Number: 26293026
  • Project Title: Elucidation of the molecular mechanism of structural dynamics of ras oncogene products for application to drug discovery.
  • Role: PI

JSPS KAKENHI_Grant-in-Aid for Scientific Research (B) (2014-2016)

  • Grant Number: 26293065
  • Project Title: Structural analysis of the role of post-translational lipid modification of the small G protein Ras.
  • Role: Research Collaborator

Health and Labour Sciences Research Grants (2011-2015)

  • Grant Number: 15ak0101006h0005
  • Project Title: Development of molecule-targeted cancer-therapeutic agents based on novel 3D structural information on ras oncogene products.
  • Role: Research Collaborator

JST_A-STEP (2011)

  • Grant Number: 122626
  • Project Title: Development of novel anti-cancer drugs that inhibits Ras/Raf signals.
  • Role: PI

JSPS_Grant-in-Aid for Scientific Research on Priority Areas (2005-2009)

  • Grant Number: 17014061
  • Project Title: Molecualr mechanism of cell proliferation by small G proteins.
  • Role: Research Collaborator

JSPS_Grant-in-Aid for Scientific Research on Priority Areas (2008-2009)

  • Grant Number: 20054011
  • Project Title: Significance in signal transduction of tertial structural polymorphisms of small G proteins.
  • Role: PI

JSPS_Grant-in-Aid for Scientific Research on Priority Areas (2006-2007)

  • Grant Number: 18057014
  • Project Title: Significance in signal transduction of tertial structural polymorphisms of small G proteins.
  • Role: PI

JSPS_Grant-in-Aid for Young Scientists (B) (2004-2005)

  • Grant Number: 16790169
  • Project Title: Elucidation of G-protein recognition mechanism via Ras/Rap binding (RA) domain.
  • Role: PI

JSPS_Grant-in-Aid for Young Scientists (B) (2002-2003)

  • Grant Number: 14770050
  • Project Title: Elucidation of G-protein recognition mechanism via Ras/Rap binding (RA) domain.
  • Role: PI

JSPS_Grant-in-Aid for Scientific Research on Priority Areas (2000-2004)

  • Grant Number: 12215098
  • Project Title: Significance in signal transduction of tertial structural polymorphisms of small G proteins.
  • Role: Research Collaborator

JSPS_Grant-in-Aid for JSPS Fellows (1999-2000)

  • Grant Number: 99J08006
  • Project Title: Elucidation of functional roles of post-translational lipid modification-acceptor that mediate effector activation by Ras protein.
  • Role: PI

(cf. The information on total allocation of each research fund and the list of grants from the Foundations have been omitted.)