Researchers Information System

日本語に切り替えるswitch to english

Matsumoto, Shigeyuki

Graduate School of Medicine, Department of Human Health Sciences Program-Specific Associate Professor

Matsumoto, Shigeyuki
list
    Last Updated :2022/09/30

    Basic Information

    Academic Degree

    • Ph. D., Pharmacy(Osaka University)
    • Master of Pharmacy(Osaka University)

    Language of Instruction

    • Japanese

    ID,URL

    researchmap URL

    list
      Last Updated :2022/09/30

      Research

      Research Topics, Overview of the research

      • Research Topics

        Extraction of protein dynamics information from cryo-EM maps using deep learning
      • Overview of the research

        Recent technical breakthroughs in cryo-EM have enabled the three dimensional structures of numerous proteins to be solved at atomic or near-atomic resolution. However, analyzing the dynamics of cryo-EM-targeted proteins is often challenging because of their large sizes and complex structural assemblies. To address the challenges, I aimed to develop an AI model to obtain dynamics information of proteins using a cryo-EM data alone.

      Research Areas

      • Life sciences, Structural biochemistry

      Papers

      • 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, 2013, Peer-reviewed
      • 2P052 Solution Structure of Variable-type Domain of Receptor for Advanced Glycation Endproducts(29. Protein structure and dynamics (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)
        Matsumoto Shigeyuki; Yoshida Takuya; Murata Hiroko; Yamamoto Hiroshi; Kobayashi Yuji; Ohkubo Tadayasu
        Seibutsu Butsuri, 2006
      • QAEmap: A Novel Local Quality Assessment Method for Protein Crystal Structures Using Machine Learning
        Ikuko Miyaguchi; Miwa Sato; Akiko Kashima; Hiroyuki Nakagawa; Yuichi Kokabu; Biao Ma; Shigeyuki Matsumoto; Atsushi Tokuhisa; Masateru Ohta; Mitsunori Ikeguchi
        09 Jul. 2021
      • 深層学習技術を用いたクライオ電子顕微鏡データに潜むタンパク質運動性情報の抽出
        松本 篤幸; 寺山 慧; 奥野 恭史
        生物物理, Jun. 2022, Peer-reviewed, Lead author
      • Integrated approach to functional analysis of an ERBB2 variant of unknown significance detected by a cancer gene panel test
        Yohei Harada; Akemi Sato; Mitsugu Araki; Shigeyuki Matsumoto; Yuta Isaka; Yukari Sagae; Tomonori Abe; Yasuko Aoyagi; Eisaburo Sueoka; Yasushi Okuno; Shinya Kimura; Naoko Sueoka-Aragane
        Cellular Oncology, 08 Jan. 2022, Peer-reviewed
      • Machine learning to estimate the local quality of protein crystal structures
        Ikuko Miyaguchi; Miwa Sato; Akiko Kashima; Hiroyuki Nakagawa; Yuichi Kokabu; Biao Ma; Shigeyuki Matsumoto; Atsushi Tokuhisa; Masateru Ohta; Mitsunori Ikeguchi
        Scientific Reports, Dec. 2021, Peer-reviewed
      • 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, Aug. 2021, Peer-reviewed, Lead author
      • Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations
        Biao Ma; Kei Terayama; Shigeyuki Matsumoto; Yuta Isaka; Yoko Sasakura; Hiroaki Iwata; Mitsugu Araki; Yasushi Okuno
        Journal of Chemical Information and Modeling, 09 Jul. 2021, Peer-reviewed
      • Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
        Mitsugu Araki; Shigeyuki Matsumoto; Gert-Jan Bekker; Yuta Isaka; Yukari Sagae; Narutoshi Kamiya; Yasushi Okuno
        Nature Communications, May 2021, Peer-reviewed
      • Microsecond-timescale MD simulation of EGFR minor mutation predicts the structural flexibility of EGFR kinase core that reflects EGFR inhibitor sensitivity
        Takahiro Yoshizawa; Ken Uchibori; Mitsugu Araki; Shigeyuki Matsumoto; Biao Ma; Ryo Kanada; Yosuke Seto; Tomoko Oh-hara; Sumie Koike; Ryo Ariyasu; Satoru Kitazono; Hironori Ninomiya; Kengo Takeuchi; Noriko Yanagitani; Satoshi Takagi; Kazuma Kishi; Naoya Fujita; Yasushi Okuno; Makoto Nishio; Ryohei Katayama
        npj Precision Oncology, Apr. 2021, Peer-reviewed
      • Extraction of protein dynamics information from cryo-EM maps using deep learning
        Shigeyuki Matsumoto; Shoichi Ishida; Mitsugu Araki; Takayuki Kato; Kei Terayama; Yasushi Okuno
        Nature Machine Intelligence, 04 Feb. 2021, Peer-reviewed, Lead author
      • E487K-Induced Disorder in Functionally Relevant Dynamics of Mitochondrial Aldehyde Dehydrogenase 2
        Shigeyuki Matsumoto; Mitsugu Araki; Yuta Isaka; Fumie Ono; Kenshiro Hirohashi; Shinya Ohashi; Manabu Muto; Yasushi Okuno
        Biophysical Journal, Aug. 2020, Peer-reviewed, Lead author
      • Landscape and function of multiple mutations within individual oncogenes
        Yuki Saito; Junji Koya; Mitsugu Araki; Yasunori Kogure; Sumito Shingaki; Mariko Tabata; Marni B. McClure; Kota Yoshifuji; Shigeyuki Matsumoto; Yuta Isaka; Hiroko Tanaka; Takanori Kanai; Satoru Miyano; Yuichi Shiraishi; Yasushi Okuno; Keisuke Kataoka
        Nature, Jun. 2020, Peer-reviewed
      • Improvement in predicting drug sensitivity changes associated with protein mutations using a molecular dynamics based alchemical mutation method
        Fumie Ono; Shuntaro Chiba; Yuta Isaka; Shigeyuki Matsumoto; Biao Ma; Ryohei Katayama; Mitsugu Araki; Yasushi Okuno
        Scientific Reports, Feb. 2020, Peer-reviewed
      • 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 Yoko; Tsuda C; Araki M; Neya M; SHIMA FUMI; Kataoka Tohru
        Biochemistry, Sep. 2018, Peer-reviewed, Lead author
      • 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, Oct. 2017, Peer-reviewed
      • 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, Aug. 2017, Peer-reviewed
      • Molecular Mechanism for Conformational Dynamics of Ras.GTP Elucidated from In-Situ Structural Transition in Crystal
        Shigeyuki Matsumoto; Nao Miyano; Seiki Baba; Jingling Liao; Takashi Kawamura; Chiemi Tsuda; Azusa Takeda; Masaki Yamamoto; Takashi Kumasaka; Tohru Kataoka; Fumi Shima
        SCIENTIFIC REPORTS, May 2016, Peer-reviewed, Lead author
      • Current status of the development of Ras inhibitors
        Fumi Shima; Shigeyuki Matsumoto; Yoko Yoshikawa; Takashi Kawamura; Masayuki Isa; Tohru Kataoka
        Journal of Biochemistry, Aug. 2015, Peer-reviewed
      • 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, May 2013, Peer-reviewed
      • Solution Structure of the Variable-Type Domain of the Receptor for Advanced Glycation End Products: New Insight into AGE−RAGE Interaction†,‡
        Shigeyuki Matsumoto; Takuya Yoshida; Hiroko Murata; Shusaku Harada; Naoko Fujita; Shota Nakamura; Yasuhiko Yamamoto; Takuo Watanabe; Hideto Yonekura; Hiroshi Yamamoto; Tadayasu Ohkubo; Yuji Kobayashi
        Biochemistry, 25 Nov. 2008, Peer-reviewed, Lead author
      • Enhanced Conformational Sampling with an Adaptive Coarse-Grained Elastic Network Model Using Short-Time All-Atom Molecular Dynamics
        Ryo Kanada; Kei Terayama; Atsushi Tokuhisa; Shigeyuki Matsumoto; Yasushi Okuno
        Journal of Chemical Theory and Computation, 24 Mar. 2022, Peer-reviewed

      Misc.

      • SACLA,SPring-8並びにNMRを用いた低分子量Gタンパク質RasのGTP加水分解過程における動的構造解析
        佐伯茉帆; 槇野義輝; 松本篤幸; 河村高志; 南後恵理子; 熊坂崇; 島扶美
        日本分子生物学会年会プログラム・要旨集(Web), 2020
      • Novel Insights into the Structural Perturbation Induced by the Oncogenic Mutations, Q61L and Q61H, in Ras State 1
        Shigeyuki Matsumoto; Haruka Taniguchi-Tamura; Mitsugu Araki; Takashi Kawamura; Ryo Miyamoto; Chiemi Tsuda; Yasushi Okuno; Fumi Shima; Takashi Kumasaka; Tohru Kataoka
        BIOPHYSICAL JOURNAL, Feb. 2020
      • 分子動力学計算を用いたアルデヒド脱水素酵素2(ALDH2)非活性型変異体の動的立体構造特性の解析
        松本篤幸; 荒木望嗣; 井阪悠太; 奥野恭史; 奥野恭史
        日本細胞生物学会大会(Web), 2019
      • rasがん遺伝子産物の新規立体構造情報を利用した分子標的がん治療薬の開発
        Nishigori Chikako; Shima Fumi; 熊坂崇; Matsumoto Shigeyuki; Yoshikawa Yoko; 山本雅貴; Kataoka Tohru
        日本放射光学会誌 放射光, 2014, Peer-reviewed

      Presentations

      • スーパーコンピューター「富岳」で挑む 新型コロナウイルス治療薬の探索
        松本篤幸
        【先端人シリーズvol.1】スーパーコンピュータで切り拓く健康と福祉の向上, 09 Dec. 2021, Invited
      • Challenges in Large-scale MD-based Docking Study Targeting SARS-CoV-2 Proteins on Fugaku
        Shigeyuki Matsumoto
        Supercomputing Asia 2021, 03 Mar. 2021, Invited
      • Challenges in Large-scale MD-based Docking Study Targeting SARS-CoV-2 Proteins on Fugaku
        Shigeyuki Matsumoto
        The 1st Fugaku Bio-supercomputing Workshop on Cellular-scale Molecular Dynamics Simulations, 07 Jan. 2021, Invited
      • 深層学習技術による cryo-EM密度マップデータに隠された動的情報の抽出
        松本篤幸
        第一回クライオ電子顕微鏡画像からの高度情報処理研究会, 23 Oct. 2020, Invited
      • Sotase Aを利用した翻訳後脂質修飾型Rasの産生と構造物学研究
        村嶋 陽亮; 柯 浩亮; Matsumoto Shigeyuki; Edamatsu Hironori; Kataoka Tohru
        第14回次世代を担う若手のためのフィジカル・ファーマフォーラム, Aug. 2016, 日本薬学会物理系薬学部会
      • Crystal Mounting Method using Humid Air and Hydrophilic Glue Coating For Ambient and Cryogenic Experiments
        Takashi Kumasaka; Masaki Yamamoto; Kataoka Tohru; Shima Fumi; Matsumoto Shigeyuki; Kawamura Takashi; Nobuo Kamiya; Yasufumi Umena; Naoto Yagi; Seiki Baba
        2015 Annual Meeting of the American Crystallographic Association, Jul. 2015, American Crystallographic Association, Invited
      • 試料雰囲気湿度調整によるRasタンパク質の結晶内構造転移
        熊坂 崇; 馬場 清喜; 宮野 菜央; Kawamura Takashi; Matsumoto Shigeyuki; 山本 雅貴; Kataoka Tohru; Shima Fumi
        第15回日本蛋白質科学会年会, Jun. 2015, 日本蛋白質科学会
      • GTP結合型H-RasのState 1結晶構造情報に基づく立体構造遷移機構の解明
        Matsumoto Shigeyuki; 宮野 菜央; 馬場 清喜; Liao Jingling; 竹田 あずさ; 山本 雅貴; 熊坂 崇; Kataoka Tohru; Shima Fumi
        第15回日本蛋白質科学会年会, Jun. 2015, 日本蛋白質科学会
      • GTP結合型H-Rasの活性調節に関与する立体構造遷移メカニズムの解明
        Matsumoto Shigeyuki
        YIAヤングインベスティゲーターアワード, Oct. 2014, 社団法人 神緑会(神戸大学医学部医学科同窓会)
      • AI・シミュレーションによる薬剤開発の迅速化
        田中良尚; 松本篤幸; 奥野恭史, Joint work
        羊土社, Aug. 2022
      • rasがん遺伝子産物Rasお分子標的としたがん治療薬開発の現状
        島扶美; 吉川陽子; 松本篤幸; 片岡徹, Joint work
        2014
      • The Enzymes, Vol. 34, Inhibitors of the Ras superfamily G-proteins, Part B / Discovery of Small-Molecule Ras Inhibitors that Display Antitumor Activity by Interfering with Ras・GTP?Effector Interaction
        Yoshikawa Yoko; Matsumoto Shigeyuki; Kataoka Tohru, Others
        Elsevier Inc., Dec. 2013, Not refereed

      Industrial Property Rights

      • 特願2021-125013, Ras/Raf結合阻害化合物
        島扶美; 吉川陽子; 松本篤幸; 槇野義輝; 窪田浩一; 幸瞳; 熊坂崇; 河村高志

      External funds: Kakenhi

      • がん遺伝子産物Rasの動的な構造特性を介した機能発現メカニズムの解明
        Grant-in-Aid for Young Scientists (B)
        Institute of Physical and Chemical Research;Kobe University
        松本 篤幸
        From 01 Apr. 2017, To 31 Mar. 2022, Granted
        Ras;state transition;がん変異体;分子動力学シミュレーション;X線結晶構造解析;立体構造;State遷移;ダイナミクス;NMR;動的平衡
      • Structural study on the role of post-translational lipid modifications of the small G protein Ras
        Grant-in-Aid for Scientific Research (B)
        Kobe University
        TOHRU KATAOKA
        From 01 Apr. 2014, To 31 Mar. 2017, Project Closed
        シグナル伝達;蛋白質;癌;脂質;高分子構造・物性
      • Research on the molecular basis of conformational dynamics of oncogene product Ras for application to the development of its specific inhibitors
        Grant-in-Aid for Scientific Research (B)
        Kobe University
        fumi shima
        From 01 Apr. 2014, To 31 Mar. 2017, Project Closed
        医薬分子設計;分子標的薬;がん;シグナル伝達;がん遺伝子;癌
      • 深層学習技術を用いた動的情報からの化合物ータンパク質結合親和性の抽出
        Grant-in-Aid for Scientific Research (C)
        Basic Section 43020:Structural biochemistry-related
        Kyoto University
        松本 篤幸
        From 01 Apr. 2022, To 31 Mar. 2026, Granted
        分子動力学計算;深層学習;結合親和性予測;低分子化合物
      • cryoEM-NMR融合構造解析の確立
        Grant-in-Aid for Challenging Research (Pioneering)
        Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
        Osaka University
        加藤 貴之
        From 30 Jun. 2022, To 31 Mar. 2025, Granted
        単粒子解析;NMR;融合構造解析;電子顕微鏡

      ページ上部へ戻る