• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Development of fully-automated system for NMR structural analysis of higher molecular weight proteins

Research Project

Project/Area Number 17H03641
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Structural biochemistry
Research InstitutionYokohama National University

Principal Investigator

KOJIMA Chojiro  横浜国立大学, 大学院工学研究院, 教授 (50333563)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2019: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2018: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2017: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
KeywordsNMR / 蛋白質 / 立体構造
Outline of Final Research Achievements

In this research, we have developed a system for determining the NMR structure of higher molecular weight proteins by making use of 950 MHz NMR equipment and fully automated structure calculation software. Specifically, the utilizitation of fully automated NMR structural determination system MagRO, amino acid selective labeling technology, and methyl group-selective deuterium labeling has enabled the structural analysis of protein-protein and protein-drug complexes.

Academic Significance and Societal Importance of the Research Achievements

NMRによる蛋白質の立体構造決定は専門性が高く、今まで専門家以外の研究者が利用することが難しかった。本研究では、大阪大学蛋白質研究所で整備されている世界最高感度のNMR装置、小林直宏博士(現理化学研究所)が開発した全自動NMR自動構造計算ソフト、独自開発の安定同位体標識技術などを用いることで、高分子量蛋白質にNMR構造解析が適用可能であることを示した。今後は蛋白質のNMR構造解析の汎用化が進むと考えられる。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (27 results)

All 2020 2019 2018 2017 Other

All Int'l Joint Research (5 results) Journal Article (14 results) (of which Int'l Joint Research: 9 results,  Peer Reviewed: 14 results,  Open Access: 6 results,  Acknowledgement Compliant: 1 results) Presentation (7 results) (of which Int'l Joint Research: 3 results,  Invited: 7 results) Remarks (1 results)

  • [Int'l Joint Research] Rutgers University(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Goethe University Frankfurt(ドイツ)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Academy of Sciences(チェコ)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Marquette University(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Universite de Sherbrooke(カナダ)

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study2020

    • Author(s)
      Bala Siqin、Shinya Shoko、Srivastava Arpita、Ishikawa Marie、Shimada Atsushi、Kobayashi Naohiro、Kojima Chojiro、Tama Florence、Miyashita Osamu、Kohda Daisuke
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: 1864 Issue: 2 Pages: 129418-129418

    • DOI

      10.1016/j.bbagen.2019.129418

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] In-cell NMR as a sensitive tool to monitor physiological condition of Escherichia coli2020

    • Author(s)
      Sugiki Toshihiko、Yamaguchi Yoshihiro、Fujiwara Toshimichi、Inouye Masayori、Ito Yutaka、Kojima Chojiro
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 2466-2466

    • DOI

      10.1038/s41598-020-59076-2

    • NAID

      120006952208

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structural instability of lamin A tail domain modulates its assembly and higher order function in Emery-Dreifuss muscular dystrophy2019

    • Author(s)
      Muneyo Mio, Toshihiko Sugiki, Chie Matsuda, Hiroaki Mitsuhashi, Chojiro Kojima, Siu Yuen Chan, Yukiko K. Hayashi, Kazuhiro Mio
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 512 Issue: 1 Pages: 22-28

    • DOI

      10.1016/j.bbrc.2019.02.138

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structural characterization of the N-terminal kinase-interacting domain of an Hsp90-cochaperone Cdc37 by CD and solution NMR spectroscopy.2019

    • Author(s)
      Ihama, F., Yamamoto, M., Kojima, C., Fujiwara, T., Matsuzaki, K., Miyata, Y., Hoshino, M.
    • Journal Title

      Biochim. Biophys. Acta-Proteins Proteom.

      Volume: 1867 Issue: 9 Pages: 813-820

    • DOI

      10.1016/j.bbapap.2019.06.007

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Noise peak filtering in multi-dimensional NMR spectra using convolutional neural networks2018

    • Author(s)
      Kobayashi, N., Hattori, Y., Nagata, T., Shinya, S., Guentert, P., Kojima, C., Fujiwara, T.
    • Journal Title

      Bioinformatics

      Volume: 34 Issue: 24 Pages: 4300-4301

    • DOI

      10.1093/bioinformatics/bty581

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] NMR spectroscopic characterization of a model RNA duplex reflecting the core sequence of hammerhead ribozymes2018

    • Author(s)
      Hattori Yoshikazu、Yamanaka Daichi、Morioka Saori、Yamaguchi Taishi、Tomonari Honoka、Kojima Chojiro、Tanaka Yoshiyuki
    • Journal Title

      Nucleosides, Nucleotides and Nucleic Acids

      Volume: 37 Issue: 7 Pages: 383-396

    • DOI

      10.1080/15257770.2018.1473877

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Phosphoinositide binding by the PH domain in ceramide transfer protein (CERT) is inhibited by hyperphosphorylation of an adjacent serine-repeat motif2018

    • Author(s)
      Sugiki Toshihiko、Egawa Daichi、Kumagai Keigo、Kojima Chojiro、Fujiwara Toshimichi、Takeuchi Koh、Shimada Ichio、Hanada Kentaro、Takahashi Hideo
    • Journal Title

      Journal of Biological Chemistry

      Volume: 293 Issue: 28 Pages: 11206-11217

    • DOI

      10.1074/jbc.ra118.002465

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Amino Acid Selective 13C Labeling and 13C Scrambling Profile Analysis of Protein α and Side-Chain Carbons in Escherichia coli Utilized for Protein Nuclear Magnetic Resonance2018

    • Author(s)
      Sugiki Toshihiko、Furuita Kyoko、Fujiwara Toshimichi、Kojima Chojiro
    • Journal Title

      Biochemistry

      Volume: 57 Issue: 26 Pages: 3576-3589

    • DOI

      10.1021/acs.biochem.8b00182

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Helix Rearrangement in the Periplasmic Domain of the Flagellar Stator B Subunit Activates Peptidoglycan Binding and Ion Influx2018

    • Author(s)
      Kojima Seiji, Takao Masato, Almira Gaby, Kawahara Ikumi, Sakuma Mayuko, Homma Michio, Kojima Chojiro, Imada Katsumi.
    • Journal Title

      Structure

      Volume: 26 Issue: 4 Pages: 590-598

    • DOI

      10.1016/j.str.2018.02.016

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] NMR line shape analysis of a multi-state ligand binding mechanism in chitosanase2017

    • Author(s)
      Shinya Shoko、Ghinet Mariana G.、Brzezinski Ryszard、Furuita Kyoko、Kojima Chojiro、Shah Sneha、Kovrigin Evgenii L.、Fukamizo Tamo
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 67 Issue: 4 Pages: 309-319

    • DOI

      10.1007/s10858-017-0109-6

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: Concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine.2017

    • Author(s)
      Jakub Sebera, Yoshikazu Hattori, Daichi Sato, David Reha, Radim Nencka, Takashi Kohno, Chojiro Kojima, Yoshiyuki Tanaka, and Vladimir Sychrovsky
    • Journal Title

      Nucleic Acids Research

      Volume: 45 Issue: 9 Pages: 5231-5242

    • DOI

      10.1093/nar/gkx157

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Protein 19F-labeling using transglutaminase for the NMR study of intermolecular interactions2017

    • Author(s)
      Hattori Yoshikazu、Heidenreich David、Ono Yuki、Sugiki Toshihiko、Yokoyama Kei-ichi、Suzuki Ei-ichiro、Fujiwara Toshimichi、Kojima Chojiro
    • Journal Title

      Journal of Biomolecular NMR

      Volume: 68 Issue: 4 Pages: 271-279

    • DOI

      10.1007/s10858-017-0125-6

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structural and Functional Analysis of the C-Terminal Region of FliG, an Essential Motor Component of Vibrio Na + -Driven Flagella2017

    • Author(s)
      Miyanoiri Yohei、Hijikata Atsushi、Nishino Yuuki、Gohara Mizuki、Onoue Yasuhiro、Kojima Seiji、Kojima Chojiro、Shirai Tsuyoshi、Kainosho Masatsune、Homma Michio
    • Journal Title

      Structure

      Volume: 25 Issue: 10 Pages: 1540-1548

    • DOI

      10.1016/j.str.2017.08.010

    • NAID

      120006375873

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Production of Single-Chain Fv Antibodies Specific for GA-Pyridine, an Advanced Glycation End-Product (AGE), with Reduced Inter-Domain Motion2017

    • Author(s)
      Fukuda N、Noi K、Weng L、Kobashigawa Y、Miyazaki H、Wakeyama Y、Takaki M、Nakahara Y、Tatsuno Y、Uchida-Kamekura M、Suwa Y、Sato T、Ichikawa-Tomikawa N、Nomizu M、Fujiwara Y、Ohsaka F、Saitoh T、Maenaka K、Kumeta H、Shinya S、Kojima C、Ogura T、Morioka H
    • Journal Title

      Molecules

      Volume: 22 Issue: 10 Pages: 1695-1695

    • DOI

      10.3390/molecules22101695

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 19F-NMR for Fragment-Based Drug Discovery2019

    • Author(s)
      Chojiro Kojima
    • Organizer
      8th Asia-Pacific NMR Symposium 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] NMRで分子集団の構造を捉える2019

    • Author(s)
      児嶋長次郎
    • Organizer
      第20回若手NMR研究会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 19F-NMR for Drug Discovery2019

    • Author(s)
      Chojiro Kojima
    • Organizer
      Chem-Bio Informatics Society (CBI) Annual Meeting 2019
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 創薬 NMR 技術の開発とその植物生理学分野への応用2018

    • Author(s)
      児嶋長次郎
    • Organizer
      日本蛋白質科学会第18回年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] NMR tools developed for protein-drug and protein-protein interaction studies2018

    • Author(s)
      Chojiro Kojima
    • Organizer
      The 6th International Symposium on Drug Discovery and Design by NMR
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 植物構造生物学研究と創薬2018

    • Author(s)
      児嶋長次郎
    • Organizer
      植物科学シンポジウム 2018
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Fully Automated NMR Structure Determination of Protein2017

    • Author(s)
      Chojiro Kojima
    • Organizer
      2017 Taiwan-Japan Biomedical Symposium on Magnetic Resonance
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Remarks] Kojima Lab top page

    • URL

      http://nmrlab.ynu.ac.jp/labotop.php

    • Related Report
      2017 Annual Research Report

URL: 

Published: 2017-04-28   Modified: 2021-02-19  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi