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In situ Protein NMR Structure Analysis

Research Project

Project/Area Number 26291013
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Structural biochemistry
Research InstitutionYokohama National University (2016-2017)
Osaka University (2014-2015)

Principal Investigator

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

Co-Investigator(Kenkyū-buntansha) 藤原 敏道  大阪大学, たんぱく質研究所, 教授 (20242381)
Co-Investigator(Renkei-kenkyūsha) MATSUKI Yoh  大阪大学, 蛋白質研究所, 准教授 (70551498)
SUGIKI Toshihiko  大阪大学, 蛋白質研究所, 特任助教 (70635698)
FURUITA Kyoko  大阪大学, 蛋白質研究所, 特任助教 (30727665)
Project Period (FY) 2014-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥16,640,000 (Direct Cost: ¥12,800,000、Indirect Cost: ¥3,840,000)
Fiscal Year 2016: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2015: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2014: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
KeywordsNMR / 蛋白質 / 立体構造 / in situ
Outline of Final Research Achievements

For in situ protein NMR structure analysis, we have developed the following NMR techniques. Amino acid selective 13C-labeling and 13C-scrambling profile analysis of protein alpha and side-chain carbons in E. coli utilized for protein NMR. Protein 19F-labeling using transglutaminase for the NMR study of intermolecular interactions. Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints.

Report

(5 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (36 results)

All 2018 2017 2016 2015 2014 Other

All Int'l Joint Research (7 results) Journal Article (23 results) (of which Int'l Joint Research: 13 results,  Peer Reviewed: 23 results,  Open Access: 7 results,  Acknowledgement Compliant: 9 results) Presentation (6 results) (of which Int'l Joint Research: 5 results,  Invited: 6 results)

  • [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(Canada)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Academy of Science/Czech Technical University(チェコ)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] University of Wisconsin-Madison/University of California(米国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] University of Athens(Greece)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] IOCB AS CR(チェコ)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] TFL1-Like Proteins in Rice Antagonize Rice FT-Like Protein in Inflorescence Development by Competition for Complex Formation with 14-3-3 and FD.2018

    • Author(s)
      Kaneko-Suzuki M, Kurihara-Ishikawa R, Okushita-Terakawa C, Kojima C, Nagano-Fujiwara M, Ohki I, Tsuji H, Shimamoto K, Taoka KI.
    • Journal Title

      Plant Cell Physiol.

      Volume: 59 Issue: 3 Pages: 458-468

    • DOI

      10.1093/pcp/pcy021

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Current NMR Techniques for Structure-Based Drug Discovery2018

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

      Molecules

      Volume: 23 Issue: 1 Pages: 148-148

    • DOI

      10.3390/molecules23010148

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [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
  • [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] 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] 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] 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] Cold-Shock Expression System in E. coli for Protein NMR Studies2017

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

      Methods Mol Biol

      Volume: 1586 Pages: 345-357

    • DOI

      10.1007/978-1-4939-6887-9_23

    • ISBN
      9781493968855, 9781493968879
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Substrate specificity of TOR complex 2 is determined by a ubiquitin-fold domain of the Sin1 subunit2017

    • Author(s)
      Hisashi Tatebe, Shinichi Murayama, Toshiya Yonekura, Tomoyuki Hatano, David Richter, Tomomi Furuya, Saori Kataoka, Kyoko Furuita, Chojiro Kojima, and Kazuhiro Shiozaki
    • Journal Title

      eLife

      Volume: 6

    • DOI

      10.7554/elife.19594

    • NAID

      120005983409

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins2016

    • Author(s)
      Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, and Toshimichi Fujiwara
    • Journal Title

      J. Biomed. Semant.

      Volume: 7 Pages: 16-16

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Expression, purification, and crystallization of a plant-specific DUF1110 protein from Oryza sativa2016

    • Author(s)
      Harada K, Yamashita E, Inoue K, Yamaguchi K, Fujiwara T, Nakagawa A, Kawasaki T, and Kojima C.
    • Journal Title

      Acta Cryst.

      Volume: 72 Issue: 6 Pages: 480-484

    • DOI

      10.1107/s2053230x16007573

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a D-isomerized serine residue2016

    • Author(s)
      Nesreen Alsanousi, Toshihiko Sugiki, Kyoko Furuita, Masatomo So, Young-Ho Lee, Toshimichi Fujiwara, and Chojiro Kojima
    • Journal Title

      Biochem. Biophys. Res. Commun.

      Volume: 477 Issue: 4 Pages: 647-653

    • DOI

      10.1016/j.bbrc.2016.06.114

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] The Structure Determination of AgI-mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with 1H/15N/109Ag NMR Spectroscopy2016

    • Author(s)
      Takenori Dairaku, Kyoko Furuita, Hajime Sato, Jakub Sebera, Katsuyuki Nakashima, Jiro Kondo, Daichi Yamanaka, Yoshinori Kondo, Itaru Okamoto, Akira Ono, Vladimir Sychrovsky, Chojiro Kojima, and Yoshiyuki Tanaka
    • Journal Title

      Chemistry

      Volume: 22 Issue: 37 Pages: 13028-13031

    • DOI

      10.1002/chem.201603048

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Noncovalent forces tune the electron transfer complex between ferredoxin and sulfite reductase to optimize enzymatic activity2016

    • Author(s)
      Ju Yaen Kim, Misaki Kinoshita, Satoshi Kume, Guy T. Hanke, Toshihiko Sugiki, John E. Ladbury, Chojiro Kojima, Takahisa Ikegami, Genji Kurisu, Yuji Goto, Toshiharu Hase, and Young-Ho Lee
    • Journal Title

      Biochem. J.

      Volume: 473 Pages: 3837-3854

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] HgII/AgI-mediated base pairs and their NMR spectroscopic studies2016

    • Author(s)
      Takenori Dairaku, Kyoko Furuita, Hajime Sato, Jakub Sebera, Katsuyuki Nakashima, Akira Ono, Vladimir Sychrovsky, Chojiro Kojima, and Yoshiyuki Tanaka
    • Journal Title

      Inorg. Chim. Acta

      Volume: 452 Pages: 34-42

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Direct Detection of the Mercury-Nitrogen Bond in the Thymine-HgII-Thymine Base-pair with 199Hg NMR Spectroscopy2015

    • Author(s)
      Takenori Dairaku, Kyoko Furuita, Hajime Sato, Jakub Sebera, Daichi Yamanaka, Hiroyuki Otaki, Shoko Kikkawa, Yoshinori Kondo, Ritsuko Katahira, F. Matthias Bickelhaupt, Celia Fonseca Guerra, Akira Ono, Vladimir Sychrovsky, Chojiro Kojima and Yoshiyuki Tanaka
    • Journal Title

      Chemical Communications

      Volume: 51 Issue: 40 Pages: 8488-8491

    • DOI

      10.1039/c5cc02423d

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Physicochemical Nature of Interfaces Controlling Ferredoxin NADP+ Reductase Activity through Its Interprotein Interactions with Ferredoxin2015

    • Author(s)
      Kinoshita Misaki, Kim Ju Yaen, Kume Satoshi, Sakakibara Yukiko, Sugiki Toshihiko, Kojima Chojiro, Kurisu Genji, Ikegami Takahisa, Hase Toshiharu, Kimata-Ariga Yoko, Lee Young-Ho
    • Journal Title

      Biochimica et Biophysica Acta-Bioenergetics

      Volume: 1847 Issue: 10 Pages: 1200-1211

    • DOI

      10.1016/j.bbabio.2015.05.023

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Exploring a DNA sequence for the three-dimensional structure determination of a silver(I)-mediated C-C base pair in a DNA duplex by 1H NMR spectroscopy2015

    • Author(s)
      Takenori Dairaku, Kyoko Furuita, Hajime Sato, Yoshinori Kondo, Chojiro Kojima, Akira Ono and Yoshiyuki Tanaka
    • Journal Title

      Nucleosides, Nucleotides & Nucleic Acids

      Volume: 34 Issue: 12 Pages: 877-900

    • DOI

      10.1080/15257770.2015.1088160

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The crystal structure of the plant small GTPase OsRacl reveals its mode of binding to NADPH oxidase.2015

    • Author(s)
      Kosami KI, Ohki I, Nagano M, Furuita F, Sugiki T, Kawano Y, Kawasaki T, Fujiwara T, Nakagawa A, Shimamoto K, Kojima C
    • Journal Title

      The Journal of Biological Chemistry

      Volume: 289 Issue: 41 Pages: 28569-78

    • DOI

      10.1074/jbc.m114.603282

    • Description
      (in press)(印刷中)
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints2015

    • Author(s)
      Kyoko Furuita, Saori Kataoka, Toshihiko Sugiki, Yoshikazu Hattori, Naohiro Kobayashi, Takahisa Ikegami, Kazuhiro Shiozaki, Toshimichi Fujiwara and Chojiro Kojima
    • Journal Title

      J. Biomol. NMR

      Volume: 61 Issue: 1 Pages: 55-64

    • DOI

      10.1007/s10858-014-9882-7

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] ^<1>H, ^<15>N and ^<13>C resonance assignments of the conserved region in the middle domain of S. pombe Sin1 protein.2014

    • Author(s)
      Kataoka S, Furuita K Hattori Y, Kobayashi N, Ikegami T, Shiozaki K, Fujiwara T, Kojima C
    • Journal Title

      Biomolecular NMR Assignments

      Volume: (印刷中) Issue: 1 Pages: 89-92

    • DOI

      10.1007/s12104-014-9550-6

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Bacterial effector modulation of host E3 ligase activity suppresses PAMP-triggered immunity in rice.2014

    • Author(s)
      Ishikawa, K., Yamaguchi, K., Sakamoto, K., Yoshimura, S., Inoue, K., Tsuge, S., Kojima, C., Kawasaki, T.
    • Journal Title

      Nature Communications

      Volume: 5 Issue: 1 Pages: 5430-5430

    • DOI

      10.1038/ncomms6430

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Latest approaches for efficient protein production in drug discovery2014

    • Author(s)
      Toshihiko Sugiki, Toshimichi Fujiwara and Chojiro Kojima
    • Journal Title

      Expert Opin. Drug Discov.

      Volume: 9 Issue: 10 Pages: 1189-1204

    • DOI

      10.1517/17460441.2014.941801

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] PRE and PCS techniques utilized for high-resolution protein structure determination2015

    • Author(s)
      Chojiro Kojima
    • Organizer
      The 2015 International Chemical Congress of Pacific Basin Societies
    • Place of Presentation
      Sheraton Waikiki (Honolulu)
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] NMR tools developed for drug discovery2015

    • Author(s)
      Chojiro Kojima
    • Organizer
      International Symposium on Structure and Folding of Disease Related Proteins
    • Place of Presentation
      Seoul National University (Seoul)
    • Year and Date
      2015-12-04
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Utilization of Paramagnetic NMR techniques for protein structure determination2015

    • Author(s)
      Chojiro Kojima
    • Organizer
      The 6th Asia-Pacific NMR Symposium
    • Place of Presentation
      The Hong Kong University of Science and Technology (Hong Kong)
    • Year and Date
      2015-08-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Paramagnetic NMR techniques utilized for protein structure analysis2015

    • Author(s)
      Chojiro Kojima
    • Organizer
      The 3rd Awaji International Workshop on “Electron Spin Science & Technology: Biological and Materials Science Oriented Applications”
    • Place of Presentation
      The Awaji Yumebutai International Conference Center (Awaji)
    • Year and Date
      2015-06-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Drug screening using NMR to regulate protein function2015

    • Author(s)
      Chojiro Kojima
    • Organizer
      The First Trilateral Workshop For Frontier Protein Studies
    • Place of Presentation
      Peking University (Beijing)
    • Year and Date
      2015-04-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Paramagnetic NMR utilized for high-resolution protein structure determination2014

    • Author(s)
      Chojiro Kojima
    • Organizer
      The 5th Japan-Taiwan bilateral NMR symposium
    • Place of Presentation
      Hokkaido University (Sapporo)
    • Year and Date
      2014-09-29 – 2014-09-30
    • Related Report
      2014 Annual Research Report
    • Invited

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Published: 2014-04-04   Modified: 2022-05-13  

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