In situ Protein NMR Structure Analysis

• Project/Area Number: 26291013
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Yokohama 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: ¥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)
• Keywords: NMR / 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.

Research Products

• [Int'l Joint Research] Academy of Sciences(チェコ)
• [Int'l Joint Research] Marquette University(米国)
• [Int'l Joint Research] Universite de Sherbrooke(Canada)
• [Int'l Joint Research] Academy of Science/Czech Technical University(チェコ)
• [Int'l Joint Research] University of Wisconsin-Madison/University of California(米国)
• [Int'l Joint Research] University of Athens(Greece)
• [Int'l Joint Research] IOCB AS CR(チェコ)
• [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
  • Peer Reviewed / Open Access
• [Journal Article] Current NMR Techniques for Structure-Based Drug Discovery (2018)
  • Author(s): Sugiki Toshihiko、Furuita Kyoko、Fujiwara Toshimichi、Kojima Chojiro
  • Journal Title: Molecules Volume: 23 Issue: 1 Pages: 148-148
  • DOI: 10.3390/molecules23010148
  • 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 Motion (2017)
  • 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
  • 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 Flagella (2017)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Protein 19F-labeling using transglutaminase for the NMR study of intermolecular interactions (2017)
  • 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
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] NMR line shape analysis of a multi-state ligand binding mechanism in chitosanase (2017)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Cold-Shock Expression System in E. coli for Protein NMR Studies (2017)
  • 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
  • Peer Reviewed
• [Journal Article] Substrate specificity of TOR complex 2 is determined by a ubiquitin-fold domain of the Sin1 subunit (2017)
  • 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
  • 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 proteins (2016)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Expression, purification, and crystallization of a plant-specific DUF1110 protein from Oryza sativa (2016)
  • 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
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a D-isomerized serine residue (2016)
  • 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
  • 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 Spectroscopy (2016)
  • 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
  • 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 activity (2016)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] HgII/AgI-mediated base pairs and their NMR spectroscopic studies (2016)
  • 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
  • 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 Spectroscopy (2015)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Physicochemical Nature of Interfaces Controlling Ferredoxin NADP+ Reductase Activity through Its Interprotein Interactions with Ferredoxin (2015)
  • 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
  • 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 spectroscopy (2015)
  • 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
  • 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)
  • 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 restraints (2015)
  • 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
  • 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
  • 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
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Latest approaches for efficient protein production in drug discovery (2014)
  • 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
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] PRE and PCS techniques utilized for high-resolution protein structure determination (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] NMR tools developed for drug discovery (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Utilization of Paramagnetic NMR techniques for protein structure determination (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Paramagnetic NMR techniques utilized for protein structure analysis (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Drug screening using NMR to regulate protein function (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Paramagnetic NMR utilized for high-resolution protein structure determination (2014)
  • 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
  • Invited