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

Folding mechanism of non-two-state proteins based on correlation analyses of kinetic folding data

Research Project

Project/Area Number 25440075
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biophysics
Research InstitutionThe University of Tokyo (2015-2016)
The Graduate University for Advanced Studies (2013-2014)

Principal Investigator

Kuwajima Kunihiro  東京大学, 大学院理学系研究科(理学部), 名誉教授 (70091444)

Research Collaborator LEE Jooyoung  韓国高等科学院, 教授
MANAVALAN Balachandran  韓国高等科学院, 研究員
Project Period (FY) 2013-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2015: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2013: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywordsフォールディング / 速度論 / データベース
Outline of Final Research Achievements

We carried out literature searching on the folding kinetics of globular proteins, and constructed a protein-folding database. The total entry number of the database is 141, consisting of 59 non-two-state proteins and 82 two-state proteins. We took the non-two-state proteins and the two-state proteins separately from the database, and investigated correlations between the logarithmic rate constant (ln kf) of folding and the structural properties of proteins. We show that using the logarithmic number of nonlocal contact clusters, a structural property proposed by us, we can clearly describe differences in the molecular mechanisms of folding between the non-two-state and the two-state proteins.

Report

(5 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (31 results)

All 2017 2016 2015 2014 2013 Other

All Int'l Joint Research (3 results) Journal Article (9 results) (of which Peer Reviewed: 9 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (17 results) (of which Int'l Joint Research: 6 results,  Invited: 15 results) Book (1 results) Remarks (1 results)

  • [Int'l Joint Research] 韓国高等科学院(韓国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Korea Institute for Advanced Study(韓国)

    • Related Report
      2015 Research-status Report
  • [Int'l Joint Research]

    • Related Report
      2015 Research-status Report
  • [Journal Article] Irreversible denaturation of maltodextrin glucosidase studied by differential scanning calorimetry, circular dichroism, and turbidity measurements.2014

    • Author(s)
      Goyal M, Chaudhuri TK, Kuwajima K.
    • Journal Title

      PLoS One

      Volume: 9 Issue: 12 Pages: e115877-e115877

    • DOI

      10.1371/journal.pone.0115877

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Dissection of the ATP-dependent conformational change cycle of a group II chaperonin.2014

    • Author(s)
      Nakagawa A, Moriya K, Arita M, Yamamoto Y, Kitamura K, Ishiguro N, Kanzaki T, Oka T, Makabe K, Kuwajima K, Yohda M.
    • Journal Title

      J Mol Biol.

      Volume: 426 Issue: 2 Pages: 447-459

    • DOI

      10.1016/j.jmb.2013.09.034

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments2013

    • Author(s)
      Mahesh S. Chandak, Takashi Nakamura, Toshio Takenaka, Tapan K. Chaudhuri, Maho Yagi-Utsumi, Jin Chen, Koichi Kato, Kunihiro Kuwajima
    • Journal Title

      Protein Science

      Volume: 22 Issue: 4 Pages: 486-491

    • DOI

      10.1002/pro.2221

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular mechanisms of the cytotoxicity of human α-lactalbumin made lethal to tumor cells (HAMLET) and other protein-oleic acid complexes.2013

    • Author(s)
      Nakamura T, Aizawa T, Kariya R, Okada S, Demura M, Kawano K, Makabe K, Kuwajima K.
    • Journal Title

      J Biol Chem.

      Volume: 288 Issue: 20 Pages: 14408-14416

    • DOI

      10.1074/jbc.m112.437889

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] The H/D-exchange Kinetics of the Escherichia coli Co-chaperonin GroES Studied by 2D-NMR and DMSO-Quenched Exchange Methods.2013

    • Author(s)
      Chandak MS, Nakamura T, Makabe K, Takenaka T, Mukaiyama A, Chaudhuri TK, Kato K, Kuwajima K.
    • Journal Title

      J Mol Biol.

      Volume: 425 Issue: 14 Pages: 2541-2560

    • DOI

      10.1016/j.jmb.2013.04.008

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] NMR characterization of interaction of GroEL with amyloid β as a model ligand.2013

    • Author(s)
      M.Yagi-Utsumi, T.Kunihara, T.Nakamura, Y.Uekusa, K.Makabe, K.Kuwajima, and K.Kato
    • Journal Title

      FEBS Lett.

      Volume: 587 Issue: 11 Pages: 605-609

    • DOI

      10.1016/j.febslet.2013.04.007

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] ATP dependent rotational motion of group II chaperonin observed by X-ray single molecule tracking.2013

    • Author(s)
      Sekiguchi H, Nakagawa A, Moriya K, Makabe K, Ichiyanagi K, Nozawa S, Sato T, Adachi S, Kuwajima K, Yohda M, Sasaki YC.
    • Journal Title

      PLoS One

      Volume: 8 Issue: 5 Pages: e64176-e64176

    • DOI

      10.1371/journal.pone.0064176

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Solvent environments significantly affect the enzymatic function of Escherichia coli dihydrofolate reductase: Comparison of wild-type protein and active-site mutant D27E2013

    • Author(s)
      E. Ohmae, Y. Miyashita, S. Tate, K. Gekko, S. Kitazawa, R. Kitahara, and K. Kuwajima
    • Journal Title

      Biocim. Biophys. Acta

      Volume: 1834 Issue: 12 Pages: 2782-2794

    • DOI

      10.1016/j.bbapap.2013.09.024

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process.2013

    • Author(s)
      A. Ochi, K. Makabe, R. Yamagami, A. Hirata, R. Sakaguchi, Y.M. Hou, K. Watanabe, O. Nureki, K. Kuwajima, and H. Hori
    • Journal Title

      J. Biol. Chem.

      Volume: 288 Issue: 35 Pages: 25562-25574

    • DOI

      10.1074/jbc.m113.485128

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] Folding mechanism of Borrelia burgdorferi Osp A, a dumbbell-shaped two-domain protein2017

    • Author(s)
      Makabe, K. & Kuwajima, K.
    • Organizer
      The 3rd Korean-Polish Conference on Protein Folding: Theoretical and Experimental Approaches
    • Place of Presentation
      Jeongsun-kun (Korea)
    • Year and Date
      2017-02-05
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Relationship between the folding rate and structure-based parameters of globular proteins2016

    • Author(s)
      Manavalan, B., Kuwajima, K. & Lee, J.
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] The problem of protein folding2016

    • Author(s)
      Kuwajima, K., Manavalan, B. & Lee, J.
    • Organizer
      The 16th KIAS Conference on Protein Structure
    • Place of Presentation
      Seoul (Korea)
    • Year and Date
      2016-09-22
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Relationship between the folding rate and structure-based parameters of globular proteins2016

    • Author(s)
      Manavalan, B., Kuwajima, K. & Lee, J.
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] The problem of protein folding2016

    • Author(s)
      Kuwajima, K., Manavalan, B. & Lee, J.
    • Organizer
      The 2nd Polish-Korean Conference on Protein Folding: Theoretical and Experimental Approaches
    • Place of Presentation
      Gdansk (Poland)
    • Year and Date
      2016-05-28
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The H/D-exchange kinetics of a fully unfolded protein studied by the DMSO-quenched and 2D NMR techniques2016

    • Author(s)
      Kuwajima, K., Chandak, M.S., Yagi-Utsumi, M., Yamaguchi, T., Nakamura, T. & Kato, K.
    • Organizer
      The 8th Japan-Korea Seminar on Biomolecular Science: Experiments and Simulations
    • Place of Presentation
      自然科学研究機構・岡崎コンファレンスセンター(愛知県岡崎市)
    • Year and Date
      2016-02-15
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] The problem of protein folding2015

    • Author(s)
      Korea Institute for Advanced Study (KIAS), Seoul, Korea
    • Organizer
      The 14th FAOBMB Congress
    • Place of Presentation
      CSIR-Centre for Cellular & Molecular Biology (CCMB), Hyderabad, India
    • Year and Date
      2015-11-27
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Formation of the chaperonin complex studied by 2D NMR and isothermal titration calorimetry2015

    • Author(s)
      Kuwajima, K.
    • Organizer
      The 15th KIAS Conference on Protein Structure
    • Place of Presentation
      Korea Institute for Advanced Study (KIAS), Seoul, Korea
    • Year and Date
      2015-09-17
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Anti-tumor complexes formed by oleic acid and molten globule intermediates of proteins2015

    • Author(s)
      Kuwajima, K.
    • Organizer
      The 1st Korean-Polish Conference on Protein Folding: Theoretical and Experimental Approaches
    • Place of Presentation
      Korea Institute for Advanced Study (KIAS), Seoul, Korea
    • Year and Date
      2015-05-24
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] A contact-based topological quantity and its relationships with the folding kinetics of non-two-state and two-state proteins2014

    • Author(s)
      Balachandran, M., Kuwajima, K., Lee, J.
    • Organizer
      The 7th Japan-Korea Seminar on Biomolecular Sciences: Experiments and Simulations
    • Place of Presentation
      Korea Institute for Advanced Study (KIAS), Seoul, Korea
    • Year and Date
      2014-11-26 – 2014-11-28
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] The problem of protein folding and its relationship to bioscience2014

    • Author(s)
      Kuwajima, K.
    • Organizer
      The Second International Symposium on Protein Folding and Dynamics
    • Place of Presentation
      National Centre for Biological Sciences (NCBS), Bangalore, India
    • Year and Date
      2014-11-05 – 2014-11-07
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] A contact-based topological quantity and its relationships with the folding kinetics of non-two-state and two-state proteins2014

    • Author(s)
      Balachandran, M., Kuwajima, K., Lee, J.
    • Organizer
      The 14th KIAS Conference on Protein Structure
    • Place of Presentation
      Korea Institute for Advanced Study (KIAS), Seoul, Korea
    • Year and Date
      2014-09-18 – 2014-09-20
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] The problem of protein folding and its relationship to bioscience2014

    • Author(s)
      Kuwajima, K.
    • Organizer
      Sokendai Special Lecture, JSPS Summer Program
    • Place of Presentation
      Shonan Village Center, Hayama, Japan
    • Year and Date
      2014-06-11
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] The problem of protein folding and its relationship to bioscience2014

    • Author(s)
      Kuwajima, K.
    • Organizer
      The 4th Asia Pacific Protein Association (APPA) Conference
    • Place of Presentation
      International Convention Center, Jeju, Korea
    • Year and Date
      2014-05-17 – 2014-05-20
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Problems of protein folding and non-folding2014

    • Author(s)
      Kuwajima K.
    • Organizer
      International Symposium "Dynamic Ordering of Biomolecular Systems for Creation of Integrated Functions"
    • Place of Presentation
      Campus Plaza, Kyoto, Japan
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Irreversible denaturation of Escherichia coli maltodextrin glucosidase studied by differential scanning calorimetry2013

    • Author(s)
      Kuwajima K.
    • Organizer
      The13th KIAS Conference on Protein Structure
    • Place of Presentation
      Korea Institute for Advanced Study (KIAS), Seoul, Korea
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Irreversible denaturation of Escherichia coli maltodextrin glucosidase2013

    • Author(s)
      Kuwajima K.
    • Organizer
      The 6th Japan-Korea Seminar on Biomolecular Sciences--Experiments and Simulations
    • Place of Presentation
      Okazaki Conference Center, Okazaki, Japan
    • Related Report
      2013 Research-status Report
    • Invited
  • [Book] Molecular Science of Fluctuations Toward Biological Functions2016

    • Author(s)
      Kuwajima, K.(第12章を分担執筆)
    • Total Pages
      270
    • Publisher
      Springer, Tokyo
    • Related Report
      2015 Research-status Report
  • [Remarks] Protein Folding Database

    • URL

      http://lee.kias.re.kr/~protein/wiki/doku.php?id=pkhd:view

    • Related Report
      2016 Annual Research Report

URL: 

Published: 2014-07-25   Modified: 2022-02-16  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi