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Studies on the transition state of protein folding by means of correlation analysis between the folding rate and the native structure

Research Project

Project/Area Number 16K07314
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biophysics
Research InstitutionThe University of Tokyo

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)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2017: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2016: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywordsフォールディング / 速度論 / 遷移状態 / 蛋白質 / 生物物理
Outline of Final Research Achievements

In this study, (1) a standardized protein folding database, in which the folding rate constant of all listed proteins are calculated at the standard temperature (25°C), has been constructed and opened on the internet homepage. (2) The correlations between the Φ values, which represent the degree of structural formation in the transition state of folding, and different structure-based properties of proteins were analyzed, and the relationships between the structure-based properties and the critical structure in the transition state were discussed. (3) Academic literatures concerning the relationships between the folding rate constant and various structure-based properties were investigated, and it has been found that the two-state and the non-two-state folding reactions of proteins apparently seem very different, but are based on essentially the same physical principles.

Academic Significance and Societal Importance of the Research Achievements

蛋白質フォールディング機構の研究は,蛋白質の間違ったフォールディングによって引き起こされる,ヒトの様々なフォールディング病(アルツハイマー病,白内障,クロイツフェルト・ヤコブ病,パーキンソン病,II型糖尿病など多数)などの原因解明や治療法の構築の応用研究に役立つと期待される,基盤的な研究である。本研究で構築されたデータベースは,蛋白質フォールディングの計算機シミュレーションや理論研究の研究者によって,広く活用されることが期待される。本研究で実施された,Φ値やフォールディング速度と構造特性との間の相関解析は,本データベースを活用するための事例研究として用いることも出来る。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (23 results)

All 2020 2019 2018 2017 2016 Other

All Int'l Joint Research (4 results) Journal Article (7 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 7 results,  Open Access: 3 results) Presentation (10 results) (of which Int'l Joint Research: 8 results,  Invited: 8 results) Remarks (2 results)

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

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] 韓国高等科学院(韓国)

    • Related Report
      2018 Research-status Report
  • [Int'l Joint Research] 韓国高等科学院(韓国)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] 韓国高等科学院(韓国)

    • Related Report
      2016 Research-status Report
  • [Journal Article] The Molten Globule, and Two-State vs. Non-Two-State Folding of Globular Proteins2020

    • Author(s)
      Kuwajima Kunihiro
    • Journal Title

      Biomolecules

      Volume: 10 Issue: 3 Pages: 407-407

    • DOI

      10.3390/biom10030407

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Determination of the Structural Ensemble of the Molten Globule State of a Protein by Computer Simulations2019

    • Author(s)
      Shimizu Masahiro、Kajikawa Yukihito、Kuwajima Kunihiro、Dobson Christopher M.、Okamoto Yuko
    • Journal Title

      Proteins: Structure, Function, and Bioinformatics

      Volume: in press Issue: 8 Pages: 635-645

    • DOI

      10.1002/prot.25688

    • Related Report
      2019 Annual Research Report 2018 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Exploring the Folding Mechanism of Small Proteins GB1 and LB12019

    • Author(s)
      Cheng Qianyi、Joung InSuk、Lee Juyong、Kuwajima Kunihiro、Lee Jooyoung
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 15 Issue: 6 Pages: 3432-3449

    • DOI

      10.1021/acs.jctc.8b01163

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] PFDB: A standardized protein folding database with temperature correction2019

    • Author(s)
      Manavalan Balachandran、Kuwajima Kunihiro、Lee Jooyoung
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1

    • DOI

      10.1038/s41598-018-36992-y

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An Overlapping Region between the Two Terminal Folding Units of the Outer Surface Protein A (OspA) Controls Its Folding Behavior2018

    • Author(s)
      Makabe Koki、Nakamura Takashi、Dhar Debanjan、Ikura Teikichi、Koide Shohei、Kuwajima Kunihiro
    • Journal Title

      Journal of Molecular Biology

      Volume: 430 Issue: 12 Pages: 1799-1813

    • DOI

      10.1016/j.jmb.2018.04.025

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] An overlapping region between the two terminal folding units of the outer surface protein A (OspA) controls its folding behavior2018

    • Author(s)
      Makabe Koki、Nakamura Takashi、Dhar Debanjan、Ikura Teikichi、Koide Shohei、Kuwajima Kunihiro
    • Journal Title

      Journal of Molecular Biology

      Volume: 印刷中

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Formation of the chaperonin complex studied by 2D NMR spectroscopy2017

    • Author(s)
      Takenaka Toshio、Nakamura Takashi、Yanaka Saeko、Yagi-Utsumi Maho、Chandak Mahesh S.、Takahashi Kazunobu、Paul Subhankar、Makabe Koki、Arai Munehito、Kato Koichi、Kuwajima Kunihiro
    • Journal Title

      PLOS ONE

      Volume: 12 Issue: 10 Pages: 187022-187022

    • DOI

      10.1371/journal.pone.0187022

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] The problem of protein folding2019

    • Author(s)
      Kuwajima, K.
    • Organizer
      The 10th Toyota RIKEN International Workshop on Science of Life Phenomena
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The H/D-exchange kinetics of unfolded ubiquitin in 6 M GdmCl studied by the DMSO-quenched 2D NMR techniques2019

    • Author(s)
      Kuwajima, K., Yagi-Utsumi, M., Yanaka, S. & Kato, K.
    • Organizer
      The 19th KIAS Conference on Protein Structure and Function
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Are there any correlations between mutational φ values and structural properties in all α two-state proteins?2018

    • Author(s)
      Kunihiro Kuwajima
    • Organizer
      The 18th KIAS Conference on Protein Structure and Function
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [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 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] An overlapping region between the two terminal folding units of outer surface protein A (OspA) controls its folding behavior2017

    • Author(s)
      真壁幸樹,桑島邦博
    • Organizer
      The 7th Conference on Protein Structure and Function
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] The Problem of Protein Folding2017

    • Author(s)
      桑島邦博
    • Organizer
      IGER International Symposium on Science of Molecular Assembly and Biomolecular Systems 2017
    • Related Report
      2017 Research-status 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 Research-status 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 Research-status 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 Research-status 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 Research-status Report
    • Int'l Joint Research / Invited
  • [Remarks] PFDB: A standardized protein folding database

    • URL

      http://lee.kias.re.kr/~bala/PFDB/

    • Related Report
      2019 Annual Research Report
  • [Remarks] 球状蛋白質フォールディイング速度のデータベース

    • URL

      http://lee.kias.re.kr/~bala/PFDB/

    • Related Report
      2018 Research-status Report

URL: 

Published: 2016-04-21   Modified: 2022-02-22  

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