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Experimental/theoretical studies on the structural stability and intermolecular interactions of proteins

Research Project

Project/Area Number 16K05657
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionOkayama University

Principal Investigator

Tomonari Sumi  岡山大学, 異分野基礎科学研究所, 准教授 (40345955)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2018: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2017: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2016: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywordsタンパク質 / 熱力学安定性 / 疎水性相互作用仮説 / 溶媒和自由エネルギー / シニョリン / 液体論 / 密度汎関数理論 / F1-ATPase / 化学-力学共役機構 / エネルギー変換効率 / SAXS / Model-potential-free解析 / 自由エネルギープロファイル / GCN4-p1 / 疎水性相互作用 / 圧力変性 / 高温変性 / 生物物理 / 蛋白質
Outline of Final Research Achievements

Understanding the dominant factor in thermodynamic stability of proteins remains an open challenge. Kauzmann’s hydrophobic interaction hypothesis, which considers hydrophobic interactions between nonpolar groups as the dominant factor, has been widely accepted for about sixty years and attracted many scientists. The hypothesis, however, has not been verified or disproved because it is difficult, both theoretically and experimentally, to quantify the solvent effects on the free energy change in protein folding. Here, we developed a computational method for extracting the dominant factor behind thermodynamic stability of proteins and applied it to a small model chignolin. Decomposition of the free energy indicated that intramolecular interactions predominantly stabilized collapsed conformations, whereas solvent-induced interactions, including hydrophobic ones, destabilized them. These results obtained for chignolin were consistent with experimental observations for globular proteins.

Academic Significance and Societal Importance of the Research Achievements

タンパク質が示す多様な物性(変性,凝集,溶解,結晶化,液-液相分離)は,基礎科学として幅広い学術分野(化学,構造生物学,医学など)から強い関心を集めているだけでなく,バイオ医薬品の設計や品質管理等の応用にも関係する,社会的に重要な研究課題である.本研究により明らかにされた、タンパク質構造安定性の分子内直接相互作用メカニズムは,これまで長年信じられてきた仮説に関し,再検討する必要性を示唆しており,この根本的理解は今後のバイオ医薬品の設計指針の確立に置いて,極めて重要な位置を占める.

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

    (44 results)

All 2019 2018 2017 2016 Other

All Int'l Joint Research (2 results) Journal Article (16 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 16 results,  Open Access: 7 results,  Acknowledgement Compliant: 6 results) Presentation (24 results) (of which Int'l Joint Research: 4 results,  Invited: 6 results) Remarks (2 results)

  • [Int'l Joint Research] University of Gottingen/Max Planck Institute, Potsdam(ドイツ)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Georg-August-University goettingen(Germany)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Theoretical analysis on thermodynamic stability of chignolin2019

    • Author(s)
      Tomonari Sumi and Kenichiro Koga
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 5186-5186

    • DOI

      10.1038/s41598-019-41518-1

    • NAID

      120006727117

    • Related Report
      2019 Annual Research Report 2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Is F1-ATPase a Rotary Motor with Nearly 100% Efficiency? Quantitative Analysis of Chemomechanical Coupling and Mechanical Slip2019

    • Author(s)
      Sumi Tomonari, Klumpp Stefan
    • Journal Title

      Nano Letters

      Volume: 19 Issue: 5 Pages: 3370-3378

    • DOI

      10.1021/acs.nanolett.9b01181

    • NAID

      120006840495

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Interaction potential surface between Raman scattering enhancing nanoparticles conjugated with a functional copolymer2019

    • Author(s)
      Morita Takeshi、Ogawa Yuki、Imamura Hiroshi、Ookubo Kouki、Uehara Nobuo、Sumi Tomonari
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 21 Issue: 31 Pages: 16889-16894

    • DOI

      10.1039/c9cp01946d

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Tracing whale myoglobin evolution by resurrecting ancient proteins2018

    • Author(s)
      Isogai Yasuhiro、Imamura Hiroshi、Nakae Setsu、Sumi Tomonari、Takahashi Ken-ichi、Nakagawa Taro、Tsuneshige Antonio、Shirai Tsuyoshi
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 16883-16883

    • DOI

      10.1038/s41598-018-34984-6

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy2017

    • Author(s)
      Sumi Tomonari、Maruyama Yutaka、Mitsutake Ayori、Mochizuki Kenji、Koga Kenichiro
    • Journal Title

      Journal of Computational Chemistry

      Volume: 39 Issue: 4 Pages: 202-217

    • DOI

      10.1002/jcc.25101

    • NAID

      120006733913

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Myosin V: Chemomechanical-coupling ratchet with load-induced mechanical slip2017

    • Author(s)
      Sumi Tomonari
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 13489-13489

    • DOI

      10.1038/s41598-017-13661-0

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Numerical calculation on a two-step subdiffusion behavior of lateral protein movement in plasma membranes2017

    • Author(s)
      Sumi Tomonari、Okumoto Atsushi、Goto Hitoshi、Sekino Hideo
    • Journal Title

      Physical Review E

      Volume: 96 Issue: 4 Pages: 042410-042410

    • DOI

      10.1103/physreve.96.042410

    • NAID

      120006733908

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Influence of co-non-solvency on hydrophobic molecules driven by excluded volume effect2017

    • Author(s)
      Mochizuki Kenji、Sumi Tomonari、Koga Kenichiro
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 19 Issue: 35 Pages: 23915-23918

    • DOI

      10.1039/c7cp04152g

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Design principles governing chemomechanical coupling of kinesin2017

    • Author(s)
      Sumi Tomonari
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1

    • DOI

      10.1038/s41598-017-01328-9

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Model-Potential-Free Determination of the Interaction Potential between Biological Sensing Nanoparticles2017

    • Author(s)
      T. Morita, N. Uehara, H. Imamura and T. Sumi
    • Journal Title

      Photon Factory Highlights 2016

      Volume: 1 Pages: 38-39

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution2016

    • Author(s)
      T. Sumi, Y. Maruyama, A. Mitsutake, K. Koga
    • Journal Title

      J. Chem. Phys.

      Volume: 144 Issue: 22 Pages: 224104-224104

    • DOI

      10.1063/1.4953191

    • NAID

      120006733911

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Interaction Potential between Biological Sensing Nanoparticles Determined by Combining Small-Angle X-ray Scattering and Model-Potential-Free Liquid Theory2016

    • Author(s)
      T. Morita, N. Uehara, K. Kuwahata, H. Imamura, T. Shimada, K. Ookubo, M. Fujita, T. Sumi
    • Journal Title

      J. Phys. Chem. C

      Volume: 120 Issue: 44 Pages: 25564-25571

    • DOI

      10.1021/acs.jpcc.6b06487

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Liquid-liquid phase separation of N-isopropylpropionamide aqueous solutions above the lower critical solution temperature2016

    • Author(s)
      K. Mochizuki, T. Sumi, and K. Koga
    • Journal Title

      Sci. Rep.

      Volume: 6 Issue: 1 Pages: 24657-24657

    • DOI

      10.1038/srep24657

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Driving forces for the pressure-induced aggregation of poly(N-isopropylacrylamide) in water2016

    • Author(s)
      K. Mochizuki, T. Sumi, K. Koga
    • Journal Title

      Phys. Chem. Chem. Phys.

      Volume: 18 Issue: 6 Pages: 4697-4703

    • DOI

      10.1039/c5cp07674a

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Mean-Field Approximation to the Hydrophobic Hydration in the Liquid-Vapor Interface of Water2016

    • Author(s)
      K. Abe, T. Sumi, and K. Koga
    • Journal Title

      J. Phys. Chem. B

      Volume: 120 Issue: 8 Pages: 2012-2019

    • DOI

      10.1021/acs.jpcb.5b10169

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Hydrophobic Polymer Chain in Water That Undergoes a Coil-to-Globule Transition Near Room Temperature2016

    • Author(s)
      I. Hatano, K. Mochizuki, T. Sumi, K. Koga
    • Journal Title

      J. Phys. Chem. B

      Volume: 120 Issue: 47 Pages: 12127-12134

    • DOI

      10.1021/acs.jpcb.6b08347

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] タンパク質の熱力学的安定性と溶媒効果2019

    • Author(s)
      墨智成,甲賀研一郎
    • Organizer
      第99回日本化学会春季大会 特別企画 分子を集める・分子を数える 「分子統計化学」を駆使したソフトマテリアル・溶液の機能構築
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] タンパク質の熱力学的安定性と溶媒効果2019

    • Author(s)
      墨智成,甲賀研一郎
    • Organizer
      応用物理学会 M&BE 研究会「繋がり広がり深まる有機分子・バイオエレクトロニクス研究」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Is F1-ATPase an ideal rotary molecular motor with nearly 100% efficiency?2019

    • Author(s)
      T. Sumi and S. Klumpp
    • Organizer
      The 13th Mini-Symposium on Liquids MSL2018
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] タンパク質折り畳みのエネルギー論と溶媒効果2019

    • Author(s)
      墨智成,甲賀研一郎
    • Organizer
      計算生命科学研究会 ~多体問題から生命システムへ~
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] タンパク質折り畳みのエネルギー論2019

    • Author(s)
      墨智成,甲賀研一郎
    • Organizer
      日本物理学会秋季大会2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] タンパク質の熱力学的安定性における主要因2019

    • Author(s)
      墨智成,甲賀研一郎
    • Organizer
      第13回分子科学討論会2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] タンパク質構造安定性のエネルギー論2019

    • Author(s)
      墨智成,甲賀研一郎
    • Organizer
      分子シミュレーション討論会2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Theoretical analysis on free energy profile for protein folding2018

    • Author(s)
      T. Sumi and K. Koga
    • Organizer
      The 12th Mini-Symposium on Liquids MSL2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Theoretical analysis of free energy profile for folding of chignolin2018

    • Author(s)
      T. Sumi and K. Koga
    • Organizer
      The 56th Annual Meeting of the Biophysical Society of Japan 2018
    • Related Report
      2018 Research-status Report
  • [Presentation] Tracing evolution of aquatic mammal myoglobin: the two adaptation mechanisms2018

    • Author(s)
      Y. Isogai, H. Imamura, S. Nakae, T. Sumi, K. Takahashi, T. Nakagawa, A. Tsuneshige and T. Shirai
    • Organizer
      The 56th Annual Meeting of the Biophysical Society of Japan 2018
    • Related Report
      2018 Research-status Report
  • [Presentation] アミン基の異なる高分子を複合化した金ナノ粒子の凝集/分散特性2018

    • Author(s)
      小川祐季,上原伸夫,墨智成,森田剛
    • Organizer
      第12回分子科学討論会2018
    • Related Report
      2018 Research-status Report
  • [Presentation] ミオシンVの化学 力学状態遷移ネットワーク2017

    • Author(s)
      墨智成
    • Organizer
      日本物理学会第72回年次大会
    • Place of Presentation
      大阪大学
    • Year and Date
      2017-03-17
    • Related Report
      2016 Research-status Report
  • [Presentation] 疎水性高分子鎖のコイル グロビュール転移における水の役割2017

    • Author(s)
      甲賀研一郎, 波多野至, 望月建爾, 墨智成
    • Organizer
      日本物理学会第72回年次大会
    • Place of Presentation
      大阪大学
    • Year and Date
      2017-03-17
    • Related Report
      2016 Research-status Report
  • [Presentation] Chemomechanical network modeling of myosin V2017

    • Author(s)
      Tomonari Sumi
    • Organizer
      The 55th Annual Meeting of the Biophysical Society of Japan 2017
    • Related Report
      2017 Research-status Report
  • [Presentation] Development of reference-modified density functional theory to improve the prediction of solvation free energy2017

    • Author(s)
      Tomonari Sumi
    • Organizer
      The 11th Mini-Symposium on Liquids MSL2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 確率的モデリングによるミオシンVの化学-力学共役機構の研究2017

    • Author(s)
      墨 智成
    • Organizer
      植物細胞骨格研究会 Plant Cytoskeleton 2017
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Theoretical analysis of a two-step relaxation on protein diffusion in the plasma membranes2016

    • Author(s)
      T Sumi, A Okumoto, H Goto, H Sekino
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tsukuba, Japan
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] Tracing evolution of whale myoglobin by resurrecting ancient proteins2016

    • Author(s)
      Y Isogai, H Imamura, S Nakae, K Takahashi, T Sumi, T Nakagawa, A Tsuneshige, T Shirai
    • Organizer
      The 54th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tsukuba, Japan
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] 小角X線散乱による構造因子と液体の統計力学を利用した粒子間二体分布関数の解析: Nelder-Mead法を用いたモデルポテンシャルフリーな計算手法2016

    • Author(s)
      澤住 亮佑,天野 健一,墨 智成,今村 比呂志,深見 一弘,西 直哉,作花 哲夫
    • Organizer
      第52回X線分析討論会
    • Place of Presentation
      筑波大学
    • Year and Date
      2016-10-26
    • Related Report
      2016 Research-status Report
  • [Presentation] 膜貫通タンパク質の細胞膜上二次元拡散における仮想格子による二段階緩和2016

    • Author(s)
      納本淳, 墨智成, 関野秀男, 後藤仁志
    • Organizer
      日本コンピュータ化学会2016秋季年会
    • Place of Presentation
      島根大学
    • Year and Date
      2016-10-22
    • Related Report
      2016 Research-status Report
  • [Presentation] 小角X線散乱によるコロイド粒子の二体分布関数の解析: モデルポテンシャルフリー法の評価と改良2016

    • Author(s)
      澤住 亮佑,天野 健一,墨 智成,今村 比呂志,深見 一弘,西 直哉,作花 哲夫
    • Organizer
      第67回コロイドおよび界面化学会
    • Place of Presentation
      北海道教育大学旭川校
    • Year and Date
      2016-09-22
    • Related Report
      2016 Research-status Report
  • [Presentation] Effect of Polymers in Nanoparticle Dispersion on Interparticle Potential2016

    • Author(s)
      M Harada, T Munekata, T Matsunag, N Kumano, M Ishii, H Nakamura, T Sumi
    • Organizer
      4th International Soft Matter Conference
    • Place of Presentation
      Grenoble, France
    • Year and Date
      2016-09-12
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 確率的モデリングによる分子モーターキネシンの化学-力学共役機構の研究2016

    • Author(s)
      墨智成
    • Organizer
      研究会「分子を使った寄せ木細工」 ~自己組織化したソフトマテリアルが織りなす「かたち」と機能
    • Place of Presentation
      島根大学
    • Year and Date
      2016-05-27
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Theoretical study of a two-step relaxation on protein diffusion in a plasma membrane2016

    • Author(s)
      T Sumi, A Okumoto, H Goto, H Sekino
    • Organizer
      The 10th Mini-Symposium on Liquids (MSL2016)
    • Place of Presentation
      Okayama University
    • Related Report
      2016 Research-status Report
  • [Remarks] 60年間支持されてきたタンパク質構造安定性理論の検証への挑戦

    • URL

      http://chem.okayama-u.ac.jp/feature/read/proteinstability.html

    • Related Report
      2019 Annual Research Report
  • [Remarks] モータータンパク質「F1回転分子モーター」のエネルギー変換効率を実証

    • URL

      http://chem.okayama-u.ac.jp/feature/read/f1_efficiency.html

    • Related Report
      2019 Annual Research Report

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Published: 2016-04-21   Modified: 2021-02-19  

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