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

Construction of protein-structure prediction method based on liquid state theory

Research Project

Project/Area Number 22300100
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionKyoto University

Principal Investigator

KINOSHITA Masahiro  京都大学, エネルギー理工学研究所, 教授 (90195339)

Co-Investigator(Renkei-kenkyūsha) TAKADA Shoji  京都大学, 大学院・理学研究科, 教授 (60304086)
Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥17,290,000 (Direct Cost: ¥13,300,000、Indirect Cost: ¥3,990,000)
Fiscal Year 2012: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2011: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2010: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Keywords蛋白質 / フォールディング / 立体構造予測 / 水和 / 自由エネルギー関数 / α-ヘリックス / エントロピー / 膜蛋白質 / ケミカルシフト / 水和エントロピー / 積分方程式論 / 形態熱力学理論 / フラグメントアセンブリ法 / 分子性流体用積分方程式論 / 比較モデリング法
Research Abstract

We analyze the structural stabilities of proteins in aqueous and nonpolar environments, thus revealing their differences. Free-energy functions are constructed for these proteins on the basis of liquid-state theories and their usefulness is demonstrated. After generating a number of candidate structures using typical bioinformatics techniques, we select the structure giving the free-energy function for a protein in aqueous environment: Promising results are obtained for several proteins tested.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (105 results)

All 2013 2012 2011 2010 Other

All Journal Article (32 results) (of which Peer Reviewed: 32 results) Presentation (67 results) (of which Invited: 1 results) Book (2 results) Remarks (4 results)

  • [Journal Article] A New Theoretical Approach to Biological Self-Assembly2013

    • Author(s)
      M. Kinoshita
    • Journal Title

      Biophys. Rev

      Volume: 5 Issue: 3 Pages: 1-11

    • DOI

      10.1007/s12551-013-0100-8

    • NAID

      120005477197

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural Stability of Proteins in Aqueous and Nonpolar Environments2013

    • Author(s)
      S. Yasuda, H. Oshima, M. Kinoshita
    • Journal Title

      Journal of Chemical Physics

      Volume: 137 Issue: 13 Pages: 1-14

    • DOI

      10.1063/1.4755755

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Entropic release of a big sphere from a cylindrical vessel2013

    • Author(s)
      Hirokazu Mishima, Hiraku oshima, Satoshi Yasuda, Ken-ichi Amano. and Masahiro Kinoshita
    • Journal Title

      Chemical Physics Letters 7

      Volume: 561-562 Pages: 159-165

    • DOI

      10.1016/j.cplett.2013.01.045

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Electrochemical Deposition of Platinum within Nanopores on Silicon: Drastic Acceleration Originating from Surface-lnduced Phase Transition2013

    • Author(s)
      K. Fukami, R. Koda, T. Sakka, Y. Ogata, and M. Kinoshita
    • Journal Title

      J. Chem. Phys

      Volume: 138 Issue: 9

    • DOI

      10.1063/1.4793526

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Simulations of Yeast F1-ATPase Before and After 16-degree Rotation of the Gamma Subunit2013

    • Author(s)
      Yuko Ito, Takashi Yoshidome, Nobuyuki Matubayashi, Masahiro Kinoshita, Mitsunori Ikeguchi
    • Journal Title

      The journal of Physical Chemistry B

      Volume: 117 Issue: 12 Pages: 3298-3307

    • DOI

      10.1021/jp312499u

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] タンパク質水和理論の新機軸III.理論的考察2012

    • Author(s)
      木下正弘,永山國昭
    • Journal Title

      生物物理

      Volume: 52 Pages: 300-303

    • NAID

      10031126107

    • URL

      https://www.jstage.jst.go.jp/article/biophys/52/6/52_300/_pdf

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] タンパク質水和理論の新機軸II.新理論の応用展開2012

    • Author(s)
      木下正弘,永山國昭
    • Journal Title

      生物物理

      Volume: 52 Pages: 250-253

    • NAID

      10030877069

    • URL

      https://www.jstage.jst.go.jp/article/biophys/52/5/52_250/_pdf

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] タンパク質水和理論の新機軸I.朝倉-大沢理論を越えて2012

    • Author(s)
      木下正弘,永山國昭
    • Journal Title

      生物物理

      Volume: 52 Pages: 203-205

    • NAID

      10030494721

    • URL

      https://www.jstage.jst.go.jp/article/biophys/52/4/52_203/_pdf

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] A scoring function based on solvation thermodynamics for protein structure prediction2012

    • Author(s)
      S. Du
    • Journal Title

      BIOPHYSICS

      Volume: 8 Issue: 0 Pages: 127-138

    • DOI

      10.2142/biophysics.8.127

    • NAID

      130002104520

    • ISSN
      1349-2942
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of Experimentally Determined Native-Structure Models of a Protein Using Energetic and Entropic Components of Free-Energy Function2012

    • Author(s)
      H. Mishima, S. Yasuda, T. Yoshidome, H. Oshima, Y. Harano, M. Ikeguchi, M. Kinoshita
    • Journal Title

      Journal of Physical Chemistry B

      Volume: 116 Issue: 27 Pages: 7776-7786

    • DOI

      10.1021/jp301541z

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Platinum electrodeposition in porous silicon : The influence of surface solvation effects on a chemical reaction in a nanospace2012

    • Author(s)
      Kazuhiro Fukami, Ryo Koda, Tetsuo Sakka,Tomoko Urata,Ken-ichi Amano,Hikaru Takaya,Masaharu Nakamura,Yukio Ogata, and Masahiro Kinoshita
    • Journal Title

      Chemical Physics Letters

      Volume: 542 Pages: 99-105

    • DOI

      10.1016/j.cplett.2012.05.078

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural Characteristics of Yeast F_1-ATPase Before and After 16-degree Rotation of the γ Subunit : Theoretical Analysis Focused on the Water-Enrtopy Effect2012

    • Author(s)
      Takashi Yoshidome, Yuko Ito, Nobuyuki Matubayashi, Mitunori Ikeguchi, Masahiro Kinoshita
    • Journal Title

      Journal of Chemical Physics

      Volume: 137 Issue: 3 Pages: 8-8

    • DOI

      10.1063/1.4734298

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Physical Origin of Hydrophobicity Studied in terms of Cold Denaturation of Proteins: Comparison between Water and Simple Fluids2012

    • Author(s)
      T. Yoshidome and M. Kinoshita
    • Journal Title

      Phys. Chem. Chem. l Phys

      Volume: 14 Issue: 42 Pages: 14554-14566

    • DOI

      10.1039/c2cp41738c

    • NAID

      120005323032

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] タンパク質水和理論の新機軸I.朝倉-大沢理論を越えて2012

    • Author(s)
      木下正弘,永山國昭
    • Journal Title

      生物物理

      Volume: 52 Pages: 203-205

    • NAID

      10030494721

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] タンパク質水和理論の新機軸II.新理論の応用展開2012

    • Author(s)
      木下正弘,永山國昭
    • Journal Title

      生物物理

      Volume: 52 Pages: 250-253

    • NAID

      10030877069

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] タンパク質水和理論の新機軸III.理論的考察2012

    • Author(s)
      木下正弘,永山國昭
    • Journal Title

      生物物理

      Volume: 52 Pages: 300-303

    • NAID

      10031126107

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evaluation of Protein-Ligand Binding Free Energy Focused on its Entropic Components2012

    • Author(s)
      S.Chiba, Y.Harano, R.Roth, M.Kinoshita, M.Sakurai
    • Journal Title

      J.Comput.Chem.

      Volume: 33 Issue: 5 Pages: 550-560

    • DOI

      10.1002/jcc.22891

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 「疎水性」の本当の物理起源:その温度依存性を通しての考察2012

    • Author(s)
      木下正弘
    • Journal Title

      低温生物工学会誌

      Volume: 58 Pages: 19-25

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Free-Energy Function for Discriminating the Native Fold of a Protein from Misfolded Decoys2011

    • Author(s)
      S.Yasuda, T.Yoshidome, Y.Harano, E.Roth, H.Oshima, K.Oda, Y.Sugita, M.Ikeguchi, M.Kinoshita
    • Journal Title

      Proteins-Structure Function and Bioinformatics

      Volume: 79 Issue: 7 Pages: 2161-2171

    • DOI

      10.1002/prot.23036

    • NAID

      120005593601

    • Related Report
      2012 Final Research Report 2011 Annual Research Report 2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rotational Mechanism of F_1-ATPase : Crucial Importance of Water-Entropy Effect2011

    • Author(s)
      T.Yoshidome, Y.Ito, M.Ikeguchi, M.Kinoshita
    • Journal Title

      Journal of the American Chemical Society

      Volume: 133 Issue: 11 Pages: 4030-4039

    • DOI

      10.1021/ja109594y

    • Related Report
      2011 Annual Research Report 2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Morphometric Approach to Thermodynamic Quantities of Solvation of Complex Molecules : Extension to Multicomponent Solvent2011

    • Author(s)
      R.Kodama, R.Roth, Y.Harano, M.Kinoshita
    • Journal Title

      Journal of Chemical Physics

      Volume: 135 Issue: 4

    • DOI

      10.1063/1.3617247

    • NAID

      120003338824

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crucial Importance of Water-Entropy Effect for Predicting Hot Spots in Protein-Protein Cotnplexes2011

    • Author(s)
      H.Oshima, S.Yasuda, T.Yoshidome, M.Ikeguchi, M.Kinoshita
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 13 Pages: 16236-16246

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Simple Theory for Entropic Interaction Induced between Large Spheres in a Binary Mixture of Small and Medium Spheres2011

    • Author(s)
      Y.Karino, R.Akiyama, M.Kinoshita
    • Journal Title

      Journal of the Physical Society of Japan

      Volume: 80 Issue: 11 Pages: 114802-114802

    • DOI

      10.1143/jpsj.80.114802

    • NAID

      210000109285

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Potential of mean force between a large solute and a biomolecular complex : A model analysis on protein flux through chaperonin system2011

    • Author(s)
      Ken-ichi Amano, Hiraku Oshima, Masahiro Kinoshita
    • Journal Title

      Journal of Chemical Physics

      Volume: 135巻 Issue: 18

    • DOI

      10.1063/1.3657856

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effects of Heme on the Thermal Stability of Mesophilic and Thermophilic Cytochromes c : Comparison between Experimental and Theoretical Results2011

    • Author(s)
      K.Oda, R.Kodama, T.Yoshidome, M.Yamanaka, Y.Sambongi, M.Kinoshita
    • Journal Title

      Journal of Chemical Physics

      Volume: 134

    • NAID

      120002753569

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An Efficient Method for Analyzing Conformational Properties of a Polymer in Solvent2011

    • Author(s)
      K.Amano, H.Oshima, M.Kinoshita
    • Journal Title

      Chemical Physics Letters

      Volume: 504 Pages: 7-12

    • NAID

      120002949761

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Model of Insertion and Release of a Large Solute into and from a Biopolymer Complex2011

    • Author(s)
      K.Amano, M.Kinoshita
    • Journal Title

      Chemical Physics Letters

      Volume: 504 Pages: 221-224

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effects of Side-Chain Packing on the Formation of Secondary Structures in Protein Folding2010

    • Author(s)
      S. Yasuda, T. Yoshidome, H. Oshima, R. Kodama, Y. Harano, and M. Kinoshita
    • Journal Title

      J. Chem. Phys

      Volume: 132 Issue: 6 Pages: 1-10

    • DOI

      10.1063/1.3319509

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Effects of Side-Chain Packing on the Formation of Secondary Structures in Protein Folding2010

    • Author(s)
      S.Yasuda, T.Yoshidome, H.Oshima, R.Kodama, Y.Harano, M.Kinoshita
    • Journal Title

      Journal of Chemical Physics

      Volume: 132

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Entropic Insertion of a Big Sphere into a Cylindrical Vessel2010

    • Author(s)
      K.Amano, M.Kinoshita
    • Journal Title

      Chemical Physics Letters

      Volume: 488 Pages: 1-6

    • NAID

      120002191875

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Entropic Potential Field Formed for a Linear-Motor Protein near a Filament : Statistical-Mechanical Analyses Using Simple Models2010

    • Author(s)
      K.Amano, T.Yoshidome, M.Iwaki, M.Suzuki, M.Kinoshita
    • Journal Title

      Journal of Chemical Physics

      Volume: 133

    • NAID

      120002511239

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 固体表面近傍における液体の構造2010

    • Author(s)
      木下正弘
    • Journal Title

      トライボロジスト,特集「固液界面の物理」

      Volume: 55 Pages: 229-235

    • NAID

      10026246333

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] Effects of Sugars on the Thermal Stability of a Protein2013

    • Author(s)
      H. Oshima and M. Kinoshita
    • Organizer
      Biophysical Society 57th Annual Meeting
    • Place of Presentation
      Philadelphia, USA
    • Related Report
      2012 Annual Research Report
  • [Presentation] Molecular Dynamics Simulations of Yeast F1-ATPase before and after 16-degree Rotation of Gamma Subunit2013

    • Author(s)
      Y. Ito, T. Yoshidome, N. Matsubayashi, M. Kinoshita, and M. Ikeguchi
    • Organizer
      Biophysical Society 57th Annual Meeting
    • Place of Presentation
      Philadelphia, USA
    • Related Report
      2012 Annual Research Report
  • [Presentation] Effects of Sugars on the Thermal Stability of a Protein2013

    • Author(s)
      H. Oshima and M. Kinoshita
    • Organizer
      International Symposium on Hydration and ATP Energy 2013
    • Place of Presentation
      Hotel Iwanumaya, Miyagi, Japan
    • Related Report
      2012 Annual Research Report
  • [Presentation] Structural Stability of Proteins in Aqueous and Nonpolar Environments2013

    • Author(s)
      S. Yasuda, H. Oshima, and M. Kinoshita
    • Organizer
      International Symposium on Hydration and ATP Energy 2013
    • Place of Presentation
      Hotel Iwanumaya, Miyagi, Japan
    • Related Report
      2012 Annual Research Report
  • [Presentation] Physics of Multidrug Efflux of a Biomolecular Complex2013

    • Author(s)
      H. Mishima, H. Oshima, S. Yasuda, K. Amano, and M. Kinoshita
    • Organizer
      International Symposium on Hydration and ATP Energy 2013
    • Place of Presentation
      Hotel Iwanumaya, Miyagi, Japan
    • Related Report
      2012 Annual Research Report
  • [Presentation] 粒子が狭い空間に入るときの溶媒の効果2012

    • Author(s)
      原諒平, 天野健一, 木下正弘, 吉森明
    • Organizer
      日本物理学会第67回年次大会
    • Place of Presentation
      関西学院大学
    • Year and Date
      2012-03-24
    • Related Report
      2011 Annual Research Report
  • [Presentation] 埋もれた界面の理論的研究:固体表面近傍における液体の構造について2012

    • Author(s)
      木下正弘
    • Organizer
      2012年(平成24年)春季第59回応用物理学関係連合講演会シンポジウム「中性子・X線のコラボレーションによる薄膜・多層膜の埋もれた界面の解析の新しい展開」
    • Place of Presentation
      早稲田大学早稲田キャンパス(招待講演)
    • Year and Date
      2012-03-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] シャペロニンの蛋白質折り畳み援助機能に関する基礎解析2012

    • Author(s)
      天野健一, 尾嶋拓, 木下正弘
    • Organizer
      次世代ナノ統合シミュレーションソフトウェアの研究開発第6回公開シンポジウム
    • Place of Presentation
      ニチイ学館,神戸ポートアイランドセンター
    • Year and Date
      2012-03-06
    • Related Report
      2011 Annual Research Report
  • [Presentation] A Novel Rotation Mechanism of F_1-ATPase Based on the Water-Entropy Effect2012

    • Author(s)
      T.Yoshidome, Y.Ito, N.Matubayasi, M.Ikeguchi, M.Kinoshita
    • Organizer
      Biophysical Society 56th Annual Meeting
    • Place of Presentation
      San Diego Convention Center, USA
    • Year and Date
      2012-02-27
    • Related Report
      2011 Annual Research Report
  • [Presentation] Prediction of Hot Spots in Protein-Protein Complexes Focused on Water Entropy2012

    • Author(s)
      S.Yasuda, H.Oshima, T.Yoshidome, M.Ikeguchi, M.Kinoshita
    • Organizer
      京都大学グローバルCOEプログラム「地球温暖化時代のエネルギー科学拠点」平成23年度年次報告会
    • Place of Presentation
      きはだホール,京都大学宇治キャンパス
    • Year and Date
      2012-01-30
    • Related Report
      2011 Annual Research Report
  • [Presentation] 水及び非水環境におけるタンパク質の立体構造安定性2012

    • Author(s)
      安田賢司、尾嶋拓、木下正弘
    • Organizer
      第52回生物物理若手の会
    • Place of Presentation
      支笏湖ユースホステル
    • Related Report
      2012 Annual Research Report
  • [Presentation] 分子機械の機能発現機構に対する横断的描像2012

    • Author(s)
      木下正弘
    • Organizer
      合同公開シンポジウム「ゆらぎと水-生命のエネルギーと機能の分子機構を探る」
    • Place of Presentation
      大阪ガーデンパレス
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 溶液中で狭い空間に溶質が入るときの経路2012

    • Author(s)
      原諒平、天野健一、木下正弘、吉森明
    • Organizer
      2012年度日本物理学会秋季大会
    • Place of Presentation
      横浜国立大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] Effects of Sugars on the Thermal Stability of Proteins2012

    • Author(s)
      H. Oshima, K. Amano, M. Kinoshita
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] Structural Stability of Proteins in Aqueous and Nonpolar Environments2012

    • Author(s)
      S. Yasuda, H. Oshima, and M. Kinoshita
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] Entropic Release of a Big Sphere from a Cylindrical Vessel2012

    • Author(s)
      H. Mishima, H. Oshima, S. Yasuda, K. Amano, and M. Kinoshita
    • Organizer
      日本生物物理学会第50回年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] Molecular Dynamics Simulations on Structural Characteristics of Yeast F1-ATPase before and after 16-degree Rotation of Gamma Subunit2012

    • Author(s)
      Y. Ito, T. Yoshidome, N. Matsubayashi, M. Kinoshita, and M. Ikeguchi
    • Organizer
      日本生物物理学会第50回年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] シャペロニンに対する蛋白質挿入のダイナミクス2012

    • Author(s)
      原諒平、天野健一、木下正弘、吉森明
    • Organizer
      第2回ソフトマター研究会
    • Place of Presentation
      九州大学西新プラザ
    • Related Report
      2012 Annual Research Report
  • [Presentation] 溶質が狭い空間に入るダイナミクスにおける溶媒のエントロピー効果2012

    • Author(s)
      原諒平、天野健一、木下正弘、吉森明
    • Organizer
      第35回溶液化学シンポジウム
    • Place of Presentation
      早稲田大学西早稲田キャンパス
    • Related Report
      2012 Annual Research Report
  • [Presentation] 溶媒の効果を含めた溶質のダイナミクス:シャペロニンへの蛋白質の挿入過程2012

    • Author(s)
      原諒平、天野健一、木下正弘、吉森明
    • Organizer
      第24回分子シュミレーション研究会
    • Place of Presentation
      九州大学西新プラザ
    • Related Report
      2012 Annual Research Report
  • [Presentation] γ-サブユニットの16度回転前後におけるイーストF_1-ATPaseの構造特性:水のエントロピー効果に焦点をあてた理論解析2012

    • Author(s)
      吉留崇, 伊藤祐子, 松林伸幸, 池口満徳, 木下正弘
    • Organizer
      新学術領域研究「水を主役としたATPエネルギー変換」第4回領域全体会議
    • Place of Presentation
      岩沼屋,仙台
    • Related Report
      2011 Annual Research Report
  • [Presentation] シャペロニンの蛋白質折り畳み援助機能に関する基礎解析2012

    • Author(s)
      天野健一, 尾嶋拓, 木下正弘
    • Organizer
      新学術領域研究「水を主役としたATPエネルギー変換」第4回領域全体会議
    • Place of Presentation
      岩沼屋,仙台
    • Related Report
      2011 Annual Research Report
  • [Presentation] 蛋白質複合体におけるホットスポットの理論的予測2012

    • Author(s)
      尾嶋拓, 安田賢司, 吉留崇, 池口満徳, 木下正弘
    • Organizer
      新学術領域研究「水を主役としたATPエネルギー変換」第4回領域全体会議
    • Place of Presentation
      岩沼屋,仙台
    • Related Report
      2011 Annual Research Report
  • [Presentation] 生命現象発現における水分子並進移動の役割2011

    • Author(s)
      木下正弘
    • Organizer
      新世代研究所第6回合同研究会
    • Place of Presentation
      明治大学紫紺館
    • Year and Date
      2011-11-29
    • Related Report
      2012 Final Research Report
  • [Presentation] 生命現象発現における水分子並進移動の役割2011

    • Author(s)
      木下正弘
    • Organizer
      新世代研究所第6回合同研究会
    • Place of Presentation
      明治大学紫紺館(招待講演)
    • Year and Date
      2011-11-29
    • Related Report
      2011 Annual Research Report
  • [Presentation] 分子認識などの生命現象における水の並進エントロピーの重要性2011

    • Author(s)
      木下正弘
    • Organizer
      日本学術振興会回折構造生物第169 委員会第36回研究会
    • Place of Presentation
      ゆうぽうと,東京都品川区
    • Year and Date
      2011-10-04
    • Related Report
      2012 Final Research Report
  • [Presentation] 分子認識などの生命現象における水の並進エントロピーの重要性2011

    • Author(s)
      木下正弘
    • Organizer
      日本学術振興会回折構造生物第169委員会第36回研究会
    • Place of Presentation
      ゆうぽうと,東京都品川区(招待講演)
    • Year and Date
      2011-10-04
    • Related Report
      2011 Annual Research Report
  • [Presentation] ATP駆動蛋白質の機能発現における水とATPの共同効果2011

    • Author(s)
      木下正弘
    • Organizer
      日本生物物理学会第49回年会シンポジウム「水とATPがつくる非対称性」
    • Place of Presentation
      兵庫県立大学(招待講演)
    • Year and Date
      2011-09-16
    • Related Report
      2011 Annual Research Report
  • [Presentation] A Theoretical Analysis on Water-Entropy Change in Yeast F_1-ATPase during 16 Degrees Rotation of Gamma Subunit2011

    • Author(s)
      吉留崇, 池口満徳, 木下正弘
    • Organizer
      第49回日本生物物理学会年会
    • Place of Presentation
      兵庫県立大学
    • Year and Date
      2011-09-16
    • Related Report
      2011 Annual Research Report
  • [Presentation] Crucial Importance of Water-Entropy Effect for Predicting Hot Spots in Protein-Protein Complexes2011

    • Author(s)
      尾嶋拓, 安田賢司, 吉留崇, 池口満徳, 木下正弘
    • Organizer
      第49回日本生物物理学会年会
    • Place of Presentation
      兵庫県立大学
    • Year and Date
      2011-09-16
    • Related Report
      2011 Annual Research Report
  • [Presentation] On the Physical Mechanism of Rotation of F_1-ATPase : Crucial Importance of the Water Entropy Effect2011

    • Author(s)
      T.Yoshidome, Y.Ito, M.Ikeguchi, M.Kinoshita
    • Organizer
      8th Liquid Matter Conference
    • Place of Presentation
      Universitat Wien, Austria
    • Year and Date
      2011-09-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] Theoretical Analysis for Hot Spots in Protein-Protein Complexes : Critical Importance of Water Entropy2011

    • Author(s)
      H.Oshima, S.Yasuda, T.Yoshidome, M.Ikeguchi, M.Kinoshita
    • Organizer
      8th Liquid Matter Conference
    • Place of Presentation
      Universitat Wien, Austria
    • Year and Date
      2011-09-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] Effects of Side-Chain Packing on the Formation of Secondary Structures in Protein Folding2011

    • Author(s)
      S.Yasuda, T.Yoshidome, H.Oshima, R.Kodama, Y.Harano, M.Kinoshita
    • Organizer
      8th Liquid Matter Conference
    • Place of Presentation
      Universitat Wien, Austria
    • Year and Date
      2011-09-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] Roles of Water and ATP in Functioning of ATP-Driven Proteins2011

    • Author(s)
      M.Kinoshita
    • Organizer
      The 7th Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII)
    • Place of Presentation
      Waseda University, Tokyo, Japan(招待講演)
    • Year and Date
      2011-09-02
    • Related Report
      2011 Annual Research Report
  • [Presentation] Free-Energy Function for Discriminating the Native Fold of a Protein from Misfolded Decoys2011

    • Author(s)
      S.Yasuda, T.Yoshidome, Y.Harano, R.Roth, H.Oshima, Y.Sugita, M.Ikeguchi, M.Kinoshita
    • Organizer
      The Third International Symposium of Kyoto University GCOE of Energy Science
    • Place of Presentation
      Ajou University, Korea
    • Year and Date
      2011-08-19
    • Related Report
      2011 Annual Research Report
  • [Presentation] ATP-駆動蛋白質の機能発現における水とATPの役割2011

    • Author(s)
      木下正弘
    • Organizer
      新学術領域研究「水を主役としたATPエネルギー変換」前期研究成果報告会
    • Place of Presentation
      大阪ガーデンパレス
    • Year and Date
      2011-08-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] Rotation Mechanism of F_1-ATPase : Crucial Importance of Water-Entropy Effect2011

    • Author(s)
      吉留崇, 伊藤祐子, 池口満徳, 木下正弘
    • Organizer
      新学術領域研究「水を主役としたATPエネルギー変換」前期研究成果報告会
    • Place of Presentation
      大阪ガーデンパレス
    • Year and Date
      2011-08-09
    • Related Report
      2011 Annual Research Report
  • [Presentation] 「疎水性」の本当の物理起源:その温度依存性を通しての考察2011

    • Author(s)
      木下正弘
    • Organizer
      第56回低温生物工学会大会セミナー
    • Place of Presentation
      いわて県民情報交流センター(招待講演)
    • Year and Date
      2011-07-07
    • Related Report
      2011 Annual Research Report
  • [Presentation] Importance of Water Entropy in Rotation Mechanism of F_1-ATPase2011

    • Author(s)
      T.Yoshidome, Y.Ito, M.Ikeguchi, M.Kinoshita
    • Organizer
      5th Mini-Symposium on Liquids
    • Place of Presentation
      Okayama University, Japan
    • Year and Date
      2011-06-25
    • Related Report
      2011 Annual Research Report
  • [Presentation] 溶媒中におけるポリマーの立体構造特性を解析するための効率的な方法2011

    • Author(s)
      天野健一, 尾嶋拓, 木下正弘
    • Organizer
      日本生物物理学会,第3回中国四国支部学会
    • Place of Presentation
      広島大学
    • Year and Date
      2011-05-14
    • Related Report
      2011 Annual Research Report
  • [Presentation] 筒状容器における大球溶質の挿入と放出:単純化モデルを用いたシヤペロニンGroELに関する理論解析2011

    • Author(s)
      天野健一, 木下正弘
    • Organizer
      日本生物物理学会,第3回中国四国支部学会
    • Place of Presentation
      広島大学
    • Year and Date
      2011-05-14
    • Related Report
      2011 Annual Research Report
  • [Presentation] 大きな溶質の生体高分子複合体への挿入およびそれからの放出2011

    • Author(s)
      木下正弘,天野健一
    • Organizer
      次世代ナノ統合シミュレーションソフトウェアの研究開発,第5回公開シンポジウム
    • Place of Presentation
      甲南大学
    • Year and Date
      2011-02-23
    • Related Report
      2010 Annual Research Report
  • [Presentation] An Efficient Method for Analyzing Conformational Properties of a Polymer in Solvent2011

    • Author(s)
      K.Amano, H.Oshima, M.Kinoshita
    • Organizer
      次世代ナノ統合シミュレーションソフトウェアの研究開発,第5回公開シンポジウム
    • Place of Presentation
      甲南大学
    • Year and Date
      2011-02-23
    • Related Report
      2010 Annual Research Report
  • [Presentation] 「疎水性」の本当の物理起源:その温度依存性を通しての考察2011

    • Author(s)
      木下正弘
    • Organizer
      第56回低温生物工学会大会セミナー
    • Place of Presentation
      いわて県民情報交流センター
    • Related Report
      2012 Final Research Report
  • [Presentation] 実験で得られた蛋白質天然構造モデルのキャラクタリゼーション2011

    • Author(s)
      三嶋浩和, 安田哲司, 吉留崇, 池口満徳, 木下正弘
    • Organizer
      第34回溶液化学シンポジウム
    • Place of Presentation
      名古屋大学ES総合館ESホール
    • Related Report
      2011 Annual Research Report
  • [Presentation] Crucial Importance of Translational Entropy of Water in Rotation Mechanism of F_1-ATPase2010

    • Author(s)
      T.Yoshidome, Y.Ito, M.Ikeguchi, M.Kinoshita
    • Organizer
      Pacifichem 2010, Topic Area-Physical, Theoretical & Computational, "New Experimental and Computational Probes of Water in Biological Systems (#130)"
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2010-12-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Statistical Thermodynamics for Cold Denaturation of Proteins2010

    • Author(s)
      H.Oshima, T.Yoshidome, K.Amano, M.Kinoshita
    • Organizer
      Pacifichem 2010, Topic Area-Physical, Theoretical & Computational, "New Experimental and Computational Probes of Water in Biological Systems (#130)"
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2010-12-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Insertion and Release of a Big Sphere into and from a Cylindrical Vessel2010

    • Author(s)
      K.Amano, M.Kinoshita
    • Organizer
      Pacifichem 2010, Topic Area-Physical, Theoretical & Computational, "New Experimental and Computational Probes of Water in Biological Systems (#130)"
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2010-12-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Effects of Heme on the Thermal Stability of Four Cytochromes c : Theoretical Analyses2010

    • Author(s)
      R.Kodama, T.Yoshidome, M.Yamanaka, Y.Sambongi, M.Kinoshita
    • Organizer
      Pacifichem 2010, Topic Area-Physical, Theoretical & Computational, "New Experimental and Computational Probes of Water in Biological Systems (#130)"
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2010-12-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Effects of Side-Chain Packing on the Formation of Secondary Structures in Protein Folding2010

    • Author(s)
      S.Yasuda, T.Yoshidome, H.Oshima, R.Kodama, Y.Harano, M.Kinoshita
    • Organizer
      Pacifichem 2010, Topic Area-Physical, Theoretical & Computational, "New Experimental and Computational Probes of Water in Biological Systems (#130)"
    • Place of Presentation
      Honolulu, Hawaii, USA
    • Year and Date
      2010-12-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Effects of Heme on the Thermal Stability of Cytochromes c : Comparison between Experimental and Theoretical Results2010

    • Author(s)
      R.Kodama, T. Yoshidome, M.Yamanaka, Y.Sambongi, M.Kinoshita
    • Organizer
      International Symposium of Advanced Energy Science
    • Place of Presentation
      Obaku Plaza, Kyoto University, Uji, Japan
    • Year and Date
      2010-11-18
    • Related Report
      2010 Annual Research Report
  • [Presentation] Free-Energy Function for Discriminating the Native Fold of a Protein from Misfolded Decoys2010

    • Author(s)
      S.Yasuda, T.Yoshidome, Y.Harano, R.Roth, H.Oshima, Y.Sugita, M.Ikeguchi, M.Kinoshita
    • Organizer
      International Symposium of Advanced Energy Science
    • Place of Presentation
      Obaku Plaza, Kyoto University, Uji, Japan
    • Year and Date
      2010-11-18
    • Related Report
      2010 Annual Research Report
  • [Presentation] F_1-ATPaseの回転のメカニズムにおける水のエントロピーの重要性2010

    • Author(s)
      吉留崇, 伊藤祐子, 池口満徳, 木下正弘
    • Organizer
      日本物理学会平成22年度秋季大会(物性関係)
    • Place of Presentation
      大阪府立大学
    • Year and Date
      2010-09-23
    • Related Report
      2010 Annual Research Report
  • [Presentation] Crucial Importance of Translational Entropy of Water in Rotation Mechanism of F_1-ATPase2010

    • Author(s)
      T.Yoshidome, Y.Ito, M.Ikeguchi, M.Kinoshita
    • Organizer
      The 48th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tohoku University, Sendai, Japan
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Theoretical Prediction of Hot Spots in Protein-Protein Complexes2010

    • Author(s)
      H.Oshima, S.Yasuda, T.Yoshidome, M.Ikeguchi, M.Kinoshita
    • Organizer
      The 48th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tohoku University, Sendai, Japan
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Import and Export of a Solute Using Solvation Effects : A Study on Chaperonin GroEL2010

    • Author(s)
      K.Amano, M.Kinoshita
    • Organizer
      The 48th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tohoku University, Sendai, Japan
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Effects of Heme on the Thermal Stability of Cytochromes c : Comparison between Experimental and Theoretical Results2010

    • Author(s)
      R.Kodama, T.Yoshidome, M.Yamanaka, Y.Sambongi, M.Kinoshita
    • Organizer
      The 48th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tohoku University, Sendai, Japan
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Development of a Free-Energy Function toward Predicting the Native Structure of a Protein2010

    • Author(s)
      S.Yasuda, T.Yoshidome, Y.Harano, R.Roth, Y.Sugita, M.Ikeguchi, M.Kinoshita
    • Organizer
      The 48th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tohoku University, Sendai, Japan
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Refinement of Modeled Protein Structure by Replica-Exchange Molecular Dynamics and Hydration Entropy Based Scoring Function2010

    • Author(s)
      S.Du, Y.Harano, M.Sakurai, M.Kinoshita
    • Organizer
      The 48th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Tohoku University, Sendai, Japan
    • Year and Date
      2010-09-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Import and Export of a Solute Using Solvation Effects : A Study on Chaperonin GroEL2010

    • Author(s)
      K.Amano, M.Kinoshita
    • Organizer
      The 2nd GCOE International Symposium(ZERO-CARBON ENERGY Kyoto 2010)
    • Place of Presentation
      Obaku Plaza, Kyoto University, Uji, Japan
    • Year and Date
      2010-08-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Effects of Heme on the Thermal Stability of Mesophilic and Thermophylic Cytochromes c : Comparison between Experimental and Theoretical Results2010

    • Author(s)
      R.Kodama, T.Yoshidome, M.Yamanaka, Y.Sambongi, M.Kinoshita
    • Organizer
      The 2nd GCOE International Symposium(ZERO-CARBON ENERGY Kyoto 2010)
    • Place of Presentation
      Obaku Plaza, Kyoto University, Uji, Japan
    • Year and Date
      2010-08-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Development of a Free-Energy Function toward Predicting the Native Structure of a Protein2010

    • Author(s)
      S.Yasuda, T.Yoshidome, Y.Harano, R.Roth, Y.Sugita, M.Ikeguchi, M.Kinoshita
    • Organizer
      The 2nd GCOE International Symposium(ZERO-CARBON ENERGY Kyoto 2010)
    • Place of Presentation
      Obaku Plaza, Kyoto University, Uji, Japan
    • Year and Date
      2010-08-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Physical Picture of Cold Denaturation of Proteins2010

    • Author(s)
      T.Yoshidome, H.Oshima, K.Amano, M.Kinoshita
    • Organizer
      International Symposium on Non-Equilibrium Soft Matter 2010
    • Place of Presentation
      Naraken Sinkoukaido, Japan
    • Year and Date
      2010-08-18
    • Related Report
      2010 Annual Research Report
  • [Presentation] F_1-ATPaseの回転のメカニズムにおける水のエントロピーの重要性2010

    • Author(s)
      吉留崇, 伊藤祐子, 池口満徳, 木下正弘
    • Organizer
      革新的ナノバイオ第5回班会議
    • Place of Presentation
      学習院大学
    • Year and Date
      2010-06-25
    • Related Report
      2010 Annual Research Report
  • [Presentation] A Solvent Effect on Insertion Path of a Solute Particle into a Cylindrical Vessel

    • Author(s)
      R. Hara, K. Amano, M. Kinoshita, A. Yoshimori
    • Organizer
      6-th Mini-Symposium on Liquid
    • Place of Presentation
      九州大学箱崎
    • Related Report
      2012 Annual Research Report
  • [Presentation] シャペロニンの中央になぜ蛋白質が入るのか

    • Author(s)
      原諒平、天野健一、木下正弘、吉森明
    • Organizer
      第118回日本物理学会九州支部例会
    • Place of Presentation
      琉球大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] エントロピー力による円筒状容器からの大球の放出

    • Author(s)
      三嶋浩和、尾嶋拓、安田賢司、天野健一、木下正弘
    • Organizer
      GCOE年次報告会
    • Place of Presentation
      京都大学時計台記念館
    • Related Report
      2012 Annual Research Report
  • [Book] 現代界面コロイド科学の事典-シャンプーから宇宙まで-2010

    • Author(s)
      木下正弘
    • Publisher
      丸善
    • Related Report
      2012 Final Research Report
  • [Book] 日本化学会・コロイドおよび界面化学部会35周年記念出版,「現代界面コロイド科学の事典-シャンプーから宇宙まで-」,10章6節2010

    • Author(s)
      木下正弘
    • Total Pages
      2
    • Publisher
      丸善
    • Related Report
      2010 Annual Research Report
  • [Remarks] 木下研究室-京都大学エネルギー理工学研究所

    • URL

      http://www.iae.kyoto-u.ac.jp/centerbunya/kinoshita

    • Related Report
      2012 Final Research Report
  • [Remarks] 木下研究室-京都大学エネルギー理工学研究所

    • URL

      http://www.iae.kyoto-u.ac.jp/centerbunya/kinoshita

    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://www.iae.kyoto-u.ac.jp/centerbunya/kinoshita/

    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://www.iae.kyoto-u.ac.jp/centerbunya/kinoshita/

    • Related Report
      2010 Annual Research Report

URL: 

Published: 2010-08-23   Modified: 2019-07-29  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi