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Molecular dynamics simulations on membrane transporting proteins

Research Project

Project/Area Number 15083201
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe Institute of Physical and Chemical Research (2007-2008)
The University of Tokyo (2003-2006)

Principal Investigator

SUGITA Yuji  The Institute of Physical and Chemical Research, 杉田理論生物化学研究室, 准主任研究員 (80311190)

Co-Investigator(Kenkyū-buntansha) KONDOU Youhei  東京大学, 分子細胞生物学研究所, 助手 (30436604)
Project Period (FY) 2003 – 2008
Project Status Completed (Fiscal Year 2008)
Budget Amount *help
¥88,800,000 (Direct Cost: ¥88,800,000)
Fiscal Year 2008: ¥16,100,000 (Direct Cost: ¥16,100,000)
Fiscal Year 2007: ¥16,100,000 (Direct Cost: ¥16,100,000)
Fiscal Year 2006: ¥15,500,000 (Direct Cost: ¥15,500,000)
Fiscal Year 2005: ¥15,600,000 (Direct Cost: ¥15,600,000)
Fiscal Year 2004: ¥17,000,000 (Direct Cost: ¥17,000,000)
Fiscal Year 2003: ¥8,500,000 (Direct Cost: ¥8,500,000)
Keywords膜蛋白質 / 分子動力学計算 / イオンポンプ / トランスロコン / 膜タンパク質 / 物質輸送 / シミュレーション / 膜透過装置 / 分子動力学 / 生体膜 / プロトン化 / 拡張アンサンブル法 / イオン能動輸送 / 分子動力学法
Research Abstract

生体膜を隔てたイオンやタンパク質の物質輸送を行う膜輸送タンパク質の立体構造を用いた分子動力学計算を行うことにより膜タンパク質の構造変化と物質輸送機構の関係を明らかにした。ターゲットとして、カルシウムイオンポンプ、その機能を制御するフォスフォランバン、タンパク質輸送を行うSecトランスロコンを選び、脂質二重膜と溶媒を露わに含む全原子分子動力学計算を実施することにより、膜インターフェイスにおけるSoftな相互作用がこれらのタンパク質の機能に果たす役割を明らかにすることができた。

Report

(7 results)
  • 2008 Annual Research Report   Final Research Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • Research Products

    (76 results)

All 2009 2008 2007 2006 2005 2004 Other

All Journal Article (43 results) (of which Peer Reviewed: 30 results) Presentation (29 results) Book (1 results) Publications (3 results)

  • [Journal Article] Transmembrane Structures of Amyloid Precursor Protein Dimer Predicted by Replica-Exchange Molecular Dynamics Simulations2009

    • Author(s)
      N. Miyashita, J. E. Straub, D. Thirumalai, Y. Sugita
    • Journal Title

      J. Am. Chem. Soc. 131(10)

      Pages: 3438-3439

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Free-energy landscapes of proteins in solution by generalized-ensemble simulations2009

    • Author(s)
      Y. Sugita
    • Journal Title

      Frontiers in Bioscience 14

      Pages: 1292-1303

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mg^<2+>-sensing mechanism of Mg^<2+> transporter MgtE probed by molecular dynamics study2008

    • Author(s)
      R. Ishitani, Y. Sugita, N. Dohmae, N. Furuya, M. Hattori, O. Nureki
    • Journal Title

      Proc. Natl. Acad. Sci. USA. 105(40)

      Pages: 15393-15398

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Conformational transition of Sec machinery inferred from bacterial SecYE structures2008

    • Author(s)
      T. Tsukazaki, H. Mori, S. Fukai, R. Ishitani, T. Mori, N. Dohmae, A. Perederina, Y. Sugita, D.G. Vassylyev, K. Ito, O. Nureki
    • Journal Title

      Nature 455

      Pages: 938-992

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Generalized-Ensemble Algorithms for Protein Folding Simulations2008

    • Author(s)
      Y. Sugita, A. Mitsutake, Y. Okamoto
    • Journal Title

      Lecture Notes in Physics 736

      Pages: 369-407

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] 生体分子の構造探索の理論2008

    • Author(s)
      杉田有治
    • Journal Title

      化学と工業 61-6

      Pages: 582-584

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] カルシウムポンプの機能制御機構2008

    • Author(s)
      杉田有治
    • Journal Title

      生化学 61-6

      Pages: 582-584

    • NAID

      10022594597

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] ぞくぞくとわかってきた膜を隔てたイオン輸送装置構造2008

    • Author(s)
      杉田有治
    • Journal Title

      生物物理 48(6)

      Pages: 330-332

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mg^<2+>-sensing mechanism of Mg^<2+> transporter MgtE probed by molecular dynamics study2008

    • Author(s)
      R. Ishitani, et al.
    • Journal Title

      Proc. Natl. Acad. Sci. USA. 105 (40)

      Pages: 15393-15398

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conformational transition of Sec machinery inferred from bacterial SecYE structures2008

    • Author(s)
      T. Tsukazaki, et al.
    • Journal Title

      Nature.

      Pages: 455988-992

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] カルシウムポンプの機能制御機構2008

    • Author(s)
      杉田 有治
    • Journal Title

      生化学 80

      Pages: 917-924

    • NAID

      10022594597

    • Related Report
      2008 Annual Research Report
  • [Journal Article] New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals2007

    • Author(s)
      J. Jung, C.H. Choi, Y. Sugita, S. Ten-no
    • Journal Title

      J. Chem. Phys. 127

      Pages: 204102-204102

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Replica-exchange molecular dynamics simulations of diffracted X-ray tracking2007

    • Author(s)
      Y. Kawashima, Y.C. Sasaki, Y. Sugita, T. Yoda, Y. Okamoto
    • Journal Title

      Molecular simulation 33

      Pages: 97-102

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Physical basis for characterizing native structures of proteins2007

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

      Chem. Phys. Lett. 437

      Pages: 112-116

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cooperative Folding Mechanism of a b-Hairpin Peptide Studied by Using a Multicanonical Replica-Exchange Molecular Dynamics Simulation2007

    • Author(s)
      Yoda T, Sugita Y, Okamoto Y
    • Journal Title

      PROTEINS : Structure, Function, and Bioinformatics 66

      Pages: 846-859

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals.2007

    • Author(s)
      J. Jung, et. al.
    • Journal Title

      J. Chem. Phys. 127

      Pages: 204102-204102

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Replica-exchange molecular dynamics simulations of diffracted X-ray tracking.2007

    • Author(s)
      Y. Kawashima, et. al.
    • Journal Title

      Molecular simulation 33

      Pages: 97-102

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Physical basis for characterizing native structures of proteins.2007

    • Author(s)
      Y. Harano, et. al.
    • Journal Title

      Chem. Phys. Lett. 437

      Pages: 112-116

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cooperative Folding Mechanism of a b-Hairpin Peptide Studied by Using a Multicanonical Replica-Exchange Molecular Dynamics Simulation.2007

    • Author(s)
      Yoda et al.
    • Journal Title

      PROTEINS : Structure, Function, and Bioinformatics 66

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Structural Changes in the Cytoplasmic Domain of Phospholamban by Phosphorylation at Ser16 : A Molecular Dynamics Study2006

    • Author(s)
      Sugita Y, Miyashita N, Yoda T, Ikeguchi M, Toyoshima C
    • Journal Title

      Biochemistry 45

      Pages: 11752-11761

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] 膜蛋白質の分子動力学2006

    • Author(s)
      杉田有治, 池口満徳
    • Journal Title

      物性研究 50

      Pages: 1271-1277

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural Changes in the Cytoplasmic Domain of Phospholamban at Serl6 : A Molecular Dynamics Study2006

    • Author(s)
      Sugita et al.
    • Journal Title

      Biochemistry 45

      Pages: 11752-11761

    • Related Report
      2006 Annual Research Report
  • [Journal Article] 膜蛋白質の分子動力学2006

    • Author(s)
      杉田 有治 et al.
    • Journal Title

      物性研究 50

      Pages: 1271-1277

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Protonation of the acidic residues in the transmembrane cation-binding sites of the Ca^<2+>-pump2005

    • Author(s)
      Sugita Y, Miyashita N, Ikeguchi M, Kidera A, Toyoshima C
    • Journal Title

      J. Am. Chem. Soc. 127

      Pages: 6150-6151

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural role of countertransport revealed in Ca^<2+> pump crystal structure in the absence of Ca^<2+>2005

    • Author(s)
      Obara K, Miyashita N, Xu C, Toyoshima I, Sugita Y, Ineshi G, Toyoshima C
    • Journal Title

      Proc. Natl. Acid, Sci. USA. 102

      Pages: 14489-14496

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] カルシウムポンプの構造と機能2005

    • Author(s)
      杉田有治, 豊島近
    • Journal Title

      蛋白質・核酸・酵素, 増刊号「生命秩序を担う生体超分子」 50

      Pages: 1271-1277

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent2005

    • Author(s)
      Sugita Y, Okamoto Y
    • Journal Title

      Biophysical J. 88

      Pages: 3180-3190

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. I. Test of sampling efficiency2005

    • Author(s)
      Murata K, Sugita Y, Okamoto Y
    • Journal Title

      J. Theor. Comp. Chem. 4

      Pages: 411-432

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling. II. Free energy analysis2005

    • Author(s)
      Murata K, Sugita Y, Okamoto Y
    • Journal Title

      J. Theor. Comp. Chem. 4

      Pages: 433-448

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structures of a peptide fragment of β_2-microgloblin studied by replica-exchange molecular dynamics simulations : towards the understanding of the mechanism of amyloid formation2005

    • Author(s)
      Nishino M, Sugita Y, Yoda T, Okamoto Y
    • Journal Title

      FEBS Lett. 579

      Pages: 5425-5429

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Effects of the Fixed End in Single-Molecular Imaging Techiques : A Replica Exchange Molecular Dynamics Simulation2005

    • Author(s)
      Kawashima Y, Sugita Y, Yoda T, Okamoto Y
    • Journal Title

      Chem. Phys. Lett. 414

      Pages: 449-455

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Protonation of the acidic residues in the transmembrane cation-binding sites of the Ca^<2+>-pump2005

    • Author(s)
      Sugita et al.
    • Journal Title

      J.Am.Chem.Soc. 127

      Pages: 6150-6151

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Structural role of countertransport revealed in Ca^<2+> pump crystal structure in the absence of Ca^<2+>.2005

    • Author(s)
      Obara et al.
    • Journal Title

      Proc.Natl.Acad.Sci.USA 102

      Pages: 14489-14496

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent.2005

    • Author(s)
      Sugita et al.
    • Journal Title

      Biophys.J. 88

      Pages: 3180-3190

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling.I.Test of sampling efficiency.2005

    • Author(s)
      Murata et al.
    • Journal Title

      J.Theor.Comp.Chem. 4

      Pages: 411-432

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling.II.Free energy analysis.2005

    • Author(s)
      Murata et al.
    • Journal Title

      J.Theor.Comp.Chem. 4

      Pages: 433-448

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Structures of a peptide fragment of β_2-microgloblin studied by replica-exchange molecular dynamics simulations : towards the understanding of the mechanism of amyloid formation.2005

    • Author(s)
      Nishino et al.
    • Journal Title

      FEBS Lett. 579

      Pages: 433-448

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Secondary-Structure Preferences of Force Fields for Proteins Evaluated by Generalized-Ensemble Simulations2004

    • Author(s)
      T. Yoda, Y. Sugita, Y. Okamoto
    • Journal Title

      Chem. Phys.

      Pages: 269-283

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Comparisons of Force Fields for Proteins by Generalized-Ensemble Simulations2004

    • Author(s)
      T. Yoda, Y. Sugita, Y. Okamoto
    • Journal Title

      Chem. Phys. Lett. 386

      Pages: 460-467

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Free energy calculations for DNA base stacking by replica-exchange umbrella sampling2004

    • Author(s)
      K. Murata, Y. Sugita, Y. Okamoto
    • Journal Title

      Chem. Phys. Lett. 385

      Pages: 1-7

    • Related Report
      2008 Final Research Report
    • Peer Reviewed
  • [Journal Article] Secondary-Structure Preferences of Force Fields for Proteins Evaluated by Generalized-Ensemble Simulations2004

    • Author(s)
      Yoda, T. et al.
    • Journal Title

      Chem.Phys. 307

      Pages: 269-283

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Comparisons of Force Fields for Proteins by Generalized-Ensemble Simulations2004

    • Author(s)
      Yoda, T. et al.
    • Journal Title

      Chem.Phys.Lett. 386

      Pages: 460-467

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Free energy calculations for DNA base stacking by replica-exchange umbrella sampling2004

    • Author(s)
      Murata, K. et al.
    • Journal Title

      Chem.Phys.Lett. 385

      Pages: 1-7

    • Related Report
      2004 Annual Research Report
  • [Presentation] Molecular Dynamics Simulations of Soft Interactions at the Membrane Interface2009

    • Author(s)
      杉田有治
    • Organizer
      International Symposium on Molecular Soft Interactions in Biological Systems
    • Place of Presentation
      大阪
    • Related Report
      2008 Final Research Report
  • [Presentation] 膜蛋白質の分子動力学計算2009

    • Author(s)
      杉田有治
    • Organizer
      計算科学研究センター・ワークショップ
    • Place of Presentation
      岡崎
    • Related Report
      2008 Final Research Report
  • [Presentation] 分子シミュレーションからカルシウムポンプの構造柔軟性を考える2008

    • Author(s)
      杉田 有治
    • Organizer
      日本生物物理学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2008-12-22
    • Related Report
      2007 Annual Research Report
  • [Presentation] Molecular Dynamics Study of Sarcoplasmic Reticulum Calcium Pump2008

    • Author(s)
      杉田 有治
    • Organizer
      第31回日本分子生物学会・第81回日本生化学会合同大会
    • Place of Presentation
      神戸ポートピアホテル
    • Year and Date
      2008-12-09
    • Related Report
      2008 Annual Research Report
  • [Presentation] Protein-Lipid Interactions Revealed by Molecular Dynamics Simulations2008

    • Author(s)
      杉田有治
    • Organizer
      九州大学次世代研究スーパースター養成プログラム公開シンポジウム
    • Place of Presentation
      博多
    • Related Report
      2008 Final Research Report
  • [Presentation] Molecular Dynamics simulations of protein dynamics in biological membrane2008

    • Author(s)
      杉田有治
    • Organizer
      次世代ナノ情報機能・材料グループ成果報告会
    • Place of Presentation
      仙台
    • Related Report
      2008 Final Research Report
  • [Presentation] Molecular Dynamics Study of Sarcoplasmic Reticulum Calcium Pump2008

    • Author(s)
      Yuji Sugita
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会 (BMB2008)
    • Place of Presentation
      神戸
    • Related Report
      2008 Final Research Report
  • [Presentation] Toward a complete understanding of molecular mechanism of ion transport by membrane proteins2008

    • Author(s)
      Yuji Sugita
    • Organizer
      1st Joint Workshop on Computational Science
    • Place of Presentation
      和光
    • Related Report
      2008 Final Research Report
  • [Presentation] Molecular mechanism for stabilizing Ca^<2+> at the transmembrane binding sites in Ca^<2+>-pump2008

    • Author(s)
      Yuji Sugita
    • Organizer
      1st CMD International Symposium Chemical Computations
    • Place of Presentation
      Seoul
    • Related Report
      2008 Final Research Report
  • [Presentation] カルシウムポンプの機能発現機構に関する分子動力学計算2008

    • Author(s)
      杉田有治
    • Organizer
      日本物理学会第63回年次大会
    • Place of Presentation
      東大阪
    • Related Report
      2008 Final Research Report
  • [Presentation] 分子シミュレーションからカルシウムポンプの構造柔軟性を考える2007

    • Author(s)
      杉田有治
    • Organizer
      日本生物物理学会第45回年会
    • Place of Presentation
      横浜
    • Related Report
      2008 Final Research Report
  • [Presentation] Molecular Dynamics Simulations on the Conformational Stability of the Ca^<2+>-binding sites in Ca^<2+>-pump2007

    • Author(s)
      Yuji Sugita
    • Organizer
      BNL-RIKEN Life Science Workshop
    • Place of Presentation
      Upton
    • Related Report
      2008 Final Research Report
  • [Presentation] カルシウムポンプによるイオン能動輸送の分子機構2007

    • Author(s)
      杉田有治
    • Organizer
      理研シンポジウム「計算機と生物学 in Silico Biology」
    • Place of Presentation
      和光
    • Related Report
      2008 Final Research Report
  • [Presentation] SR Ca^<2+>-ATPaseによるCa^<2+>輸送とプロトン対抗輸送の分子機構2006

    • Author(s)
      杉田有治
    • Organizer
      第4回特定領域研究「膜インターフェイス」公開シンポジウム
    • Place of Presentation
      京都大学百周年記念ホール
    • Year and Date
      2006-07-05
    • Related Report
      2008 Final Research Report
  • [Presentation] レプリカ交換法による蛋白質機能解析2006

    • Author(s)
      杉田有治
    • Organizer
      第6回蛋白質科学会年会
    • Place of Presentation
      京都国際会議場
    • Year and Date
      2006-04-26
    • Related Report
      2008 Final Research Report
  • [Presentation] 分子動力学計算による蛋白質原子揺らぎの収束性について2006

    • Author(s)
      杉田有治
    • Organizer
      大阪大学蛋白研セミナー
    • Place of Presentation
      大阪大学蛋白質研究所
    • Related Report
      2008 Final Research Report
  • [Presentation] Molecular dynamics simulations of sarcoplasimc reticulum calcium pump in membrane2006

    • Author(s)
      Yuji Sugita
    • Organizer
      In Satellite meeting for 20^<th> IUBMB International Congress of Biochemistry and Molecular Biology & 11^<th> FAOBMB Congress on Molecular Mechanism and Regulation in Cation Transport ATPases and Related Genetic Diseases
    • Place of Presentation
      京都リサーチパーク
    • Related Report
      2008 Final Research Report
  • [Presentation] 分子動力学計算によるカルシウムポンプの機能制御機構の解析2006

    • Author(s)
      杉田有治
    • Organizer
      大阪大学蛋白研セミナー
    • Place of Presentation
      大阪大学蛋白質研究所
    • Related Report
      2008 Final Research Report
  • [Presentation] カルシウムポンプとその阻害剤の分子動力学計算2006

    • Author(s)
      杉田有治
    • Organizer
      スーパーコンピュータワークショップ
    • Place of Presentation
      自然科学機構・岡崎共通研究施設・計算科学研究センター
    • Related Report
      2008 Final Research Report
  • [Presentation] Theoretical studies on the proton countertransport by sarcoplasmic reticulum calcium pump2006

    • Author(s)
      Yuji Sugita
    • Organizer
      In KAIST seminar
    • Place of Presentation
      KAIST、Korea
    • Related Report
      2008 Final Research Report
  • [Presentation] カルシウムポンプの分子動力学計算 : 構造から機能の理解へ2006

    • Author(s)
      杉田有治
    • Organizer
      京都大学ウイルス研セミナー
    • Place of Presentation
      京都大学ウイルス研究所
    • Related Report
      2008 Final Research Report
  • [Presentation] 筋小胞体Ca^<2+>-ATPaseの機能に関する分子動力学計算2005

    • Author(s)
      杉田有治
    • Organizer
      第28回日本分子生物学会年会
    • Place of Presentation
      福岡ドーム
    • Related Report
      2008 Final Research Report
  • [Presentation] Molecular dynamics studies on the biological functions of sarcoplasmic reticulum Ca^<2+>-ATPase.2005

    • Author(s)
      Yuji Sugita
    • Organizer
      In P-Chem seminar
    • Place of Presentation
      Boston University、Boston
    • Related Report
      2008 Final Research Report
  • [Presentation] SR Ca^<2+>-ATPase Atomic Structure and Molecular Dynamics Simulations2005

    • Author(s)
      Yuji Sugita, Chikashi Toyoshima
    • Organizer
      In 11-th International ATPase Conference and 59-th Annual Meeting and Symposium of the Society of General Physiologists
    • Place of Presentation
      Marine Biological Laboratory, Woods Hole, Massachusetts
    • Related Report
      2008 Final Research Report
  • [Presentation] 脂質二重膜中におけるカルシウムポンプの運動と機能2005

    • Author(s)
      杉田有治
    • Organizer
      生体分子ダイナミックス研究会
    • Place of Presentation
      東京大学農学部
    • Related Report
      2008 Final Research Report
  • [Presentation] Molecular dynamics studies on Sarcoplasmic reticulum Ca^<2+>-ATPase2005

    • Author(s)
      Yuji Sugita
    • Organizer
      In Theoretical Biophysics Seminar
    • Place of Presentation
      Rutgars University, New Jersey
    • Related Report
      2008 Final Research Report
  • [Presentation] Molecular dynamics simulations SR Ca^<2+>-ATPase in the Ca^<2+>-bound and unbound states2005

    • Author(s)
      Yuji Sugita, Chikashi Toyoshima
    • Organizer
      In 2005 FASEB Summer Research Conferences
    • Place of Presentation
      Vermont Academy, Saxton River, Vermont, USA
    • Related Report
      2008 Final Research Report
  • [Presentation] Molecular Mechanism of cooperative Ca^<2+>-binding by Ca2+-ATPase, insight from molecular dynamics simulations2005

    • Author(s)
      Yuji Sugita
    • Organizer
      In the 2^<nd> symposium of membrane interface
    • Place of Presentation
      ホテル阪急エキスポパーク
    • Related Report
      2008 Final Research Report
  • [Presentation] 脂質二重膜中でのカルシウムポンプの分子動力学2004

    • Author(s)
      杉田有治
    • Organizer
      第1回特定領域研究「膜インターフェイス」公開シンポジウム
    • Place of Presentation
      東京大学山上会館
    • Related Report
      2008 Final Research Report
  • [Book] Rugged Free Energy Landscapes2008

    • Author(s)
      Y. Sugita, et al.
    • Total Pages
      412
    • Publisher
      Springer
    • Related Report
      2008 Annual Research Report
  • [Publications] Mitsutake et al.: "Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptide I.Formulation and benchmark test"J.Chem.Phys.. 118. 6664-6675 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Mitsutake, A. et al.: "Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptide II.Application to a more complex system"J.Chem.Phys.. 118. 6676-6688 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Funahashi J. et al.: "How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions?"Protein Eng. 16. 665-671 (2003)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2018-03-28  

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