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Molecular dynamics study of membrane properties of lipid bilayers with asymmetric lipid composition

Research Project

Project/Area Number 16K21094
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Physical chemistry
Biophysics
Research InstitutionNagoya University

Principal Investigator

Andoh Yoshimichi  名古屋大学, 工学研究科, 特任准教授 (80509076)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2019: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2018: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2017: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywords細胞膜 / 肝臓細胞 / 脂質組成の非対称性 / 分子動力学計算 / リン脂質 / スフィンゴミエリン / コレステロール / ミクロドメイン / 非対称な脂質分布 / 膜流動性 / 脂質二重層膜 / 非対称性な脂質組成 / グリセロリン脂質 / スフィンゴ脂質 / 膜物性 / 脂質ラフト / 非対称な脂質組成 / 化学物理 / 生物物理 / 統計力学 / 表面・界面物性
Outline of Final Research Achievements

All-atomistic molecular dynamics (MD) calculations were carried out on fully-hydrated lipid bilayer systems modeling asymmetric lipid composition between outer and inner leaflets of hepatocyte plasma membranes. Differences in membrane physico-chemical properties, such as membrane structure, degree of order, and fluidity, between outer and inner leaflets were clarified in a molecular level. Large space-scale and long time-scale MD simulations enabled to explore a molecular picture of the lateral clustering of specific lipid molecules (e.g. cholesterol) and its difference between outer and inner leaflets. Degree of correlation of membrane properties induced by the interdigitation of lipid tails was also investigated. Simulation protocol used in this research can be widely applied to other MD simulation researches with an aim to reveal membrane properties of actual cell plasma membranes.

Academic Significance and Societal Importance of the Research Achievements

細胞膜は単に細胞を形作る隔壁の役割だけでなく, 細胞内で生成される物質の代謝やシグナル伝達, さらにウィルス感染経路においても重要な役割を果たしている. 本研究は細胞膜の構造的基礎となるリン脂質二重層膜について特に興味が持たれている, 内外単層膜間での物性の違い, および膜内でのミクロドメイン形成についての分子論的知見を与えるものである. 研究成果は興隆しつつある膜脂質標的型治療 (membrane-lipid therapy) や脂質標的薬剤 (lipid-targeted drugs) 研究への展開が期待される.

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

    (39 results)

All 2020 2019 2018 2017 2016 Other

All Journal Article (11 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 10 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (24 results) (of which Int'l Joint Research: 6 results,  Invited: 2 results) Book (3 results) Remarks (1 results)

  • [Journal Article] Molecular dynamics study of lipid bilayers modeling outer and inner leaflets of plasma membranes of mouse hepatocytes. I: Differences in physicochemical properties between the two leaflets2020

    • Author(s)
      Yoshimichi Andoh, Shiho Hayakawa, and Susumu Okazaki
    • Journal Title

      The Journal of Chemical Physics

      Volume: -

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Extension of the fast multipole method for the rectangular cells with an anisotropic partition tree structure2020

    • Author(s)
      Y. Andoh, N. Yoshii, S Okazaki
    • Journal Title

      Journal of Computational Chemistry

      Volume: - Issue: 14 Pages: 1353-1367

    • DOI

      10.1002/jcc.26180

    • NAID

      120007127374

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fast multipole method for three dimensional systems with periodic boundary condition in two directions2020

    • Author(s)
      N. Yoshii, Y. Andoh, S Okazaki
    • Journal Title

      Journal of Computational Chemistry

      Volume: 41 Issue: 9 Pages: 940-948

    • DOI

      10.1002/jcc.26141

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] All-atom Molecular Dynamics Simulation Study ofSelf-assemblies of Amphiphilic Molecules in Solution2019

    • Author(s)
      ANDOH Yoshimichi、OKAZAKI Susumu
    • Journal Title

      Oleoscience

      Volume: 19 Issue: 11 Pages: 447-453

    • DOI

      10.5650/oleoscience.19.447

    • NAID

      130007742439

    • ISSN
      1345-8949, 2187-3461
    • Related Report
      2019 Annual Research Report
    • Open Access
  • [Journal Article] Molecular Behavior of Linear Alkylbenzene Sulfonate in Hydrated Crystal, Tilted Gel, and Liquid Crystal Phases Studied by Molecular Dynamics Simulation2019

    • Author(s)
      Takeda Kosuke、Andoh Yoshimichi、Shinoda Wataru、Okazaki Susumu
    • Journal Title

      Langmuir

      Volume: 35 Issue: 33 Pages: 10877-10884

    • DOI

      10.1021/acs.langmuir.9b01607

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of Hydrated Crystal (Lc), Tilted Gel (Lβ′), and Liquid Crystal (Lα) Phases of Linear Alkylbenzene Sulfonate (LAS) Studied by X-ray Diffraction and Molecular Dynamics Simulation2019

    • Author(s)
      Takeda Kosuke、Andoh Yoshimichi、Shinoda Wataru、Okazaki Susumu
    • Journal Title

      Langmuir

      Volume: 35 Issue: 27 Pages: 9011-9019

    • DOI

      10.1021/acs.langmuir.9b01199

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Difference in molecular mechanisms governing changes in membrane properties of phospholipid bilayers induced by addition of nonionic and zwitterionic surfactants2018

    • Author(s)
      Yoshimichi Andoh, Sakiho Kitou, Susumu Okazaki
    • Journal Title

      Journal of Molecular Liquids

      Volume: 271 Pages: 933-941

    • DOI

      10.1016/j.molliq.2018.09.018

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] A thread-level parallelization of pairwise additive potential and force calculations suitable for current many-core architectures2018

    • Author(s)
      Y. Andoh, S. Suzuki, S. Ohshima, T. Sakashita, M. Ogino, T. Katagiri, N. Yoshii, S. Okazaki
    • Journal Title

      Journal of Supercomputing

      Volume: 印刷中 Issue: 6 Pages: 2449-2469

    • DOI

      10.1007/s11227-018-2272-2

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Pressure tensor for electrostatic interaction calculated by fast multipole method with periodic boundary condition2018

    • Author(s)
      Noriyuki Yoshii, Yoshimichi Andoh, Susumu Okazaki
    • Journal Title

      Journal of Computational Chemistry

      Volume: 印刷中 Issue: 19 Pages: 1192-1199

    • DOI

      10.1002/jcc.25179

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural ordering of lipid bilayers induced by surfactant molecules with small hydrophilic head group2017

    • Author(s)
      Andoh Yoshimichi、Mohamed Siti Nor Syafawani、Kitou Sakiho、Okazaki Susumu
    • Journal Title

      Molecular Simulation

      Volume: 43 Issue: 13-16 Pages: 1247-1255

    • DOI

      10.1080/08927022.2017.1319061

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Evaluation of atomic pressure in the multiple time-step integration algorithm2017

    • Author(s)
      Y Andoh, A. Yamada, N. Yoshii, S Okazaki
    • Journal Title

      Journal of Computational Chemistry

      Volume: 38 Issue: 10 Pages: 704-713

    • DOI

      10.1002/jcc.24731

    • NAID

      120006305599

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] 非対称な脂質組成を持った脂質二重層膜内での脂質分子側方凝集に関する理論的研究2019

    • Author(s)
      安藤嘉倫、早川志保、岡崎進
    • Organizer
      第13回分子科学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 細胞膜内でのコレステロール分子側方凝集に関する理論的研究2019

    • Author(s)
      安藤嘉倫、 早川志保、 岡崎進
    • Organizer
      第42回溶液化学シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] Molecular dynamics study on correlation of membrane properties between outer and inner leaflets of cell plasma membranes2019

    • Author(s)
      Andoh Yoshimichi, Hayakawa Shiho, Okazaki Susumu
    • Organizer
      The 5th International Conference on Molecular Simulation
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 次期スパコン「富岳」での大規模・長時間分子動力学計算実現のためのソフトウェアMODYLASの性能向上2019

    • Author(s)
      安藤嘉倫、 坂下達哉、 張家超、 朱喆、 浦野諒、 藤本和士、 吉井範行、 岡崎進
    • Organizer
      第33回分子シミュレーション討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 非対称な脂質組成を持った脂質二重層膜モデル内での脂質分子側方凝集に関する理論的研究2019

    • Author(s)
      安藤 嘉倫, 早川 志保, 岡崎 進
    • Organizer
      第10回生体界面研究会
    • Related Report
      2018 Research-status Report
  • [Presentation] 汎用分子動力学計算ソフトウェアMODYLASへの自動チューニング技術適用の展望2019

    • Author(s)
      安藤 嘉倫
    • Organizer
      第10回自動チューニング技術の現状と応用に関するシンポジウム
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 脂質組成に非対称性をもつモデル脂質二重膜の分子動力学計算2018

    • Author(s)
      安藤 嘉倫, 早川 志保, 岡崎 進
    • Organizer
      第12回分子科学討論会2018
    • Related Report
      2018 Research-status Report
  • [Presentation] Yoshimichi Andoh, Shiho Hayakawa, Susumu Okazaki2018

    • Author(s)
      Molecular dynamics study on lipid bilayers with asymmetric lipid composition modeling cell plasma membranes
    • Organizer
      Joint Conference of EMLG/JMLG Annual Meeting 2018 and 41st Symposium on Solution Chemistry of Japan
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Ayato Matsuoka, Yoshimichi Andoh, Susumu Okazaki2018

    • Author(s)
      Solvent effect on lateral interaction between two cholesterol molecules in lipid bilayers
    • Organizer
      Joint Conference of EMLG/JMLG Annual Meeting 2018 and 41st Symposium on Solution Chemistry of Japan
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 大規模分子動力学計算高速化のための新規MPI通信方法の開発2018

    • Author(s)
      安藤 嘉倫, 坂下 達哉, 吉井 範行, 岡崎 進
    • Organizer
      第32回分子シミュレーション討論会
    • Related Report
      2018 Research-status Report
  • [Presentation] 脂質二重層膜中のコレステロール二分子間側方相互作用にリン脂質および水が果たす役割の解明2018

    • Author(s)
      松岡漢斗, 安藤嘉倫, 岡崎進
    • Organizer
      第32回分子シミュレーション討論会
    • Related Report
      2018 Research-status Report
  • [Presentation] Recent developments of molecular dynamics calculation software MODYLAS2018

    • Author(s)
      Andoh Yoshimichi
    • Organizer
      5th ADAC workshop
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 細胞膜の外単層膜と内単層膜間での膜物性の違いに関する研究2017

    • Author(s)
      早川志保, 安藤嘉倫, 岡崎進
    • Organizer
      第11回分子科学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] 脂質組成の非対称性を考慮したモデル脂質二重膜の分子動力学計算2017

    • Author(s)
      早川志保, 安藤嘉倫, 岡崎進
    • Organizer
      第11回分子科学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] Molecular dynamics study of differences in membrane properties between outer and inner leaflets of cell plasma membranes2017

    • Author(s)
      Andoh Yoshimichi, Hayakawa Shiho, Okazaki Suzumu
    • Organizer
      Joint EMLG/JMLG Meeting 2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] 脂質組成の非対称性を考慮したモデル脂質二重膜の分子動力学計算2017

    • Author(s)
      安藤嘉倫, 早川志保, 岡崎進
    • Organizer
      第40回溶液化学シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] 脂質二重膜中のコレステロール2分子間側方相互作用への溶媒効果の解明2017

    • Author(s)
      松岡漢斗,安藤嘉倫,岡崎進
    • Organizer
      第31回分子シミュレーション討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] 細胞膜の外単層膜と内単層膜間での膜物性の違いに関する研究2017

    • Author(s)
      早川志保, 安藤嘉倫, 岡崎進
    • Organizer
      第31回分子シミュレーション討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] マルチタイムステップ数値積分法(RESPA) に基 づく分子動力学計算での圧力値算出における問題2016

    • Author(s)
      安藤嘉倫, 吉井範行, 山田篤志, 岡崎進
    • Organizer
      第30 回分子シミュレーション討論会
    • Place of Presentation
      大阪
    • Year and Date
      2016-11-30
    • Related Report
      2016 Research-status Report
  • [Presentation] リン脂質二重層膜中でのコレステロール間側方相互作用のリン脂質種依存性2016

    • Author(s)
      松岡漢斗, 安藤嘉倫, 岡崎進
    • Organizer
      第30 回分子シミュレーション討論会
    • Place of Presentation
      大阪
    • Year and Date
      2016-11-30
    • Related Report
      2016 Research-status Report
  • [Presentation] 親水性および疎水性の異なる直鎖界面活性剤分子添加によるDMPC 脂質二重層膜の物性変化2016

    • Author(s)
      鬼頭咲帆, 安藤嘉倫, 岡崎進
    • Organizer
      第39回溶液化学シンポジウム
    • Place of Presentation
      筑波
    • Year and Date
      2016-11-09
    • Related Report
      2016 Research-status Report
  • [Presentation] リン脂質二重層膜中でのコレステロール間側方相互作用のリン脂質種依存性2016

    • Author(s)
      松岡漢斗, 安藤嘉倫, 岡崎進
    • Organizer
      第39回溶液化学シンポジウム
    • Place of Presentation
      筑波
    • Year and Date
      2016-11-09
    • Related Report
      2016 Research-status Report
  • [Presentation] An attempt to estimate correct atomic pressure in the multiple time-step integration algorithm2016

    • Author(s)
      Y. Andoh, N. Yoshii, A. Yamada, S. Okazaki
    • Organizer
      The 4th International Conference on Molecular Simulation
    • Place of Presentation
      Shanghai
    • Year and Date
      2016-10-23
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 肝臓細胞膜を模した脂質二重層膜の全原子分子動力学計算2016

    • Author(s)
      安藤嘉倫, 青木則之, 岡崎進
    • Organizer
      第10回分子科学討論会
    • Place of Presentation
      神戸
    • Year and Date
      2016-09-13
    • Related Report
      2016 Research-status Report
  • [Book] The Art of High Performance Computing for Computational Science: Advanced techniques and examples for materials science, vol. 2, 117-157. Acceleration of Classical Molecular Dynamics Simulations2019

    • Author(s)
      M. Geshi (Ed.), Y Andoh, N Yoshii, J Jung, Y Sugita (Chapter 5)
    • Total Pages
      41
    • Publisher
      Springer Singapore
    • ISBN
      9789811398018
    • Related Report
      2019 Annual Research Report
  • [Book] 月刊細胞 50巻 (3), 43-44. 分子シミュレーションによる非対称な脂質組成をもった脂質二重層膜物性の解明2018

    • Author(s)
      安藤嘉倫
    • Total Pages
      2
    • Publisher
      ニューサイエンス社
    • Related Report
      2017 Research-status Report
  • [Book] 計算科学のためのHPC技術22017

    • Author(s)
      下司 雅章(編)、安藤嘉倫(第6章分担)
    • Total Pages
      32
    • Publisher
      大阪大学出版会
    • ISBN
      9784872595871
    • Related Report
      2017 Research-status Report
  • [Remarks] 名古屋大学 教員情報検索

    • URL

      http://profs.provost.nagoya-u.ac.jp/view/html/100007950_ja.html

    • Related Report
      2018 Research-status Report

URL: 

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

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