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Multiscale Molecular Modeling of Membrane Fusion

Research Project

Project/Area Number 23350014
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical chemistry
Research InstitutionNagoya University (2013-2014)
National Institute of Advanced Industrial Science and Technology (2011-2012)

Principal Investigator

SHINODA Wataru  名古屋大学, 工学(系)研究科(研究院), 准教授 (70357193)

Co-Investigator(Kenkyū-buntansha) TSUZUKI Seiji  産業技術総合研究所, 上級主任研究員 (10357527)
Co-Investigator(Renkei-kenkyūsha) KLEIN Michael  Temple University, College of Science and Technology, Dean
Project Period (FY) 2011-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000)
Fiscal Year 2014: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2013: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2012: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2011: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Keywords膜融合 / 分子シミュレーション / 自由エネルギー / 粗視化モデル / 生体膜融合 / 生物物理 / 分子動力学シミュレーション / ストーク / ストレス / 膜弾性 / ベシクル間相互作用 / 脂質混合効果
Outline of Final Research Achievements

In order to understand the molecular mechanism in the membrane fusion process, a series of molecular dynamics simulation of membrane systems including vesicles has been conducted using a newly developed (semi)-quantitative coarse-grained molecular model on the basis of all-atom molecular dynamics trajectories. Interaction between curved membranes such as vesicles and fusion process has been investigated in terms of free energy analysis. Effects of lipid components and the presence of the peptides have been analyzed in the free energy calculations. New methods to accurately evaluate the line tension and curvature moduli of membranes have been also developed. The calculated physical constants were used to compare a simple continuum model and molecular dynamics for the free energy barriers of membrane fusion, which elucidated that the elastic energy contribution explains the fusion energy barrier only qualitatively.

Report

(5 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (36 results)

All 2015 2014 2013 2012 2011

All Journal Article (12 results) (of which Peer Reviewed: 12 results,  Acknowledgement Compliant: 2 results) Presentation (24 results) (of which Invited: 10 results)

  • [Journal Article] Precise Calculation of the Local Pressure Tensor in Cartesian and Spherical Coordinates in LAMMPS2015

    • Author(s)
      中村壮伸、川本周平、篠田 渉
    • Journal Title

      Computer Physics Communications

      Volume: 190 Pages: 120-128

    • DOI

      10.1016/j.cpc.2014.11.017

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Free energy analysis along the stalk mechanism of membrane fusion2014

    • Author(s)
      川本周平、篠田 渉
    • Journal Title

      Soft Matter

      Volume: 10 Issue: 17 Pages: 3048-3054

    • DOI

      10.1039/c3sm52344f

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] 脂質膜透過現象の分子シミュレーションによる研究2014

    • Author(s)
      篠田 渉
    • Journal Title

      膜(MEMBRANE)

      Volume: 39 Pages: 372-378

    • NAID

      130005069452

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effective interaction between small unilamellar vesicles as probed by coarse-grained molecular dynamics simulations2014

    • Author(s)
      篠田 渉、Michael L Klein
    • Journal Title

      Pure and Applied Chemistry

      Volume: 86 Issue: 2 Pages: 215-222

    • DOI

      10.1515/pac-2014-5023

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation2013

    • Author(s)
      川本周平、中村壮伸、Steven O. Nilesen、篠田 渉
    • Journal Title

      Journal of Chemical Physics

      Volume: 139 Issue: 3

    • DOI

      10.1063/1.4811677

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Probing the structure of PEGylated-lipid assemblies by coarse-grained molecular dynamics2013

    • Author(s)
      篠田 渉、Dennis E. Discher、Michael L. Klein、Sharon M. Loverde
    • Journal Title

      Soft Matter

      Volume: 9 Issue: 48 Pages: 11549-11556

    • DOI

      10.1039/c3sm52290c

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory2013

    • Author(s)
      中村壮伸、篠田 渉
    • Journal Title

      Journal of Chemical Physics

      Volume: 138 Issue: 12

    • DOI

      10.1063/1.4795579

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 脂質膜の粗視化分子シミュレーション2013

    • Author(s)
      篠田 渉
    • Journal Title

      Colloid & Interface Communication

      Volume: 12 Pages: 55-61

    • NAID

      40020187316

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computer simulation studies of self-assembling macromolecules2012

    • Author(s)
      篠田 渉、Russell DeVane、Michael L Klein
    • Journal Title

      Current Opinions in Structural Biology

      Volume: 22 Issue: 2 Pages: 175-186

    • DOI

      10.1016/j.sbi.2012.01.011

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Free energy analysis of vesicle-to-bicelle transformation2011

    • Author(s)
      篠田渉、中村壮伸、Steven O.Nielsen
    • Journal Title

      Soft Matter

      Volume: 7 Issue: 19 Pages: 9012-9020

    • DOI

      10.1039/c1sm05404j

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Novel numerical method for calculating the pressure tensor in spherical coordinates for molecular systems2011

    • Author(s)
      中村壮伸、篠田渉、池庄司民夫
    • Journal Title

      Journal of Chemical Physics

      Volume: 135 Issue: 9

    • DOI

      10.1063/1.3626410

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers : A Molecular Dynamics Study2011

    • Author(s)
      斎藤大明、篠田渉
    • Journal Title

      Journal of Physical Chemistry B

      Volume: 115 Issue: 51 Pages: 15241-15250

    • DOI

      10.1021/jp201611p

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] 膜の粗視化分子シミュレーション2015

    • Author(s)
      篠田 渉
    • Organizer
      第359回CBI学会講演会「粗視化による生体分子系のシミュレーション」
    • Place of Presentation
      東大、東京
    • Year and Date
      2015-02-24
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 膜タンパクの粗視化モデル2014

    • Author(s)
      川本周平, Giacomo Fiorin, Chris MacDermaid, Russell DeVane, 篠田渉, Michael L. Klein
    • Organizer
      第28回分子シミュレーション討論会
    • Place of Presentation
      仙台
    • Year and Date
      2014-11-12 – 2014-11-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] Membrane Fusion: Free Energy Analysis2014

    • Author(s)
      篠田 渉、川本周平、Michael L. Klein
    • Organizer
      International Symposium on Extended Molecular Dynamics and Enhanced Sampling: Nosé Dynamics 30 Years (NOSE30)
    • Place of Presentation
      慶應大、東京
    • Year and Date
      2014-11-10 – 2014-11-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] Coarse-grained model of membrane protein2014

    • Author(s)
      川本周平, Giacomo Fiorin, Chris MacDermaid, Russell DeVane, 篠田渉, Michael L. Klein
    • Organizer
      International Symposium on Extended Molecular Dynamics and Enhanced Sampling: Nosé Dynamics 30 Years (NOSE30)
    • Place of Presentation
      慶應大、東京
    • Year and Date
      2014-11-10 – 2014-11-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] Free Energy Analysis of Membrane Fusion2014

    • Author(s)
      川本周平、篠田渉、Michael L Klein
    • Organizer
      XXVI IUPAP Conference on Computational Physics, CCP2014
    • Place of Presentation
      Boston, USA
    • Year and Date
      2014-08-11 – 2014-08-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] 膜の柔らかさと機能:分子シミュレーションによるアプローチ2014

    • Author(s)
      篠田 渉
    • Organizer
      日本化学会第94春期年会
    • Place of Presentation
      名古屋
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 膜構造形成の分子シミュレーション2014

    • Author(s)
      篠田 渉
    • Organizer
      日本物理学会第69回年次大会
    • Place of Presentation
      神奈川
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Coarse-grained molecular dynamics study on stability of liposome and effect of carbon nanoparticles2013

    • Author(s)
      篠田 渉
    • Organizer
      246th ACS National Meeting
    • Place of Presentation
      Indianapolis, IN, USA
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Free Energy Analysis of Topological and Morphological Changes in Lipid Membranes: Molecular Dynamics Study2013

    • Author(s)
      篠田 渉、川本周平
    • Organizer
      3rd International Conference on Molecular Simulation 2013 (ICMS2013)
    • Place of Presentation
      神戸
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Coarse-Grained molecular Dynamics Study of Self-assembled Macromolecules2013

    • Author(s)
      篠田 渉
    • Organizer
      International Conference on Biomolecular Simulations & Dynamics
    • Place of Presentation
      Chennai, India
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Molecular Dynamics Study of Lipid Self-Assembly2013

    • Author(s)
      篠田 渉
    • Organizer
      33rd International Conference on Solution Chemistry
    • Place of Presentation
      京都
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Coarse-Grained Molecular Simulation of Lipid Self-Assembly2013

    • Author(s)
      篠田 渉
    • Organizer
      APS March Meeting 2013
    • Place of Presentation
      Baltimore, MD, USA
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 膜融合の分子メカニズムの解析2012

    • Author(s)
      川本周平、篠田渉
    • Organizer
      第67回日本物理学会
    • Place of Presentation
      関西学院大学(大阪)
    • Year and Date
      2012-03-24
    • Related Report
      2011 Annual Research Report
  • [Presentation] Molecular Dynamics Study of Self-Assembly of Amphiphiles2012

    • Author(s)
      篠田渉
    • Organizer
      International Workshop : Mathematical approach to emerging topics in Material Science 2012
    • Place of Presentation
      東北大学(宮城)(招待講演)
    • Year and Date
      2012-02-19
    • Related Report
      2011 Annual Research Report
  • [Presentation] Molecular Dynamics Study of Effective Interaction Between Liposomes2012

    • Author(s)
      篠田 渉
    • Organizer
      IACIS2012 (International Association of Colloid and Interface Scientists, Conference)
    • Place of Presentation
      仙台
    • Related Report
      2012 Annual Research Report
  • [Presentation] Effect of lipid components on the stability of stalk of membrane fusion2012

    • Author(s)
      川本周平、篠田 渉
    • Organizer
      IACIS2012 (International Association of Colloid and Interface Scientists, Conference)
    • Place of Presentation
      仙台
    • Related Report
      2012 Annual Research Report
  • [Presentation] Coarse Grained Molecular Simulations of Lipid Self-Assembly2012

    • Author(s)
      篠田 渉
    • Organizer
      Bridging Scales in Computational Polymer Chemistry
    • Place of Presentation
      Providence, RI, USA
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 生体膜融合における融合細孔の形成過程のシミュレーション2012

    • Author(s)
      川本周平、篠田 渉
    • Organizer
      日本物理学会2012秋季大会
    • Place of Presentation
      横浜
    • Related Report
      2012 Annual Research Report
  • [Presentation] Morphology change of fusion stalk of lipid bilayer membrane studied by molecular dynamics simulation2012

    • Author(s)
      川本周平、篠田 渉
    • Organizer
      第50回日本物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Annual Research Report
  • [Presentation] 膜融合過程の自由エネルギー解析2012

    • Author(s)
      川本周平、篠田 渉
    • Organizer
      第26回分子シミュレーション討論会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] 曲げ応力による膜の曲げ弾性係数の解析手法2012

    • Author(s)
      川本周平、篠田 渉
    • Organizer
      第26回分子シミュレーション討論会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] 階層的分子シミュレーションによる脂質膜・ベシクルの研究2012

    • Author(s)
      篠田 渉
    • Organizer
      第16回ペプチドフォーラム
    • Place of Presentation
      京都
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Stability of Liposome : Free Energy Analysis of Vesicle-to-Bicelle Transformation2011

    • Author(s)
      篠田渉、中村壮伸、Steven O Nielsen
    • Organizer
      Conference on Computational Physics 2011
    • Place of Presentation
      Gatlinburg, Tennessee
    • Year and Date
      2011-11-02
    • Related Report
      2011 Annual Research Report
  • [Presentation] Molecular Simulation of Liposomal Membranes2011

    • Author(s)
      篠田渉
    • Organizer
      The 2nd international symposium on "Multi-scale Simulations of Biological and Soft Materials" (MSBSM 2011)
    • Place of Presentation
      京都大学芝蘭会館稲盛ホール(京都)(招待講演)
    • Year and Date
      2011-09-10
    • Related Report
      2011 Annual Research Report

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Published: 2011-04-06   Modified: 2019-07-29  

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