Free energy analysis along the stalk mechanism of membrane fusion

Shuhei Kawamoto, Wataru Shinoda

Research output: Contribution to journalArticlepeer-review

43 Citations (Scopus)


The free energy profile of the stalk model of membrane fusion has been calculated using coarse-grained molecular dynamics simulations. The proposed method guides the lipid configuration using a guiding wall potential to make the transition from two apposed membranes to a stalk and a fusion pore. The free energy profile is obtained with a thermodynamic integration scheme using the mean force working on the guiding wall as a response of the system. We applied the method to two apposed flat bilayers composed of dioleoyl phosphatidylethanolamine/dioleoyl phosphatidylcholine expanding over the simulation box under the periodic boundary conditions. The two transition states are identified as pre-stalk and pre-pore states. The free energy barrier for the latter is confirmed to be in good agreement with that estimated by the pulling method. The present method provides a practical way to calculate the free energy profile along the stalk mechanism. This journal is

Original languageEnglish
Pages (from-to)3048-3054
Number of pages7
JournalSoft Matter
Issue number17
Publication statusPublished - May 7 2014
Externally publishedYes

ASJC Scopus subject areas

  • Chemistry(all)
  • Condensed Matter Physics


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