Issue 17, 2014

Free energy analysis along the stalk mechanism of membrane fusion

Abstract

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.

Graphical abstract: Free energy analysis along the stalk mechanism of membrane fusion

Supplementary files

Article information

Article type
Paper
Submitted
05 Sep 2013
Accepted
11 Dec 2013
First published
23 Jan 2014

Soft Matter, 2014,10, 3048-3054

Free energy analysis along the stalk mechanism of membrane fusion

S. Kawamoto and W. Shinoda, Soft Matter, 2014, 10, 3048 DOI: 10.1039/C3SM52344F

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