title: Free energy calculations of gramicidin dimer dissociation.
abstract: Molecular dynamics simulations, combined with umbrella sampling, is used to study how gramicidin A (gA) dimers dissociate in the lipid bilayer. The potential of mean force and intermolecular potential energy are computed as functions of the distance between center of masses of the two gA monomers in two directions of separation: parallel to the bilayer surface and parallel to the membrane normal. Results from this study show that the dissociation of gA dimers occurs via lateral displacement of gA monomers followed by tilting of dimers with respect to the lipid bilayer normal. It is found that the dissociation energy of gA dimers in the dimyristoylphosphatidylcholine bilayer is 14 kcal mol(-1) (~22 kT), which is approximately equal to the energy of breaking six intermolecular hydrogen bonds that stabilize the gA channel dimer.
authors: Department of Electrical and Computer Engineering, University of British Columbia, 5500 - 2332 Main Mall, Vancouver, BC, V6T 1Z4 Canada.
authors: Surajith N
authors: SN
authors: Wanasundara
authors: Vikram
authors: V
authors: Krishnamurthy
authors: Shin-Ho
authors: SH
authors: Chung
mesh_terms: D019281:Dimerization; D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry; D006096:Gramicidin / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D008051:Lipid Bilayers; D006096:Gramicidin; D004134:Dimyristoylphosphatidylcholine