On Bilayer Deformation Energetics With and Without Gramicidin A Channel

Lipid membranes are not simply passive barriers. Embedded proteins are coupled to the membrane and can deform the surrounding bilayer, which incurs an energetic penalty. To minimize these penalties, proteins are known to tilt, aggregate, and experience major conformation changes. The degree to which the protein is influenced by the bilayer is dependent on the bilayer material properties and protein-bilayer coupling strength, for example. In this dissertation, the effects of bilayer material properties and protein-bilayer coupling are detailed using gramicidin A channel. This simple channel experiences one major conformational change, its transmembrane dimerization, which produces a bilayer deformation if the bilayer and dimer do not have the same hydrophobic lengths. Herein, molecular dynamics simulations are used to describe bilayer material properties, channel-bilayer coupling, and general lipid energetics with and without gramicidin A