Surface Binding of Alamethicin Stabilizes its Helical Structure: Molecular Dynamics Simulations

AbstractAlamethicin is an amphipathic α-helical peptide that forms ion channels. An early event in channel formation is believed to be the binding of alamethicin to the surface of a lipid bilayer. Molecular dynamics simulations are used to compare the structural and dynamic properties of alamethicin in water and alamethicin bound to the surface of a phosphatidylcholine bilayer. The bilayer surface simulation corresponded to a loosely bound alamethicin molecule that interacted with lipid headgroups but did not penetrate the hydrophobic core of the bilayer. Both simulations started with the peptide molecule in an α-helical conformation and lasted 2ns. In water, the helix started to unfold after ∼300ps and by the end of the simulation only the N-terminal region of the peptide remained α-helical and the molecule had collapsed into a more compact form. At the surface of the bilayer, loss of helicity was restricted to the C-terminal third of the molecule and the rod-shaped structure of the peptide was retained. In the surface simulation about 10% of the peptide/water H-bonds were replaced by peptide/lipid H-bonds. These simulations suggest that some degree of stabilization of an amphipathic α-helix occurs at a bilayer surface even without interactions between hydrophobic side chains and the acyl chain core of the bilayer