Calculations suggest a pathway for the transverse diffusion of a hydrophobic peptide across a lipid bilayer

Alamethicin is a hydrophobic antibiotic peptide 20 amino acids in length. I t is predominantly helical and partitions into lipid bilayers mostly in tra nsmembrane orientations. The rate of the peptide transverse diffusion (flip -flop) in palmitoyl-oleyl-phosphatidylcholine vesicles has been measured re cently and the results suggest that it involves an energy barrier, presumab ly due to the free energy of transfer of the peptide termini across the bil ayer. We used continuum-solvent model calculations, the known x-ray crystal structure of alamethicin and a simplified representation of the lipid bila yer as a slab of low dielectric constant to calculate the flip-flop rate. W e assumed that the lipids adjust rapidly to each configuration of alamethic in in the bilayer because their motions are significantly faster than the a verage peptide flip-flop time. Thus, we considered the process as a sequenc e of discrete peptide-membrane configurations, representing critical steps in the diffusion, and estimated the transmembrane flip-flop rate from the c alculated free energy of the system in each configuration. Our calculations indicate that the simplest possible pathway, i.e., the rotation of the hel ix around the bilayer midplane, involving the simultaneous burial of the tw o termini in the membrane, is energetically unfavorable. The most plausible alternative is a two-step process, comprised of a rotation of alamethicin around its C-terminus residue from the initial transmembrane orientation to a surface orientation, followed by a rotation around the N-terminus residu e from the surface to the final reversed transmembrane orientation. This pr ocess involves the burial of one terminus at a time and is much more likely than the rotation of the helix around the bilayer midplane. Our calculatio ns give flip-flop rates of similar to 10(-7)/s for this pathway, in accord with the measured value of 1.7 x 10(-6)/s.