Two approaches employing nuclear magnetic resonance (NMR) were used to investigate the transmembrane migration rate of the C- terminal end of native alamethicin and a more hydrophobic analog called L1. Native alamethicin exhibits a very slow transmembrane migration rate when bound to phosphatidylcholine vesicles, which is no greater than 1 x 10-4 min-1. This rate is much slower than expected, based on the hydrophobic partition energies of the amino acid side chains and the backbone of the exposed C-terminal end of alamethicin. The alamethicin analog L1 exhibits crossing rates that are at least 1000 times faster than that of native alamethicin. A comparison of the equilibrium positions of these two peptides shows that L1 sits ~3-4 Å, deeper in the membrane than does native alamethicin (Barranger-Mathys and Cafiso. 1996. Biochemistry. 35:489). The slow rate of alamethicin crossing can be explained if the peptide helix is irregular at its C-terminus and hydrogen bonded to solvent or lipid. We postulate that L1 does not experience as large a barrier to transport because its C-terminus is already buried within the membrane interface. This difference is most easily explained by conformational differences between L1 and alamethicin rather than differences in hydrophobicity. The results obtained here demonstrate that side-chain hydrophobicity alone cannot account for the energy barriers to peptide and protein transport across membranes.
Jayasinghe, S., Barranger-Mathys, M., Ellena, J. F., Franklin, C., & Cafiso, D. S. (1998). Structural features that modulate the transmembrane migration of a hydrophobic peptide in lipid vesicles. Biophysical Journal, 74(6), 3023–3030. https://doi.org/10.1016/S0006-3495(98)78010-5