De novo design of a peptide which partitions between water and phospholipid bilayers as a monomeric alpha-helix.

Abstract

To dissect the determinants of protein insertion into membranes, we designed a model peptide which partitions between water and phospholipid bilayers as an alpha-helical monomer. We used a simplex method to optimize the 'a, d hydrophobicity' and 'e, g charge' of a series of five peptides, where 'abcdefg' correspond to the positions in two turns of an alpha-helix. Circular dichroism and analytical ultra-centrifugation experiments showed that the final peptide (helix5) is monomeric and has an alpha-helix content of approximately 89% at 0 degrees C in aqueous solution. In the presence of large unilamellar vesicles (LUVs), helix5 partitions between the aqueous and membranous phases with a partition constant well suited for measurements by electron paramagnetic resonance (EPR) spectroscopy. EPR power saturation experiments with a cysteine-scanning strategy showed that the alpha-helicity of helix5 is conserved upon binding to LUVs and that the alpha-helix binds parallel to the membrane surface with the central axis approximately 5 A below the lipid phosphate groups. Helix5 should be a useful model peptide for studies aimed at dissecting the determinants of the membrane binding of alpha-helices. The simplex-based strategy may be useful in the rational design of proteins when desired structural or partitioning properties cannot be selected or screened from libraries.