Evidence for phenylalanine zipper-mediated dimerization in the X-ray crystal structure of a magainin 2 analogue

Abstract

High-resolution structure elucidation has been challenging for the large group of host-defense peptides that form helices on or within membranes but do not manifest a strong folding propensity in aqueous solution. Here we report the crystal structure of an analogue of the widely studied host-defense peptide magainin 2. Magainin 2 (S8A, G13A, G18A) is a designed variant that displays enhanced antibacterial activity relative to the natural peptide. The crystal structure of magainin 2 (S8A, G13A, G18A), obtained for the racemic form, features a dimerization mode that has previously been proposed to play a role in the antibacterial activity of magainin 2 and related peptides.

Figure 1

Sequences of magainin 2 and several designed analogues. Positions of amino acid substitutions, relative to magainin 2, are shown in red.

Figure 2

Ala^8,13,18-magainin is α-helical under the crystallization condition. Circular dichroism (CD) spectra of L- and D- ala^8,13,18-magainin peptides. All solutions contained 0.1 M sodium citrate, pH 5.6.

Figure 3

Crystal structure of Ala^8,13,18-magainin 2. (A) Residues 1-22 of Ala^8,13,18-magainin 2 are incorporated into a single α-helix. (B) The helical conformation of Ala^8,13,18-magainin is globally amphiphilic. All hydrophilic side chains (green) are clustered along one side of the helix, and nearly all of the hydrophobic side chains (blue) are clustered on the opposite side of the helix.

Figure 4

(A) Dimeric association of L-Ala^8,13,18 magainin 2 and intercalated phenylalanine side chains. 2Fo-Fc electron density corresponding to side chain atoms is shown at a contour of 1.5σ. (B) Crystal packing between dimers of L- and D-Ala^8,13,18-magainin 2 (blue and yellow, respectively) results in burial of hydrophobic surfaces.