High-Resolution Structures and Orientations of Antimicrobial Peptides Piscidin 1 and Piscidin 3 in Fluid Bilayers Reveal Tilting, Kinking, and Bilayer Immersion

While antimicrobial peptides (AMPs) have been widely investigated as potential therapeutics, high-resolution structures obtained under biologically relevant conditions are lacking. Here, the high-resolution structures of the homologous 22-residue long AMPs piscidin 1 (p1) and piscidin 3 (p3) are determined in fluid-phase 3:1 phosphatidylcholine/phosphatidylglycerol (PC/PG) and 1:1 phosphatidylethanolamine/phosphatidylglycerol (PE/PG) bilayers to identify molecular features important for membrane destabilization in bacterial cell membrane mimics. Structural refinement of H-1-N-15 dipolar couplings and N-15 chemical shifts measured by oriented sample solid-state NMR and all-atom molecular dynamics (MD) simulations provide structural and orientational information of high precision and accuracy about these interfacially bound alpha-helical peptides. The tilt of the helical axis, tau, is between 83 degrees and 93 degrees with respect to the bilayer normal for all systems and analysis methods. The average azimuthal rotation, rho, is 235 degrees, which results in burial of hydrophobic residues in the bilayer. The refined NMR and MD structures reveal a slight kink at G13 that delineates two helical segments characterized by a small difference in their T angles (<10 degrees) and significant difference in their rho angles (similar to 25 degrees). Remarkably, the kink, at the end of a G(X)(4)G motif highly conserved among members of the piscidin family, allows p1 and p3 to adopt rho angles that maximize their hydrophobic moments. Two structural features differentiate the more potent pl from p3: p1 has a larger rho angle and less N-terminal fraying. The peptides have comparable depths of insertion in PC/PG, but p3 is 1.2 angstrom more deeply inserted than p1 in PE/PG. In contrast to the ideal a-helical structures typically assumed in mechanistic models of AMPs, p1 and p3 adopt disrupted alpha-helical backbones that correct for differences in the amphipathicity of their N- and C-ends, and their centers of mass lie similar to 1.2-3.6 angstrom below the plane defined by the C2 atoms of the lipid acyl chains.