All-Atom Molecular Dynamic Simulations of Piscidin 1 and Piscidin 3 in Lipid Bilayers

Piscidin 1 (p1) and the less active piscidin 3 (p3) are α-helical, amphipathic, and cationic antimicrobial peptides (AMPs). They adsorb onto the anionic outer membrane of pathogenic species and induce leakage beyond a threshold peptide concentration. While different mechanisms of membrane disruption have been proposed, an atomic-level description of the events leading to cell death is lacking and elucidating these mechanisms aid in the antibiotic design. Here, p1 and p3 in three different lipid bilayers (3:1 DMPC:DMPG, 1:1 POPE:POPG, and 4:1 POPC:Cholesterol) are studied by solid-state NMR spectroscopy and all-atom molecular dynamics (MD) simulations to identify factors that differentiate the structure, orientation, and depth of insertion of piscidin. 15N-H dipolar coupling calculated for the membrane-bound peptides are in good agreement with values measured by NMR. The tilts of the peptides in the bilayer (τ) determined by fitting dipolar waves to the coupling data agree with those of the NMR-derived and MD-average structures when deviation from an ideal α-helix is included; when ideal values are assumed for the dipolar wave fitting, deviations range from 4° to 6°. While the instantaneous tilt fluctuates approximately ± 10° in the simulation, averaging over a time series of structures yields the same tilt as one for an average structure (as might be obtained from NMR-based structure determination). This is because τ ≈ 90. For transmembrane helices (τ ≈ 0), the average over a MD time series may be significantly different from a single averaged structure. Correlation between τ and the depth of insertion for p1 shows that as the peptide becomes more buried, the peptide tilts to bury the C-terminus. Moreover, the depth of insertion is 0.5 to 1.5A greater for p3 than p1, which likely reduces the activity of p3.