The Disruptive State of the Membrane Active Antimicrobial Peptide Piscidin 1 Investigated by Multi-μS All-Atom Simulations and Solid-State NMR: Surface Defects are Favored over Stable Pores

Abstract

Antimicrobial peptides (AMPs) that disrupt bacterial inner membranes are promising therapeutics against the growing number of antibiotic-resistant bacteria. The mechanism of membrane disruption by the AMP piscidin 1 was examined with multi-microsecond all-atom molecular dynamics simulations and solid-state NMR spectroscopy. A 14-μs control simulation of an archetype barrel-stave alamethicin pore validated the methodology. The primary simulation was initialized with 20 peptides in 4 barrel-stave pores in a fully hydrated POPC/POPG bilayer. The 4 pores relaxed to toroidal by 200 ns, only one pore containing 2 transmembrane helices remained at 20 μs, and none of the 18 peptides released to the surface reinserted to form pores. These results imply that the population of toroidal pores is <4% (consistent with 15N NMR). This simulation and a separate 2.5-μs trajectory of surface-bound peptides show large distortions of the bilayer/water interface (consistent with 31P NMR), which could be responsible for membrane disruption by piscidin.