Indolicidin Interactions with Bacterial Membranes: Sequence and Secondary-Structure Effects

Abstract Purpose Antimicrobial peptides (AMPs) are promising antibiotic alternatives, yet how sequence and secondary structure tune membrane activity remains incompletely understood. Methods We performed all-atom molecular dynamics (MD) to compare, at OPM-predicted membrane-bound configurations, linear indolicidin (AMP1) and a disulfi de-stabilized cyclic analogue (AMP2) interacting with lipid bilayers representative of mammalian and bacterial inner membranes: POPC, POPS, POPG, POPE, POPC/POPG (7:3), POPC/POPS (7:3), and POPG/POPE at 1:3 (Gram-negative) and 3:1 (Gram-positive). Results Simulations reveal that cationic Arg/Lys residues drive salt-bridge formation with anionic headgroups, while Trp, Ile and Leu strengthen van der Waals (vdW) contacts with acyl chains. During the simulations, AMP1 remained within the bilayer, and its presence increased area-per-lipid while reducing thickness and order parameters, —hallmarks of destabilization, —particularly in POPG/POPE (3:1). AMP2 remained primarily associated with the membrane interface, redistributing interfacial water and counterions with limited penetration depth.AQ1 MM-GBSA decomposition indicates that electrostatic contributions dominate the peptide-bilayer interaction energy, with the strongest interaction trends for anionic membranes; AMP1 shows more favorable total interaction energies thanAMP2. The observed membrane thinning and lipid disordering accompanying AMP1’s bilayer-spanning configuration are consistent with localized disruptions associated with pore-like or interfacial insertion mechanisms, whereas AMP2’s predominantly interfacial adsorption is more consistent with a carpet-type mechanism; however, protease resistance of AMP2 may compensate for its weaker single-peptide membrane interaction trends. Conclusions These results highlight how secondary structure and residue composition jointly modulate AMP-– membrane complexation and provide design cues for optimizing potency while mitigating hemolysis.