Exploring the Mechanism of Alyteserin-1c in Gram-Positive and Gram-Negative Bacterial Membrane Models Using a Computational Approach.

Alyteserin-1c is a 23-amino-acid cationic antimicrobial peptide exhibiting greater activity against Gram-negative than Gram-positive bacteria (Conlon et al. 2009), yet the molecular basis of this differential membrane selectivity remains incompletely understood. Using all-atom molecular dynamics simulations (200 ns × 3 independent replicates per system), we examined the interactions of a pre-assembled Alyteserin-1c hexamer with simplified bilayer models representing Gram-positive (75% PG/25% PE) and Gram-negative (75% PE/25% PG) bacterial inner membranes. The hexameric assembly maintained structural stability and substantial α-helical content throughout all simulations, with oligomeric cohesion associated primarily with hydrophobic packing of residues L10, L13, V14, I17, and F6. Cationic residues K7 and K15 remained lipid-exposed with near-permanent headgroup contact occupancy, suggesting their role as principal membrane-anchoring sites. Comparative membrane analyses indicated greater lateral lipid mobility, lower bilayer density, and stronger local acyl chain perturbation in the Gram-negative membrane model, consistent with greater membrane susceptibility at lower peptide concentrations. Helix orientation and pore geometry analyses were inconsistent with stable barrel-stave transmembrane pore formation and instead supported interfacial or transient toroidal-like membrane perturbations. Transient single-file water threading was observed in the Gram-positive system, while perturbations in the Gram-negative membrane remained predominantly surface-localized. These findings provide a computationally derived mechanistic framework for the membrane selectivity of Alyteserin-1c and may inform rational design of membrane-targeting antimicrobial peptides. Given the simplified bilayer models, pre-assembled oligomeric assumption, and accessible simulation timescales, the proposed mechanisms should be interpreted as hypothesis-generating rather than definitive.