Molecular Basis for the Role of Cationic Residues in Antimicrobial Peptide Interactions

Antimicrobial peptides (AMPs) play a vital role in the innate immune response and represent promising templates for developing broad-spectrum alternatives to conventional antibiotics. Most AMPs are charged amino acid sequences that interact more strongly with negatively charged prokaryotic membranes than net neutral eukaryotic ones. Both AMPs and synthetic analogues with arginine-like guanidine groups show a greater toxic effect against bacteria than those with lysine-like amine groups, though the atomistic mechanism for this increase in potency remains unclear. To examine this, we have conducted comparative molecular dynamics simulations of two mutants of a model AMP, KR-12: one with all lysine residues mutated to arginine (R-KR12), and one with all arginine residues mutated to lysine (K-KR12). Both peptides were simulated in two model membrane systems: prokaryotic (POPC/POPG) or eukaryotic (pure POPC). Simulations show that both peptides demonstrate similar favorability for the POPC/POPG bilayer over POPC, partition analogously to the bilayer, and display a preference for forming hydrogen bonds with the anionic POPGs. However, R-KR12 has a significantly higher propensity for hydrogen bonding with the bilayer than K-KR12, resulting in considerably longer interaction times. Overall, these results help elucidate the greater toxicity of arginine-rich AMPs and offer potential insights for designing more potent therapeutic analogues in the future.