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

Abstract

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 guanidinium 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 a model prokaryotic membrane system (POPC/POPG) interacting with two different mutants of a prototypical AMP, KR-12: one with all lysine residues mutated to arginine (R-KR12), and one with all arginine residues mutated to lysine (K-KR12). Simulations show that both peptides partition analogously to the bilayer and display similar preferences 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, as well as stronger peptide-bilayer hydrogen bonds, resulting in considerably longer interaction times. Additional simulations with single and double methylated R-KR12 mutants show that the strength of these hydrogen bonds, rather than the number of bonds formed, is responsible for the extensive peptide-bilayer interaction seen in the R-KR12 system. Finally, free energy simulations reveal that both peptides are unstructured in solution and adopt a highly helical amphipathic structure when inserted into the bilayer. Overall, these results help elucidate the greater toxicity of arginine-rich AMPs and offer potential insights for designing more potent analogues in the future.