Probing the disparate effects of arginine and lysine residues on antimicrobial peptide/bilayer association

Abstract

Antimicrobial peptides (AMPs) are key components of the innate immune response and represent promising templates for the development of broad-spectrum alternatives to conventional antibiotics. Most AMPs are short, cationic peptides that interact more strongly with negatively charged prokaryotic membranes than net neutral eukaryotic ones. Both AMPs and synthetic analogues with arginine-like side chains are more active against bacteria than those with lysine-like amine groups, though the atomistic mechanism for this increase in potency remains unclear. To examine this, we conducted comparative molecular dynamics simulations of a model negatively-charged membrane system interacting with two mutants of the AMP KR-12: one with lysine residues mutated to arginines (R-KR12) and one with arginine residues mutated to lysine (K-KR12). Simulations show that both partition analogously to the bilayer and display similar preferences for hydrogen bonding with the anionic POPGs. However, R-KR12 binds stronger to the bilayer than K-KR12 and forms significantly more hydrogen bonds, leading to considerably longer interaction times. Additional simulations with methylated R-KR12 and charge-modified K-KR12 mutants show that the extensive interaction seen in the R-KR12 system is partly due to arginines strong atomic charge distribution, rather than being purely an effect of the greater number of hydrogen bond donors. Finally, free energy simulations reveal that both peptides are disordered in solution but form an amphipathic α-helix when inserted into the bilayer headgroup region. Overall, these results highlight the role of charge and hydrogen bond strength in peptide bilayer insertion, and offer potential insights for designing more potent analogues in the future.

Cartilage penetrating cationic peptide carriers for applications in drug delivery to avascular negatively charged tissues

“…The work highlights that while the net charge of a carrier can help predict its electro-diffusive behavior, the type of amino acid moiety in the peptide [43, 47, 48] and its spatial distribution [33, 49–51] are also important to consider. The change in uptake of arginine rich CPCs between 50% and 90% GAG depletion, was less significant than the change from healthy to 50% GAG depleted cartilage.…”

Arginine‐enveloped virus inactivation and potential mechanisms

“…The zwitterionic properties of arginine and butyroyl arginine likely enhance viral inactivation through strong lipid binding and self‐interactions. Alone, guanidinium is able to form multiple hydrogen bonds with lipids . However, in combination with the strong charge distribution of arginine, the hydrogen binding of guanidinium to lipids is strengthened .…”

“…In support of Hypothesis 2, arginine does interact with the lipid bilayer through binding and lipid deformations. Specifically, arginine‐rich peptides deform membranes in order to translocate into the cell for drug delivery . At low arginine concentrations, endocytosis has been observed as the sole route for arginine peptide translocation .…”

“…Although arginine peptides do have a different charge/size ratio in comparison to a single arginine molecule, the guanidinium group on arginine is a large component of peptide activity . Membrane deformations result from the guanidinium moiety binding to negative charges on the lipid bilayer, and/or the hydrophilic peptides interacting with the hydrophobic lipids . Arginine side chains also maintain their charge when exposed to the hydrophobic membrane environment where no other amino acid can, aiding further in membrane deformations .…”

“…In several studies, arginine‐rich peptides have been shown to cross the lipid bilayer through the formation of a water pore . Pores are hypothesized to form in a similar manner to membrane deformations, through electrostatic or hydrophilic interactions . For example, preferential binding to negative charges in zwitterionic lipids (common in mammalian membranes) results in lipid sorting and membrane tension.…”