Binding of indolicidin to the DMPC bilayer using molecular dynamics simulations

Abstract

Antimicrobial peptides (AMPs) are part of the innate immune system and fight bacterial infections by disrupting bacterial lipid bilayers or encouraging water permeation. Indolicidin, a cationic AMP with 13 amino acids, has garnered attention due to its broad-spectrum activity, unique secondary structure profile compared to other AMPs, and short sequence. We used molecular dynamics simulations to study the binding of indolicidin peptides to the DMPC bilayer. We analyzed this system by extracting the atomic coordinates as a function of time and computing the distance between indolicidin and the DMPC bilayer. We also performed secondary structure analysis to understand the effect of binding on indolicidin structure. Overall, our molecular dynamics simulations assess the physicochemical mechanisms of indolicidin’s initial docking process to the DMPC bilayer. In future studies, we will extend these simulations to establish the impact of indolicidin’s equilibrium binding profile on its antimicrobial activity.