The cell membrane is arguably one of the most important and complex features of a cell, serving to demarcate “self” from “environment” and... Show moreThe cell membrane is arguably one of the most important and complex features of a cell, serving to demarcate “self” from “environment” and selectively controlling the flow of material in and out of the cell. Bacterial cell membranes are of additional interest since they serve as the first point of contact for antibiotic drugs or other antimicrobial agents. In this work, I use atomistic molecular dynamics simulations to study factors that alter bacterial susceptibility to antimicrobial agents and their environment, with the goal of better understanding how bacteria are able to modulate their sensitivity.First, I present results from a series of simulations of antimicrobial peptides (AMP) interacting with phospholipid bilayers to elucidate the observed interaction differences between arginine and lysine-containing AMPs. Simulations show that the extensive interaction with arginine is due in part to arginine's strong atomic charge distribution, rather than being purely an effect of the greater hydrogen bond capacity. 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.Next, the effects of bacterial lipopolysaccharide (LPS) modifications are examined, first to understand study how three key modifications observed in S. enterica affect bilayer properties, as well as to examine the role these modifications play in AMP resistance. We hypothesize that defects at the crystalline/liquid-ordered boundary facilitate LL-37 intercalation into the outer membrane, whereas LPS modification protects against this process by having already increased crystallinity and packing efficiency. These results further improve our understanding of outer membrane chemical properties and help elucidate how outer membrane modification systems are able to alter bacterial virulence and susceptibility. Lastly, I investigate the effects of ion type and phosphate charge on four distinct LPS types. Simulations show that bilayer properties are highly influenced by the choice of cation type, ion parameterization, and phosphate group charges. Additional free energy perturbation simulations predict that the protonated LPS state should dominate at physiological pH, in contrast to the deprotonated state utilized by many LPS force fields. Overall, these results reveal inaccuracies in the existing LPS force fields and establish guidelines to better reproduce experimental LPS membrane properties. Show less
