Complexity matters: Polymyxins and the E. coli cell envelope

We present a computational study of the effects of biomolecular crowding on the behaviour of the antimicrobial peptides (AMPs) polymyxin B1 (PMB) and polymyxin E (PME) within the periplasm of E. coli. We have employed atomistic molecular dynamics simulations to explore the nature of the interaction between these AMPs and both Braun's lipoprotein (BLP) and the peptidoglycan (PGN) cell wall in models of the periplasm that are crowded to different extents. The most crowded model of the periplasm contained a range of osmolytes as well as crowding proteins (ubiquitin) in addition to the peptides, cell wall and Braun's lipoprotein. All systems also included a model of the E. coli outer membrane. Overall, three x 250 ns replicates of each system were performed (with both just neutralising ions and also 150 mMol concentration of NaCl); giving a total simulation time of 10.5 microseconds. Our results show the importance of D-phenylalanine to the primarily hydrophobic interaction between PMB and BLP; we characterise the change in this interaction with increased molecular crowding and highlight how the replacement of this moiety by D-leucine in PME altered the balance of interactions. A similar analysis of the interactions between the peptides and the cell wall highlight the prevalence of electrostatic interactions between the specific (DAP) residues of the cell wall and both polymyxins. Finally, the impacts of both polymyxins on the dimensions of the ‘mesh’ of the cell wall are discussed. Our results highlight the importance of considering the full biological complexity of a system when attempting to characterise details about the function and behaviour of antimicrobial peptides in vivo; as evidenced by an increase in the range of observed behavioural states of polymyxins as the complexity of the system increased.