Polymyxins, critical last-resort antibiotics, impact the distribution of membrane-bound divalent cations in the outer membrane of Gram-negative bacteria. We employed atomistic molecular dynamics simulations to model the effect of displacing these ions. Two polymyxin-sensitive and two polymyxin-resistant models of the outer membrane of Salmonella enterica were investigated. First, we found that the removal of all calcium ions induces global stress on the model membranes, leading to substantial membrane restructuring. Next, we used enhanced sampling methods to explore the effects of localized stress by displacing membrane-bound ions. Our findings indicate that creating defects in the membrane-bound ion network facilitates polymyxin permeation. Additionally, our study of polymyxin-resistant mutations revealed that divalent ions in resistant model membranes are less likely to be displaced, potentially contributing to the increased resistance associated with these mutations. Lastly, we compared results from all-atom molecular dynamics simulations with coarse-grained simulations, demonstrating that the choice of force field significantly influences the behavior of membrane-bound ions under stress.

Central European Institute of Technology Masaryk University Brno60200 Czech Republic

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague16000 Czech Republic

Laboratoire Chrono Environnement UMR CNRS 6249 Université de Bourgogne Franche Comté Besançon25000 France

National Centre for Biomolecular Research Faculty of Science Masaryk University Brno60200 Czech Republic

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