Atomistic modeling of molecule-lipid interactions to understand small-molecule induced outer membrane vesicle biogenesis in Gram-negative bacteria

With the role of packing biochemical cargos, outer membrane vesicles (OMVs) of Gram-negative bacteria have great importance in many disease-related processes. Recent studies have shown a strong link between a self-produced small molecule, Pseudomonas Quinolone Signal (PQS), and OMV biogenesis in Pseudomonas aeruginosa. We conducted all-atom molecular dynamics simulations to elucidate the interactions between PQS and a model outer membrane. We discovered two characteristic states of PQS, namely attachment on the membrane surface and insertion into the Lipid A leaflet. The time-resolved position of PQS and the angle between its heterocyclic ring and alkyl side chain reveal a four-staged dynamical process: flotation, attachment, folding, and insertion. Remarkably, PQS bends its hydrophobic chain into a closed conformation to lower the energy barrier for penetration through the hydrophilic Lipid A head-group zone, which was confirmed by the potential of mean force (PMF) measurements. Simulation with multiple PQS exhibit significant aggregation of these amphiphilic molecules in the surrounding aqueous phase. Yet, both attached and inserted states were simultaneously observed even in the presence of PQS aggregation. These findings provide critical insight into OMV biogenesis.