Accurate molecular dynamics modeling of Pseudomonas aeruginosa outer membrane interaction with signaling molecules.

Abstract

Pseudomonas aeruginosa is an opportunistic pathogen responsible for lungs, urinary tract, and surgical wound infections. This gram-negative bacterium releases outer membrane vesicles (OMV) derived from the cell's outer membrane (OM), serving diverse functions in bacterial survival, including nutrient acquisition, signaling, antibiotic resistance, delivery vehicle, and host-immune response modulation. This work aims to develop an accurate in silico model of P. aeruginosa outer membrane using all-atom molecular dynamics (MD) to understand OMV biogenesis formation based on the prediction of the bilayer-couple model. This model predicts the intercalation of a signaling molecule name Pseudomonas Quinolone Signal (PQS) to the OM as the main driver for the vesicle formation. In this study, the asymmetric model OM is composed of PA14 Lipid A in the outer leaflet and a mixture of POPE and POPG phospholipids in the inner leaflet. Due to the use of periodic boundary conditions in MD simulations, the compositional asymmetry imposes a fixed ratio of lipid numbers between the two leaflets, which needs to be set with caution. It has been shown that many widely used methods of defining this ratio lack control over the stress state of the membrane. As a result, the generated membrane could have a non-zero per leaflet tension. We investigate the role of the initial stress state on the intercalation of PQS to the OM. Free energy calculation shows that the favorable position of PQS within the membrane would shift significantly by variation of per leaflet tension, which could have important implications on the bilayer-couple model of OMV biogenesis. In addition, we model various PQS analogs to probe the role of different functional groups of PQS on the spontaneous intercalation of this signaling molecule to the membrane.