Mechanistic Details of Drug Translocation in MexAB-OprM Efflux Pump

Abstract

Antibiotic efflux is one of the most important mechanisms of bacterial multi-drug resistance. Antibiotics are pumped out of the bacterial cell by tripartite efflux pumps containing three protein components (outer-membrane, periplasmic, and inner-membrane proteins). Together they are able to actively extrude both noxious and hazardless compounds from the internal bacterial compartments to the extracellular environment.Despite the efforts to characterize both the mechanism and dynamics of the tripartite pump complex, there are still several important answers that remain elusive. Here, we have used multi-scale molecular dynamics to get insights into the mechanism of drug translocation across the whole protein machinery. We have considered the MexAB-OprM pump complex of Pseudomonas aeruginosa in a lipid model membrane that contains many components of a gram-negative bacterium. Our results suggest that the drug translocation depends on the size of the molecule. While drugs with varying sizes enter through a vestibule accessible from periplasm, only smaller drugs can enter the pump through a channel from the cytoplasmic leaflet of the inner-membrane component. Overall, drug binding leads to subtle conformational changes that are transmitted along the components in the periplasmic region. The influence of such drug induced conformational changes on the periplasmic and outer-membrane components and the coupling to the proton motive force are being probed. Subsequent extrusion of the drug through the outer membrane component is a passive process and concentration dependent. The free energy landscape of the drug translocation through this pump is evaluated as well.