On How the Conformational Cycle of the AcrB Efflux Pump is Coupled to Proton Translocation: A Theoretical Study Based on High-Resolution Structural Data

Abstract

The AcrA/AcrB/TolC multidrug efflux pump confers Escherichia coli with antibiotic resistance by sequestering toxic compounds found within the periplasm and inner membrane and extruding them into the extracellular space. The AcrB trimer is the central component of this efflux complex; anchored in the inner membrane, it forms an asymmetric assembly that undergoes a conformational cycle in which each protomer adopts three different structures. As a result, substrates bound in the periplasmic domain of AcrB are projected into the TolC channel, which reaches beyond the outer membrane. Crucially, the conformational cycle within AcrB is driven by the translocation of protons down the gradient sustained by the inner membrane, through a mechanism that has not been characterized so far.Here, we investigate this microscopic mechanism through atomistic free-energy molecular dynamics simulations and electrostatic calculations, based upon novel high-resolution structural data for wild-type and mutagenized AcrB. Specifically, we assess the events associated with binding and release of protons within the membrane domain, and determine the mechanism by which these events are coupled to the reorganization of key transmembrane helices within each protomer. This investigation reveals how proton translocation influences both local and remote interactions within the protein, thereby modulating its structure.