Simulating bacterial efflux: how molecular features affect functional rotation

The major tripartite efflux pump AcrAB-TolC is responsible for the intrinsic and acquired multidrug resistance in Escherichia coli. At heart of the extrusion machinery there is the homotrimeric transporter AcrB, which is in charge of the selective binding of structurally and chemically different substrates and energy transduction. The effects of conformational changes, which have been proposed as the key features of the extrusion of drugs, are investigated at molecular level using different computational methods like targeted molecular dynamics. Simulations, including almost half a million atoms, have been used to assess several hypotheses concerning the structure-dynamics-function relationship of the AcrB protein. The results indicate that, upon induction of conformational changes, the substrate detaches from the binding pocket and approaches the gate to the central funnel. In addition, we provide evidence for the proposed peristaltic transport involving a zipper-like closure of the binding pocket, responsible for the displacement of the drug. Using these atomistic simulations the role of specific amino acids during the transitions can be identified, providing an interpretation of sitedirected mutagenesis experiments. Additionally, we discuss a possible role of water molecules in the extrusion process.