From closed to open: Addressing the role of the efflux pump AcrAB-TolC in antibiotic resistance

The emergence of antibiotic-resistant bacterial infections is an escalating public health challenge. In particular, Gram-negative bacteria are difficult to treat due to the additional outer membrane with embedded porins and efflux pumps that confer natural and acquired mechanisms of antibiotic resistance. AcrAB-TolC is a well-studied trans-envelope efflux pump in E. coli that expels toxic substrates and other small molecules. The complex is assembled from three main components: AcrA, AcrB, and TolC. AcrB in the inner membrane recognizes, binds, and extrudes a wide variety of substrates into the channel formed by AcrA-TolC using the proton-motive force. Due to the integral role of efflux pumps in expelling antibiotics, drugs targeting the pumps, which can inhibit efflux of existing antibiotics, have been investigated. Cryo-EM structures of the full protein have been solved in which both closed and open conformations of the AcrA-TolC channel are observed. In our present study, the conformational changes of the full protein complex, in going from the closed conformation to the open one, were resolved utilizing Targeted Molecular Dynamics. Both the original apo system and the system with a bound inhibitor, NSC 60339, were simulated, in order to quantify the effect of the compound on these conformational changes and to suggest possible mechanisms of action of the drug.