Simulating Efflux Pumps: The Extrusion Mechanism of Substrates

Schulz R;VARGIU, ATTILIO VITTORIO;Collu F;CECCARELLI, MATTEO;Kleinekathöfer U;RUGGERONE, PAOLO

2009-01-01

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Abstract

Bacteria use multidrug efflux pumps to extrude toxic substrates through their cell membranes. The RND transporters of the AcrAB-TolC (E.Coli) and MexAB-OprM (P.Aeruginosa) systems are able to export structurally and chemically different substrates, being responsible of multidrug resistance. While the energy conversion takes place in the transmembrane domain of AcrB and MexB, the energy is transducted towards the periplasmic part and used there to initiate what is believed to be a three-cyclic peristaltic pumping. Using different computational methods like adaptive bias force (ABF) and targeted molecular dynamics (TMD), we have investigated the mechanism of substrate uptake and pumping. With ABF we have studied the passage of antibiotics from the periplasm and protein-lipid interface into the inner pore of the pump, while TMD has been used to assess the effect of conformational changes on the extrusion of drugs (located into one of the proposed binding pockets). Finally, analysis of water distribution in the transmembrane region represents an important step to identify features of the energy transduction process. Comparison between the active pumps AcrB and MexB (which show different resistance patterns despite their homology) provide insights into the microscopic details of their functioning.