Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump

Efflux pumps of the Resistance-Nodulation-cell Division superfamily confer multi-drug resistance to Gram-negative bacteria. AcrB of Escherichia coli is a paradigm model of these polyspecific transporters. The molecular determinants and the energetics of the functional rotation mechanism proposed for the export of substrates by this protein have not yet been unveiled. To this aim, we implemented an original protocol that allows mimicking substrate transport in silico. We show that the conformational changes occurring in AcrB enable the formation of a layer of structured waters on the surface of the substrate transport channel. This, in turn, allows for a fairly constant hydration of the substrate that facilitates its diffusion. Our findings reveal a new molecular mechanism of transport in polyspecific systems, whereby waters contribute by screening potentially strong substrate-protein interactions. The mechanistic understanding of a fundamental process related to multi-drug transport provided here could help rationalizing the behavior of other polyspecific systems.