In a new study published online in the open access journal PLoS Biology, Gaby Sennhauser, Marcus Gruetter, and colleagues use structural biology techniques to probe the molecular mechanisms of the major drug efflux pump in E. coli AcrB.
Bacterial resistance to antibiotics is a major challenge for the current treatment of infectious diseases. One way bacteria can escape destruction is by pumping out administered drugs through specific transporter proteins that span the cell membrane, such as AcrB.
Making use of designer proteins that bind to and stabilize proteins of interest, the researchers were able to obtain better resolution structural data for the AcrB complex. After selecting for designed ankyrin repeat proteins (DARPins) that inhibit this pump, Sennhauser and colleagues solved the crystal structure of the DARPin inhibitor in complex with AcrB. They were able to confirm that the AcrB pump is split into three subunits, each of which exhibit distinctly different conformations.
Each subunit has a differently shaped substrate transport channel; these variable channels provide unique snapshots of the different phases employed by AcrB during transport of a substrate. The structure also offers an explanation for how substrate export is structurally coupled to simultaneous proton import--thus significantly improving our understanding of the mechanism of AcrB. This is the first report of the selection and co-crystallization of a DARPin with a membrane protein, which demonstrates not only DARPins' potential as inhibitors, but also as tools for the structural investigation of integral membrane proteins.