Researchers publish insights into transporter EmrE, utilize new method of imaging

Photo of Katie Henzler-Wildman
Professor Katie Henzler-Wildman.

Biochemistry Professor Katie Henzler-Wildman and her team of researchers have published findings on the structure and dynamics of EmrE, utilizing a new method to determine the protein’s structure in greater detail than had been previously available. EmrE is a membrane protein that may provide key insight into antibiotic resistance, a rising public health concern.

EmrE has been understood to play a critical role as a multi-drug transporter, typically transporting compounds that are toxic from inside the cell to the outside. This family of transporters are only found in bacteria; they pump antibiotics, antiseptics and other bacterial toxins out of the cell. This allows the bacteria to thrive unhindered, contributing to the broader public health problem of drug resistance.

Previously, Henzler-Wildman and her team had reported data suggesting that EmrE may be a more promiscuous transporter, not just exporting a wide array of toxic molecules, but perhaps also pumping protons or toxins into bacteria.

“The EmrE transporter is not specifically relevant to antibiotic resistance in E. coli,” said Henzler-Wildman. “We have data suggesting this transporter may not just transport toxins out of bacteria, and those other transport activities may lead to [drug] susceptibility rather than resistance.”

The ability to confer susceptibility could have broad implications for designing more effective antibiotic treatments. In order to understand how EmrE recognizes so many different molecules and perhaps transports them in different ways, a better structural model of the transporter is needed.

In a study published in Nature Communications, Henzler-Wildman and her team, in collaboration with Mei Hong (MIT), share a more precise structure of EmrE bound to a substrate. Previous crystal structure models produced only a modest resolution structure of the EmrE molecule, so the team used a new method of study that combines solid-state NMR and a fluorinated substrate to measure precise distances between the substrate and different sites on the protein.

NMR structure and binding pocket illustration.
Distance-constrained NMR structure model of the drug-binding site. Key residues, including E14, Y40, Y60, and W63, surround the substrate (left). One of the four phenylene Hζ atoms, marked as F13, is tightly coordinated by residues from both monomer A (yellow) and monomer B (green).

Since many small molecule drugs contain fluorine, this method will allow researchers to explore with greater precision how EmrE – and other transporters of the same family – binds to a small molecule, and then changes shape to release it onto the other side of the cell membrane. As researchers learn more about how the transporters interact with other molecules, they’ll be able to better target treatments to disease.

“This new method allows researchers to understand much more precisely where exactly the substrate is interacting,” said Henzler-Wildman, “and how dynamic it is when bound to the transporter.”

While this study utilized the collaboration of off-site facilities, co-directors Henzler-Wildman and Chad Rienstra now have the capability to do these experiments here at the National Magnetic Resonance Facility at Madison (NMRFAM), located in the Hector F. DeLuca Biochemistry Labs building on the UW-Madison campus.