Determining the secondary structure and orientation of EmrE, a multi-drug transporter, indicates a transmembrane four-helix bundle.

EmrE is a member of a newly emerging family of MiniTEXANS, a family of multi-drug antiporters from bacteria characterized by their small size of roughly 100 amino acids. In this report we have obtained transmission FTIR spectra of EmrE in CHCl3:MeOH, DMPC vesicles, and Escherichia coli lipid vesicles. Secondary structure analysis has shown that both in DMPC vesicles and in CHCl3: MeOH the protein adopts a highly helical secondary structure that correlates remarkably well with that predicted by hydropathy analysis. The protein was shown to be resistant to amide proton H/D exchange, providing evidence that most of the protein is embedded in the lipid bilayer. Polarized ATR-FTIR spectra of the protein in DMPC vesicles have shown that the helices are oriented with an average tilt angle of 27 degrees from the bilayer normal. The protein was found to be less oriented in E. coli lipid vesicles, most likely as a result of the poor orientation of the bilayer lipids themselves. Thus, the protein is identified as a transmembrane four-helix bundle providing valuable structural data for this family of multi-drug transporters. The results set the stage for further studies aimed at deriving a detailed model for this protein.