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° 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.