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Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels

dc.contributor.authorYardeni, Eliane H.
dc.contributor.authorBahrenberg, Thorsten
dc.contributor.authorStein, Richard A.
dc.contributor.authorMishra, Smriti
dc.contributor.authorZomot, Elia
dc.contributor.authorGraham, Bim
dc.contributor.authorTuck, Kellie L.
dc.contributor.authorHuber, Thomas
dc.contributor.authorBibi, Eitan
dc.contributor.authorMchaourab, Hassane S.
dc.contributor.authorGoldfarb, Danielle
dc.identifier.citationYardeni, E.H., Bahrenberg, T., Stein, R.A. et al. Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels. Sci Rep 9, 12528 (2019).
dc.description.abstractMethodological and technological advances in EPR spectroscopy have enabled novel insight into the structural and dynamic aspects of integral membrane proteins. In addition to an extensive toolkit of EPR methods, multiple spin labels have been developed and utilized, among them Gd(III)-chelates which offer high sensitivity at high magnetic fields. Here, we applied a dual labeling approach, employing nitroxide and Gd(III) spin labels, in conjunction with Q-band and W-band double electron-electron resonance (DEER) measurements to characterize the solution structure of the detergent-solubilized multidrug transporter MdfA from E. coli. Our results identify highly flexible regions of MdfA, which may play an important role in its functional dynamics. Comparison of distance distribution of spin label pairs on the periplasm with those calculated using inward- and outward-facing crystal structures of MdfA, show that in detergent micelles, the protein adopts a predominantly outward-facing conformation, although more closed than the crystal structure. The cytoplasmic pairs suggest a small preference to the outward-facing crystal structure, with a somewhat more open conformation than the crystal structure. Parallel DEER measurements with the two types of labels led to similar distance distributions, demonstrating the feasibility of using W-band spectroscopy with a Gd(III) label for investigation of the structural dynamics of membrane proteins.en_US
dc.description.sponsorshipThis work was supported by the German-Israeli Foundation for Scientific Research and Development to E.B. (GIF, Grant Number I-1202-248.9/2012), the Clore Center of Biological Physics at the Weizmann Institute of Science to D.G. and E.B., by a grant from the United States - Israel Binational Science Foundation (BSF), Jerusalem, Israel to H.S.M. and E.B., and by a grant from the Minerva Foundation to D.G. E.H.Y is the recipient of a Professor Rahamimoff Travel Grant from the United States - Israel Binational Science Foundation. T.B. acknowledges financial support from the Minerva Foundation. The authors would like to thank Dr. Akiva Feintuch for his support with Gd(III) AWG-DEER measurements.en_US
dc.publisherScientific Reportsen_US
dc.rightsOpen Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit
dc.titleProbing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labelsen_US

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