Department of Physics and Astronomy
Iowa State University
Office Phone: 515-294-4955
Office Location: A115 Physics
Email: ewyu@iastate.edu

Research Interests

Multidrug efflux pumps are now known to exist in most living cells. These membrane proteins recognize a number of structurally unrelated toxic compounds and actively extrude them from cells. Our long-term goal is to elucidate the structures and fundamental mechanisms that give rise to multiple drug recognition and extrusion in these multidrug transporters. The primary target of our work is the Escherichia coli AcrB multidrug efflux pump, which shows the widest substrate specificity among all known multidrug transporters, ranging from most of the currently used antibiotics, disinfectants, dyes, detergents, to simple solvents. This inner membrane efflux pump, AcrB, interacts with a periplasmic membrane fusion protein, AcrA, to mediate the extrusion of drugs from E. coli.

We have determined the x-ray structures of AcrB in the presence of four structurally different agents. These are the first structures of any transporter that have been solved in complex with a variety of ligands by x-ray crystallography. The crystal structures illustrate that three molecules of ligands bind simultaneously to the extremely large central cavity of 5000 cubic Angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. The subsequent study of the efflux pump by crystallizing a mutant AcrB with five structurally diverse ligands indicates that AcrB consists of two distinct binding sites. These five ligands not only bind to various positions of the central cavity, but also to residues lining the deep external depression formed by the C-terminal periplasmic domain.

We are studying the structural and functional relationships of the transmembrane AcrB efflux pump by x-ray crystallography and site-directed mutagenesis. The specific aims are to: (i) identify important residues for multiple drug binding in AcrB, (ii) examine the mechanism of multidrug transport in the efflux pump, (iii) determine the x-ray structure of the AcrAB efflux complex.

Timeric AcrB with three bound R6G molecules

Selected Publications

Yu, E.W., McDermott, G., Koshland, D.E., Jr., and Nikaido, H. (2004) "Mechanism of Drug Transport in the AcrB Multidrug Efflux Pump" submitted.

Yu, E.W., McDermott, G., Zgurskaya, H.I., Nikaido, H., and Koshland, D.E., Jr. (2003) "Structural Basis of Multiple Drug-Binding Capacity of the AcrB Multidrug Efflux Pump" Science 300, 976.

Commentaries on this paper include: Chemical & Engineering News 81 (19), 7 (2003); Nature Biotechnology 21, 633 (2003); Nature Reviews Drug Discovery 2, 510 (2003); Drug Discovery Today 8, 566 (2003); The Scientist On-line Daily News, May 9 (2003); and Chemical & Engineering News 81 (51), 39 (2003).

Yu, E.W., Aires, J.R., and Nikaido, H. (2003) "AcrB Multidrug Efflux Pump of Escherichia coli: A composite substrate-binding cavity of an exceptional flexibility generates its extremely wide substrate specificity" J. Bacteriol. 185, 5657.

Made the cover of this issue of Journal of Bacteriology.

Yu, E.W., and Koshland, D.E., Jr. (2001) "Propagating Conformational Changes Over Long (and Short) Distances in Proteins" Proc. Nat. Acad. Sci. U.S.A. 98, 9517.