Edward Yu, PhD

Department of Pharmacology
School of Medicine
Cleveland Center for Membrane & Structural Biology

Since I began my tenure track position in 2004, I have developed a highly successful independent research program that focuses on the structure, assembly, and mechanism of the resistance-nodulation-cell division (RND)-superfamily efflux pumps as well as the
factors that regulate their expression. These efflux pumps are key components for Gram-negative pathogens to ensure their survival in toxic environments by extruding a variety of antimicrobial agents from bacterial cells. Typically, RND efflux pumps work in
conjunction with a periplasmic membrane fusion protein and an outer membrane channel to form a functional protein efflux system. One such RND-type efflux system is the Escherichia coli CusCFBA tetrapartite heavy-metal efflux system, which specifically recognizes and confers resistance to Ag(I) and Cu(I) ions. My lab has determined the crystal structures of the CusA heavy-metal efflux pump. We have also resolved the crystal structure of the CusBA adaptor-transporter efflux complex. This is the only adaptor-transporter efflux complex structure that has been determined using X-ray crystallography. In addition, we have determined two mutant structures of the CusC efflux channel to identify conformational changes accompanying the folding and transmembrane channel formation of this outer membrane protein.

Interestingly, certain RND membrane proteins are also involved in cell wall biogenesis to remodel and strengthen bacterial cell walls to withstand harsh environmental conditions. We determined the structures of Burkholderia multivorans HpnN and Mycobacterium smegmatis MmpL3 transporters, which play major roles in remodeling the cell envelopes of these two bacterial species. These two cell wall remodeling machinery structures were separately published in the journal PNAS in 2017 and 2019.

I am also very interested in developing a cryo-EM methodology to study membrane proteomes of Gram-negative bacteria. To that end, we have recently developed a cryo-electron microscopy (Cryo-EM) methodology termed “Build and Retrieve” (BaR) that allows us to simultaneously solve structures of a variety of proteins from heterogeneous samples. We have successfully used BaR to determine structures from impure membrane fractions as well as from raw lysates from several tissues, including the liver, kidney, and brain. Coupled with other techniques such as proteomics and interactomics, the BaR methodology should help illuminate the details of biological networks at near-atomic resolution. It is expected that in the future, cryo-EM will enable a new perspective on the elucidation of the human interactome at the atomic level.



Selected Publications:
1.  F. Long, C.-C. Su, M.T. Zimmermann, S.E. Boyken, K.R. Rajashankar, R.L. Jernigan, and E.W. Yu. 2010. Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport. Nature. 467:484-488. PMID: 20865003. PMCID: PMC2946090

2.  C.-C. Su, F. Long, M.T. Zimmermann, K.R. Rajashankar, R.L. Jernigan, and E.W. Yu. 2011. Crystal structure of the CusBA heavy metal efflux complex of Escherichia coli. Nature. 470:558-562. PMID: 21350490.  PMCID: PMC3078058

3. N. Kumar, C.-C. Su, T.-H. Chou, A. Radhakrishnan, J.A. Delmar, K.R. Rajashankar and E.W. Yu. 2017. Crystal structures of the Burkholderia multivorans hopanoid transporter HpnN. Proc. Natl. Acad. Sci. Jun 20;114(25):114:6557-6562. PMID: 28584102. PMCID: PMC5488925

4. C.-C. Su, P.A. Klenotic, J.R. Bolla, G.E. Purdy, C.V. Robinson, E.W. Yu. 2019. MmpL3 is a lipid transporter that binds trehalose monomycolate and phosphatidylethanolamine. Proc Natl Acad Sci. Jun 4;116(23):11241-11246. PMID: 31113875. PMCID: PMC6561238

5. C.-C. Su, M. Lyu, C.E. Morgan, J.R. Bolla, C.V. Robinson, E.W.Yu. 2021. A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins. Nat Methods. Jan;18(1):69-75. PMID: 33408407. PMCID: PMC7808410

6. C.E. Morgan, Z. Zhang, M. Miyagi, M. Golczak, E.W. Yu. 2022. Toward structural-omics of the bovine retinal pigment epithelium. Cell Rep. Dec 27;41(13):111876. doi: 10.1016/j.celrep.2022.111876. PMID: 36577381. PMCID: PMC9875382

7. M.A. Moseng, C.-C. Su, K. Rios, M. Cui, M. Lyu, P. Glaza, P.A. Klenotic, E. Delpire, E.W. Yu. 2022. Inhibition mechanism of NKCC1 involves the carboxyl terminus and long-range conformational coupling. Sci Adv. Oct 28;8(43) PMID: 36306358. PMCID: PMC9616490