Associate Professor
Thomas C. Jenkins Department of Biophysics
Krieger School of Arts & Sciences

karen.fleming@jhu.edu

420 Jenkins Hall
3400 N. Charles Street
Baltimore, MD 21218

Office: 410-516-7256
Lab: 410-516-5452

Nearly one third of open reading frames encode proteins that live in membranes. These membrane proteins are essential for many biological functions including ion transport, molecular sorting, energy transduction, bacterial pathogenesis, and cell signaling. Over half of the drugs on the market today are thought to target membrane proteins, emphasizing their medical importance. Paradoxically, very little is known about how membrane proteins attain their native folds and how membrane proteins attain their native folds and how membrane proteins assemble into molecular complexes.

Research in my laboratory addresses fundamental biological questions concerning the formation of native structures in membrane proteins:

• How does the sequence for a membrane protein specify the fold?
• What are the physical principles dictating membrane protein folding and interactions?
• What is the role of the lipid bilayer environment?
• What principles for protein folding are similar between soluble and membrane proteins?

To address these questions our research efforts are focused on developing a physical understanding of membrane proteins, their folding and interactions, their specificity, their stability, their regulation, and their evolution. We carry out experiments that probe the chemistry of both helical and beta-barrel transmembrane proteins. Our tools include standard molecular biology and protein chemistry manipulations, analytical ultracentrifugation, light scattering, fluorescence spectroscopy, and molecular modeling. Through these biophysical studies on a variety of membrane proteins with a diversity of folds we aim to elucidate governing principles for membrane protein folding and interactions.

Selected Publications
Burgess, N.K., T.P. Dao, A.M. Stanley, and K.G. Fleming. (2008) Beta-barrel proteins that reside in the E. coli outer membrane in vivo demonstrate varied folding behavior in vitro. J. Biol. Chem. 283:26748-26758.

Mackenzie, K.R., and K.G. Fleming. (2008) Association energetics of membrane spanning alpha-helices. Curr. Opin. Struct. Biol. 18:412-419.

Stanley, A.M., and K.G. Fleming. (2008) The process of folding proteins into membranes: challenges and progress. Arch. Biochem. Biophys. 469:46-66.

Burgess, N.K., A.M. Stanley, and K.G. Fleming. (2008) Determination of membrane protein molecular weights and association equilibrium constants using sedimentation equilibrium and sedimentation velocity. Methods Cell Biol. 84:181-211.

Duong, M.T., T.M. Jaszewski, K.G. Fleming, and K.R. Mackenzie. (2007) Changes in apparent free energy of helix-helix dimerization in a biological membrane due to point mutations. J. Mol. Biol. May 18 [Epub ahead of print]

Stanley, A.M., and K.G. Fleming. (2007) The role of a hydrogen bonding network in the transmembrane beta-barrel OMPLA. J. Mol. Biol. 370:912-924.

Stanley, A.M., A.M. Treubrodt, P. Chuawong, T.L. Hendrickson, and K.G. Fleming. (2007) Lipid chain selectivity by outer membrane phospholipase A. J. Mol. Biol. 366:461-468.

Ebie, A.Z., and K.G. Fleming. (2007) Dimerization of the erythropoietin receptor transmembrane domain in micelles. J. Mol. Biol. 366:517-524.

Stanley, A.M., P. Chuawong, T.L. Hendrickson, and K.G. Fleming. (2006) Energetics of outer membrane phospholipase A (OMPLA) dimerization. J. Mol. Biol. 358:120-131.

Kroch, A.E., and K.G. Fleming. (2006) Alternate interfaces may mediate homomeric and heteromeric assembly in the transmembrane domains of SNARE proteins. J. Mol. Biol. 357:184-94.

Fleming, K.G. (2005) Analysis of membrane proteins using analytical ultracentrifugation. (Invited book chapter) Analytical Ultracentrifugation, Techniques and Methods, (Scott DJ, Harding SE, & Rowe AJ, Eds.) Royal Society of Chemistry Publishing, Cambridge, UK.

Stanley, A.M. and K.G. Fleming. (2005) The transmembrane domains of the ErbB receptors do not dimerize strongly in micelles. J. Mol. Biol. 347:759-772.

Kobus, F.J. and K.G. Fleming. (2005) The GxxxG-containing transmembrane domain of the CCK4 oncogene does not encode preferential self-interactions. Biochemistry 44:1464-1470.

Doura, A.K. and K.G. Fleming. (2004) Complex interactions at the helix-helix interface stabilize the glycophorin A transmembrane dimer. J. Mol. Biol. 343:1487-1497.

Raasi, S., I. Orlov, K.G. Fleming and C.M. Pickart. (2004) Binding of polyubiquitin chains to ubiquitin-associated (UBA) domains of HHR23A. J. Mol. Biol. 341:1367-1379.

Doura, A.K., F.J. Kobus, L. Dubrovsky, E. Hibbard and K.G. Fleming. (2004) Sequence context modulates the stability of a GxxxG mediated transmembrane helix-helix dimer. J. Mol. Biol. 341:991-998.

Fleming, K.G., C.C. Ren, A.K. Doura, F.J. Kobus, M.E. Eisley and A.M. Stanley. (2004) Thermodynamics of glycophorin A transmembrane helix-helix association in C14 betaine micelles. Biophys. Chem. 108:43-49.

Fleming, K.G. (2002) Standardizing the free energy change of transmembrane helix-helix interactions. J. Mol. Biol. 323:563-571.

Vergis, J.M., K.G. Bulock, K.G. Fleming and G.P. Beardsley. (2001) Human AICAR transformylase/IMP cyclohydrolase: A bifunctional protein requiring dimerization for transformylase activity but not for cyclohydrolase activity. J. Biol. Chem. 276:7727-7733.

Trombetta, E.S., K.G. Fleming and A. Helenius. (2001) Quaternary and domain structure of glycoprotein processing glucosidase II. Biochemistry 40:10717-10722.

Fleming, K.G. and D.M. Engelman. (2001) Specificity in transmembrane helix-helix interactions defines a hierarchy of stability for sequence variants. Proc. Natl. Acad. Sci. USA 98:14340-14344.

Fleming, K.G., and D.M. Engelman. (2001) Computation and mutagenesis suggest a right-handed structure for the synaptobrevin transmembrane dimer. Proteins 45:313-317.