[ Research Interests ] [ Representative Publications ]

Karen Fleming Associate Professor Biophysics B.A. University of Notre Dame Ph.D. Georgetown University  Postdoctoral Yale University

Department of Biophysics Johns Hopkins University 3400 North Charles Street Baltimore, MD 21218-2685 U.S.A. Office Telephone: Fax: Email: 410.516.7256 410.516.4118 Karen.Fleming@jhu.edu

Research Interests We study membrane proteins. Proteins that live in membranes are encoded by about one quarter of open reading frames from all organisms. Membrane proteins are integral to 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 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 and to develop 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. Representative Publications Stanley, A.M. and Fleming, K.G. 2008. The process of folding proteins into membranes: Challenges and progress. Arch Biochem Biophys. Accepted. Burgess, N.K., Stanley, A.M., and Fleming, K.G. 2007. Determination of membrane protein molecular weights and association equilibrium constants using sedimentation equilibrium and sedimentation velocity. Chapter 7 in Methods in Cell Biology. JJ Correia, editor. Volume 84. Duong, M.T, Jaszewski, T.M, Fleming, K.G, and MacKenzie, K.T. 2007. Changes in apparent free energy of helix-helix dimerization in a biological membrane due to point mutations. J Mol Biol. 371:422-434. Stanley, A.M. and Fleming, K.G. 2007. The role of a hydrogen bonding network in the transmembrane beta-barrel OMPLA. J Mol Biol. 370:912-924. Stanley, A.M., Treubodt, A.M., Chauwang, P., Hendrickson, T.L., and Fleming, K.G. 2007. Lipid chain selectivity of outer membrane phospholipase A. J Mol Biol. 366:461-468. Ebie, A.Z. and Fleming, K.G. 2007. Dimerization of the erythropoietin receptor transmembrane domain in micelles. Journal of Molecular Biology 366: 517-524. Ebie AZ and KG Fleming 2006. The transmembrane domain of the Erythropoeitin receptor dimerizes weakly in micelles J Mol Biol, in press. Stanley, A.M., Treubodt, A.M., Chauwang, P., Hendrickson, T.L. and Fleming, K.G. 2006. Lipid chain selectivity of outer membrane phospholipase A. Under Review at J Mol Biol. Stanley, A.M., Chauwang, P., Hendrickson, T.L., and Fleming, K.G. 2006. Energetics of Outer Membrane Phospholipase A (OMPLA) Dimerization. J Mol Biol 358: 120-131. Kroch, A.E. and Fleming, K.G. 2006. Alternate Interfaces May Mediate Homomeric and Heteromeric Assembly in the transmembrane domains of SNARE Proteins. J Mol Biol 357: 184-197. Fleming, KG. 2005. Analysis of Membrane Proteins using Analytical Ultracentrifugation Analytical Ultracentrifugation, Techniques and Methods, (Scott DJ, Harding SE, & Rowe AJ, Eds.) Royal Society of Chemistry Publishing, Cambridge, UK. Stanley, A.M., and Fleming, K.G. 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 inter stabilize the glycophorin A transmembrane dimer J Mol Biol, 343: 1487-1497. Raasi S., Orlov I., Fleming K.G. and C.M. Pickart. 2004. Binding of polyubiquitin chains to ubiquitin-associated (UBA) domains of HHR23A changeme J Mol Biol, 341: 1367-1379. Doura A.K., Kobus F.J., Dubrovsky L., Hibbard E. 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., Ren C-C., Doura A.K., Eisley M.E., Kobus F.J. and Stanley A.M. 2004. Thermodynamics of glycophorin A transmembrane helix dimerization 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. Fleming, K.G.* and D.M. Engelman. 2001. *Corresponding author Specificity in transmembrane helix association defines a hierarchy of stability for sequence variants PNAS, 98: 14340-14344. Fleming, K.G.* and Engelman, D.M. 2001. *Corresponding author Computation and mutagenesis suggest a right-handed dimer for the synaptobrevin transmembrane domain Proteins, 45: 313-317. Trombetta, E.S., Fleming, K.G, and A. Helenius. 2001. Quaternary and domain structure of glycoprotein processing glucosidase II Biochemistry 40: 10717-10722. Vergis, J.M, Bulock, K.G, Fleming, K.G and Beardsley, G.P. 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. Fleming, K.G. 2000. Riding the wave: structural and energetic principles of helical membrane proteins Current Opinion in Biotechnology (P. Hensley & D. Myszka, eds) Vol. 11: 67-71. Fleming, K.G. 2000. Probing the Stability of Helical Transmembrane Proteins Energetics of Biological Macromolecules, Part C, a volume of Meth. Enzymol. (M. L. Johnson & G. Ackers, eds.) Academic Press, 323: 63-77.

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