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Karen Fleming
Associate Professor
Department of Biophysics
Assistant Professor
Department of Biology
CMDB Graduate Program Faculty
B.A.
University of Notre Dame
Ph.D.
Georgetown University
Postdoctoral
Yale University
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Department of Biophysics
Johns Hopkins University
3400 North Charles Street
Baltimore, MD 21218-2685
U.S.A. |
Office Telephone:
Fax:
Email:
Lab Web Page |
410.516.7256
410.516.4118
Karen.Fleming@jhu.edu
http://freedom.bph.jhu.edu |
Jenkins Hall
Office - Jenkins 420 |
[Research Interests] [Representative Publications]
RESEARCH INTERESTS
Structural and Energetic Principles of Helical Membrane Proteins
Genome sequencing efforts are revealing that perhaps as many as 20-40% of open reading frames in complex organisms may encode
proteins containing at least one helical transmembrane segment. Contrasting with the approaching tidal wave of helical membrane
proteins is the fact that our understanding of the sequence-structure-function relationships for membrane proteins lags far behind
that of soluble proteins. This paradox emphasizes the extensive biophysical and structural work that remains to be done in the field
of helical membrane proteins.
Our research is aimed at elucidating structural and energetic principles of membrane proteins. We are especially focused on
understanding the structural and energetic basis of transmembrane helix-helix recognition. Our lab takes a multidisciplinary
approach to address scientific questions employing molecular biology techniques, structural studies, thermodynamic investigations
and computational analysis and modeling.
Currently our research projects include:
1. Structural and energetic dissection of the glycophorin A transmembrane dimer. A paradigm for transmembrane helix-helix
interactions, we are probing the structural and energetic effects on dimerization of single and multiple point mutants. Our
interaction studies on glycophorin A suggest the idea that specificity in helix-helix interactions for this protein may be
independent of the hydrophobic environment.
2. Transmembrane interactions in SNARE fusion proteins. We are using computational modeling and thermodynamics to probe
the transmembrane helix-helix interactions of synaptobrevin and other SNARE proteins. Our studies on the dimerization of
synaptobrevin offer an opportunity for protein engineering and design of a membrane protein as a means to understanding its
structural stability.
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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