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Elizabeth Komives
Structure, function, dynamics and thermodynamics of protein-protein interactions: NMR, mass spectrometry and kinetics
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| Contact Information |
| Office: NSB 4324 |
| Phone: (858) 534-3058 |
| Fax: (858) 534-6174 |
| Email: ekomives@ucsd.edu |
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| Education and Appointments |
| 1987 |
Ph.D., UC San Francisco
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| 1982 |
BS, Massachusetts Institute of Technology
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| 1982 |
MS, Massachusetts Institute of Technology
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| Awards and Academic Honors |
| 2000 |
Kaiser Award for Excellence in Teaching |
| 2000 |
Barany Award for Contributions to Biophysics |
| 1992-1995 |
Searle Scholar |
| 1991-1996 |
Rita Allen Scholar |
| 1987-1990 |
N.I.H. Postdoctoral Fellow, Harvard University |
| Research Interests |
The long-term goal of research in the Komives lab is to understand the parameters that govern protein-protein recognition and the mechanisms by which these interactions contribute to biological function. The relative importance of factors such as hydrophobic effects, electrostatic interactions and dynamics are being defined for several different interactions. These parameters are explored by a combination of molecular biological techniques, protein chemistry, surface plasmon resonance, multidimensional NMR, and mass spectrometry. One project aims to discover how thrombomodulin (TM) converts the pro-coagulant activity of thrombin to anti-coagulant activity. The thrombin-TM interaction involves diffusion-controlled association that is highly electrostatically steered. The binding has no favorable enthalpy change, but is instead driven by entropy. The favorable entropy of association is probably due to release of water molecules from the interface into the bulk as a large number of amides are completely solvent inaccessible in the interface. When TM binds to thrombin, it appears to transmit conformational changes to the active site loops which we can observe with amide exchange.
A second project in the lab involves the interactions of the LDL-receptor-related protein (LRP-1), which is a 515 kD protein that is responsible for clearing many ligands that are genetically linked to Alzheimers disease. So far, we have been able to narrow-down the binding site of two of these ligands and are solving the NMR structure of the complement repeats that contain the binding sites. For one of the ligands, apolipoprotein E, we were able to define a 20 residue peptide with full LRP-1 binding capacity. This peptide causes chemical shift perturbation within the binding fragment, and we are also solving the structure of the complex. We have also characterized the interaction of the intracellular domain of LRP-1 with signaling molecules such as Shc, cSrc kinase, phospholipase Cg, and several PTN homologs in collaboration with P. van der Geer. We have found that phosphorylation regulates the folded structure of the intracellular domain exposing a secondary interaction site. Proteomics experiments are underway to define which proteins bind to which sites and how binding is dependent on phosphorylation.
A third project in the lab is a joint effort with the G. Ghosh, A. Hoffmann, P. Wolynes and J. Dyson labs. This involves understanding the signal transduction mediated by the family of NF-kB transcription factors and their IkB inhibitors. We determined that the binding energy of the complex between IkBa and NF-kB (p50/p65) lies at the ends of the binding interface. We also determined that IkBa folds upon binding to NF-kB. We are now trying to understand how the weakly-folded parts of IkBa behave when IkBa is free in solution, and how these parts are important for facilitating removal of NF-kB from transcription sites.
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| Primary Research Area: |
Interdisciplinary Specialties: |
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Biochemistry
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Biophysics
Macromolecular Structure
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| Selected Publications |
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Croy, J. E., Brandon, T. & Komives, E. A. (2004) Two apolipoprotein E mimetic peptides, apoE(130-149) and apoE(141-155)2, bind to LRP1 Biochemistry 43, 7328-35.
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Croy, C. H, Bergqvist, S. P., Huxford, T., Ghosh, G. & Komives, E. A. (2004) Biophysical Characterization of Free IkBa in Solution Protein Science 13, 1767-77.
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Prieto, J. H., Sampoli Benitez, B. A., Melacini, G., Johnson, D. A., Wood, M. A. & Komives, E. A. (2005) "Dynamics of the Fragment of Thrombomodulin containing the fourth and fifth EGF-like domains correlate with function" Biochemistry 44, 1225-1233.
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Koeppe, J. R., Seitova, A., Mather, T. & Komives, E. A. (2005) "Thrombomodulin tightens the thrombin active site loops to promote protein C activation" Biochemistry 44, 14784-91.
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Bergqvist, S., Croy, C. H., Kjaergaard, M., Huxford, T., Ghosh, G. & Komives, E. A. (2006) Thermodynamics reveal that helix four in the NLS of NF-kappaB p65 anchors IkappaBalpha, forming a very stable complex. J. Mol. Biol. 360, 421-34.
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Truhlar, S. M. E., Torpey, J. W., & Komives, E. A. (2006) Regions of IkBa that are critical for its inhibition of NF kB"DNA interaction fold upon binding to NF-kB. Proc. Nat. Acad. Sci. U. S. A. 103, 18951-6..
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Koeppe, J. R. and Komives, E. A. (2006) Amide H/2H Exchange Reveals a Mechanism of Thrombin Activation. Biochemistry 45, 7724-32.
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Ferreiro, D. U., Cervantes, C. F., Truhlar, S. M. E., Cho, S. S., Wolynes, P. G., and Komives, E. A. (2007) Stabilizing IkBa by 'consensus' design. J. Mol. Biol. 365, 1201-16.
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