Structure, function, dynamics and thermodynamics of protein-protein interactions: NMR, mass spectrometry and kinetics
UC San Francisco
Massachusetts Institute of Technology
Massachusetts Institute of Technology
Awards and Academic Honors
Kaiser Award for Excellence in Teaching
Barany Award for Contributions to Biophysics
Rita Allen Scholar
N.I.H. Postdoctoral Fellow, Harvard University
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. In collaboration with the McCammon group, we have obtained evidence from Accelerated Molecular Dynamics that the TM binding site is dynamically coupled to motions at the thrombin active site. We recently were able to obtain beautiful NMR spectra for thrombin, and are now characterizing its dynamics.
A second 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 NFkB transcription factors and their IkB inhibitors. We determined that the binding energy of the complex between IkBa and NFkB (p50/p65) lies at the ends of the binding interface. We showed that IkBa folds upon binding to NFkB and that the fifth and sixth ankyrin repeats are weakly folded according to amide exchange experiments. The weakly-folded parts of IkBa appear to be important for facilitating removal of NFkB from transcription sites and we showed by single molecule FRET that they slowly fluctuate between folded and unfolded states. Taking off on this project, we are now investigating other protein-protein interactions mediated by ankyrin-repeat domain proteins. In particular, we are studying the interaction between ASB9, one member of a large family of E3 ubiquitin ligases, and its target, Creatine Kinase.
A third project in the lab is to develop novel proteases for proteomics applications. Starting from alphalytic protease, a particularly stable and highly active protease, we are evolving a family of proteases with unique substrate specificity to expand the protein sequence coverage in proteomics experiments.
Primary Research Area
Minority Access to Careers committee member, Biophysical Society (helped develop summer course in Biophysics for underrepresented students that was recently funded by the NIH)
Diversity Coordinator Department of Chemistry and Biochemistry
Steering Committee member in charge of recruitment of underrepresented students for Molecular Biophysics Training Program
Ph. D. thesis advisor for several underrepresented minorities.
Mentor for underrepresented minority undergraduates and postdoctoral scholars.
Hosted Preuss School students in lab for Science Fair Projects
Founding Faculty of Academic Connections Research Scholars Program – this program brings 15-20 high school students to UCSD for 3 weeks to work in a research lab.
Ensemble of thrombin structures that best represents the NMR-derived residual dipolar couplings
Single molecule FRET traces showing the fluctuations within the IkBa molecule
- Cervantes CF, Bergqvist S, Kjaergaard M, Kroon G, Sue SC, Dyson HJ, Komives EA, "The RelA nuclear localization signal folds upon binding to IκBα.", J Mol Biol, 2011, Vol. 405, Issue 3, 754-64
- DeVries I, Ferreiro DU, Sánchez IE, Komives EA, "Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain.", J Mol Biol, 2011, Vol. 408, Issue 1, 163-76
- Treuheit NA, Beach MA, Komives EA, "Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin.", Biochemistry, 2011, Vol. 50, Issue 21, 4590-6
- Ferreiro DU, Komives EA, "Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha.", Biochemistry, 2010, Vol. 49, Issue 8, 1560-7
- Guttman M, Prieto JH, Croy JE, Komives EA, "Decoding of lipoprotein-receptor interactions: properties of ligand binding modules governing interactions with apolipoprotein E.", Biochemistry, 2010, Vol. 49, Issue 6, 1207-16
- Guttman M, Prieto JH, Handel TM, Domaille PJ, Komives EA, "Structure of the minimal interface between ApoE and LRP.", J Mol Biol, 2010, Vol. 398, Issue 2, 306-19
- Bergqvist S, Alverdi V, Mengel B, Hoffmann A, Ghosh G, Komives EA, "Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha.", Proc Natl Acad Sci U S A, 2009, Vol. 106, Issue 46, 19328-33
- Cervantes CF, Markwick PR, Sue SC, McCammon JA, Dyson HJ, Komives EA, "Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance.", Biochemistry, 2009, Vol. 48, Issue 33, 8023-31
- Guttman M, Betts GN, Barnes H, Ghassemian M, van der Geer P, Komives EA, "Interactions of the NPXY microdomains of the low density lipoprotein receptor-related protein 1.", Proteomics, 2009, Vol. 9, Issue 22, 5016-28
- Koeppe JR, Beach MA, Baerga-Ortiz A, Kerns SJ, Komives EA, "Mutations in the fourth EGF-like domain affect thrombomodulin-induced changes in the active site of thrombin.", Biochemistry, 2008, Vol. 47, Issue 41, 10933-9