Determination of an Atomic-level Description of Protein Structure and Function
Research in my laboratory addresses three questions:
1. How did proteins evolve?
2. How do proteins fold?
3. How do folded proteins assemble into regulated multiprotein complexes?
To address the questions of how proteins evolved and how they fold, we are studying a class of modular proteins that contain simple, repetitive architectures. These proteins are built from simple units of supersecondary structure that are repeated in multiple, tandem copies. Examples include ankyrin repeats and leucine-rich repeats.
This simple architecture suggests a major simplification to the evolutionary origins of proteins. Through recombination events, the simple building blocks illustrated above can be duplicated, fused, and mixed, providing a route to large proteins with diverse sequences, bypassing the need to start from large (and improbable) folded domains. We are currently looking at the effects of deletion, insertion, and recombination on stability and structure formation in repeat proteins. These measurements will provide us with an assessment of the fitness of such recombinant constructs.
In addition to the evolutionary implications of repeat architecture, repeat proteins provide a unique framework in which to understand protein folding thermodynamics and kinetics. Since repeat-proteins are linear, they provide an excellent system to determine the maximum radius of coupling between elements of protein structure, and are amenable to statistical thermodynamic modeling to help us quantify the origin and extent of coupling. And since the close contacts in repeat-proteins are made exclusively from neighboring segments of the polypeptide, their kinetics of folding should be fast, based on current ideas relating topology to folding rates. We are using deletion and point substitutions to map the equilibrium energy landscape of repeat proteins, and map kinetic flux onto these surfaces.
We are studying how proteins assemble into regulated multiprotein complexes using a system that is critical for transmembrane signal transduction, the Notch pathway. The Notch pathway controls cellular differentiation during development, and disruption of normal function in humans has been implicated in stroke, dementia, and in certain forms of leukemia. Our goal is to determine how the Notch receptor and its intracellular effectors interact, both structurally and thermodynamically, using techniques such as spectroscopy, light-scattering, calorimetry, and x-ray crystallography. Through studies of interactions between different components of this pathway, we hope to identify key allosteric regulatory mechanisms that control signaling, with the ultimate goal of describing the signal transduction process in terms of a binding partition function.
Dao, T., Majumdar, A., & Barrick D. (2015) The highly polarized C-terminal transition state of the leucine-rich repeat domain of PP32 is governed by local stability. PNAS, 112 (18), E2298-306.
Preimesberger, M.R., Majumdar, A., Aksel, T., Sforza, K., Leckta, T., Barrick, D, & Lecomte, J.T.J. (2015) Direct NMR Detection of Bifurcated Hydrogen Bonding in the a-Helix N-Caps of Ankyrin Repeat Proteins. J. Am. Chem. Soc., in press.
Aksel, T., & Barrick, D (2014) Direct observation of parallel folding pathways revealed using a symmetric repeat protein system. Biophysical Journal 107, 220-232.
Dao, T., Majumdar, A., & Barrick, D (2014). The role of the capping motifs in stabilizing the structure of the PP32 leucine-rich repeat domain. Protein Science 23 (6), 801-811.
Cunha, E., Hatem, C., & Barrick, D (2013) Insertion of Endocellulase Catalytic Domains into Thermostable Consensus Ankyrin Scaffolds: Effects on Stability and Cellulolytic Activity. Applied Environmental Microbiology 79, 6684-6696.
Johnson, S.E. & Barrick, D. (2012) Dissecting and cirumventing the requirement for RAM in Notch signaling. PLos One 7(8) 39093.
Allgood, A.G, & Barrick, D. (2011) Mapping the Deltex binding surface on the Notch Ankyrin domain using analytical ultracentrifugation. J. Mol. Biol. 414, 243-259.
Cunha, E., Hatem, C.L., & Barrick, D. (2011). Natural and designed enzymes for cellulose degradation, in Advanced Biofuels and Bioproducts, Springer Publishing, 339-370.
Vieux, E.F., & Barrick, D. (2011). Deletion of internal structured repeats increases the stability of a leucine-rich repeat protein, YopM. Biophysical Chemistry 159, 152-161.
Rouget, J. B., Aksel, T., Roche, J., Saldana, J. L., Garcia, A. E., Barrick, D., & Royer, C. A. (2011). Size and Sequence and the volume change of protein folding. J. Am. Chem. Soc., 133, 6020-6027.
Sosnick, T.R., & Barrick, D. (2011). The folding of single domain proteins – have we reached a consensus? Curr. Op. Struct. Biol. 21, 12-24.
Aksel, T., Majumdar, A., & Barrick, D. (2011) The contribution of entropy, enthalpy, and hydrophobic desolvation ito cooperativity in repeat-protein folding. Structure, 19, 349-360.
Johnson, S.E. Ilagan, M.X.G., Kopan, R., & Barrick, D (2010) Thermodynamic analysis of the CSL:Notch interaction: Distribution of binding energy of the Notch RAM region to the CSL beta-trefoil domain and the mode of competition with the viral transactivator EBNA2. J. Biol. Chem, 285, 6681-6692.
Kloss, E. & Barick, D. (2009) C-terminal deletion of leucine-rich repeats from YopM reveals a heterogeneous distribution of stability in a cooperatively folded protein. Protein Science, 18, 1948-1960.
Aksel, T., & Barrick, D. (2009) Analysis of repeat-protein folding using nearest-neighbor statistical mechanical models. Meth. Enzymol. 455, 95-125.
Street, T.O., Bradley, C.M., & Barrick, D. (2009) Predicting repeat-protein folding kinetics from an experimentally determined folding energy landscape. Prot. Sci. 18, 58-68.
Kloss, E., & Barrick, D. (2008) Thermodynamics, kinetics, and salt dependence of folding of YopM, a large leucine-rich repeat protein. J. Mol. Biol. 383, 1195-1209.
Courtemanche, N., & Barrick, D. (2008) The leucine-rich repeat domain of Internalin B folds along a polarized N-terminal pathway. Structure 16, 705-712.
Tripp, K.W., & Barrick, D. (2008) Rerouting the folding pathway of the Notch ankyrin domain by reshaping the energy landscape. J. Am. Chem. Soc. 130, 5681-5688.
Bertagna, A., Toptygin, D., Brand, L., & Barrick, D. (2008) The effects of conformational heterogeneity on the binding of the Notch intracellular domain to effector proteins: a case of biologically tuned disorder. Biochem. Soc. Trans. 36, 157-166.
Courtemanche, N., & Barrick, D. (2008) Folding thermodynamics and kinetics of the Leucine-rich repeat domain of the virulence factor Internalin B. Protein Science 17, 43-53.
Kloss, E., Courtemanche, N., & Barrick, D. (2007) Repeat-protein folding: new insights into origins of cooperativity, stability, and topology. Archives of Biochemistry and Biophyics 469, 83-99.
Street, T.O., Courtemanche, N., & Barrick, D. (2007B) Protein folding and stability using denaturants. Methods in Cell Biology: Biophysical Tools for Biologists. Correia, J.J. & Detrich, H.W. III, eds. Academic Press, Vol 84, 295-325.