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. - Street, T.O., C.M. Bradley, and D. Barrick. (2007) Predicting coupling limits from an experimentally determined energy landscape. Proc. Natl. Acad. Sci. USA 104:4907-4912.
- Lubman, O.Y., M.X.G. Ilagan, R. Kopan, and D. Barrick. (2007) Quantitative dissection of the Notch:CSL interaction: Insights into the Notch-mediated transcriptional switch. J. Mol. Biol. 365:577-589.
- Tripp, K.W., and D. Barrick. (2007) Enhancing the stability and folding rate of a repeat protein through the addition of consensus repeats. J. Mol. Biol. 365:1187-1200.
- Bradley, C.M., and D. Barrick. (2006) The Notch Ankyrin domain folds through a discrete, centralized pathway. Structure 14:1303-1312.
- Street, T.O., G.D. Rose, and D. Barrick. (2006) The role of introns in repeat-protein gene formation. J. Mol. Biol. 360:258-266.
- Zweifel, M.E., D.J. Leahy, and D. Barrick. (2005) Structure and Notch-receptor binding of the tandem WWE domain of Deltex. Structure 13:1599-1611.
- Mello, C., C.M. Bradley, K.W. Tripp, and D. Barrick. (2005) Experimental Characterization of the Folding Kinetics of the Notch Ankyrin Domain. J. Mol. Biol. 352:266-281.
- Street, T.O., C.M. Bradley, and D. Barrick. (2005) An improved experimental system for measuring small folding entropy changes resulting from proline -->alanine substitutions. Prot. Sci. 14:2129-2135.
- Mello, C.C., and D. Barrick. (2004) An experimentally determined energy landscape for protein folding. Proc. Natl. Acad. Sci. USA 101:169-178.
- Zweifel, M.E., D.J. Leahy, F.M. Hughson, and D. Barrick. (2003) Structure and stability of the ankyrin domain of the Drosophila Notch receptor. Protein Sci. 12:2622-2632.
- Zweifel, M.E., and D. Barrick. (2001) Studies of ankyrin repeats of the Drosophila melanogaster Notch receptor: II. Solution stability and folding cooperativity. Biochemistry 40:14357-14367.
- Barrick, D., N.T. Ho, V. Simplaceanu, F.W. Dahlquist, and C. Ho. (1997) Molecular signaling in hemoglobin: A test of the Perutz model for cooperativity. Nat. Struct. Biol. 4:78-83.
- Scholtz, J.M., D. Barrick, E.J. York, J.M. Stewart, and R.L. Baldwin. (1995) Urea unfolding of peptide helices as a model for interpreting protein unfolding. Proc. Natl. Acad. Sci. USA 92:185-189.
- Barrick, D. (1994) Replacement of the proximal ligand of sperm whale myoglobin with free imidazole in the mutant His-93->Gly. Biochemistry 33:6546-6554.
- Barrick, D., and R.L. Baldwin. (1993) A three-state analysis of apomyoglobin unfolding. Biochemistry 32:3790-3796.
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