Chemical and molecular basis of transcription: design of functional miniature proteins and assemblies

Alanna Schepartz, Ph.D. Milton Harris '29 Ph.D. Professor of Chemistry; Professor of Molecular, Cellular, & Developmental Biology Yale University, KCL 120 PO Box 208103, 266 Whitney Ave New Haven, CT 06520 Email: alanna.schepartz@yale.edu Phone: (203) 432-5094 Fax: (203) 432-3486 Web site B.S. SUNY Albany 1982; Ph.D. Columbia University 1987

Research in the Schepartz laboratory explores the chemical biology of protein–protein and protein–DNA interactions inside the cell. We are interested in the structural and energetic factors that distinguish specific protein interfaces and how the assembly and disassembly of these complexes define biology.

Many of these studies originate from a long-term effort to design ligands for diverse protein surfaces, including those in proteins currently considered “undruggable”. These ligands fall into two classes, miniature proteins and foldamers.

Our miniature protein design strategy has been applied to inhibit the formation and function of many important and challenging protein-DNA and protein-protein interactions, including those between pro- and anti-apoptotic Bcl-2 protein paralogs, between the transcriptional co-activator CBP and the phosphorylated CREB activation domain, and between EVH1 domains and cell surface proteins of the human pathogen Listeria monocytogenes. Most recently we have demonstrated that a miniature protein can increase the kinase specificity of a potent but non-specific small molecule kinase inhibitor.

Our foldamer design strategy has been applied to inhibit the formation of the complex between the oncoprotein hDM2 and p53; the molecule we described represents the very first helical b-peptide that specifically recognizes a cellular target. Our results suggest that b-peptides can be applied broadly to mimic the functions of natural a-helices.

Using miniature proteins and foldamers that we design, we are asking questions such as: how cells effectively use a limited number of SH3 domains to achieve a precisely controlled and robust cell signaling network; how different EVH1 domains control actin-dependent cytoskeletal dynamics, can natural cell signaling networks be usurped using synthetic molecules that mimic or surpass the functions of proteins found in Nature; and can we design new miniature proteins or foldamers that inhibit processes such as HIV infectivity, TRAF signaling, or CBP-dependent transcriptional activation.

Selected Publications

Paralog-selective ligands for Bcl-2 proteins. A. C. Gemperli, S. E. Rutledge, A. Maranda & A. Schepartz, submitted.

Specific Recognition of hDM2 by b-Peptide Helices. J.A. Kritzer, J.D. Lear, M.E. Hodsdon & A. Schepartz, J. Am. Chem. Soc. 2004, 126, 9468.

High affinity, paralog-specific recognition of the Mena EVH1 domain by a miniature protein. D. Golemi-Kotra, R. Mahaffy, M.J. Footer, J.H. Holtzman, T.D. Pollard, J.A. Theriot & A. Schepartz, J. Am. Chem. Soc. 2004, 126, 4-5.

Molecular recognition of protein surfaces: High affinity ligands for the CBP KIX domain. S.E. Rutledge, H.M. Volkman & A. Schepartz, J. Am. Chem. Soc. 2003, 125, 14336.

Helix macrodipole control of ß-peptide 14-helix stability in water. S.A. Hart, A.B.F. Bahadoor, E.E. Matthews, & A. Schepartz, J. Am. Chem. Soc. 2003, 125, 4022.

Design and evolution of a miniature Bcl-2 binding protein. J.W. Chin & A. Schepartz, Angew. Chem. Int. Ed. Eng. 2001, 40, 3806-3809.

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