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Amy Keating


A.B. Physics, Harvard, 1992
Ph.D. Chemistry, University of California, Los Angeles, 1998
Helen Hay Whitney Postdoctoral Fellow, Whitehead Institute and MIT
Dept. of Chemistry, 1998
Assistant Professor, Dept. of Biology, 2002
Associate Professor, Dept. of Biology, 2007

The Keating lab studies the specificity of protein-protein interactions using a combination of bioinformatic analysis, structural modeling, computational design, and experimental screening and characterization. Our aim is to understand, at a high level of detail, how the interaction properties of proteins are encoded in their sequences and structures. Our work with CDP focuses on the Bcl-2 family of apoptosis-regulating proteins because interaction specificity among proteins of this family participate in a key decision point critical for regulating cell death.

Keating lab website

Research summary

In humans, the Bcl-2 family consists of ~15 known proteins important for controlling apoptosis, or programmed cell death. Critical junctures that govern cellular life-vs-death decisions are regulated by specific interactions among pro- and antiapoptotic members of this family. The delicate balance between the two types of proteins is often disrupted in cancer, making inhibition of the interactions a promising therapeutic strategy. Associations between family members are characterized by the docking of a BH3 (Bcl-2 homology 3) alpha-helix into a groove of an antiapoptotic protein. Such binding is simple enough to allow comprehensive experimental analysis and extensive computational sampling, yet complex enough to extend our understanding beyond the limits of other common protein interaction models.

We explore the interaction specificity of Bcl-2 family proteins by applying computational modeling, experimental screens, mutational analysis and x-ray crystallography. Using new computational methods for varying the backbone structure of alpha helices, we designed several novel BH3 ligands to bind the antiapoptotic protein Bcl-xL. Solution binding studies confirmed that many of these designed peptides bind with low- to mid- nanomolar affinity. As a complement to structure-based computational design, we have also applied yeast display screening as an experimental route to discovering new peptides with desired binding properties. In our first such study, we identified new peptides specific for binding Mcl-1 over 4 other human anti-apoptotic receptors. We also identified peptides specific for binding Bcl-xL in preference to Mcl-1. To understand the origins of binding specificity, we have used SPOT peptide array technology to characterize the effects of large numbers of point mutations in wild-type and engineered peptides. Such large-scale interaction data enables the construction of preliminary models, which we have shown capture some key determinants of specific binding to Bcl-xL vs. Mcl-1. We have also solved structures of several Mcl-1 complexes to provide insights into the structural plasticity that influences binding specificity.

Designed peptides that bind specifically to desired targets could be used to dissect complex apoptotic signaling networks or to provide leads for the development of targeted therapies. We also anticipate that elucidation of the relationship between structure and function in the Bcl-2 family of proteins will broaden our understanding of the general principles underlying interaction specificity, and are likely to improve systems-level models of apoptosis. In collaboration with the Sorger lab, we have updated models of apoptosis to include additional Bcl-2 family proteins and their interactions, and in the future we look forward to CDP collaborations that will allow us to profile the activities of engineered, specific BH3 peptides in cells.

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