Analysis and design of protein interactions that regulate cell death

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Protein-protein interactions control myriad biological processes important for human health. Tools for discovering, predicting and designing such interactions can provide insights into biological mechanisms and highlight possible routes to therapeutic intervention. This project will integrate computational and experimental approaches to advance our understanding of the relationships between sequence and function for protein interactions among Bcl-2 family proteins. The Bcl-2 family regulates apoptosis and autophagy by forming specific complexes, some of which inhibit and some of which promote cell death. Competition between pro- and anti-apoptotic Bcl-2 family proteins for binding to short alpha helices encoded by a Bcl-2 homology 3 (BH3) motif controls key cell survival decisions. It is now well established that peptides and small molecules can mimic or inhibit BH3 interactions. Such molecules provide a way to control signaling outcomes using exogenous reagents, as demonstrated by the first drug approved for treating cancer by targeting Bcl-2. Despite exciting progress, open questions about Bcl-2 protein interactions with BH3 motifs provide additional opportunities for discovery. In particular: Do as-yet undiscovered BH3 motif-containing proteins in the human proteome influence signaling through Bcl-2 family proteins? Why do some proteins that contain BH3 motifs trigger mitochondrial pore formation by pro-apoptotic BAK and BAX whereas others do not? What are the mechanisms of BH3 binding-induced conformational changes that lead to mitochondrial membrane pore formation and cell death? What opportunities exist for promoting or blocking such processes using designed peptides or proteins? Answers to these questions will impact analysis of Bcl-2 pathways important for multiple human diseases, provide new reagents, and guide development of therapies for cancer and other diseases. Building on the substantial successes that we realized in the previous funding period, we will drive progress in these areas by applying new methodology that integrates interaction screening with structural modeling and prediction. We will apply novel computational methods for predicting new Bcl-2 binding partners, test predictions of our models, and highlight candidate new interaction partners of biological significance. We will propose molecular mechanisms of BAK and BAX activation and test them using libraries of BH3 motif variants. We will apply new computational design methods to make peptides and mini-proteins that activate or inhibit BAK and BAX-mediated cell death. Collectively, our contributions will provide a map of the sequence-function landscape of BH3 motifs, which are critical factors controlling cell survival. The methods and tools developed in this work will also be useful for discovering and inhibiting other protein-protein interactions. !