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. !

Public Health Relevance

Helix-mediated interactions among Bcl-2 family proteins can promote or inhibit apoptotic cell death. This project integrates computational modeling, interaction prediction, and structure-based design with experimental screening and biophysical analysis to map and manipulate protein-protein interactions of Bcl-2 family proteins. !

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM110048-05
Application #
9735640
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Fabian, Miles
Project Start
2014-06-01
Project End
2021-08-31
Budget Start
2019-09-15
Budget End
2020-08-31
Support Year
5
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Massachusetts Institute of Technology
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
001425594
City
Cambridge
State
MA
Country
United States
Zip Code
02142
Jenson, Justin M; Xue, Vincent; Stretz, Lindsey et al. (2018) Peptide design by optimization on a data-parameterized protein interaction landscape. Proc Natl Acad Sci U S A 115:E10342-E10351
Rezaei Araghi, Raheleh; Bird, Gregory H; Ryan, Jeremy A et al. (2018) Iterative optimization yields Mcl-1-targeting stapled peptides with selective cytotoxicity to Mcl-1-dependent cancer cells. Proc Natl Acad Sci U S A 115:E886-E895
Frappier, Vincent; Duran, Madeleine; Keating, Amy E (2018) PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode. Protein Sci 27:276-285
Foight, Glenna Wink; Chen, T Scott; Richman, Daniel et al. (2017) Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design. Methods Mol Biol 1561:213-232
Jenson, Justin M; Ryan, Jeremy A; Grant, Robert A et al. (2017) Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1. Elife 6:
Rezaei Araghi, Raheleh; Ryan, Jeremy A; Letai, Anthony et al. (2016) Rapid Optimization of Mcl-1 Inhibitors using Stapled Peptide Libraries Including Non-Natural Side Chains. ACS Chem Biol 11:1238-44
Rezaei Araghi, Raheleh; Keating, Amy E (2016) Designing helical peptide inhibitors of protein-protein interactions. Curr Opin Struct Biol 39:27-38
Burrer, Christine M; Foight, Glenna W; Keating, Amy E et al. (2016) Selective peptide inhibitors of antiapoptotic cellular and viral Bcl-2 proteins lead to cytochrome c release during latent Kaposi's sarcoma-associated herpesvirus infection. Virus Res 211:86-8
Foight, Glenna Wink; Keating, Amy E (2015) Locating Herpesvirus Bcl-2 Homologs in the Specificity Landscape of Anti-Apoptotic Bcl-2 Proteins. J Mol Biol 427:2468-2490
Dutta, Sanjib; Ryan, Jeremy; Chen, T Scott et al. (2015) Potent and specific peptide inhibitors of human pro-survival protein Bcl-xL. J Mol Biol 427:1241-1253