# Analysis and design of protein interactions that regulate cell death

> **NIH NIH R01** · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · 2020 · $312,211

## Abstract

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.
!

## Key facts

- **NIH application ID:** 10018034
- **Project number:** 5R01GM110048-06
- **Recipient organization:** MASSACHUSETTS INSTITUTE OF TECHNOLOGY
- **Principal Investigator:** AMY E KEATING
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $312,211
- **Award type:** 5
- **Project period:** 2014-06-01 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10018034

## Citation

> US National Institutes of Health, RePORTER application 10018034, Analysis and design of protein interactions that regulate cell death (5R01GM110048-06). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10018034. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*