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Deciphering the language of cellular protein interaction networks using spectrally encoded peptide-bead libraries

Seed Grants
Awarded in 2016

Interdisciplinary Initiatives Program Round 8 - 2016

Martha Cyert, Biology
Polly Fordyce, Genetics and Bioengineering

Precision medicine aims to develop targeted treatments for each individual. However, scientists must first understand how normal cells respond to biological signals (nutrients, hormones, etc.) to appreciate how these decisions are hijacked during disease. Cells are built from networks of proteins that ‘talk’ to each through weak, transient physical interactions that change during signaling, when proteins and their partners are reversibly modified. One example of such a signaling mechanism is phosphorylation, whereby the regulated addition or removal of a single phosphate molecule to proteins drastically alters their interaction networks. Although technological advances have provided a detailed protein ‘parts list’ for each cell, we still need to map how the parts connect to each other and how these connections change, especially during disease, to produce different outcomes. We propose development of a new technology that will transform our knowledge of cellular information networks by efficiently and quantitatively mapping the weak interactions that occur between proteins under different phosphorylation states.

Technology: We have recently developed a new method of producing libraries of tiny beads that are 1,000 different colors, allowing us to track individual beads even when mixed together. Here, we propose to attach short protein sequences (peptides) to the surface of these beads with each protein sequence uniquely associated with a particular color. By mixing these bead-bound peptide libraries with candidate binding partners, we can then resolve how each binding partner interacts with thousands of peptide sequences in a single low-cost experiment that uses very small amounts of material. Furthermore, the phosphate content of each peptide can be varied to reveal how these interactions change during cell signaling.

Biology: This technology will first be applied to identify partners for a critical enzyme, calcineurin. In cells of the immune system, calcineurin removes phosphate groups from key proteins to activate the immune response. As a result, transplant patients receive drugs that inhibit calcineurin to suppress rejection of the new organ. However, long-term use of these drugs creates other problems by inhibiting calcineurin in tissues outside the immune system. We aim to discover many of the proteins calcineurin ‘talks’ to and modifies to better understand the adverse effects of immunosuppression therapy. After successful application of the new technology to map calcineurin networks, we will map protein interactions that occur after DNA is damaged, a response that is perturbed by many types of cancer.