# Designed proteins to study and modulate cellular processes

> **NIH NIH R01** · YALE UNIVERSITY · 2020 · $306,203

## Abstract

A grand challenge of biomedicine is to understand biological processes at a level that allows us to
manipulate them in a predictable fashion. Such knowledge lays the foundation for preventing and treating
diseases that result from the malfunction of such processes. To accomplish this goal, we must develop
experimental tools that permit us to perturb cellular processes with exquisite precision. In addition, we must
develop quantitative, testable, predictive models. The ramifications of accomplishing this grand challenge
are many fold: We will have delineated the minimal components of a cellular process; we will be able to
predict the responses of that process to perturbations in a quantitative fashion; and we will have fabricated
new tools for manipulating cellular pathways – for example, to engineer metabolic pathways to produce
desired products, including drugs. In this proposal, we focus on the key process of protein degradation. We
present a powerful and widely applicable new strategy to specifically target proteins for degradation in yeast
(S. cerevisiae). Working in yeast provides great scope for the use of genetic screens and selections to
accomplish our goals. Moreover, the wealth of proteomic information available for yeast far surpasses that
of any other organism. We employ our expertise in protein engineering and design to create an `orthogonal'
degradation pathway. We will engineer the E3 ligase, CHIP, changing its substrate recognition specificity by
switching its tetratricopeptide repeat (TPR) domain for different TPR domains that we have designed. CHIP
is not an endogenous yeast protein, so no cellular processes depend on its activity. Thus, there is huge
scope for us to change the amount and activity of CHIP without effecting normal cellular function. Such
capability will allow us to test quantitative models of the CHIP-mediated degradation, by significantly
perturbing both the cellular concentration and specific activity of CHIP. Moreover, our strategy provides
great scope to use targeted degradation by CHIP as a means to manipulate metabolic pathways and thus
define the products produced. A unique advantage of our proposed scheme is that multiple proteins can be
targeted for degradation, in the same cell, each controlled by a different specificity CHIP. We will
demonstrate this facility by engineering the Violacein pathway, targeting two enzymes of the pathway (either
individually or at the same time) to define the metabolic products that are produced in the cell.

## Key facts

- **NIH application ID:** 9856499
- **Project number:** 5R01GM118528-04
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** Simon Mochrie
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $306,203
- **Award type:** 5
- **Project period:** 2017-02-01 → 2023-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9856499

## Citation

> US National Institutes of Health, RePORTER application 9856499, Designed proteins to study and modulate cellular processes (5R01GM118528-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9856499. Licensed CC0.

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