Investigating forced proximity and its application to targeted autophagy-mediated protein aggregate clearance

This is a summer student position supervised by Christopher Green in Anne Schreiber's lab.

Introduction to the science

Targeted protein degradation is a rapidly growing field where currently undruggable protein targets are recruited to the cellular degradation machinery directly to selectively achieve its degradation either by the ubiquitin-proteasome system or autophagy. We are specifically interested in recruiting the autophagy machinery to targets due to its ability to engulf and acidify protein targets and even organelles. To mimic this, in the lab we have optimized a chemically inducible-dimerization system, in which addition of a small molecule forces the interaction of two proteins. We are using this system to identify the best autophagy effectors to achieve the autophagy-dependent degradation of our targets of interest. By utilising this system, we can establish which autophagy protein to recruit to targets to selectively degrade them. We can also determine whether it is optimal to degrade specific targets by autophagy or the proteasome.

About the project

This project will include validating hits from our screens where we have identified good autophagy effectors that degrade our targets of interest. We have developed a system that will allow us to directly compare degradation of simple, monomeric proteins against complex oligomeric proteins. To do this we have fused our targets with mKeima, a fluorescent protein that changes its wavelengths based on its pH environment. Hence, we can detect when a target has been delivered to the autophagy pathway for acidification and degradation. Using mKeima means we can utilise techniques such as flow cytometry and live cell imaging by confocal microscopy to quantify delivery of the target to the autophagy pathway. We will also use molecular biology techniques to mutate our autophagy proteins of interest to help understand or confirm their mechanism of action.

Candidate background