Identification of Biologically Relevant Binding Targets of SH3 Domains Using a Compensatory Mutation Approach
Year: 2018
Type: dissertation
Abstract: Protein-protein interactions are crucial for cellular function. Many protein-protein interactions are mediated by peptide recognition modules (PRMs), small domains in proteins that recognize and interact with short peptide sequences in target proteins. In many systems, the interactions between PRMs and target proteins have been investigated using high-throughput methods. These studies have revealed protein-protein interaction networks where single PRMs apparently interact with dozens of different proteins. Some of these interactions may be false positives, may never occur in vivo, or may not be involved in any biological function. Thus, a key challenge arising from these studies is to identity protein-protein interactions that are “biologically relevant”. In this thesis, I define a biologically relevant interaction as one where specific disruption of the interaction can be definitively shown to cause a detectable phenotype under some genetic background or environmental condition. The goal of my work has been to design and test a generalizable approach, which I call “the compensatory mutation approach”, for determining whether particular protein-protein interactions are biologically relevant. To develop my approach, I studied the function of SH3 domains in budding yeast, Saccharomyces cerevisiae, as a model system. In particular, I focused on the SH3 domains found in two yeast proteins, Abp1p and Nbp2p. Using the compensatory mutation approach, I identified biologically relevant binding targets for both of these domains. Importantly, I showed that the biologically relevant binding targets may change depending on the phenotype tested and the assay conditions. I also demonstrated that the pathway involving Abp1p can be re-wired in such a way as to eliminate the requirement for the Abp1p SH3 domain. This study has provided the first unequivocal identification of biologically relevant targets for the Nbp2p and Abp1p SH3 domains, and established that the compensatory mutation approach can supply unique insights into the functioning of biological pathways.
Source: TSpace (University of Toronto)
Author: Yun Zhu
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2963512215