Date of Award
Summer 7-19-2024
Embargo Period
7-19-2026
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Cell and Molecular Pharmacology and Experimental Therapeutics
College
College of Graduate Studies
First Advisor
Lalima Madan
Abstract
Protein tyrosine phosphatases (PTPs), a critical class of signaling enzymes, are principally responsible for balancing the actions of kinases through the dephosphorylation of tyrosine residues on substrate proteins. As such, this family is involved in myriad pathways and individual members are able to perform both oncogenic and tumor-suppressing roles. However, while clinical success has been achieved in targeting kinases, PTPs have remained therapeutically challenging. Orthosteric inhibition is limited in PTPs due to their highly conserved fold, leading to off-target effects, and their highly charged active site, requiring highly polar molecules with poor bioavailability. These challenges posit the allosteric inhibition of PTPs as an attractive therapeutic avenue. In kinases, a key milestone to the development of allosteric inhibitors was the identification of active and inactive conformations in the structure of these proteins, such as the alignment of the regulatory spine residues and various conformations of the DFG motif. However, no analogous definition exists for PTPs. We seek to define such conformations through molecular dynamics simulations, biochemical characterization, and large-scale analysis of publicly available crystal structures. Through investigating the dynamics of three diverse PTPs (PTP1B from Homo sapiens, YopH from Yersinia pestis, and TbPTP1 from Trypanosoma brucei) we have identified residues that drive the basal dynamics required for catalysis. Additionally, we have characterized a unique residues in PTP1B, centered around F225, that includes residues involved in allosteric regulation. Through examining the interface of the dual PTP domains in the receptor PTP LAR, we have determined the mechanism for substrate specificity induced by the otherwise inactive D2 domain. Finally, by employing a modified algorithm originally used to identify the kinase regulatory spine in conjunction with modern machine learning techniques, we have analyzed available crystal structures of diverse PTP domains. This has led to the identification of a conformational change in F225 (PTP1B numbering) that is required for PTPs to adopt their active conformation. In total, we have defined a conserved dynamic architecture in PTPs that enables their regulation in a complex signaling environment.
Recommended Citation
Welsh, Colin L., "Defining a Dynamic Architecture of Protein Tyrosine Phosphatases" (2024). MUSC Theses and Dissertations. 947.
https://medica-musc.researchcommons.org/theses/947
Rights
Copyright is held by the author. All rights reserved.