Dissertations, Theses, and Capstone Projects

Date of Degree

6-2023

Document Type

Dissertation

Degree Name

Ph.D.

Program

Biochemistry

Advisor

Daniel A. Keedy

Committee Members

Kevin Gardner

Ranajeet Ghose

Thomas Kurtzman

Avner Schlessinger

Subject Categories

Biochemistry, Biophysics, and Structural Biology

Keywords

PTP1B, allostery, multitemperature X-ray crystallography, ligand binding, structure based drug design (SBDD), computational structural biology

Abstract

Allostery is central to regulation of protein function, but our mechanistic understanding remains incomplete. A deeper understanding of how redistributions of conformational states drive allostery in proteins could allow us to better grasp natural regulatory principles in cells and open new doors to therapeutic development. Conformationally dynamic human Protein Tyrosine Phosphatases (PTPs) exemplify the challenges and opportunities associated with allostery. The archetypal PTP, PTP1B, has been highly validated as a therapeutic target but no allosteric inhibitors have been approved for clinical use. This is largely because our understanding of the mechanisms underlying allostery in PTP1B remains limited, despite the discovery of putative allosteric sites in PTP1B.

In the work described in this dissertation, I used high-throughput small-molecule fragment soaking and room-temperature X-ray crystallography to determine how temperature affects the occupancy, pose, and location of small-molecule fragments binding to PTP1B. These structures also indicated that temperature can modulate protein conformational responses to ligand binding, leading to new insights into allosteric networks. Building on fragment-bound structures, I worked to apply structure based drug design (SBDD) methods to design allosteric molecules that can modulate PTP1B function. In particular, I designed a new approach to bias the conformational ensemble of the targeted allosteric site using multistate docking simulations. I also worked with biotech companies who applied their technologies to a SBDD approach to design potential allosteric modulators. We uncovered both allosteric inhibitors and benign binders, and I determined the crystal structure of a designed compound bound to the targeted allosteric site in PTP1B. Lastly, I used computational and molecular modeling to map clinically relevant PTP mutations onto the structures of PTP1B and a close homolog, T-Cell Protein Tyrosine Phosphatase (TCPTP), and uncovered that the mutations likely enact their functional effects by perturbing allosteric sites and allosteric networks of the protein.

Overall, this research, which marries unique techniques in experimental X-ray crystallography and computational structural biology, provides unique insights into protein-ligand interactions, particularly for allosteric sites, and provides promising new allosteric ligand footholds for a biomedically important enzyme. More broadly, this work will improve our general understanding of how transitions between multiple conformational states underlie allosteric regulation.

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