Investigating the role of allostery through changes in protein stability and dynamics

Abstract

Allostery is the presence of a communication network that links functional sites of a protein that are distal from one another. The existence of an allosteric network can be observed through conformational change or a change in protein dynamics. These networks can be used to provide insight into the mechanistic function of proteins or protein complexes. In this thesis, four protein complexes were studied (RPA, HBV, Cascade, and Csy) and allosteric networks within the complexes were observed by monitoring the changes in protein dynamics upon an energy perturbation. To measure the changes in protein dynamics, hydrogen deuterium exchange mass spectrometry was used. This technique allows for the determination of how often the hydrogen bonding within a protein structure is broken. By tracking the longevity of the hydrogen bonding network that comprises the studied protein's structure, the dynamics of the protein can be studied. In this work, each of the proteins had changes in protein dynamics that were distal from the site of the energy perturbation that had functional impacts on each of the protein complexes. The combined presence of the distal changes in dynamics with an effect on protein function fits the definition of allostery. If allostery is present in these four diverse systems, is it possible that allostery is present in all proteins?