Methods and Informatics for Gas-Phase Structural Biology and Drug Discovery

Abstract

Methods for rapid interrogation of structure and stability attributes of proteins and protein complexes are becoming increasingly important for developing our understanding of biology and the development of pharmaceuticals. Gas-phase technologies such as mass spectrometry and ion mobility spectrometry have proven valuable in these endeavors, as they provide unique perspectives on the solution-phase equilibrium of protein complexes and their conformations. Before fully harnessing the information derived from these gas-phase techniques, new approaches for data analysis and mechanistic understanding of gas-phase protein structure are necessary. In this dissertation, we develop ion mobility mass spectrometry methods and informatics for the study of gas-phase proteins, multiprotein complexes, and protein-small molecule complexes. In the first half of the dissertation, novel data analysis tools and experimental methodologies are outlined for the study of gas-phase protein unfolding. After providing the software tools necessary for robust analysis of gas-phase unfolding trajectories in Chapter 2, we turned our attention to understanding the mechanism of unfolding for large multidomain proteins. In Chapter 3, we focus on the factors driving changes in unfolding trajectories for a variety of serum albumin homologues, and through the use of novel unfolding experiments utilizing chemical probes and non-covalent protein constructs, a detailed mechanism for solvent-free protein unfolding is provided.

Subsequent chapters in the dissertation focus on the characterization of multiprotein complexes, especially through the use of ion mobility-mass spectrometry and coarse-grained modeling. In chapter 4, we develop and benchmark new algorithms for translating ion mobility and mass spectrometry datasets into coarse grained models. These studies outline the limits in current coarse-graining methodologies, and define the minimum restraint sets necessary to generate high confidence multiprotein models. Additionally, best practices for dealing with ambiguous models resulting from sparse datasets are described. In chapter 5, the tools developed in the previous chapter are applied to structurally characterize the urease pre-activation complex, a transient 18-subunit complex that is a target for inhibition of urease-related pathology. When our ion mobility-mass spectrometry datasets are combined with previously published chemical crosslinking and x-ray scattering data, a discrete population of conformations for the urease pre-activation complex emerges which compares favorably to previous models generated using computational techniques. In Chapter 6, I highlight more applications of ion mobility-mass spectrometry to engineered and naturally occurring protein complexes. These applications highlight the power of ion mobility mass-mass spectrometry datasets for rapid analysis of protein oligomerization state and structure, providing a basis for further integration of the technology into pharmaceutical and structural biology workflows.