Mass spectrometry (MS) serves as an indispensable technology for modern pharmaceutical drug discovery and development processes, where it is used to assess ligand binding to target proteins and to search for biomarkers that can be used to gauge disease progression and drug action. However, MS is rarely treated as a screening technology for the structural consequences of drug binding. Instead, more time-consuming technologies capable of projecting atomic models of protein-drug interactions are utilized. In this thesis, ion mobility-mass spectrometry (IM-MS) methods are developed in order to fill these technology gaps. Principle among these is collision induced unfolding (CIU), which leverages the ability of IM to separate ions according to their size and charge, in order to fingerprint gas-phase unfolding pathways for non-covalent protein complexes.
Following a comprehensive introductory chapter, we demonstrate the consequences of sugar binding on the CIU of Concanavalin A (Con A) in Chapter 2. Our CIU assay reveals cooperative stabilization upon small molecule binding, and such effect cannot be easily detected by solution phase assays, or by MS alone. In Chapter 3, the underlying mechanism of multi-protein unfolding is systematically investigated by IM-MS and molecular modeling approaches. Our results show a strong positive correlation between monomeric Coulombic unfolding and the tetrameric CIU process. This provides strong evidence that multi-protein unfolding events are initiated primarily by charge migration from the complex to a single monomer. In Chapter 4, the interactions between human histone deacetylase 8 (HDAC8) and poly-r(C)-binding protein 1 (PCBP1) are investigated by IM-MS. Our data suggest that these proteins interact with each other in a specific manner, a fact revealed by our optimized ESI-MS workflow for quantifying binding affinity (KD) for weakly-associated hetero-protein complexes. In Chapter 5, the translocator protein (TSPO) dimer from Rhodobacter sphaeroides, as well as its disease-associated variant forms, is analyzed by IM-MS and CIU assays. By utilizing a combination of CIU and collision induced dissociation (CID) stability data, an unknown endogenous ligand bound to TSPO is detected and identified.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/116693/1/shuainiu_1.pd
