Development and application of methods towards the structural characterization of gas-phase biomolecular assemblies

Sipe, Sarah Natalie
Journal Title
Journal ISSN
Volume Title

The utility of ultraviolet photodissociation mass spectrometry (UVPD-MS) in native MS approaches, including ion mobility spectrometry (IMS), for protein complexes is described in this dissertation. A modular drift tube demonstrated suitability for measuring collision cross sections (CCSs) of native-like ions on an Orbitrap mass spectrometer with high resolution using acquisition times as short as one minute. This IMS method is used throughout this dissertation for measurement of native-like and disordered structures. A fundamental study for determining the charge-dependent behavior of UVPD for protein complexes was evaluated using the homomeric Cu/Zn superoxide dismutase dimer, streptavidin tetramer, transthyretin tetramer, and C reactive protein pentamer as well as the heteromeric hemoglobin tetramer. A wide range of charge states were irradiated with 193 nm photons resulting in asymmetric charge partitioning of subcomplexes at lower energies (0.5 to 1.5 mJ/pulse) and symmetric dissociation at higher energies (1.5 to 3.0 mJ/pulse). The ability to access both of these competing dissociation pathways is unique to UVPD and contributes to the vast array of sequence ions and enhanced sequence coverage for protein complexes not obtained by any other activation method. With its ability to generate useful sequence information, UVPD was employed to study an intrinsically disordered protein, a set of asymmetric and symmetric trimers, and three membrane protein complexes. The vast population of structures adopted by the intrinsically disordered protein, high mobility group protein AT-hook 2 (HMGA2), was characterized using UVPD and the probable binding location of two DNA hairpins was determined. Trimers in the tautomerase superfamily that have nearly identical secondary structures differ in their quaternary arrangements to form asymmetric and symmetric homooligomers. In combination with collision-induced unfolding, UVPD proved capable of differentiating the two structures owing to the preservation of noncovalent interactions in the gas phase. Aquaporin z (AqpZ), mechanosensitive channel of large conductance (MscL), and the E. coli ammonia channel (AmtB) comprise the membrane protein complexes studied herein. UVPD of these complexes resulted in unprecedented levels of characterization with backbone cleavages demonstrating no significant influence from the hydrophobicity of the residues or the mobile proton-directed cleavages, which contrasts reports using electron- and collision-based dissociation methods, respectively. UVPD has also proven effective for localizing phosphorylated residues along the C-terminal domain (CTD) of RNA polymerase II, shedding light on the CTD code that mediates transcription regulation.