Fundamental and Quantitative Analysis of Gas-Phase Protein Structure and Structural Transitions Using Ion Mobility-Mass Spectrometry
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Date
2020-09-24
Authors
Donor, Micah
Journal Title
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Publisher
University of Oregon
Abstract
Ion mobility-mass spectrometry has become a capable, powerful tool for studying biomolecular structure and interactions. Preservation of weak non-covalent interactions into the gas phase via electrospray ionization has enabled native mass spectrometry investigations of protein complexes and protein-ligand systems. The coupling of mass spectrometry with ion mobility has allowed measurement of ion size and shape alongside mass. In addition, methods to obtain quantitative energetic information for many systems of moderate size have been introduced. However, the large size, structural dispersity, and conformational flexibility of proteins have greatly limited quantitative studies of their properties using extant methods. An additional contributing factor to this gap in knowledge has been an incomplete understanding of several mechanisms and processes commonly used in ion mobility-mass spectrometry analysis of proteins. These gaps in understanding have, in turn, constrained the range of systems and processes amenable to investigation. Introduction of creative new approaches will continue to expand the set of biological questions addressable by mass spectrometry methods.
Here, novel quantitative methods are developed and used to study the gas-phase structures and structural transitions of proteins, yielding fundamental insights into key gas-phase processes. First, the structures of highly-extended protein ions produced by supercharging electrospray ionization are found to be one-dimensional, and mechanistic insights into supercharging are obtained. Focus is then shifted to manipulating protein structure in the gas phase. The energy scales of two methods that can unfold proteins in the gas phase, collisional and surface activation, are calibrated and the efficiencies of each process studied. Surface activation is found to be much more efficient for larger proteins, and its efficiency is highly dependent on structure. Next, a method for determining activation energies for protein unfolding is introduced. Energies for protein unfolding are found to support the mobile proton model as the universal gas-phase unfolding mechanism. Lastly, the energetics of non-specific binding of lipid head groups to soluble proteins are probed.
This dissertation included previously published and unpublished co-authored material.
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Keywords
Ion energetics, Ion mobility, Native mass spectrometry, Protein Structure, Protein unfolding