QUANTITATIVE DETERMINATION OF GAS-PHASE THERMODYNAMIC BARRIERS OF PROTEINS FOR NATIVE ION MOBILITY-MASS SPECTROMETRY: APPLICATIONS AND IMPLEMENTATION OF AN IMPROVED IMPULSIVE COLLISION THEORY
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Date
2024-08-07
Authors
Shepherd, Samantha
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Publisher
University of Oregon
Abstract
Ion mobility-mass spectrometry is a powerful tool for identifying and elucidating biomolecular structures and behaviors. This technique is able to retain even weak and non-covalent interactions permitting the study of native or native-like gas-phase biomolecular complexes including folded proteins, protein-protein complexes, and protein-ligand complexes. Historically, energetic and thermodynamic information has been limited to techniques on specialized instrumentation and/or computationally expensive strategies. This changed with the development of “proto-IonSPA” to allow rapid determination of thermochemical barriers for protein dissociation and unfolding on modern, commercially available instrumentation. In this work, reproducibility, repeatability, and applications of the use of thermochemical measurements on modern, commercially available instruments are assessed, inspired by a need to compare gas-phase dissociation and unfolding of proteins more broadly. This groundwork enables the development of an Improved Impulsive Collision Theory (IICT) in a Monte-Carlo python script, which in turn improves qualitative and quantitative understanding of activation in Collision Induced Unfolding and Dissociation. This program further enables the determination of gas-phase thermochemical barriers for the dissociation of proteins in modern commercially available mass spectrometers. Reasonable agreement is shown with literature standards and between different mass spectrometer designs and experimental parameters. This agreement is particularly noteworthy due to the drastic difference in timescales being compared (seconds in the literature to as low as microseconds in this work) This dissertation includes previously published co-authored material.
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Keywords
collision induced dissociation, Collision induced unfolding, Ion mobility-mass spectrometry, native mass spectrometry, protein structure