Semester
Fall
Date of Graduation
2024
Document Type
Dissertation
Degree Type
PhD
College
Eberly College of Arts and Sciences
Department
Chemistry
Committee Chair
Stephen J. Valentine
Committee Member
Peng Li
Committee Member
Brian Dolinar
Committee Member
Fabien Goulay
Committee Member
Mikel Holcomb
Abstract
Over the last two decades, mass spectrometry (MS) has received significant interest in biological study platforms, especially in the areas of proteomics and metabolomics. With the development of soft ionization methods like electrospray ionization (ESI), mass spectrometry has emerged as a potent method for directly characterizing proteins in their native state. The recent invention of capillary vibrating sharp-edge spray ionization has opened new avenues for the study of biopolymer native structure including the usage of droplet charge tuning and in-droplet hydrogen-deuterium exchange (HDX) labeling. With this new technique comes the opportunity to study biopolymer ion structure preservation with molecular dynamics (MD) simulations. In this work, cVSSI-MS-based techniques and MD simulations have been used to explore protein structure and conformation under different analyte and solution conditions. In Chapter 2, experiments revealed a connection between a protein’s ability to form salt-bridge stabilization and the number of attached adducts. This suggests transfer of adduct species via the charged residue model (CRM) of ionization. Additionally, MD simulations have been utilized to propose ion production via various putative ionization pathways for proteins with increased conformational flexibility in solutions. It is shown in Chapter 3 that using cVSSI in combination with supercharging techniques results in greater average charge state and ion intensity as observed for ESI. Further experiments employing a dual-emitter cVSSI setup for in-droplet HDX reveal isotopic distributions of different ions of supercharged ubiquitin that are very similar to those obtained upon protein denaturation by incubation in 10% to 40% methanol. Thus, for the first time, a degree of protein denaturation achieved by increased organic solvent is tied to that inflicted by supercharging. In Chapter 4, MD simulations are conducted to understand the degree of protein denaturation achieved with this methanol addition. This work represents the first attempt to locate preferred sites of deuterium incorporation in a 40% methanol solution using MD simulations. Finally, Chapter 5 explores potential applications for utilizing cVSSI experiments complemented by theoretical methods to obtain more information about large biomolecule structures and conformational dynamics under different conditions.
Recommended Citation
Hajian Foroushani, Samira, "Conformational Investigation of Biopolymers through Molecular Dynamics (MD) Simulations and in-Droplet HDX-MS utilizing cVSSI" (2024). Graduate Theses, Dissertations, and Problem Reports. 12649.
https://researchrepository.wvu.edu/etd/12649
