Repositioning ion mobility spectrometry-mass spectrometry for novel applications: Structural elucidation of amyloid oligomers and detection of endogenous peptides

Author

Sarah Summers HirschbeckFollow

Orcid ID

0009-0000-0201-6960

Date of Award

5-2025

Degree Type

Dissertation

Degree Name

Doctor of Philosophy

Major

Chemistry

Major Professor

Thanh Do

Committee Members

Tessa Calhoun, Michael Best, Francisco Barrera

Abstract

A hallmark of neurodegenerative diseases is the misfolding and aggregation of small peptides into soluble oligomers and insoluble fibrils. Amyloid oligomers (AOs) are particularly toxic, making their study crucial for therapeutic development. However, their transient and heterogeneous nature complicates detection using traditional methods. Ion mobility spectrometry-mass spectrometry (IMS-MS) addresses this by separating oligomers of the same m/z based on size and charge. This dissertation leverages IMS-MS to study the structure and mechanisms of AOs and endogenous peptides.

Chapter 2 explores how IMS-MS supports X-ray crystallography (XRC) by identifying SOD1 peptides that form stable oligomers, improving their crystallization likelihood. Key traits include abundant high-order oligomers, sharp oligomer peaks, a single monomer peak, and resistance to fibril formation. This work also suggests that AOs may adopt multiple configurations, with XRC capturing the most stable forms.

Chapter 3 examines the toxic mechanisms of a mutant αB-crystallin peptide, G6W, which forms a double-helix dodecamer resembling lipid transport proteins. G6W binds strongly to lipids with unsaturated, 16-carbon alkyl chains which is a specificity not observed in other AOs lacking the double-helix motif. While current hypotheses suggest amyloid-lipid complexes perforate membranes, our findings propose a novel mechanism in which soluble AOs disrupt lipid homeostasis through selective protein-ligand interactions.

In Chapter 4, we investigate tau oligomers and their role in seeding toxic fibrils. We examine the interactions between two tau peptides, Tau_PHF43 and jR2R3^P301L, which form hetero-oligomers potentially initiating jR2R3^P301L’s fibril seeding mechanism. Since soluble AOs have a high potential for cell-to-cell transmission, their ability to spread may exacerbate tau pathology and understanding their mechanisms is essential for the development of future drug treatments.

Chapter 5 presents an LC-IMS-MS homogenization method to detect structural features of endogenous peptides and proteins. This method can reveal conformational changes due to post-translational modifications and elucidate 3D atomic structures. Conformations like these are overlooked in traditional proteomics and peptidomics studies but are important to detect due to their potential in implicating diseases, highlighting the importance of utilizing IMS-MS for endogenous studies.

Recommended Citation

Hirschbeck, Sarah Summers, "Repositioning ion mobility spectrometry-mass spectrometry for novel applications: Structural elucidation of amyloid oligomers and detection of endogenous peptides. " PhD diss., University of Tennessee, 2025.
https://trace.tennessee.edu/utk_graddiss/12368