An investigation of proteoforms in health and disease using peptide-level readouts

Abstract

Proteins are the biomolecules that drive the functions of life. To fully appreciate and understand the role of protein diversity in health and disease, we must seek a deeper understanding of proteoforms - the molecular variants of canonical proteins. Although humans have around 20,000 protein-coding genes, millions of proteoforms arise through mutations, splicing, and post-translational modifications. My thesis work focuses on two proteoform types: missense mutations and phosphorylation. In Chapter 2, I demonstrate the utility of pooled mass spectrometry (MS)-based assays to measure solubility and thermal stability of missense mutations. Using ten disease-causing mutants of the human phosphoglucomutase 1 (PGM1) protein, we achieved improved resolution using our pooled MS assays compared to previously published studies that relied on individually purified mutants. Scaling of this approach to larger mutant libraries and diverse biochemical assays will significantly enhance our understanding of how missense mutations affect protein function and contribute to variant classification in disease contexts. Chapter 3 discusses proteoforms generated by phosphorylation, a post-translational modification that enables proteins to rapidly and reversibly alter their properties and functions. We investigate the phosphorylation signatures in response to osmotic, heat, and oxidative stresses. We identify shared and stress-type specific phosphorylation signatures that align with previously reported data. We also identify phosphorylation sites on proteins known to localize to stress granules, providing a candidate list of stress granule phosphorylation sites for mechanistic investigation. Together, these chapters highlight the power of MS-based methods for characterizing proteoforms and their roles in health and disease.