Thesis advisor: Eranthie Weerapana / Disulfide-bonding cysteine residues perform critical roles in the structural stabilization and redox regulation of protein function. Secreted proteins are often enriched for structural disulfide bonds conferring conformational stability in the oxidizing extracellular environment. The controlled formation of disulfide bonds in secreted proteins is regulated in the endoplasmic reticulum (ER) by the protein disulfide isomerase (PDI) family. To investigate disulfide-bond formation in the ER, quantitative chemical-proteomic methods were coupled to subcellular-fractionation-based ER enrichment. Cysteine reactivity studies identified highly reactive post-translationally modified cysteine residues including disulfide-bonding cysteines. Upon discovering a highly reactive population of traditionally oxidized cysteines, the percentage of oxidation for cysteines localizing to the ER was determined. Next, ER function was chemically perturbed to evaluate changes to cysteine oxidation following upregulation of the unfolded protein response (UPR). Disulfide bond formation was specifically disrupted in the ER by CRISPR-Cas9-mediated PDIA1 and PDIA4 knockout. The effects of PDI knockout on cancer cell phenotype and changes to cysteine oxidation states were evaluated. Finally, in vitro studies were performed to evaluate PDIA4 oxidase activity and identify potential PDIA4-selective inhibitors. In the future, the platforms developed within may be applied to profiling changes to cysteine oxidation in other biological systems such as other organelles and disease states. / Thesis (PhD) — Boston College, 2019. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.