Abstract
The transition of structural biology from the study of isolated proteins to the characterization of complex macromolecular assemblies has revolutionized our understanding of neurodegenerative diseases (NDs). As of January 2024, the field of structural proteomics has emerged as a cornerstone for elucidating the aberrant protein-protein interactions (PPIs) that drive pathologies such as Alzheimer’s, Parkinson’s, and Amyotrophic Lateral Sclerosis. This study employs an integrated structural proteomics workflow—combining chemical cross-linking mass spectrometry (XL-MS), nuclear magnetic resonance (NMR) spectroscopy, and advanced computational modeling—to map the interactome of key pathogenic proteins including alpha-synuclein and tau. Our methodology identified several high-confidence PPIs within mitochondrial networks that are significantly altered in disease states, particularly those involving the Arfaptin2 complex and redox-regulated ligases. Quantitative analysis revealed that post-translational modifications (PTMs), specifically phosphorylation and oxidative stress-induced changes, act as critical molecular switches that modulate the affinity and stability of these toxic assemblies. Furthermore, we utilized in silico docking and molecular dynamics to screen for small-molecule inhibitors capable of disrupting these pathological interfaces. Our results demonstrate that targeting specific PPI interfaces, rather than individual monomers, provides a more precise therapeutic strategy. The findings highlight the utility of structural proteomics in identifying novel 'druggable' pockets within the interactome, offering a roadmap for the development of next-generation neuroprotective agents. By mapping the spatial and temporal dynamics of the neurodegenerative interactome, this research facilitates a deeper understanding of the molecular mechanisms underlying cellular toxicity and provides a robust framework for future drug discovery efforts.