Mechanism of Aggregation of the NACore of α-Synuclein: Stable Oligomer Formation Competes with Fibril Formation with Implications for the Etiology of Parkinson’s Disease

NACore peptides, derived from the hydrophobic core region of α-synuclein, serve as a critical model for understanding amyloid fibril formation, a hallmark of neurodegenerative diseases such as Parkinson's. This study integrates atomic force microscopy (AFM), ion mobility-mass spectrometry (IM-MS), and molecular dynamics (MD) simulations to investigate the structural dynamics of NACore aggregation under varying conditions of time, concentration, and pH. The results reveal distinct concentration-dependent aggregation pathways, where stable early-stage oligomers such as tetramers and hexamers form at low concentrations while fibril formation predominates at higher concentrations. A subtle change in environmental pH significantly modulates these pathways: neutral pH (7.4) facilitates the formation of diverse and relatively stable oligomeric species, including hexamers and octamers, while basic pH (8.0) stabilizes tetramers as off-pathway intermediates that may delay fibril formation. Conversely, at acidic pH (6.8), oligomerization is limited, with the system predominantly remaining monomeric and small, with unstable oligomers likely acting as fibril precursors. AFM and IM-MS characterize oligomer size and stability, while MD simulations highlight the molecular stability of cylindrin-like tetramers and hexamers. These findings emphasize the complexity of NACore aggregation and provide valuable insights into oligomer formation pathways, thereby providing opportunities to design potential therapeutic strategies targeting specific intermediates to modulate amyloid formation.