Quantitative analysis of structural polymorphism in alpha-synuclein and mammalian prion protein amyloid filaments

Amyloid fibril polymorphism has direct implications for neurodegenerative disease, and distinct fibril polymorphs often underlie different disease strains and responses to treatments. Quantifying polymorphism is therefore key to understanding disease heterogeneity and will aid greatly in the development of novel therapeutics and locating drug targets. While the development of imaging techniques like cryo-EM has highlighted the existence of polymorphism in amyloid fibrils, larger scale quantitative assessment of their diversity has garnered little attention. The aim of this study was to further the understanding of structural polymorphism through comparative analysis of helical parameters between alpha-synuclein and Prion protein fibrils. Hierarchical agglomerative clustering of helical parameters and cryo-EM images was employed as complementary analysis to highlight commonalities and trends present in their geometrical variations. The analysis revealed a significant overlap in both helical parameters and local structural features between the two proteins. The most significant separations in the data were linked to disease association, experimental conditions and biological origin suggesting that external conditions have a significant impact on fibril morphology. Opposing our initial expectations, observations of cross-sectional images, analysis of 16 different helical parameters, and the clustering of both resulted in no entirely distinct or consistent preferential conformations which was further backed up with PCA and PERMANOVA statistical testing. Overall, the findings put forward a quantitative representation of fibril polymorphism and highlight how selective pressures contribute to both conformational restriction and structural flexibility. Whilst explicit therapeutic targets were not identified, this research provides both a quantitative and qualitative map of conformations between a-syn and prp on a scale not seen previously, and a framework for future investigation into selective pressures and the identification of therapeutic targets present in disease associated conformations.