Discriminating Strains of Self-Propagating Protein Aggregates Using a Conformational Stability Assay

Prions and other self-propagating protein aggregates can exist as distinct strains, which are thought to represent different conformations of aggregates. There is growing evidence that protein aggregate strains may be important for understanding the biology of common neurodegenerative disorders, such as Alzheimer's disease and Parkinson's disease. While methodology for discriminating prion strains is in widespread use, there is a paucity of tools for comparing the conformational properties of aggregates composed of β-amyloid (Aβ) peptide or α-synuclein protein, particularly when present in complex samples such as brain extracts. The conformational stability assay (CSA) is a simple technique that measures the relative resistance of protein aggregates to chemical denaturation. While originally developed to differentiate prion strains, the CSA has since been adapted for use with other protein aggregates. Here, we describe the CSA in detail and outline its utility for distinguishing prion strains as well as unique conformational states of Aβ and α-synuclein aggregates.