Nanoscopy

Misfolding of prion protein and its subsequent aggregation is the cause of various prion related diseases. Prions are composed of aggregates of a misfolded prion protein. Although primary structure of prion protein is the same, its infectious form, amyloid fibrils, exist as multiple strains. The ability of prions to generate multiple strains poses an immediate health threat, which renders studies of this phenomenon very important. The strains are thought to represent structurally dif- ferent prion protein molecules packed into amyloid fibrils. The biophysical prop- erties of the fibrils, such as fragility, represent a major mechanism of prion amplification. Here, we demonstrate that variations in environmental conditions such as pH, salt concentration, temperature and mechanical stress (stirring) pro- duces a variety of fibrillar polymorphs for a short peptide CGNNQQNY from yeast prion protein Sup35. The fibrils differ by their length and diameter as well as their ability to bundle together. We have used Tip-Enhanced Raman Scat- tering (TERS) in combination with AFM to study underlying conformational pe- culiarities of peptides within individual aggregates. Two types of fibrils were investigated, one formed in water and another one at pH 5.6. These conditions produce morphologically distinct fibrils in terms of their length and diameter. They also exhibited different kinetics of aggregation. The Raman spectra ob- tained with TERS also revealed the peptide conformational differences between these two types of fibrils. The observed differences are mostly manifested in the positions of the characteristic amide bands (I and III), suggesting that peptides in these two types of fibrils have different conformational states. This study dem- onstrates potentials of such a combined method as TERS/AFM for structural analysis of individual protein aggregates.