Identification and removal of proteins that co-purify with infectious prion protein improves the analysis of its secondary structure

Prion diseases are neurodegenerative disorders associated with the accumulation of an abnormal isoform of the mammalian prion protein (PrP). Fourier transform infrared spectroscopy (FTIR) has previously been used to show that the conformation of aggregated, infectious PrP (PrP ^Sc) varies between prion strains and these unique conformations may determine strain-specific disease phenotypes. However, the relative amounts of α-helix, β-sheet and other secondary structures have not always been consistent between studies, suggesting that other proteins might be confounding the analysis of PrP ^Sc secondary structure. We have used FTIR and LC-MS/MS to analyze enriched PrP ^Sc from mouse and hamster prion strains both before and after the removal of protein contaminants that commonly co-purify with PrP ^Sc. Our data show that non-PrP proteins do contribute to absorbances that have been associated with α-helical, loop, turn and β-sheet structures attributed to PrP ^Sc. The major contaminant, the α-helical protein ferritin, absorbs strongly at 1652cm ^-1 in the FTIR spectrum associated with PrP ^Sc. However, even the removal of more than 99% of the ferritin from PrP ^Sc did not completely abolish absorbance at 1652cm ^-1. Our results show that contaminating proteins alter the FTIR spectrum attributed to PrP ^Sc and suggest that the α-helical, loop/turn and β-sheet secondary structure that remains following their removal are derived from PrP ^Sc itself.