Phase separation leads to significant conformational change in the N-terminal region of the prion protein

Abstract

Understanding the link between phase separation (PS) of disease-linked proteins to form liquid-like condensates, and their aggregation, requires insights into the conformational changes that the proteins undergo inside the condensates as they age and become solid-like. In this study, the structural changes undergone by the mouse prion protein (moPrP) inside condensate induced by PS have been characterized. Hydrogen-deuterium exchange in conjunction with mass spectrometry reveals that the N-terminal region (NTR), which is unstructured in monomeric native moPrP, gains significant stable structure as the condensate ages. The structured C-terminal domain remains native-like, albeit with higher stability, but subtle changes are seen. Conformational change initiates in the native monomer inside the condensate, with different regions undergoing rapid, slow, or no conformational change as it ages. The β1-α1 loop undergoes rapid conformational change to lose stability, while the NTR gains structure slowly concomitantly with conformational change at the C-terminal end of α3. Infrared (IR) spectroscopy shows that β-structure forms, IR and circular dichroism spectroscopy indicate that secondary structure becomes heterogeneous, and dynamic light scattering measurements reveal that the protein forms oligomeric nanoscale assemblies as the condensate ages. The formation of the nanoscale assemblies inside the condensate is responsible for the fraction of protein present as mobile monomer decreasing with time of aging, when fluorescence recovery after photobleaching is quantified. Such assembly and the resultant conformational change in the protein appear to be responsible for a change in its material properties of the condensate, which manifests itself as a liquid-like to solid-like transition.