Distinct Prion Strains Are Defined by Amyloid Core Structure and Chaperone Binding Site Dynamics

• Amyloid cores of strong and weak prion fibers are structurally distinct
• Chaperone binding site is more dynamic in weak prion fibers than strong prion fibers
• Interaction of weak and strong prion fibers with Hsp104 are different in vivo
• Both the amyloid core and the dynamics of chaperone binding define prion strains

SummaryYeast prions are self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that produce distinct phenotypes. Using magic-angle spinning nuclear magnetic resonance spectroscopy, we provide a detailed look at the dynamic properties of these forms over a broad range of timescales. We establish that different prion strains have distinct amyloid structures, with many side chains in different chemical environments. Surprisingly, the prion strain with a larger fraction of rigid residues also has a larger fraction of highly mobile residues. Differences in mobility correlate with differences in interaction with the prion-partitioning factor Hsp104 in vivo, perhaps explaining strain-specific differences in inheritance.