Orientation of aromatic residues in amyloid cores: Structural insights into prion fiber diversity

Significance Amyloids, which are protein fiber aggregates, are often associated with neurodegenerative diseases such as Alzheimer’s, but they can also be beneficial, as in yeasts, where they help cells adapt to environmental changes. Intriguingly, the same protein has the ability to aggregate into different fiber forms, known as strains, that generate distinct biological phenotypes. Structurally, little is known about strains. Using polarized light spectroscopy, we provide structural information on two distinct phenotypic strains of the yeast translation termination factor, Sup35. Remarkably, they show similar orientation of aromatic residues in the fiber core relative to the fiber direction, suggesting similar structures. Small variations are observed, indicating different local environments for aromatic residues outside the core, reflecting differences in fiber packing. Structural conversion of one given protein sequence into different amyloid states, resulting in distinct phenotypes, is one of the most intriguing phenomena of protein biology. Despite great efforts the structural origin of prion diversity remains elusive, mainly because amyloids are insoluble yet noncrystalline and therefore not easily amenable to traditional structural-biology methods. We investigate two different phenotypic prion strains, weak and strong, of yeast translation termination factor Sup35 with respect to angular orientation of tyrosines using polarized light spectroscopy. By applying a combination of alignment methods the degree of fiber orientation can be assessed, which allows a relatively accurate determination of the aromatic ring angles. Surprisingly, the strains show identical average orientations of the tyrosines, which are evenly spread through the amyloid core. Small variations between the two strains are related to the local environment of a fraction of tyrosines outside the core, potentially reflecting differences in fibril packing.