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

Abstract

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.linear dichroism | polarized light | prion proteins | Sup35 strains | tyrosine

Modulation of prion polymerization and toxicity by rationally designed peptidomimetics

“…These results corroborated that the large ring structure of Trp could entail steric hindrance to the amyloidogenic assembly of prions [103]. Our results are in agreement with a recent report by Reymer et al [104] where heterogeneity in orientation and environment of aromatic residues was shown to define the variations in Sup35 prion strains. Due to their hydrophobic bispidine scaffold and specific amino acid residues, interaction between BPMs and HuPrP could hinder/facilitate HuPrP self-assembly and hence block/trigger amyloid aggregation.…”

Combining DNP NMR with segmental and specific labeling to study a yeast prion protein strain that is not parallel in-register

“…1). To do so, we prepared chimeric His 6 -NM[ (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14) ]-Npu[ (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25) ]-His 6 , expressed in natural-abundance media (Fig. 1C).…”

“…However, the PITHIRDS-CT does not report on the chemical identity of the other isotopically labeled site, and the extracted distances are very sensitive to how the geometry of neighboring spins is modeled (16). Moreover, the highly degenerate nature of NM complicates interpretation of inter-versus intramolecular interactions for specifically labeled molecules, particularly for aromatic residues that may participate in ring stacking (19). Thus, differentiating between these two models for amyloid quaternary structure requires additional experimental approaches.…”

The Structure and Dynamics of Higher-Order Assemblies: Amyloids, Signalosomes, and Granules

“…Different amyloid strains formed under different conditions can exhibit alternative contacts within the same sequence (Sawaya et al, 2007). Yeast prion Sup35 strains show variations in core lengths, intermolecular contacts, and side chain chemical environments or orientations (Frederick et al, 2014; Krishnan and Lindquist, 2005; Reymer et al, 2014). Additionally, the sequence of the Sup35 LCD can be randomized without blocking amyloid formation (Ross et al, 2005).…”