Some proteins can undergo non-covalent polymerization coupled with conformational rearrangement, resulting in the formation of amyloid fibrils with regular cross-β-sheet structure. Such fibrils tend to stick together, forming intra- or extracellular amyloid aggregates. Amyloid formation causes about 30 diseases, also called amyloidoses, many of which are neurodegenerative, including Alzheimer, Parkinson, and Huntington diseases 
. Amyloidoses are thought to be noninfectious, except for the prion diseases related to the PrP protein, which include Creutzfeldt-Jacob disease, sheep scrapie, and other transmissible spongiform encephalopathies.
Prions were also found in fungi, mostly in the yeast Saccharomyces cerevisiae
, where they define various heritable phenotypes. Yeast prions represent a convenient model for studying the basic properties of prions. Among them, [PSI+
] is probably the best studied. This prion is related to the heritable polymerization of translation termination factor eRF3, also called Sup35, which reduces efficiency of translation termination resulting in a nonsense-suppressor phenotype. The S. cerevisiae
Sup35 protein consists of three domains 
. Its amino-terminal N domain (amino acid residues (aa) 1–123), also called prion domain (PrD), is responsible for the prion properties of the protein, being necessary for its polymerization both in vivo
and in vitro
. The Sup35 PrD can be split into two areas, one of which (aa 1–40) is especially rich in glutamine (Q) and asparagine (N), while another (aa 41–123) contains five and a half imperfect oligopeptide repeats and has a high proportion of tyrosine, glycine and proline. The carboxyl-terminal C domain of Sup35 (aa 254–685) is responsible for the translation termination activity of the protein 
. The Sup35 middle M domain (aa 124–253) probably serves as a spacer between the N and C domains and contains a binding site (aa 129–148) for the Hsp104 chaperone 
. The propagation of [PSI+
] requires Hsp104 
, which fragments Sup35 polymers, thus multiplying Sup35 prion particles 
. Similarly to mammalian prions, yeast prions, and [PSI+
] in particular, can exist in different phenotypic variants. “Strong” [PSI+
] variants, as compared to “weak” ones, show more efficient nonsense suppression and higher mitotic stability. These phenotypic differences are defined by variation in the fragmentation frequency of Sup35 polymers, which is higher in strong [PSI+
] variants 
. However, the structural elements of prion polymers, which determine their fragmentation frequency, remain unclear.
Amyloid and prion polymers are distinguished by high physical strength. In contrast to other large protein structures, they are insoluble at room temperature in strong ionic detergents such as sodium lauroyl sarcosinate (Sarcosyl) and sodium dodecyl sulphate (SDS), allowing to analyze the size of these polymers using agarose electrophoresis in the presence of these detergents (SDD-AGE) 
. The fragmentation frequency can be judged by the size of prion polymers, with one being inversely proportional to the other. Remarkably, this dependence is unambiguous, i.e. the size should not depend on other parameters, such as rate constants for polymerization and prion synthesis 
The prionogenic properties of Sup35 and most other yeast proteins rely on their Q/N-rich PrDs, which makes them similar to amyloidogenic proteins with expanded polyglutamine (polyQ) domains, such as the human huntingtin protein. However, in contrast to yeast prions, polymers of polyQ proteins are poorly fragmented in yeast and have a large size 
Chaperones are known to recognize misfolded proteins by binding to exposed hydrophobic residues 
, and so we proposed that the frequency of amyloid polymer fragmentation mainly depends on recognition of such residues by Hsp104 and/or its co-chaperones. In agreement with this, insertion of tyrosine residues into polyQ stretches strongly decreased the size of SDS-resistant polymers, indicating that polymer fragmentation was greatly increased 
. Another factor which is thought to influence the fragmentation of amyloid polymers by chaperones is physical stability of polymers. This assumption stems from the observation that the better fragmentation of strong [PSI+
] Sup35 polymers correlates with their higher fragility 
. The fragility of these polymers can be related to observations that in them a smaller portion of the PrD is tightly packed into the amyloid core.
Here, we studied the effects of various amino acid residues inserted into polyQ stretches on amyloid formation and fragmentation in yeast. The most efficient fragmentation was caused by insertion of aromatic residues tyrosine, tryptophan and phenylalanine, while strongly hydrophobic residues valine and isoleucine did not promote fragmentation. Our data also show that the size of amyloid polymers does not always correlate with their thermal stability, indicating that physical stability of polymers does not define the susceptibility to fragmentation.