Amyloids of shuffled prion domains that form prions have a parallel in-register beta-sheet structure

The URE3] and PSI (+)] prions of Saccharomyces cerevisiae are self-propagating amyloid forms of Ure2p and Sup35p, respectively. The Q/N-rich N-terminal domains of each protein are necessary and sufficient for the prion properties of these proteins, forming in each case their amyloid cores. Surprisingly, shuffling either prion domain, leaving amino acid content unchanged, does not abrogate the ability of the proteins to become prions. The discovery that the amino acid composition of a polypeptide, not the specific sequence order, determines prion capability seems contrary to the standard folding paradigm that amino acid sequence determines protein fold. The shuffleability of a prion domain further suggests that the beta-sheet structure is of the parallel in-register type, and indeed, the normal Ure2 and Sup35 prion domains have such a structure. We demonstrate that two shuffled Ure2 prion domains capable of being prions form parallel in-register beta-sheet structures, and our data indicate the same conclusion for a single shuffled Sup35 prion domain. This result confirms our inference that shuffleability indicates parallel in-register structure.