Hydrogen-deuterium exchange/mass spec analysis of PrPSc derived from mouse brains reveals that the infectious form of the prion adopts conformations that differ substantially from those previously postulated by various structural models. One of the mysteries in prion research is the structure of the infectious form of mammalian prion protein PrPSc. Here we used mass spectrometry analysis of hydrogen-deuterium exchange to examine brain-derived PrPSc. Our data indicate that, contrary to popular models, prion-protein conversion involves refolding of the entire region from residue ~80–90 to the C-terminus, which in PrPSc consists of β-strands and relatively short turns and/or loops, with no native α-helices present.