The cerebral prion protein (PrP) isolated in the absence of proteinase K digestion, from ruminants prion sources transmitted to ovine transgenic mice, was studied by Western blot analysis. A C2 PrP fragment, showing strain-specific cleavages, similar to those observed after proteinase K or thermolysin digestion, accumulated in the brain. 'CH1641-like' scrapie was characterized by the unique accumulation of a more C-terminally cleaved PrP fragment (CTF14). A similar, protease-resistant, PrP product was observed after proteinase K or thermolysin digestion. Whereas classical BSE appeared highly resistant to thermolysin digestion, CH1641 and 'CH1641-like' natural isolates did not show any remarkable feature regarding resistance to thermolysin. Thus, the molecular strain-specific features in the brain of transmissible spongiform encephalopathy infected mice essentially reflect the PrP proteolytic processing occurring in vivo.