Heterogeneity in transmissible spongiform encephalopathy is thought to have derived from conformational variation in an abnormal isoform of the prion protein (PrPSc). To characterize PrPSc in bovine spongiform encephalopathy (BSE) and scrapie, we analyzed the newly generated N-terminus of PrPSc isoforms by digestion with proteinase K (PK). With a lower concentration of PK, the terminal amino acid of BSE PrPSc converged at N-96. Under the same conditions, however, the terminal amino acid of scrapie PrPSc was G(81) or G(85). Furthermore, with an increase of PK concentration, the N-terminal amino acid was shifted and converged at G(89). The results suggest that the PK cleavage site of BSE PrPSc is uniform and is different from the cleavage site of scrapie PrPSc. (C) 2005 Elsevier Inc. All rights reserved.