Imals, characterized by an abnormal accumulation of prion protein (PrP) [1,2], primarily in the brain. Prions replicate by converting the normal non-infectious cellular prion protein (PrPC) into a prion (PrPSc), via a poorly characterized post-translational conformational transformation. In mice, PrP contains approximately 209 amino acids (numbered 23?31 after cleavage of a 22?mer Epigenetics signal peptide) and has four covalent post-translational modifications: two Epigenetic Reader Domain asparagine N-linked glycans at residues N180 and N196, a disulfide bridge between residues C178 213 and a glycosylphosphatidylinositol (GPI) anchor attached to the Cterminus of the protein (residue S231) [2,3]. Mouse PrPC is a monomer, while PrPSc is a heterogeneous multimer [2,3]. There have been no demonstrated covalent differences between mouse PrPSc and PrPC. The only difference between PrPSc and PrPC is conformational; they are isoforms [2]. The structure of folded, monomeric, recombinant PrP, highly likely to be identical to that of PrPC, has been solved by NMR spectroscopy [4] and X-ray crystallography [5]. In contrast, the structure of PrPSc remains unclear because the insolubility of PrPScand the failure to crystallize the heterogeneous PrPSc multimers prevent the application of the mentioned high resolution analytical techniques. However, a variety of lower resolution instrumental techniques have provided some information about the structure of PrPSc. 
Unlike PrPC, PrPSc is partially resistant to proteinase K (PK) digestion [2,6]. The secondary structure of PrPC is largely composed of unstructured and a-helical regions, while PrPSc is largely composed of b-sheet with little, if any, a-helix [7,8,9]. The structure of PrPSc has also been studied using electron microscopybased analysis of two-dimensional crystals of the PK resistant core of Syrian hamster (SHa) PrPSc (PrP27?0) [10,11] and mass spectrometry(MS)-based analysis of hydrogen/deuterium exchange [9]. Although theoretical models for PrPSc have been proposed [10,12], there is an insufficient amount of experimental data to reach a definitive consensus. In a previous study, we used limited proteolysis to elucidate structural features of PrPSc [13]. Conformational parameters such as surface exposure of amino acids, flexibility, and local interactions correlate well with limited proteolysis. Peptide bonds located within b-strands are resistant to proteolytic cleavage, whereas peptide bonds within loops and, more rarely, a-helices may be cleaved [14]. Therefore, the targets for limited proteolysisStructural Organization of Mammalian Prionsare locally unfolded or highly flexible segments [14]. In our previous study [13], we demonstrated the usefulness of combining limited proteolysis and mass spectrometry (MS) to obtain structural information about two strains of hamster PrPSc. We concluded that the amino-terminal half of PrPSc features a series of short PK-resistant stretches, presumably b-strands, interspersed with short PK-sensitive stretches, likely loops and turns. Unfortunately, the structural information was largely limited to the Nterminal portion of the protein, as a consequence of the covalent attachment of the heterogeneous GPI anchor and the heterogeneous asparagine-linked sugar antennae to amino acids in the Cterminal portion of the molecule, which prevented MS-based analysis of this part of the molecule. Here we extended our studies of the structure of PrPSc, by using transgenic (tg) mice expressing PrPC lacking t.Imals, characterized by an abnormal accumulation of prion protein (PrP) [1,2], primarily in the brain. Prions replicate by converting the normal non-infectious cellular prion protein (PrPC) into a prion (PrPSc), via a poorly characterized post-translational conformational transformation. In mice, PrP contains approximately 209 amino acids (numbered 23?31 after cleavage of a 22?mer signal peptide) and has four covalent post-translational modifications: two asparagine N-linked glycans at residues N180 and N196, a disulfide bridge between residues C178 213 and a glycosylphosphatidylinositol (GPI) anchor attached to the Cterminus of the protein (residue S231) [2,3]. Mouse PrPC is a monomer, while PrPSc is a heterogeneous multimer [2,3]. There have been no demonstrated covalent differences between mouse PrPSc and PrPC. The only difference between PrPSc and PrPC is conformational; they are isoforms [2]. The structure of folded, monomeric, recombinant PrP, highly likely to be identical to that of PrPC, has been solved by NMR spectroscopy [4] and X-ray crystallography [5]. In contrast, the structure of PrPSc remains unclear because the insolubility of PrPScand the failure to crystallize the heterogeneous PrPSc multimers prevent the application of the mentioned high resolution analytical techniques. However, a variety of lower resolution instrumental techniques have provided some information about the structure of PrPSc. Unlike PrPC, PrPSc is partially resistant to proteinase K (PK) digestion [2,6]. The secondary structure of PrPC is largely composed of unstructured and a-helical regions, while PrPSc is largely composed of b-sheet with little, if any, a-helix [7,8,9]. The structure of PrPSc has also been studied using electron microscopybased analysis of two-dimensional crystals of the PK resistant core of Syrian hamster (SHa) PrPSc (PrP27?0) [10,11] and mass spectrometry(MS)-based analysis of hydrogen/deuterium exchange [9]. Although theoretical models for PrPSc have been proposed [10,12], there is an insufficient amount of experimental data to reach a definitive consensus. In a previous study, we used limited proteolysis to elucidate structural features of PrPSc [13]. Conformational parameters such as surface exposure of amino acids, flexibility, and local interactions correlate well with limited proteolysis. Peptide bonds located within b-strands are resistant to proteolytic cleavage, whereas peptide bonds within loops and, more rarely, a-helices may be cleaved [14]. 
Therefore, the targets for limited proteolysisStructural Organization of Mammalian Prionsare locally unfolded or highly flexible segments [14]. In our previous study [13], we demonstrated the usefulness of combining limited proteolysis and mass spectrometry (MS) to obtain structural information about two strains of hamster PrPSc. We concluded that the amino-terminal half of PrPSc features a series of short PK-resistant stretches, presumably b-strands, interspersed with short PK-sensitive stretches, likely loops and turns. Unfortunately, the structural information was largely limited to the Nterminal portion of the protein, as a consequence of the covalent attachment of the heterogeneous GPI anchor and the heterogeneous asparagine-linked sugar antennae to amino acids in the Cterminal portion of the molecule, which prevented MS-based analysis of this part of the molecule. Here we extended our studies of the structure of PrPSc, by using transgenic (tg) mice expressing PrPC lacking t.