Elucidation of the structure of PrP Sc continues to be one of the most important and difficult challenges in prion research. This task, essential for gaining an understanding of the basis of prion infectivity, has been hampered by the insoluble, aggregated nature of this molecule. We used a combination of chemical cross-linking, proteolytic digestion, and mass spectrometry (MALDI-TOF and nanoLC-ESI-QqTOF), in an attempt to gain structural information about PrP 27-30 purified from the brains of Syrian hamsters infected with scrapie. The rationale of this approach is to identify pairs of specific amino acid residues that are close enough to each other to react with a bifunctional reagent of a given chain length. We cross-linked PrP 27-30 with the amino-specific reagent bis(sulfosuccinimidyl) suberate (BS 3 ), obtaining dimers, trimers, and higher-order oligomers that were separated by SDS-PAGE. In-gel digestion followed by mass spectrometric analysis showed that BS 3 reacted preferentially with Gly90. A cross-link involving two Gly90 amino termini was found in cross-linked PrP 27-30 dimers, but not in intramolecularly crosslinked monomers or control samples. This observation indicates the spatial proximity of Gly90 amino termini in PrP 27-30 fibrils. The Gly90-Gly90 cross-link is consistent with a recent model of PrP 27-30, based on electron crystallographic data, featuring a fiber composed of stacked trimers of PrP monomers; specifically, it is compatible with cross-linking of monomers stacked vertically along the fiber axis but not those adjacent to each other horizontally in the trimeric building block. Our results constitute the first measured distance constraint in PrP Sc .Prions were originally defined as "proteinaceous infectious particles", and very substantial and diverse evidence has accumulated to suggest that, indeed, their only component might be an intrinsically infectious protein (2). Transmissible spongiform encephalopathies (TSEs), 1 a group of fatal neurodegenerative diseases affecting humans and animals, are associated with a prion, termed PrP (prion protein) (2-6). PrP can exhibit two conformations, PrP C and PrP Sc . The latter is associated with TSEs, and PrP showing the physicochemical characteristics of PrP Sc is isolated as the main and most probably only component of the TSE infectious agent. PrP C can convert into PrP Sc in the presence of preformed PrP Sc , through a poorly understood molecular process (6, 7). The structure of PrP C has been characterized by NMR (8), but that of PrP Sc is largely unknown, as its insolubility in nondenaturing solvents has seriously hampered analytical efforts. It is known, however, that PrP Sc and PrP C differ with respect to secondary, tertiary, and quaternary structure (3,9). No covalent differences have been detected between the two molecules (10), although the possibility that post-translational modifications of a small set of PrP C molecules could trigger structural changes relevant to initiation of conversion to PrP Sc cannot be ruled out...