Figure 1.

Protein fold determination by disulfide cross-linking. The example shows two models, but the method readily handles tens or even hundreds of models. (left) Two models, TS125_3 (green) and TS194_2 (magenta), for CASP target T0351, are of reasonable quality but have rather different topologies. (middle) The three-dimensional structures are compiled into graphs on the secondary structure elements (SSEs), representing the topology in terms of contacting SSE pairs. A topological fingerprint is selected based on differences in SSE contacts (e.g., 1-2, 2-4, 3-5, etc.) that together distinguish the models. (right) For each SSE pair in the topological fingerprint, a set of residue pairs is selected for disulfide cross-linking, in order to robustly determine whether or not the SSE pair is actually in contact. The figure shows the selected cross-links (yellow) to test for SSE pair (1, 2). Residues selected for cross-linking are colored red.