Fig. 3.
Cross-links of rHDL-2-100. Intermolecular (A) and intramolecular (B) distance maps of Cα from simulation (colored points, 15.1 Å cutoff) compared with experimental cross-linking data with three qualitative signal strengths (circle, strong; square, medium; triangle, weak). (C) Twenty-microsecond snapshot from Simulation 1 highlighting critical intramolecular cross-links; Cα atoms of residues involved in experimentally observed cross-links are shown as balls, and cross-links that are consistent with the experiment are shown by red dotted lines. Inset of A shows an intermolecular distance map of Cα from an ideal belt model with LL5/4 registry (see SI Appendix, Fig. S8, for LL4/4 and LL5/2 registries).