Fig. 2. Panel A: the three lowest energy binding modes for the Aβ40/Ub complex. Aβ40 sections are shown by yellow ribbons, Ub sections are shown by green ribbons. The residues of Ub interacting with Aβ40 are shown by solid sticks and those involved in salt-bridge interactions are also labeled. The internal energies of the Aβ40/Ub complex in the three binding poses (a)–(c) are –4490 kcal mol^–1, –4404 kcal mol^–1 and –4271 kcal mol^–1, respectively. Panel B: DSBU cross-links mapped onto the three lowest energy binding modes for the Aβ40/Ub complex. Aβ40 sections are shown in yellow, Ub sections are shown in green. The cross-linked residues of Aβ40 are shown by blue solid sticks and cross-linked residues of Ub are represented as red solid sticks. All the measured Cα–Cα Euclidean distances are shorter than 27 Å as required by the DSBU cross-linker.