Fig. 5. MD analysis predicts S1^A conformational transition.

a, An exemplar molecular dynamics simulation trajectory. Docking of the disialoside (purple diamonds) into the apo cryo-EM model (top) converts S1^A into the stable holo state (bottom). b, New key hydrogen bonds and hydrophobic contacts form within 500 ns, altering the topologies of the e1 loop (shown in yellow in a) and the p1 and p2 pockets. Changes in inter-residue distances (y axis) plotted against time (x axis). See also Supplementary Video 7.