Fig. 4. Molecular dynamics simulations of apo or complexed E6AP-LXXLL motifs.

Different states of the E6AP LXXLL motif peptide (tan), determined by clustering the entire MD trajectories (refer to Materials and Methods). The parental LXXLL motif conformation is highlighted in red, featuring both the AlphaFold 2 (left) and cryoEM conformations (all other panels). Initial configurations for the MD simulation are as follows: a apo-E6AP protein as predicted by AF2, b apo-E6AP after removing p53 and 16E6 from our CryoEM complex, c binary complex of 16E6-bound E6AP, derived from the cryoEM structure with p53 removed, d ternary complex of p53-16E6-E6AP-LXXLL motif, using only the mentioned section and omitting the rest of the E6AP construct from the cryoEM and e ternary complex of p53-16E6-E6AP as observed in our cryoEM.