*4.1. Choice of Peptide Systems*

We chose a set of five peptides for this study: the sequence from the *p53* binding epitope, two high affinity inhibitors (*pdiq* [39] and *ATSP*-7041) [25] and two control peptides, based on the poly-Ala sequence (*Ala1* and *Ala2*; see Table 1). Of the two control sequences, *Ala1* sequence conserves the set of hydrophobic residues that allow binding, and *Ala2* does not. *ATSP*-7041 is a stapled peptide using three non-standard amino acids, where one of the three anchoring residues (Leucine) is substituted by a non-canonical amino acid.

For *p53* and *pdiq*, we used crystal structures of the peptides binding to MDM2 (PDB codes 1ycr [30] and 3jzs [39]. For *ATSP*-7041, we used the structure bound to MDMX (PDB code 4n5t [25]) and superposed the active site onto MDM2 to have the reference structure of the peptide on the active site of MDM2. For the two control peptides bases on poly-ALA, there is no native structure. We compare it to the *p53*-MDM2 conformation for those two peptides. Parameters for the *ATSP*-7041 peptide are derived from the general amber force field (GAFF) [40], deriving charges based on the AM1 model [41].
