*2.1. Free Peptide Simulation Ensembles Show the IDP Nature of p53*

We simulated five peptides in their free form (see Methods and Table 1), capturing their intrinsic degree of disorder. All peptides are able to visit multiple states with short life times. A 2D-RMSD clustering of the ensemble reveals many clusters with low populations for the *p53* and two control peptides, consistent with their intrinsically disordered nature (see unrestrained Molecular Dynamics (MD) column in Table 2). The peptide *pdiq* adopts stable helix conformations for a significant amount of time, while *ATSP*-7041 is an outlier in this analysis, adopting very stable helical conformations due to the presence of a chemical staple. We used these simulations to define a common reference frame to compare simulations for all peptides in their free and binding simulations (see Methods). Each peptide ensemble was projected onto the corresponding eigenvectors that showed a good separation between helical and non-helical states—as those are the states required for binding (see left panels in Figures 2 and A1–A4). Clustering on the space defined by the top 14 eigenvectors shows

that only *ATSP*-7041 and, to a lesser extent, *pdiq* adopt stable helical structures—consistent with the IDP nature of the other three peptides.

**Figure 2.** Comparison of the conformational space for free peptide versus binding simulations for the *ATSP*-7041 peptide. (**a**) The peptide ensembles are projected onto the third and fifth tICA eigenvectors common to all five peptides. (**b**) The metastable states sampled for the free peptide. (**c**) Top clusters by population from MELD×MD binding simulations.

**Table 1.** Peptides used in the current work. Bold letters represent the anchoring residues.



**Table 2.** Populations for peptides in free and MELD binding simulations. Clustering is done on the lowest temperature replica using hierarchical clustering with *ǫ* = 1.5 .
