AlphaFold Ensemble Competition Screens Enable Peptide Binder Design with Single-Residue Sensitivity.

Understanding the relationship between the sequence and binding energy in peptide-protein interactions is an important challenge in chemical biology. A prominent example is ubiquitin interacting motifs (UIMs), which are short peptide sequences that recognize ubiquitin and which bind individual ubiquitin proteins with a weak affinity. Though the sequence characteristics of UIMs are well understood, the relationship between the sequence and ubiquitin binding affinity has not yet been fully characterized.

An engineered ubiquitin binding coiled coil peptide.

Recognition of ubiquitin (Ub) is often mediated by small Ub binding domains such as the Ubiquitin Interacting Motif (UIM). Most Ub binding events are low affinity interactions, and designing stronger binders for Ub can be challenging. We here report the design of a short crosslinked coiled coil (CC) which is conformationally and chemically stable, and which can act as a scaffold to present the key binding residues from known UIM sequences.