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

Area of Science:

• Chemical Biology
• Structural Biology
• Computational Biology

Background:

• Peptide-protein interactions are crucial in chemical biology.
• Ubiquitin interacting motifs (UIMs) are short peptides that bind ubiquitin with weak affinity.
• The sequence-binding energy relationship for UIMs is not fully understood.

Purpose of the Study:

• To investigate the sequence-binding energy relationship in UIMs using Vps27's first UIM as a model.
• To assess the utility of AlphaFold in predicting binding affinity changes due to single-residue variations.

Main Methods:

• Experimental alanine scan of hydrophobic residues in the UIM.
• AlphaFold displacement studies using large ensembles of predicted models.
• Incorporation of decoy binding sites in AlphaFold simulations to prevent interference.

Main Results:

• Alanine scan successfully ranked the contribution of hydrophobic residues to ubiquitin binding.
• AlphaFold competition experiments, with large model ensembles, detected single-residue variations.
• Optimized AlphaFold simulations accurately recapitulated experimental binding trends.

Conclusions:

• AlphaFold is a powerful tool for peptide binder design.
• Large ensembles of AlphaFold models can detect subtle energetic changes from single-residue alterations.
• Computational methods can effectively guide the design of peptides with specific binding affinities.