Mutational Scanning

High-resolution structure-activity analysis of polypeptides requires amino acid structures that are not present in the universal genetic code. Examination of peptide and protein interactions with this resolution has been limited by the need to individually synthesize and test peptides containing nonproteinogenic amino acids.

Scientists in the Suga Laboratory at the University of Tokyo, published in PNAS, describe a method to scan entire peptide sequences with multiple nonproteinogenic amino acids and, in parallel, determine the thermodynamics of binding to a partner protein.

By coupling genetic code reprogramming to deep mutational scanning, any number of amino acids can be exhaustively substituted into peptides, and single experiments can return all free energy changes of binding.

The group members validate this approach by scanning two model protein-binding peptides with 21 diverse nonproteinogenic amino acids. The produced dense structure–activity maps at the resolution of single aliphatic atom insertions and deletions. This permits rapid interrogation of interaction interfaces, as well as optimization of affinity, fine-tuning of physical properties, and systematic assessment of nonproteinogenic amino acids in binding and folding.

Nonproteinogenic Deep Mutational Scanning of Linear and Cyclic Peptides
Joseph M. Rogers, Toby Passioura, and Hiroaki Suga
PNAS, October 23, 2018, vol. 115, no. 43, 10959-10964