In Vitro Selection of Functional Neoproteins Containing Highly Fluorinated Cores

The inclusion of non-proteinogenic amino acids (npAAs) into proteins vastly expands their chemical repertoire and hence possible functional diversity. However, it remains challenging to obtain non-proteinogenic sequences that carry out a specific task. Here we develop a platform to discover functional non-standard proteins and illustrate its utility by generating a family of bioactive proteins whose hydrophobic cores are built using fluorinated amino acids (fAAs). Starting from the protein chymotrypsin inhibitor 2 (CI2), we use genetic code reprogramming, combinatorial mutagenesis and mRNA display-based in vitro selection to discover fluorinated mutant sequences with optimised inhibitory activity. Using microwave-assisted solid-phase peptide synthesis, we perform preparative chemical synthesis of 14 selected proteins, which contain up to eight fAAs-or 19 fluorine atoms. All are nanomolar inhibitors of chymotrypsin; several hits are more active than the wildtype, and possess thermostabilities of up to 70°C. Crystal structures reveal that these proteins maintain native-like folds, with fluorine atoms forming close and epistatically coupled packing contacts within the core. This work demonstrates how to generate functional protein sequences with multiple interacting npAAs, namely neoproteins, and thereby provides a framework for exploring the use of unnatural building blocks in protein design.