Design and engineering of catalytic proteins

Spurred by advances in computational protein science, de novo protein design and engineering has seen great success in recent years. No longer restricted to biological protein sequences, protein engineers can construct protein molecules of almost arbitrary shape, arrangement, and properties. De novo designed proteins are seeing applications in therapeutics, diagnostics, and materials science.

A continuing challenge is the design and engineering of catalytic proteins - enzymes - using the principles of de novo protein design. Using a de novo TIM barrel protein scaffold and drawing from a growing library of validated de novo protein domains, we designed a hyperstable fusion protein with a sizeable internal cavity. This protein is robust to sequence substitutions, allowing for the generation of a programmable active site in a protein scaffold never before seen by nature.

In this de novo TIM barrel fusion protein, we engineered a binding site for metals of low biological abundance, including terbium and europium. The bound metal ion lies within the internal cavity delineated by de novo protein domains. The metal presents open coordination sites to the cavity, which remains solvent accessible. This protein and promises the ability to engineer novel chemistries into a human-designed protein scaffold. In addition to remarkably low affinities for lanthanide ions, we believe this scaffold to be an important advance in the development of fully de novo catalytic proteins.