Minimalist de novo Design of Protein Catalysts

Abstract

The field of protein design has grown enormously in the past few decades. In this review we discuss the minimalist approach to design of artificial enzymes, in which protein sequences are created with the minimum number of elements for folding and function. This method relies on identifying starting points in catalytically inert scaffolds for active site installation. The progress of the field from the original helical assemblies of the 1980s to the more complex structures of the present day is discussed, highlighting the variety of catalytic reactions which have been achieved using these methods. We outline the strengths and weaknesses of the minimalist approaches, describe representative design cases and put it in the general context of the de novo design of proteins.

Keywords: Protein design; catalysis; design approaches; enzymology; minimalism.

Figure 1

Protein design requires consideration of the correct method to apply to materials for optimal outcome.

Figure 2

Schematic representation and representative cases of the A) docking approach with a representative example from ref. ; B) minimalist approach with a representative example from ref. ; and C) theozyme approach to design of protein catalysts with a representative example from ref. .

Figure 2

Schematic representation and representative cases of the A) docking approach with a representative example from ref. ; B) minimalist approach with a representative example from ref. ; and C) theozyme approach to design of protein catalysts with a representative example from ref. .

Figure 3

Hierarchical approach to create secondary structure elements by hydrophobic patterning (green circles – hydrophobic residues, blue circles – polar residues) that can self-assemble or be assembled in complex structures. This patterning can be applied to the formation of large libraries which can be screened for activity.

Figure 4

Schematic representative of the general minimalist approach to creation of metalloproteins using the trimeric coiled coils.

Figure 5

Minimalist design of a catalytic triad in a helical coiled coil bundle CC-Hept. Catalytic residues are arranged in close proximity in a peptide that upon self-assembly from an efficient p-nitrophenol esterase (PDB code 5EZC).