Catalytic efficiency of designed catalytic proteins

Abstract

The de novo design of catalysts that mimic the affinity and specificity of natural enzymes remains one of the Holy Grails of chemistry. Despite decades of concerted effort we are still unable to design catalysts as efficient as enzymes. Here we critically evaluate approaches to (re)design of novel catalytic function in proteins using two test cases: Kemp elimination and ester hydrolysis. We show that the degree of success thus far has been modest when the rate enhancements seen for the designed proteins are compared with the rate enhancements by small molecule catalysts in solvents with properties similar to the active site. Nevertheless, there are reasons for optimism: the design methods are ever improving and the resulting catalyst can be efficiently improved using directed evolution.

Figure 1

Reactions and common substrates used to test various protein design methodologies.

Figure 2

Comparison of the catalytic efficiencies (left) and turnover numbers (right) of Kemp eliminases obtained by various approaches. The efficiencies of the computationally (re)designed catalyst are shown in green and blue, the subsequent improvement by directed evolution is shown in red.

Figure 3

Minimalistic approach to designing a Kemp eliminase [16].

Figure 4

De novo designed peptides self-assemble to form amyloid-like fibrils that catalyze ester hydrolysis [37••].