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.

A redox-mediated Kemp eliminase

“…Various protein scaffolds have been reported as Kemp eliminases, all operating by the traditional acid/base mechanism234567891011121314151617. In contrast, we have identified a Kemp eliminase that functions by a fundamentally different mechanism based on a redox process.…”

“…Combining computational design methodology with 17 rounds of state-of-the-art directed evolution Hilvert, Mayo and coworkers reported the artificial enzyme HG3.17, which employs a Brønsted acid/base mechanism to catalyse Kemp elimination with an unprecedented catalytic efficiency that approaches the activities of natural enzyme ( k cat =700 s −1 and k cat / K m =230,000 M −1  s −1 )16. While these numbers are truly impressive, analysis of the possible efficiency limits for base-catalysed Kemp elimination shows that additional improvement is still possible in principle17. Along a different line, it has been postulated that an oxidoreductase breaks down 5-nitrobenzisoxazole possibly by an oxidative process, although no mechanistic evidence was reported18.…”

Coordination complexes and biomolecules: A wise wedding for catalysis upgrade

“….) might also be standardized [105]. These would bring a more convenient comparison of the different approaches.…”

Enhancing Mn(II)-Binding and Manganese Peroxidase Activity in a Designed Cytochrome c Peroxidase through Fine-Tuning Secondary-Sphere Interactions

“…4–15 Despite progress made in this field, most designed metalloproteins display much lower binding affinity for metal ions and lower activity than native enzymes. 16 One contributing factor is a lack of appreciation for the role of non-covalent secondary coordination shell interactions around the metal binding site in determining the metal-binding affinity and functionality, as most studies so far have focused mainly on reproducing the primary coordination sphere of native metalloproteins. Recently, we and others have explored the roles of electrostatics, hydrogen bonding, and hydrophobic interactions around the primary coordination sphere in fine-tuning the reduction potentials of metalloproteins.…”