Engineering enzymes

Abstract

Fundamental research into bioinorganic catalysis of the kind presented at this Faraday Discussion has the potential to turn inspiration drawn from impressive natural energy and chemical transformations into artificial catalyst constructions useful to mankind. Creating bio-inspired artificial constructions requires a level of understanding well beyond simple description of structures and mechanisms of natural enzymes. To be useful, such description must be augmented by a practical sense of structural and energetic engineering tolerances of the mechanism. Significant barriers to achieving an engineering understanding of enzyme mechanisms arise from natural protein complexity. In certain cases we can surmount these barriers to understanding, such as natural electron tunneling, coupling of electron tunneling to light capture and proton exchange as well as simpler bond breaking redox catalysis. Hope for similar solutions of more complex bioinorganic enzymes is indicated in several papers presented in this Discussion. Armed with an engineering understanding of mechanism, the current serious frustrations to successful creation of functional artificial proteins that are rooted in protein complexity can fall away. Here we discuss the genetic and biological roots of protein complexity and show how to dodge and minimize the effects of complexity. In the best-understood cases, artificial enzymes can be designed from scratch using the simplest of protein scaffolds.

Fig. 1

Pie chart of the principal Faraday speakers grouped into topics.

Fig. 2

Pie chart of oxidoreductases taken from the IUBMB Enzyme Classification resource. The data was abstracted by inspection of the enzyme classification in 2009. Shown is the 74% population of different enzymes in nature engaged catalysis that does not involve net oxidation and reduction of substrates (blue); the remaining 26% are oxidoreductases of different types. These are sectioned into those known to transfer hydride to/from substrates and generally called dehydrogenases which are common in intermediary metabolism (red slice), and those that promote single electron tunneling through extended chains of cofactors common in photosynthesis and respiration and oxidative and reductive metabolism terminated by dehydrogenase activity (orange slice) or terminated by sites containing clusters of cofactors catalyzing multiple electron chemistry (yellow slice). See ref. .

Fig. 3

Muller’s ratchet explains the source of fragility, amino acid interdependence and irreversible complexity in proteins.

Fig. 4

Darwin’s principle of multiple utility at the protein level. In maquette design red segments 1, 11 and 12 would be excluded, as initially would 5 and 6. Green segments 2, 3, 4 and 7 represent minimal utilities for the simplest maquette incorporating a bioinorganic cofactor; green/red segments 8, 9 and 10 represent catalytic utilities.

Fig. 5

Complexity derived from Mullerian and Darwinian sources in natural protein and in simple proteins engineered from scratch (maquettes). The figure explains that any amino acid serves a number of utilities in a protein. It also demonstrates that an amino acid or a function in a protein displays interdependencies, close and far, with a number of other amino acids. The maquette approach to protein construction diminishes both the number of utilities and interdependencies.