Changing the enantioselectivity of enzymes by directed evolution

Directed Evolution of Protein Catalysts

Directed evolution is a powerful technique for generating tailor-made enzymes for a wide range of biocatalytic applications. Following the principles of natural evolution, iterative cycles of mutagenesis and screening or selection are applied to modify protein properties, enhance catalytic activities, or develop completely new protein catalysts for non-natural chemical transformations. This review briefly surveys the experimental methods used to generate genetic diversity and screen or select for improved enzyme variants. Emphasis is placed on a key challenge, namely how to generate novel catalytic activities that expand the scope of natural reactions. Two particularly effective strategies, exploiting catalytic promiscuity and rational design, are illustrated by representative examples of successfully evolved enzymes. Opportunities for extending these approaches to more complex biocatalytic systems are also considered.

Light-driven biocatalytic oxidation and reduction reactions: scope and limitations

The quest for practical regeneration concepts for nicotinamide-dependent oxidoreductases continues. Recently we proposed the use of visible light to promote the direct reductive regeneration of a flavin-dependent monooxygenase. With this enzyme (PAMO-P3) light-driven enantioselective Baeyer-Villiger oxidations were performed. In spite of the significant reduction in the complexity achieved, catalytic performance of the novel approach did not meet the requirements for an efficient biocatalytic oxygenation system. Driven by this ultimate goal, we further investigated the limiting factors of our particular system. We discovered that oxidative uncoupling of the flavin-regeneration reaction from enzymatic O2-activation accounts for the futile consumption of approximately 95% of the reducing equivalents provided by the sacrificial electron donor, EDTA. Furthermore, it was found that the apparent turnover frequency (TOF) for PAMO-P3 in the present setup is approximately two orders of magnitude lower than in conventional setups that use NADPH as reductant. This finding was traced to sluggish electron transfer kinetics that arose from an impeded interaction between PAMO-P3-bound FAD and the reducing catalyst. The limiting factors and potential approaches for their circumvention are discussed. Furthermore, we broadened the light-driven regeneration approach to the class of flavin-dependent reductases. By using the Old Yellow Enzyme homologue YqjM as a model system, a significantly higher catalytic turnover for the enzyme catalyst was achieved, which we assign to a higher accessibility of the prosthetic group as well as to the absence of oxidative uncoupling.

The stability effects of protein mutations appear to be universally distributed

How the thermodynamic stability effects of protein mutations (DeltaDeltaG) are distributed is a fundamental property related to the architecture, tolerance to mutations (mutational robustness), and evolutionary history of proteins. The stability effects of mutations also dictate the rate and dynamics of protein evolution, with deleterious mutations being the main inhibitory factor. Using the FoldX algorithm that attempts to computationally predict DeltaDeltaG effects of mutations, we deduced the overall distributions of stability effects for all possible mutations in 21 different globular, single domain proteins. We found that these distributions are strikingly similar despite a range of sizes and folds, and largely follow a bi-Gaussian function: The surface residues exhibit a narrow distribution with a mildly destabilizing mean DeltaDeltaG ( approximately 0.6 kcal/mol), whereas the core residues exhibit a wider distribution with a stronger destabilizing mean ( approximately 1.4 kcal/mol). Since smaller proteins have a higher fraction of surface residues, the relative weight of these single distributions correlates with size. We also found that proteins evolved in the laboratory follow an essentially identical distribution, whereas de novo designed folds show markedly less destabilizing distributions (i.e. they seem more robust to the effects of mutations). This bi-Gaussian model provides an analytical description of the predicted distributions of mutational stability effects. It comprises a novel tool for analyzing proteins and protein models, for simulating the effect of mutations under evolutionary processes, and a quantitative description of mutational robustness.

A novel screening assay for hydroxynitrile lyases suitable for high-throughput screening

Hydroxynitrile lyases (Hnls) are important biocatalysts for the synthesis of optically pure cyanohydrins, which are used as precursors and building blocks for a wide range of high price fine chemicals. Although two Hnl enzymes, from the tropical rubber tree Hevea brasiliensis and from the almond tree Prunus amygdalus, are already used for large scale industrial applications, the enzymes still need to be improved and adapted to the special demands of industrial processes. In many cases directed evolution has been the method of choice to improve enzymes, which are applied as industrial biocatalysts. The screening procedure is the most crucial point in every directed evolution experiment. Herein, we describe the successful development of a novel screening assay for Hnls and its application in high-throughput screening of Escherichia coli mutant libraries. The new assay allows rapid screening of mutant libraries and facilitates the discovery of improved enzyme variants. Hnls catalyze the cleavage of cyanohydrins to hydrocyanic acid and the corresponding aldehyde or ketone. The enzyme assay is based on the detection of hydrocyanic acid produced, making it an all-purpose screening assay, without restriction to any kind of substrate. The gaseous HCN liberated within the Hnl reaction is detected by a visible colorimetric reaction. The facile, highly sensitive and reproducible screening method was validated by identifying new enzyme variants with novel substrate specificities.

Designed evolution of artificial metalloenzymes: protein catalysts made to order

Artificial metalloenzymes based on biotin-streptavidin technology, a "fusion" of chemistry and biology, illustrate how asymmetric catalysts can be improved and evolved using chemogenetic approaches.

Evolving the substrate specificity of O6-alkylguanine-DNA alkyltransferase through loop insertion for applications in molecular imaging

We introduce a strategy for evolving protein substrate specificity by the insertion of random amino acid loops into the protein backbone. Application of this strategy to human O6-alkylguanine-DNA alkyltransferase (AGT) led to the isolation of mutants that react with the non-natural substrate O6-propargylguanine. Libraries generated by conventional random or targeted saturation mutagenesis, by contrast, did not yield any mutants with activity towards this new substrate. The strategy of loop insertion to alter enzyme specificity should be general and applicable to other classes of proteins. An important application of the isolated AGT mutant is in molecular imaging, where the mutant and parental AGTs are used to label two different AGT fusion proteins with different fluorophores in the same living cell or in vitro . This allowed the establishment of fluorescence-based assays to detect protein-protein interactions and measure enzymatic activities.

Metal ions dramatically enhance the enantioselectivity for lipase-catalysed reactions in organic solvents

We propose a simple and a powerful method to enhance the enantioselectivity for lipase-catalysed transformations in organic solvents by an addition of metal ion-containing water to the reaction mixture. In this paper, various metal ions such as LiCl or MgCl2 are tested to improve the enantioselectivity for the model reactions. The enantioselectivities obtained are dramatically enhanced, the E values of which are about 100-fold as compared with the ordinary conditions without a metal ion, for example, E = 200 by addition of LiCl. Furthermore, lowering the reaction temperature led to an almost perfect enantioselectivity of lipase in the presence of a metal ion, for example, E = 1,300 by addition of LiCl. Also, a mechanism for the drastic enhancement by metal ions is discussed briefly on the basis of the EPR spectroscopic study and the initial rate for each enantiomer of the substrate.

Creation of GPCR-based chemical sensors by directed evolution in yeast

G protein-coupled receptors (GPCRs) form a class of biological chemical sensors with an enormous diversity in ligand binding and sensitivity. To explore structural aspects of ligand recognition, we subjected the human UDP-glucose receptor (P2Y14) functionally expressed in the yeast Saccharomyces to directed evolution. We sought to generate new receptor subtypes with ligand-binding properties that would be useful in the development of practical biosensors. Mutagenesis of the entire UDP-glucose receptor gene yielded receptors with increased activity but similar ligand specificities, while random mutagenesis of residues in the immediate vicinity of the ligand-binding pocket yielded mutants with altered ligand specificity. By first sensitizing the P2Y14 receptor and then redirecting ligand specificity, we were able to create mutant receptors suitable for a simple biosensor. Our results demonstrate the feasibility of altering receptor ligand-binding properties via a directed evolution strategy, using standard yeast genetic techniques. The novel receptor mutants can be used to detect chemical ligands in complex mixtures and to discriminate among chemically or stereochemically related compounds. Specifically, we demonstrate how engineered receptors can be applied in a pairwise manner to differentiate among several chemical analytes that would be indistinguishable with a single receptor. These experiments demonstrate the feasibility of a combinatorial approach to detector design based on the principles of olfaction.