Today, enzymes are extensively used for many industrial applications, this includes bulk and fine-chemical synthesis, pharmaceuticals and consumer products. Though Nature has perfected enzymes for many millions of years, they seldom reach industrial performance targets. Natural enzymes could benefit from protein redesign experiments to gain novel functions or optimize existing functions. Glutathione transferases (GSTs) are detoxification enzymes, they also display disparate functions. Two Mu-class GSTs, M1-1 and M2-2, are closely related but display dissimilar substrate selectivity profiles. Saturation mutagenesis of a previously recognized hypervariable amino acid in GST M2-2, generated twenty enzyme variants with altered substrate selectivity profiles, as well as modified thermostabilities and expressivities. This indicates an evolutionary significance; GST Mu-class enzymes could easily alter functions in a duplicate gene by a single-point mutation. To further identify residues responsible for substrate selectivity in the GST M2-2 active site, three residues were chosen for iterative saturation mutagenesis. Mutations in position10, identified as highly conserved, rendered enzyme variants with substrate selectivity profiles resembling that of specialist enzymes. Ile10 could be conserved to sustain the broad substrate acceptance displayed by GST Mu-class enzymes. Enzymes are constructed from primarily twenty amino acids, it is a reasonable assumption that expansion of the amino acid repertoire could result in functional properties that cannot be accomplished with the natural set of building blocks. A combination approach of site-directed mutagenesis and chemical modifications in GST M2-2 and GST M1-1 resulted in novel enzyme variants that displayed altered substrate selectivity patterns as well as improved enantioselectivities. The results presented in this thesis demonstrate the use of different protein redesign techniques to modulate various functions in Mu-class GSTs. These techniques could be useful in search of optimized enzyme variants for industrial targets. / biokemi och organisk kemi

Directed evolution is generally regarded as a useful approach in protein engineering. By subjecting members of a mutant library to the power of Darwinian evolution, desired protein properties are obtained. Numerous reports have appeared in the literature showing the success of tailoring proteins for various applications by this method. Is it a one-way track that protein practitioners can only learn from nature to enable more efficient protein engineering? A structure-and-mechanism-based approach, supplemented with the use of reduced amino acid alphabets, was proposed as a general means for semi-rational enzyme engineering. Using human GST A2-2*E, the most active human enzyme in the bioactivation of azathioprine, as a parental enzyme to test this approach, a L107G/L108D/F222H triple-point mutant of GST A2-2*E (thereafter designated as GDH) was discovered with 70-fold increased activity, approaching the upper limit of specific activity of the GST scaffold. The approach was further experimentally verified to be more successful than intuitively choosing active-site residues in proximity to the bound substrate for the improvement of enzyme performance. By constructing all intermediates along all putative mutational paths leading from GST A2-2*E to mutant GDH and assaying them with nine alternative substrates, the fitness landscapes were found to be “rugged” in differential fashions in substrate-activity space. The multidimensional fitness landscapes stemming from functional promiscuity can lead to alternative outcomes with enzymes optimized for other features than the selectable markers that were relevant at the origin of the evolutionary process. The results in this thesis suggest that in this manner an evolutionary response to changing environmental conditions can readily be mounted. In summary, the thesis demonstrates the attractive features of the structure-and-mechanism-based semi-rational directed evolution approach for optimizing enzyme performance. Moreover, the results gained from the studies show that laboratory evolution may refine our understanding of evolutionary process in nature.

Glutathione transferase (GST) A2-2 is the human enzyme most efficient in catalyzing azathioprine activation. Structure-function relationships were sought explaining the higher catalytic efficiency compared to other alpha class GSTs. By screening a DNA shuffling library, five recombined segments were identified that were conserved among the most active mutants. Mutational analysis confirmed the importance of these short segments as their insertion into low-active GSTs introduced higher azathioprine activity. Besides, H-site mutagenesis led to decreased azathioprine activity when the targeted positions belonged to these conserved segments and mainly enhanced activity when other positions were targeted. Hydrophobic residues were preferred in positions 208 and 213. The prodrug azathioprine is today primarily used for maintaining remission in inflammatory bowel disease. Therapy leads to adverse effects for 30 % of the patients and genotyping of the metabolic genes involved can explain some of these incidences. Five genotypes of human A2-2 were characterized and variant A2*E had 3–4-fold higher catalytic efficiency with azathioprine, due to a proline mutated close to the H-site. Faster activation might lead to different metabolite distributions and possibly more adverse effects. Genotyping of GSTs is recommended for further studies. Molecular docking of azathioprine into a modeled structure of A2*E suggested three positions for mutagenesis. The most active mutants had small or polar residues in the mutated positions. Mutant L107G/L108D/F222H displayed a 70-fold improved catalytic efficiency with azathioprine. Determination of its structure by X-ray crystallography showed a widened H-site, suggesting that the transition state could be accommodated in a mode better suited for catalysis. The mutational analysis increased our understanding of the azathioprine activation in alpha class GSTs and highlighted A2*E as one factor possibly behind the adverse drug-effects. A successfully redesigned GST, with 200-fold enhanced catalytic efficiency towards azathioprine compared to the starting point A2*C, might find use in targeted enzyme-prodrug therapies.

La transcétolase thermostable de Geobacillus stearothermophilus (TKgst, EC 2.2.1.1) permet de synthétiser efficacement à haute température des cétoses à 4, 5 et 6 atomes de carbone de configuration d-thréo (3S, 4R), par formation stéréosélective d’une liaison C-C, à partir d’aldéhydes α-hydroxylés (2R) à courte chaîne. L’objectif de ces travaux est d’utiliser la TKgst à 60°C pour gagner en efficacité et étendre son spectre de substrats à de nouveaux donneurs et accepteurs par Evolution dirigée, selon une approche semi-rationnelle, basée sur la mutagenèse par saturation de site. Ainsi, à l’issue du criblage des banques générées, les TKgst mutées les plus performantes (L382D/D470S, L191I, L382F/F435Y, R521Y/H462N et R521V/S385D/H462S) ont été sélectionnées pour leurs activités spécifiques supérieures à celle de la TKgst sauvage (gain de 3,3 à 5) vis-à-vis d’aldéhydes α-hydroxylés (2S) et d’aldéhydes α-hydroxylés (2R) à longue chaîne polyhydroxylée (C5-C6). La TKgst sauvage, ainsi que ces TKgst mutées performantes ont permis d’obtenir, à 60°C, onze cétoses, dont neuf de configuration l-érythro (3S, 4S) à 5 à 6 atomes de carbone et de configuration d-thréo (3S, 4R) de 4 à 8 atomes de carbone d’intérêt biologique, avec de très bons rendements, quatre étant inaccessibles avec les TKs microbiennes utilisées jusqu’alors. D’autres TKgst mutées ont par ailleurs conduit à une amélioration significative de l’activité de la TKgst vis-à-vis d’aldéhydes aliphatiques et aromatiques, mais également vis-à-vis d’un nouveau substrat donneur, l’acide pyruvique et d’analogues, ouvrant le champs des applications aux 1-désoxycétoses. De plus, ces travaux ont permis de développer un procédé multi-enzymatique innovant et éco-comptatible, dans lequel les substrats donneurs et accepteurs de la TKgst sont générés par voie enzymatique, via l’utilisation d’une transaminase ou d’une d-aminoacide oxydase et d’une aldolase, à partir de composés naturels et peu coûteux. Cette stratégie pourra être appliquée aux TKgst mutées, afin d’accéder efficacement et à moindre coût, à d’autres cétoses rares hautement valorisables. / Thermostable transketolase from Geobacillus stearothermophilus (TKgst, EC 2.2.1.1) catalyzes efficiently the synthesis of d-threo (3S, 4R) ketoses having 4, 5 and 6 carbon atoms, by the stereoselective formation of a new C-C bond, from short chain (2R)-α-hydroxylated aldehydes. The aim of this work is to use TKgst at 60°C, in order to increase reaction rates and to broad its substrate scope to new donors and acceptors by Directed Evolution, according to a semi-rationnal approach, based on site saturation mutagenesis. Thus, the screening of the libraries led to TKgst variants (L382D/D470S, L191I, L382F/F435Y, R521Y/H462N and R521V/S385D/H462S) having significantly improved specific activities towards (2S)-α-hydroxylated aldehydes and (2R)-α-hydroxylated aldehydes having a long polyhydroxylated chain (C5-C6), compared to wild type TKgst (3,3 to 5-fold increased activity). Wild-type TKgst as well as these TKgst variants were used, at 60°C, to obtain eleven, including nine l-erythro (3S, 4S) ketoses having 5 and 6 carbon atoms and d-threo (3S, 4R) ketoses having from 4 to 8 carbon atoms of biological interest, with good yields, four being inaccessible using common TK sources. Besides, other TKgst variants led to significantly improved activities towards hydrophobic aldehydes and towards a new donor substrate, pyruvic acid and derivatives, extending TKgst product scope to 1-deoxyketoses. In addition, a multienzymatic innovative and environmentally friendly process, in which TKgst substrates are generated through enzymatic pathways, using a transaminase or a d-aminoacid oxidase and an aldolase, from non-expensive and natural compounds was developed, in the presence of wild-type TKgst and will be able to be applied to TKgst variants, in order to synthesize efficiently and at lower cost, other highly valuable rare ketoses.