Cell-free protein synthesis (CFPS) is a powerful protein expression platform where protein synthesis machinery is borrowed from living organisms. Target proteins are synthesized in a reaction tube together with cell extract, amino acids, energy source, and DNA. This reaction is versatile, and dynamic optimizations of the reaction conditions can be performed. The "œopen" nature of CFPS makes it a compelling candidate for many technologies and applications. This dissertation reports new and innovative applications of CFPS including 1) enzyme encapsulation in a virus-like particle, 2) detection of endocrine disrupting chemicals in the presence of blood and urine, and 3) expression of a multi-disulfide bond therapeutic protein. Two major limitations of enzymes are their instability and recycling difficulty. To overcome these limitations, we report the first enzyme encapsulation in the CFPS by immobilizing in a virus-like particle using an RNA aptamer. This technique allows simple and fast enzyme production and encapsulation We demonstrate, for the first time, the Rapid Adaptable Portable In vitro Detection biosensor platform (RAPID) for detecting endocrine disrupting chemicals (EDCs) in human blood and urine samples. Current living cell-based assays can take a week to detect EDCs, but RAPID requires only 2 hours. It utilizes the versatile nature of CFPS for biosensor protein complex production and EDC detection. Biotherapeutic protein expression in E. coli suffers from inclusion body formation, insolubility, and mis-folding. Since CFPS is not restricted by a cell wall, dynamic optimization can take place during the protein synthesis process. We report the first expression of full-length tissue plasminogen activator (tPA) using CFPS. These research works demonstrate the powerful and versatile nature of the CFPS.

The colonization of immersed surfaces by a myriad of marine organisms is a complex, multi-stage, species-specific process giving rise to economic and environmental costs. This unwanted accumulation of organisms in the marine environment, called biofouling, has been attacked from different fronts, going from the ‘problem-elimination-as-problem-solving’ strategy (essentially through the use of biocides) to more elaborated and environmentally-friendly options based on the principle of ‘non-stick’ or ‘easy foul-release’ surfaces, which do not jeopardize marine life viability. Several marine organisms rely on proteinaceous adhesives to secure a holdfast to surfaces. Proteolytic enzymes have been demonstrated to be effective agents against settlement and settlement consolidation onto surfaces of marine bacteria, algae, and invertebrates, their proposed mode-of-action being the enzymatic degradation of the proteinaceous components of the adhesives. So far, however, the evidence remains inconclusive since most of the published investigations refer to commercial preparations where the enzyme is mixed with other components, like additives, which obviously act as additional experimental variables. This work aims at providing clear, conclusive evidence about the potential of serine proteases to target the adhesives produced by a group of model marine biofoulers. The strategy towards the goal consisted in the preparation and characterization of maleic anhydride copolymer nanocoatings modified by a surface-bound enzyme, Subtilisin A, the active constituent of the commercial preparations reported as effective against biofouling. The enzyme-containing maleic anhydride copolymer films were characterized (enzyme surface concentration, activity, stability, roughness and wettability) and thereafter tested in biological assays with three major biofoulers: spores of the green alga Ulva linza, cells of the pennate diatom Navicula perminuta, and cyprid larvae of the barnacle Balanus amphitrite. The purpose of the biological assays was to elucidate the efficacy of the immobilized catalyst to discourage settlement and/or to facilitate removal of these organisms from the bioactive layers. Results confirmed the initial hypotheses related to the enzymatic degradation of the biological adhesives: the immobilized protease was effective at reducing the adhesion strength of Ulva spores and Navicula diatoms in a manner that correlated with the enzyme activity and surface concentration, and deterred settlement of Balanus amphitrite barnacle cyprids even at the lowest surface activity tested. By facilitating the removal of biofilm-forming diatoms and of spores of the troublesome alga Ulva linza, as well as by interfering with the consolidation of adhesion of the calcareous Balanus amphitrite macrofouler, the enzyme-containing coatings here disclosed are considered to constitute an appealing and promising alternative to control marine biofouling without jeopardizing marine life.

Polyketides are natural products with complex chemical structures and immense pharmaceutical potential that are synthesized via secondary metabolic pathways. The in-vitro synthesis of these molecules requires high supply of building blocks such as acetyl Co-enzyme A, and cofactors (adenosine triphosphate (ATP). These precursor and cofactor are synthesized from respective soluble enzymes. Owing to the expensive nature of the enzymes, it is important to immobilize enzymes to improve the process economics by enabling multiple uses of catalyst and improving overall productivity and robustness. The polymer-based particles of nano and submicron size have become attractive material for their role in the life sciences. With the advances in synthetic protocols of the microgels and commercial availability of many of the monomers, it is feasible to tune the properties of the particles as per the process requirement. The core shell microgel with functional shell allows high loading of ligands onto the microgel particles due to increased availability of functional group on the outer surface. The aim of the thesis thus was to study biochemical reactions on the smart microgels support using single (acetyl CoA synthetase (Acs)) and dual (pyruvate kinase (Pk) and L-lactic dehydrogenase (Ldh)) enzyme/s systems. The study indicated that the enzyme immobilization significantly depends on the enzyme, conjugation strategy and the support. The covalent immobilization provides rigidity to the enzyme structure as in case of Acs immobilized on PNIPAm-AEMA microgels but at the same time leads to loss in enzyme activity. Whereas, in the case of covalent immobilization of Ldh on microgel showed improved in enzyme activity. On the other hand adsorption of the enzyme via ionic interaction provide better kinetic profile of enzymes hence the membrane reactor was prepared using PNIPAm-PEI conjugates for acetyl CoA synthesis. The better outcome of work with PNIPAm-PEI resulted in its further evaluation for dual enzyme system. This work is unique in the view that the immobilization strategies were well adapted to immobilize single and dual enzymes to achieve stable bioconjugates for their respective applications in precursor biosynthesis (Acetyl Co enzyme A) and co-factor dependent processes (ACoA and ATP). The positive end results of microgels as the support (particles in solution and as the thin film (membrane)) opens further prospective to explore these systems for other precursor biomolecule production.

Approche multi-échelle pour l’étude de la réaction de N-acylation enzymatique d’acides aminés La réaction de N-acylation d’acides aminés ou de peptides permet l’obtention de dérivés de ces molécules présentant des propriétés bioactives et/ou techno-fonctionnelles, avec une biodisponibilité, une hydrophobie et une stabilité accrue. Les acides aminés acylés ont été largement décrits comme constituant une classe d'agents tensioactifs avec d'excellentes propriétés de surface, des activités biologiques intéressantes, un faible potentiel de toxicité et un faible impact environnemental. Actuellement réalisée de manière chimique à l’échelle industrielle, l’acylation de ces acides aminés ou peptides présente des contraintes en termes de sélectivité réactionnelle et d’innocuité vis-à-vis de l’environnement ainsi qu’en termes de coût de retraitement des effluents polluants. Une alternative à cette voie chimique est l’utilisation d’enzymes capables de catalyser ces réactions d’acylation. Dans la littérature, différents couples d’enzymes et de solvants ont déjà été décrits. Néanmoins, les performances réactionnelles de ces systèmes demeurent parfois limitées. L’objectif de cette thèse a donc été l’amélioration du procédé d’acylation par une approche à différentes échelles. À l’échelle moléculaire, une étude a été réalisée avec la lipase B de Candida antarctica (CALB). Une approche de modélisation moléculaire a été utilisée afin de mettre au point une méthodologie associant des simulations de docking et des calculs d’interaction permettant d’améliorer la compréhension et permettre la prédiction de la régiosélectivité de CALB lors de l’acylation de la lysine par différents acides gras. Des études ont également été conduites à l’échelle réactionnelle, notamment avec la recherche de nouveaux biocatalyseurs de type aminoacylases dans l’extrait brut de Streptomyces ambofaciens. La régiosélectivité et les performances de la réaction catalysée par ces enzymes ont été comparés à celles de CALB. Les résultats ont mis en évidence un potentiel très prometteur des aminoacylases de S. ambofaciens concernant la synthèse d’acide aminés/peptides acylés. En effet, en plus de leur aptitude à réaliser la réaction d’acylation en milieu aqueux, ces enzymes possèdent une régio-sélectivité qui diffère de celle de CALB. Cette régio-sélectivité orientée vers les groupements N-terminaux est un atout très peu décrit à ce jour, car elle permet d’acyler ces molécules sans modifier les chaînes latérales des acides aminés ou des peptides et donc leurs fonctionnalités. Dans la dernière partie de ces travaux, des études à l’échelle procédé ont été menées. Tout d’abord, l’immobilisation des aminoacylases sur des matériaux mésoporeux silicatés a été réalisée et différentes méthodes d’immobilisation ont pu être comparées. Cette étude a permis de proposer une méthode d’immobilisation des aminoacylases de S. ambofaciens par physisorption, permettant de conserver l’activité spécifique pendant au moins 3 cycles. Puis, dans une dernière partie, l’intensification de la réaction d’acylation en réacteur micro-ondes ou microstructurés a été abordée. Les expérimentations réalisées dans un réacteur chauffé par irradiation micro-onde ont montré que ce type de réacteur était adapté à la réaction d’acylation catalysé par CALB sous sa forme immobilisée commerciale (Novozym435®) en solvant organique, ce qui n’est pas le cas avec des aminoacylases de S. ambofaciens libres, en milieux aqueux. Pour cette réaction, d’autres méthodes d’intensification ont été envisagées, notamment en réacteur microstructuré de type microfluidique. L’efficacité du mélange étant primordiale notamment en milieu biphasique, celle-ci a pu être améliorée avec un taux de conversion supérieur dans ce réacteur comparativement à un réacteur classique agité mécaniquement / N-acylation of amino acids or peptides results in bioactive and/or functional molecules showing increased bioavailability, hydrophobicity and stability. Acylated amino acids have been broadly described as being a kind of surfactant with great surface chemistry properties, interesting biological activities, weak toxicity and low environmental impact. Acylation of amino acids or peptides is being performed chemically at industrial scale. It creates constraints in term of reaction selectivity, environmental safety and cost of polluted wastewater treatment. Enzymatic catalysis is an alternative to chemical acylation reaction. Several enzyme/solvent pairs have already been described in the literature. Their performance are however somewhat limited. The objective of this thesis work was thus to improve the capacity of acylation processes at different scales. At the molecular scale, a study was performed using Candida antarctica’s (CALB) lipase B. Molecular modeling was used to create a methodology coupling docking simulation and interaction calculus that would allow for a better understanding of CALB regioselectivity during lysine acylation by different fatty acids. Studies were also conducted at the reaction level, especially by searching for new aminoacylase-type of biocatalysts in Streptomyces ambofaciens raw extract. Regioselectivity and performance of these enzyme’s catalytic reactions were compared to those of CALB. Results brought into light a promising potential from S. ambofaciens’ aminoacylases in synthesizing acylated amino acids/peptides. Indeed, on top of their ability to catalyse acylation reaction in aqueous solution, these enzymes have a different regioselectivity compared to CALB’s. Regioselectivity targeting N-terminal groups is a rarely researched phenomenon allowing acylation to be performed without modifying amino acids or peptides lateral chains and hence their functionality. In the last part part of this work, studies at process scale were performed. Aminoacylase were first immobilized on mesoporous silicates and several immobilisation methods were compared. Using physisorption, a method for the immobilisation of S. ambofaciens’ aminoacylases was developed to reach a conserved specific activity during 3 cycles. Finally, intensification of acylation reaction was examined in microwave or microstructured reactors. First, an experimental set up was performed in an heated reactor using microwaves irradiation. This kind of reactor was demonstrated as being adapted to acylation reaction using a commercial immobilized form of CALB (Novozym435®) as catalyst in organic solvent. The microwave reactor was however not suited for free S. ambofaciens aminoacylase in aqueous solution. For that latter reaction, intensification had to be approached through other aspects of the process. Hydrodynamic appeared indeed as an important aspect for this reaction occurring in a biphasic medium composed of fatty acids and aqueous solution. A microstructured microfluidic reactor was hence tested. Conversion yield were increased with this system. This study demonstrated how mixing quality was an important factor for acylation reaction and could be a way to intensify the enzymatic process at larger scale

Conselho Nacional de Desenvolvimento Científico e Tecnológico / Immobilized enzymes provide many advantages when compared to the usage of their free forms. Among these ones, remarkable advantages are the possibility of the biocatalyst reusability, easy separation at the end of the process, its usage in continuous way and the enhancement of its stability. This work was performed aiming the immobilization of the α-galactosidase enzyme from Aspergillus niger in ion exchange resin and the evaluation of its catalytic activity. Firstly, tests were performed in five different resins: Amberlite 252-Na, Dowex Marathon A, Dowex Marathon C, Duolite A-568 e Duolite S-761. According to the results, Duolite A-568 was chosen as the best support. Therefore, studies were done aiming the optimization of the immobilization process in this resin. Glutaraldehyde 1% (v/v) was used before the enzyme adsorption process and it enhanced the operational stability of the immobilized enzyme. Preliminary tests did not showed difference for the immobilization process at the temperatures of 25 and 40°C. A full factorial design and a central composite design were performed to study the best immobilization conditions varying the pH, the α-galactosidase concentration and the immobilization time. The results led to use the following immobilization conditions: pH 4.5; 15 g/L of α-galactosidase and 3 hours of immobilization. The temperature of maximum activity occurred at 60°C for both free and immobilized enzyme. The activation energy calculated by linear adjustment of Arrhenius equation was 5.66 kcal/mol for soluble α-galactosidase and 4.48 kcal/mol for immobilized α-galactosidase. The optimum pH range obtained for free enzyme was 4.0-5.0 and for immobilized enzyme it was 3.0-6.0. The immobilization process improved the α-galactosidase activity in alkaline pHs. Analysis of pH stability showed that both forms of enzyme were resistant for the pH ranges studied (3.5 to 7.5 for free and 3.0 to 8.0 for immobilized). However, the thermal stability of the biocatalyst immobilized in the support decreased. The kinetic studies without inhibition showed closed values of maximum speed (Vmax) for both enzyme forms (194.5 U for free and 187.7 U for immobilized). Although, the Michaelis-Menten constant (Km) of immobilized enzyme was higher than the free one (18.8 and 12.5 g/L, respectively). The hydrolysis reaction of raffinose was inhibited by the addition of the reaction products, sucrose and galactose, and the results of inhibition by galactose pointed for the competitive inhibition type. Then, storage tests of immobilized α-galactosidase showed that the enzyme maintained its activity even after 145 days when kept at the temperature of 4°C. / O uso de enzimas imobilizadas proporciona muitas vantagens em relação ao seu uso na forma livre. Dentre estas vantagens se destacam a possibilidade de reutilização do biocatalisador, a sua fácil separação ao final do processo, a utilização em modo contínuo e o aumento de sua estabilidade. Este trabalho foi desenvolvido com o objetivo de imobilizar a enzima α-galactosidase de Aspergillus niger em resina de troca iônica e avaliar a sua atividade catalítica. Inicialmente, foram feitos testes preliminares de imobilização em 5 tipos de resinas: Amberlite 252-Na, Dowex Marathon A, Dowex Marathon C, Duolite A-568 e Duolite S-761. Pelos resultados obtidos, Duolite A-568 foi selecionada como melhor suporte e, portanto, estudos foram feitos para a otimização do processo de imobilização nesta resina. Glutaraldeído na concentração de 1% (v/v) foi utilizado anteriormente ao processo de adsorção da enzima e melhorou a estabilidade operacional da α-galactosidase imobilizada. Testes preliminares não indicaram diferença do processo de imobilização para temperaturas de 25 e 40°C. Realizou-se um planejamento fatorial completo e um planejamento composto central para estudar as melhores condições de imobilização variando-se o pH, concentração de α-galactosidase e tempo de imobilização. Os resultados obtidos levaram a utilizar as seguintes condições de imobilização: pH 4,5, concentração de α-galactosidase de 15 g/L e tempo de imobilização de 3 horas. A temperatura de máxima atividade enzimática foi 60°C tanto para a enzima livre quanto imobilizada. O valor da energia de ativação encontrado pelo ajuste linear da equação de Arrhenius foi de 5,66 kcal/mol para α-galactosidase solúvel e 4,48 kcal/mol para α-galactosidase imobilizada. A faixa de pH ótimo obtido para a enzima livre foi 4,0-6,0 e para a enzima imobilizada foi 3,0-6,0. O processo de imobilização melhorou a atividade da α-galactosidase para pHs mais alcalinos. A análise de resistência ao pH mostrou que ambas as formas da enzima foram resistentes para as faixas estudadas (3,5 a 7,5 para livre e 3,0 a 8,0 para imobilizada). No entanto, a resistência térmica do biocatalisador retido no suporte foi menor. O estudo cinético sem inibição apresentou valores de velocidade máxima (Vmáx) próximos para as duas formas da α-galactosidase (194,5 U para livre e 187,7 U para imobilizada), porém o Km da forma imobilizada foi maior que o da livre (18,8 g/L e 12, 5 g/L de rafinose, respectivamente). A reação de hidrólise da rafinose foi inibida pela adição dos produtos da reação, sacarose e galactose, sendo que os resultados de inibição por galactose apontam para o tipo de inibição competitiva Por fim, testes de estocagem da α-galactosidase imobilizada mostraram que a enzima manteve sua atividade mesmo após 145 dias mantida a temperatura de 4°C. / Mestre em Engenharia Química

The colonization of immersed surfaces by a myriad of marine organisms is a complex, multi-stage, species-specific process giving rise to economic and environmental costs. This unwanted accumulation of organisms in the marine environment, called biofouling, has been attacked from different fronts, going from the ‘problem-elimination-as-problem-solving’ strategy (essentially through the use of biocides) to more elaborated and environmentally-friendly options based on the principle of ‘non-stick’ or ‘easy foul-release’ surfaces, which do not jeopardize marine life viability. Several marine organisms rely on proteinaceous adhesives to secure a holdfast to surfaces. Proteolytic enzymes have been demonstrated to be effective agents against settlement and settlement consolidation onto surfaces of marine bacteria, algae, and invertebrates, their proposed mode-of-action being the enzymatic degradation of the proteinaceous components of the adhesives. So far, however, the evidence remains inconclusive since most of the published investigations refer to commercial preparations where the enzyme is mixed with other components, like additives, which obviously act as additional experimental variables. This work aims at providing clear, conclusive evidence about the potential of serine proteases to target the adhesives produced by a group of model marine biofoulers. The strategy towards the goal consisted in the preparation and characterization of maleic anhydride copolymer nanocoatings modified by a surface-bound enzyme, Subtilisin A, the active constituent of the commercial preparations reported as effective against biofouling. The enzyme-containing maleic anhydride copolymer films were characterized (enzyme surface concentration, activity, stability, roughness and wettability) and thereafter tested in biological assays with three major biofoulers: spores of the green alga Ulva linza, cells of the pennate diatom Navicula perminuta, and cyprid larvae of the barnacle Balanus amphitrite. The purpose of the biological assays was to elucidate the efficacy of the immobilized catalyst to discourage settlement and/or to facilitate removal of these organisms from the bioactive layers. Results confirmed the initial hypotheses related to the enzymatic degradation of the biological adhesives: the immobilized protease was effective at reducing the adhesion strength of Ulva spores and Navicula diatoms in a manner that correlated with the enzyme activity and surface concentration, and deterred settlement of Balanus amphitrite barnacle cyprids even at the lowest surface activity tested. By facilitating the removal of biofilm-forming diatoms and of spores of the troublesome alga Ulva linza, as well as by interfering with the consolidation of adhesion of the calcareous Balanus amphitrite macrofouler, the enzyme-containing coatings here disclosed are considered to constitute an appealing and promising alternative to control marine biofouling without jeopardizing marine life.

Amine transaminases (ATA) catalyse the transfer of an amino group from one molecule and replaces a ketone or aldehyde with the amino group, the amino group on the amino-donor is replaced with a ketone or aldehyde. This enzyme, ATA from Chromobacterium violaceum, has previously been used to catalyse the reaction involving amphetamine, therefore, it might be possible to use this enzyme to convert amphetamine and the product absorbs in the UV spectrum and can therefore be measured spectrophotometrically. The aim of the project was to explore the possibility of using ATA in a portable biosensor for the detection of amphetamine. A literature study of commercially available portable biosensors was performed, activity of the free enzyme was tested against two substrates, methylbenzylamine (MBA) and amphetamine. Research on immobilization techniques, materials, and surface functionalization was done to chose suitable methods for immobilizing ATA. Two immobilization methods were suggested and one of the methods, ionic immobilization through His-tag towards Ni2+ on the surface, was tested for enzyme activity toward MBA. The enzyme activity of the free enzyme in solution towards MBA was comparable to previously reported enzyme activity, however, no enzyme activity towards amphetamine was observed. No activity was observed for the immobilized enzyme, but it might be due to the experimental design, more experiments need to be performed to draw conclusions. / Amintransaminaser (ATA) katalyserar överförandet av en amingrupp från en molekyl och ersätter en keton eller aldehyd med den amingruppen, amingruppen på amin-donatorn ersätts med en keton eller aldehyd. Det här enzymet, ATA från Chromobacterium violaceum (CvATA), har tidigare använts för att katalysera en reaktion som involverar amfetamin, därför skulle detta enzym kunna användas på amfetamin. Produkten av reaktionen absorberar i UV spektrumet och kan mätas med en spektrofotometer. Målet med projektet var att utforska möjligheten av att använda CvATA i en biosensor för att detektera amfetamin. En litteraturstudie på kommersiellt tillgängliga bärbara biosensorer genomfördes, aktiviteten av det fria enzymet testades mot två substrat, metylbenzylamin (MBA) och amfetamin. Information samlades om immobiliseringstekniker, material, och ytfunktionalisering gjordes för att välja ut lämpliga metoder för immobilisering av CvATA. Två immobiliseringsmetoder föreslogs och en av metoderna, immobilisering via enzymets His6-tagg och Ni2+ joner på ytan, testades för enzymaktivitet mot MBA. Enzymaktiviteten av det fria enzymet i lösning mot MBA var i samma storleksordning som tidigare rapporterad enzymaktivitet, men ingen enzymaktivitet mot amfetamin kunde observeras. Ingen aktivitet kunde observeras för det immobiliserade enzymet, men det kan vara på grund av designen på experimentet, fler experiment behöver göras för att kunna dra några fler slutsatser.

Den nära förestående bristen på fossila resurser i kombination med deras associerade miljöfarlighet betonar behovet av utveckling av alternativa, mer hållbara kemikalier. I denna studie utvecklades en enzymatisk kaskad för förädling av 5-(hydroxymetyl)furfural (HMF) till 5-(aminometyl)-2-furfuraldehyd (AMFA). Kaskaden omfattar transaminering av HMF till 5-(hydroxymetyl)furfurylamin (HMFA) följt av oxidation av HMFA till AMFA. Transaminas från Silicibacter pomeroyi (SpATA) immobiliserades via his6-taggar på EziG-proteinbärare från EnginZyme AB. Proteinbärarna placerades i spin-kolonner under transamineringen vilket möjliggjorde omhändertagande av SpATA efter transamineringen av HMF. För oxidationen utvärderades alkoholdyhydrogenas från Thermoanaerobacter brockii och hästlever samt galaktosoxidas från Dactylium dendroides (GOase). Omsättning och produktbildning analyserades med HPLC. Resultaten indikerar att SpATA effektivt katalyserar transamineringen av HMF, att alkohol dehydrogenasen inte förmår katalysera oxidationen av HMF till HMFA och att galaktosoxidaset kan oxidera HMFA med hög omsättning vilket leder oss att tro att den föreslagna kaskaden för förädling av HMF till AMFA är möjlig. / The imminent shortage of fossil resources coupled with their associated environmental hazards stresses the need for the development of alternative, more sustainable chemicals. In this study an enzymatic cascade was developed for the valorisation of 5-(hydroxymethyl)furfural (HMF) into 5-(aminomethyl)-2-furfuraldehyde (AMFA). The cascade involves the transamination of HMF into 5-(hydroxymethyl)furfurylamine (HMFA) followed by the oxidation of HMFA into AMFA. Transaminases from Silicibacter pomeroyi (SpATA) was immobilised via his6-tags onto EziG-protein carriers from EnginZyme AB. The protein carriers were placed in spin-columns during the transamination which allowed for salvaging of the SpATA after the transamination of HMF. For the oxidation, alcohol dehydrogenases from Thermoanaerobacter brockii and horse liver as well as galactose oxidase from Dactylium dendroides (GOase) were evaluated. The conversion and product formation were analysed by HPLC. The results indicate that the SpATA efficiently catalyses the transamination of HMF, that the alcohol dehydrogenases are not able to catalyse the oxidation of HMF nor HMFA and that the GOase can oxidize HMFA with high conversion which leads us to believe that the proposed cascade for the valorisation of HMF to AMFA is feasible.

Les enzymes et leur diversité d’actions sont appréciées dans des domaines d’applications variés allant del’agroalimentaire à la thérapeutique. Ainsi, une attention toute particulière est portée à leur étude afin d’améliorer uneaction (contre le vieillissement de la peau, antivirale, anticancéreuse…) ou un procédé de synthèse. Ce projet derecherche s’inscrit dans une démarche de développement d’outils analytiques basés sur la spectrométrie de masse,permettant le suivi rapide et sensible d’interactions enzyme-ligand.Dans une première étude, l’approche TLC couplée à une détection par UV a été évaluée pour la déterminationde constantes enzymatiques de l’enzyme invertase. Cette approche couplée à un MALDI/TOF MS a permis d’identifierdes substrats spécifiques de l’invertase au sein d’extraits de plantes. Pour preuve de concept, l’interactioncellobiohydrolase II–ligand est présentée dans le cadre de l’identification d’inhibiteur par TLC-MALDI/TOF et TLCENALDIMS.En seconde étude, nos travaux ont porté sur la caractérisation directe de différentes enzymes kinases, puis auxsuivis des réactions de phosphorylation de nucléosides /tides endogènes. Ces études, basées sur des approches « offline» (Flow Injection Analysis, FIA) et « on-line » (Frontal Affinity Chromatography, FAC) couplées à unspectromètre de masse haute résolution, ont été réalisées au moyen de ces kinases libres et immobilisées. Dans le cadrede la recherche de nouveaux candidats médicamenteux antiviraux, le suivi d’une phosphorylation spécifique desmolécules de synthèse, au regard de souches humaine ou virale de kinase, a également été évalué par ces deuxméthodologies. / Enzymes are very appreciated and useful in various application fields from agri-business to therapeutic due to theirdiversity of actions. Therefore, their action mechanisms are widely studied in order to enhance an action (anti-aging ofskin, antiviral, antitumorous) or a synthesis process. This research project is part of the approach to propose analyticaltools based on mass spectrometry, allowing rapid and sensitive follow-up of enzyme-ligand interactions.In a first study, the Thin-Layer Chromatography (TLC) approach coupled with UV detection was evaluated forthe determination of invertase kinetic constants. This approach coupled with a MALDI / TOF-MS led to theidentification of invertase substrates in plant extracts. As a proof of concept, the cellobiohydrolase II - ligand interactionwas presented in the framework of the identification of inhibitor by TLC-MALDI / TOF and TLC-ENALDI MS.In the second study, our work aimed at developing a direct method for the determination of kinetic parametersof kinases and following-up the phosphorylation reactions of endogenous nucleosides / tides. These studies, based on“off-line” (Flow Injection Analysis, FIA) and “on-line” (Frontal Affinity Chromatography, FAC) approaches coupledwith a high-resolution mass spectrometer, were carried out using free and immobilized kinases. In the context of thesearch for new antiviral drug candidates, a specific phosphorylation of synthetic molecules regards to human or viralkinase was also evaluated by these both approaches.

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No. of bitstreams: 1 TeseTSSM.pdf: 23662587 bytes, checksum: 4ef26b2b65e46560d905cc700258cd0d (MD5) Previous issue date: 2017-03-30 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / In ethanol production process from hemicellulosic fraction, the use of xylooligomers (XOS) as substrate reduce the contamination risk, favoring its application at industrial scale. Thus, a biocatalyst, containing xylanases, xylose isomerase (XI) and yeast co-immobilized in calcium alginate gel, was developed and XOS simultaneous hydrolysis, isomerization and fermentation (SHIF) process was studied. Firstly, xylanases from Multifect CX XL A03139 (XAS-5), a commercial enzyme preparation, and the recombinant xylanase from Bacillus subtilis (XynA) were selected to compose biocatalyst beads. XAS-5 presented better conversion (78.7%) and higher xylose production in the hydrolysis of beechwood xylan, while XynA showed exclusive endoxylanase activity. The immobilization and stabilization of XynA were performed in chitosan-glutaraldehyde, chitosan-glyoxyl and agarose-glyoxyl. Although the enzyme was efficiently immobilized on all supports, the agarose-glyoxyl-XynA derivative was notable for exhibiting remarkable stabilization under tested conditions (8600 times). Studies of SHIF process were carried out with birchwood xylan, leading to ethanol production (0.160 g/g and 0.092 g/L.h) and xylose accumulation, which indicated XI activity decrease. Further experiments were then performed to to identify possible inhibitors of XI (pH, Ca2+, Mg2+ and xylooligosaccharides). Ca2+ was identified as an inhibitor, while Mg2+ acts as an activator of the enzyme, and both actions are potentiated at acidic pHs. XI is also inhibited by XOS, with a decrease of 31.6% in XI activity in the presence of 7.0 g/L of xylobiose. For this reason, it was decided to evaluate SIF process with a recombinant yeast, capable of expressing XI. In batch runs, GSE16-T18 (T18) yeast encapsulated in alginate gel was capable to ferment xylose efficiently, consuming 40 g/L of xylose in 4 h and producing 14.4 g/L of ethanol, with yield of 0.422 g/g and productivity of 3.61 g/L.h. Calcium alginate gel encapsulation also contributed to protect yeast from the action of inhibitors, such as acetic acid. The encapsulated T18 was able to perform 10 consecutive cycles in repeated batch (yeast extract-peptone medium with 40 g/L of xylose), keeping the same productivity and high yields. It also fermented efficiently sugarcane bagasse hydrolysate, containing 60 g/L of fermentable sugars and high grade of inhibitors. The modified yeast to be more tolerant to acetic acid, GSE16-T18 HAA1, was also studied, exhibiting superior performance in comparison to T18 for hydrolysate fermentations. Continuous experiments were conducted in a fixed bed reactor using the T18-HAA1 yeast immobilized, with different xylose concentrations (40, 60, 80 and 120 g/L) in the feed medium. The reactor was operated up to 15 days, without bacterial contamination, with yield of 0.45 g/g, productivity of 4.8 g/L.h and selectivity of 31 gethanol/gxylitol (60 g/L of xylose in the feed). For the concentrations higher than 60 g/L, the conversion decreased after 4 days of continuous operation, indicating loss of cell viability due to hazardous effect of ethanol when present at 30 g/L or more, as well as limitation of oxygen and nutrients in the system. / No processo de produção de etanol a partir da fração hemicelulósica, a utilização de xilooligômeros como substrato reduz o risco de contaminação, favorecendo o emprego da tecnologia em escala industrial. Para isso, um biocatalisador contendo xilanases, xilose isomerase (XI) e levedura co-imobilizadas em gel de alginato de cálcio foi desenvolvido e o processo de hidrólise, isomerização e fermentação simultâneos (SHIF) de xilooligômeros foi estudado. Primeiramente, as xilanases presentes no produto Multifect CX XL A03139 (XAS- 5) e a xilanase recombinante de Bacillus subtilis (XynA) foram selecionadas para compor os beads do biocatalisador. XAS-5 apresentou melhor conversão (78,7%) e maior produção de xilose na hidrólise da xilana de faia, enquanto XynA apresentou exclusiva atividade de endoxilanase. Realizou-se a imobilização e estabilização da XynA em quitosanaglutaraldeído, quitosana-glioxil e agarose-glioxil. Apesar da enzima ser eficientemente imobilizada nos três suportes, o derivado agarose-glioxil-XynA se destacou por apresentar uma estabilização notável nas condições testadas (8600 vezes). Estudos do processo SHIF foram realizados com xilana de bétula, observando-se produção de etanol (0,160 g/g e 0,092 g/L.h) e acúmulo de xilose, indicando redução da atividade da XI. Realizou-se então, um estudo para identificar possíveis inibidores da XI (pH, Ca2+, Mg2+ e XOS), constatando-se que Ca2+ é um inibidor enquanto Mg2+ é um ativador da enzima, sendo suas ações potencializadas em pHs ácidos. Comprovou-se também que XI é inibida por XOS, observando-se queda da atividade de XI (31,6%) na presença de 7,0 g/L de xilobiose. Desta forma, tornou-se interessante avaliar o processo SIF com uma levedura recombinante, capaz de expressar XI. Em ensaios em batelada, a levedura GSE16-T18 (T18), encapsulada em gel de alginato, mostrou-se eficiente na fermentação de xilose, consumindo 40 g/L de xilose em 4 h e produzindo 14,4 g/L de etanol, com rendimento de 0,422 g/g e produtividade de 3,61 g/L.h. O encapsulamento em gel de alginato de cálcio também protegeu a levedura da ação de inibidores, como o ácido acético. A T18 encapsulada foi capaz de realizar 10 ciclos consecutivos em bateladas repetidas (meio contendo extrato de levedura, peptona e 40 g/L de substrato), mantendo mesma produtividade e elevado rendimento, além de fermentar eficientemente hidrolisado hemicelulósico de bagaço de cana, contendo 60 g/L de açúcares fermentescíveis e alto teor de inibidores. A levedura GSE16-T18 HAA1, modificada geneticamente para ser mais tolerante ao ácido acético, foi também estudada, com resultados superiores a T18 nas fermentações de hidrolisado. Fermentações em modo contínuo foram realizadas em reator de leito fixo utilizando a levedura T18-HAA1 imobilizada, com diferentes concentrações de xilose na alimentação (40, 60, 80 e 120 g/L). O reator foi operado por até 15 dias, sem ocorrência de contaminação por bactérias, com rendimento 0,45 g/g, produtividade em etanol de 4,8 g/L.h e seletividade de 31 getanol/gxilitol (60 g/L de xilose na alimentação). Para as concentrações superiores a 60 g/L, a conversão diminuiu após 4 dias de operação contínua, indicando perda de viabilidade celular devido à ação do etanol quando presente em concentrações acima de 30 g/L e da limitação de oxigênio e nutrientes no sistema.