Dissertations / Theses on the topic 'Enzymatic modifications'

Doutoramento em Bioquímica
A glicosilação não-enzimática e o stress oxidativo representam dois processos importantes visto desempenharem um papel importante no que respeita às complicações de vários processos patofisiológicos. No presente, a associação entre a glicosilação não-enzimática e a oxidação de proteínas é reconhecida como sendo um dos principais responsáveis pela acumulação de proteínas não-funcionais que, por sua vez, promove uma contínua sensibilização para um aumento do stress oxidativo ao nível celular. Embora esteja disponível bastante informação no que respeita aos dois processos e suas consequências ao nível estrutural e funcional, permanecem questões por esclarecer acerca do que se desenvolve ao nível molecular. Com o objectivo de contribuir para uma melhor compreensão da relação entre a glicosilação não-enzimática e a oxidação, proteínas modelo (albumina, insulina e histonas H2B e H1) foram submetidas a sistemas in vitro de glicosilação não-enzimática e oxidação em condições controladas e durante um período de tempo específico. A identificação dos locais de glicosilação e oxidação foi realizada através de uma abordagem proteómica, na qual após digestão enzimática se procedeu à análise por cromatografia líquida acoplada a espectrometria de massa tandem (MALDI-TOF/TOF). Esta abordagem permitiu a obtenção de elevadas taxas de cobertura das sequências proteicas, permitindo a identificação dos locais preferenciais de glicosilação e oxidação nas diferentes proteínas estudadas. Como esperado, os resíduos de lisina foram os preferencialmente glicosilados. No que respeita à oxidação, além das modificações envolvendo hidroxilações e adições de oxigénio, foram identificadas deamidações, carbamilações e conversões oxidativas específicas de vários aminoácidos. No geral, os resíduos mais afectados pela oxidação foram os resíduos de cisteína, metionina, triptofano, tirosina, prolina, lisina e fenilalanina. Ao longo do período de tempo estudado, os resultados indicaram que a oxidação teve início em zonas expostas da proteína e/ou localizadas na vizinhança de resíduos de cisteína e metionina, ao invés de exibir um comportamente aleatório, ocorrendo de uma forma nãolinear por sua vez dependente da estabilidade conformacional da proteína. O estudo ao longo do tempo mostrou igualmente que, no caso das proteínas préglicosiladas, a oxidação das mesmas ocorreu de forma mais rápida e acentuada, sugerindo que as alterações estruturais induzidas pela glicosilação promovem um estado pro-oxidativo. No caso das proteínas pré-glicosiladas e oxidadas, foi identificado um maior número de modificações oxidativas assim como de resíduos modificados na vizinhança de resíduos glicosilados. Com esta abordagem é realizada uma importante contribuição na investigação das consequências do dano ‘glico-oxidativo’ em proteínas ao nível molecular através da combinação da espectrometria de massa e da bioinformática.
Glycation and oxidative stress are two important processes known to play a key role in complications of many pathophysiological processes. It is nowadays acknowledged the association between glycation and oxidation events as a major responsible for the accumulation of non-functional damaged proteins that in turn promote continuous sensitization to further oxidative stress at the cellular level. Despite the large amount of information concerning both events and their consequences at structural and functional levels, questions remain to answer on what happens at the protein molecular level. With the aim of contributing to better understand the interrelationship between glycation and oxidation, model proteins (BSA, insulin and histones H2B and H1) were submitted to in vitro systems of glycation and oxidation under controlled conditions and through a specific period of time. Identification of glycation and oxidation sites was performed through a proteomics approach. Protein samples were enzimatically digested and further analyzed by nano-liquid chromatography coupled to MALDI-TOF/TOF mass spectrometry. This approach allowed obtaining high protein coverage rates, enabling the identification of the most susceptible sites of glycation and oxidation in the different studied proteins. As expected, lysine residues were preferentially glycated and with respect to oxidation, besides protein hydroxyl derivatives and oxygen additions, modifications such as deamidations, carbamylations and specific amino acid oxidative conversions were detected. In general, the main affected amino acids by oxidative damage were cysteine, methionine, tryptophan, tyrosine, proline, lysine and phenylalanine. The time-course study of the oxidative damage indicated the oxidative attack, rather than occurring randomly, initiates at surface-exposed regions and/or near cysteine and methionine residues and occurs in a non-linear way depending on the conformational stability of the protein. Time-course analysis also showed a more pronounced and earlier occurrence of the oxidative damage in the case of preglycated proteins, suggesting that structural changes caused by glycation induce a pro-oxidant state. This increased oxidative damage included not only a greater number of oxidative modifications, but also of oxidized residues, occurring in the vicinity of the glycated residues. Through this kind of approach, an important contribution is made in the investigation of the consequences of protein ‘glycoxidative’ damage at a molecular level through the profit combination of mass spectrometry and bioinformatics.

Malaria is a disease caused by the protozoan parasite Plasmodium where the species that causes the most severe form of malaria in humans is known as Plasmodium falciparum. At least 40% of the global population is at risk of contracting malaria with 627 000 people dying as a result of this disease in 2012. Approximately 90% of all malaria deaths occur in sub-Saharan Africa, where approximately every 30 seconds a young child dies, making malaria the leading cause of death in children under the age of five years old. The malaria parasite has a complex life cycle utilising both invertebrate and vertebrate hosts across sexual and asexual stages. The erythrocyte invasion stage of the life cycle in the human whereby the invasive merozoite form of the parasite enters the erythrocyte is a central and essential step, and it is during this stage that the clinical symptoms of malaria manifest themselves. Merozoites invade erythrocytes utilising multiple, highly specific receptor-ligand interactions in a series of co-ordinated events. The aim of this study was to better understand the interactions occurring between the merozoite and erythrocyte during invasion by using modern, cutting-edge proteomic techniques. This was done in the hope of laying the foundation for the discovery of new key therapeutic targets for antimalarial drug and vaccine-based strategies, as there is currently no commercially available antimalarial vaccine and no drug to which the parasite has not at least started showing resistance. In this study healthy human erythrocytes were treated separately with different protein-altering enzymes and chemicals being trypsin, the potent oxidant sodium periodate (NaIO4), the amine cross-linker tris(2-chloroethyl)amine hydrochloride (TCEA) and the thiol cross-linker 1,11-bis(maleimido)triethylene glycol (BM(PEG)3). The resulting erythrocyte protein alterations were visualised as protein band differences on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE), where treated and untreated control erythrocyte ghost protein fingerprints were visually compared to one another. The protein bands showing differences between treated and control samples were in-gel digested using trypsin then sequenced by liquid chromatography tandem mass spectrometry (LC-MS/MS) and identified using proteomics-based software. In this way, the erythrocyte proteins altered by each enzyme/chemical treatment were identified. Malaria invasion assays were performed where each treatment group of erythrocytes as well as the control erythrocytes were incubated separately with schizont stage malaria parasites for the duration of one complete life cycle. Using fluorescent staining and flow cytometry, the invasion inhibition efficiency for each treatment group was evaluated. By utilising these methods, the identification and the relative importance of the erythrocyte proteins involved in the invasion process were determined. Protein fingerprints of control and treated erythrocyte ghosts were visualised and optimised on SDS PAGE where induced protein band differences were successfully identified by LC-MS/MS. It was found that each treatment altered erythrocyte proteins with changes found in Band 3, actin, phosphoglycerate kinase 1, spectrin alpha, spectrin beta, ankyrin, haemoglobin, Bands 4.1 and 4.2, glycophorin A and stomatin. The invasion assays revealed that TCEA inhibited invasion to the greatest extent as compared to the other treatments, followed by BM(PEG)3 and trypsin. Sodium periodate-treated erythrocytes could not be assessed using the invasion assay due to auto-haemolysis. Band 3, glycophorin A, Band 4.1 and stomatin appear to be of higher relative importance in the invasion process as compared to the other altered erythrocyte proteins. These results confirmed the known roles of spectrin alpha, spectrin beta, glycophorin A, Band 3 and Band 4.1 in invasion, and suggested that ankyrin, Band 4.2 and stomatin may also be involved. This study highlighted the potential that modern, cutting-edge proteomic techniques provide when applied to previous comparative studies found in older literature, as previously unidentified proteins that can be involved in invasion were revealed. These results can be used as a foundation in future studies in order to identify new key targets for the development of new antimalarial drug- and vaccine-based strategies, with the hope of preventing the suffering of the millions of malaria-inflicted people worldwide, and ultimately eradicating this deadly disease.
Dissertation (MSc)--University of Pretoria, 2014.
tm2015
Pharmacology
MSc
Unrestricted

Les dextrane-saccharases utilisent le saccharose comme glucosyle donneur pour la biosynthese de dextranes. Des saccharoses modifies ont ete synthetises puis testes comme analogues de substrat de ces enzymes. Le 3-oxo-saccharose, obtenu par biooxydation du saccharose, a ete utilise comme compose precurseur pour les modifications en c-3. Les 3-oximino, 3-amino et 3-thio-saccharoses ont ete obtenus avec de bons rendements. La strategie developpee pour les modifications en position c-4 a permis d'obtenir, de facon stereoselective, les 4-amino, 4-thio et 4-fluoro-saccharoses. Des tests enzymatiques en presence de dextrane-saccharases ont mis en evidence le caractere inhibiteur des amino et thio-saccharoses

All eukaryotic mRNAs analyzed to date contain, at their 5' end, a cap structure consisting of a reversed 7-methyl guanosine residue linked at the 5' position of the ribose by a triphosphate to the 5'- position of the terminal residue. Since its discovery, the cap structure has been shown to play an important role in the control of initiation of protein synthesis. Further characterization of mRNAs has revealed other unique properties. Its 3' terminus in most eukaryotes is enriched with a sequence of adenylic acid residues called the poly(A) tail. Photoaffinity binding studies, using photoaffinity capped mRNAs and mRNAs polyadenylated with a photoaffinity label translated in a rabbit reticulocyte lysate system, suggest that proteins or initiation factors are associated with both the 5' and 3' ends. The ability for ribosomes to form complexes in a rabbit reticulocyte lysate system was tested by modi fying mRNAs using 8-azido-[32P]GTP and 8-azido-[32P]ATP. The extent of binding was measured by the total amount of photoaffinity label recovered from a 12% SDS-polyacrylamide gel cut into 1 mm stripes and counted in a LS 7000 scintillation counter. Several proteins labeled both at the 5' and 3' ends with the photoaffinity probe appear to be ribonuclear proteins.

En les últimes dècades han augmentat els problemes derivats de la sobreproducció i acumulació de residus de la industria, així com els problemes mediambientals i la disminució de fonts de matèries primeres. En aquest sentit, ha incrementant l’interès en reutilitzar-los, per tal de re-valoritzar-los produint productes d’interès, acostant-nos cada cop més al concepte de residu zero. Un dels majors subproductes de la industria agroalimentària és el conegut amb el terme de biomassa. En aquest treball, ens hem centrat en investigar la re-valorització d’una petita part dels poliols presents en la biomassa, entre ells alguns carbohidrats i el glicerol.
En las últimas décadas han aumentado los problemas derivados de la sobreproducción y acumulación de residuos de la industria agroalimentaria, así como los problemas medioambientales y la disminución de fuentes de materias primas. Incrementando así el interés en reutilizarlos, revalorizándolos produciendo productos de interés, acercándonos cada vez más al concepto de residuo cero. Uno de los mayores subproductos de la industria es el conocido con el término de biomasa. En este trabajo, nos hemos centrado en investigar la revalorización de una pequeña parte de los polioles presentes en la biomasa, entre ellos algunos carbohidratos y el glicerol.
In the last decades, problems related with overproduction and industry waste accumulation have increased, causing environmental problems and depletion of raw material sources. Because of that, there has been an increasing interest in the reuse of wastes to prepare valuable products, getting closer to the zero waste concept. Biomass is one of the major agroindustrial by-products. In this work, we were focused on adding-value to a small portion of the polyols present in biomass, including some carbohydrates and glycerol.

Starch is the major energy reserve in plants, extensively present in many food and non-food applications, and is one of the most abundant carbohydrates in human diet. In addition to starch native form currently used as a raw material for industrial applications, modified starches have become very attractive to develop numerous products that have greatly expanded starch use and utility. Enzymatic modifications are carried out to enhance starch functionality with the aim of overcoming technological constraints and to improve final product quality. Above all starches, corn starch is widely produced and consumed, and used as main ingredient to produce gluten-free products. This Thesis focuses to the study of the individual effect of three different enzymes, fungal alpha-amylase, amyloglucosidase and cyclodextrin glycosyltransferase, on the above sub-gelatinization temperature of corn starch, in order to modify its properties and extend its applications. Different analyses have been performed to improve the understanding of functional and structural changes promoted by the enzyme action. Moreover, corn starch modified with cyclodextrin glycosyltransferase was selected to investigate the glycemic response in mice. The presence/absence of hydrolysis products released from the enzyme catalytic activity and gelatinization properties were related to glycemic index. Enzymatically modified corn starch resulted in a diversity of functional starch granules that may be used in food applications for many purposes.
El almidón es la principal fuente de reserva de energía en las plantas, está ampliamente presente en diversas aplicaciones alimentarias y no alimentarias, y constituye uno de los hidratos de carbono más abundantes en la dieta humana. Además del uso frecuente y clásico del almidón nativo como materia prima en la producción de alimentos, los almidones modificados han experimentado gran expansión en el desarrollo de numerosos productos debido a su carácter versátil. Las modificaciones enzimáticas se llevan a cabo para realzar la funcionalidad del almidón con objeto de soslayar las restricciones tecnológicas y mejorar la calidad del producto final. En concreto, el almidón de maíz ampliamente producido y consumido, es apropiado como ingrediente principal en la producción de alimentos libres de gluten. Esta Tesis aborda el estudio del efecto individual de tres diferentes enzimas, alfa-amylasa fúngica, amiloglucosidasa y ciclodextrina glucosiltransferasa, sobre la temperatura de sub-gelatinización del almidón de maíz. Se realizaron diferentes análisis para ampliar el conocimiento de los cambios estructurales y funcionales asociados a la acción de la enzima. Así mismo, se seleccionó el almidón de maíz modificado con ciclodextrina glucosiltransferasa para investigar la respuesta glicémica en ratones. El índice glicémico se relacionó con la ausencia/presencia de productos de hidrólisis liberados por la acción catalítica de la enzima y las propiedades de gelatinización. Los almidones de maíz enzimáticamente modificados presentaron alteraciones funcionales en los gránulos de almidón, lo que les confiere características de interés para diversos usos alimentarios.
El midó és la principal font de reserva d'energia en les plantes, està àmpliament present en diverses aplicacions alimentàries i no alimentàries, i constitueix un dels hidrats de carboni més abundants en la dieta humana. A més de l'ús freqüent i clàssic del midó natiu com a matèria primera en la producció d'aliments, els midons modificats han experimentat gran expansió en el desenvolupament de nombrosos productes a causa del seu caràcter versàtil. Les modificacions enzimàtiques es duen a terme per a realçar la funcionalitat del midó a fi d'esbiaixar les restriccions tecnològiques i millorar la qualitat del producte final. En concret, el midó de dacsa àmpliament produït i consumit, és apropiat com a ingredient principal en la producció d'aliments lliures de gluten. Aquesta Tesi aborda l'estudi de l'efecte individual de tres diferents enzims, alfa-amylasa fúngica, amiloglucosidasa i ciclodextrina glucosiltransferasa, sobre la temperatura de sub-gelatinizació del midó de dacsa. Es van realitzar diferents anàlisi per a ampliar el coneixement dels canvis estructurals i funcionals associats a l'acció de l'enzim. Així mateix, es va seleccionar el midó de dacsa modificat amb ciclodextrina glucosiltransferasa per a investigar la resposta glicémica en ratolins. L'índex glicémic es va relacionar amb l'absència/presencia de productes d'hidròlisis alliberats per l'acció catalítica de l'enzim i les propietats de gelatinización. Els midons de dacsa enzimàticament modificats van presentar alteracions funcionals en els grànuls de midó, la qual cosa els confereix característiques d'interès per a diversos usos alimentaris.
Durá De Miguel, Á. (2017). EFFECT OF ENZYMATIC TREATMENTS ON CARBOHYDRATE MATRICES TOWARDS HEALTHY GLUTEN FREE FOODS APPLICATION [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/79509
TESIS

Vegetable oils are a cheap and abundant chemical feedstock which can be readily broken down into fatty acid methyl esters (FAMEs) by transesterification using methanol and a base catalyst. These FAMEs contain reactive unsaturated double bonds which can be targeted for modification. In this study, enzymatic and chemical modifications of the unsaturated double bonds of FAMEs are explored with the goal of producing higher value products. Specifically the enzymatic modification of methyl linoleate using soybean lipoxygenase and the chemical modification of methyl oleate using hypobromantion are studied.

Doutoramento em Bioquímica
Os polissacarídeos são os componentes maioritários dos grãos de café verde e torrado e da bebida de café. Os mais abundantes são as galactomananas, seguindo-se as arabinogalactanas. Durante o processo de torra, as galactomananas e arabinogalactanas sofrem modificações estruturais, as quais estão longe de estar completamente elucidadas devido à sua diversidade e à complexidade estrutural dos compostos formados. Durante o processo de torra, as galactomananas e arabinogalactanas reagem com proteínas, ácidos clorogénicos e sacarose, originando compostos castanhos de alto peso molecular contendo nitrogénio, designados de melanoidinas. As melanoidinas do café apresentam diversas atividades biológicas e efeitos benéficos para a saúde. No entanto, a sua estrutura exata e os mecanismos envolvidos na sua formação permanecem desconhecidos, bem como a relação estrutura-atividade biológica. A utilização de sistemas modelo e a análise por espectrometria de massa permitem obter uma visão global e, simultaneamente, detalhada das modificações estruturais nos polissacarídeos do café promovidas pela torra, contribuindo para a elucidação das estruturas e mecanismos de formação das melanoidinas. Com base nesta tese, oligossacarídeos estruturalmente relacionados com a cadeia principal das galactomananas, (β1→4)-Dmanotriose (Man3), e as cadeias laterais das arabinogalactanas, (α1→5)-Larabinotriose (Ara3), isoladamente ou em misturas com ácido 5-Ocafeoilquínico (5-CQA), o ácido clorogénico mais abundante nos grãos de café verde, e péptidos compostos por tirosina e leucina, usados como modelos das proteínas, foram sujeitos a tratamento térmico a seco, mimetizando o processo de torra. A oxidação induzida por radicais hidroxilo (HO•) foi também estudada, uma vez que estes radicais parecem estar envolvidos na modificação dos polissacarídeos durante a torra. A identificação das modificações estruturais induzidas por tratamento térmico e oxidativo dos compostos modelo foi feita por estratégias analíticas baseadas principalmente em espectrometria de massa, mas também em cromatografia líquida. A cromatografia de gás foi usada na análise de açúcares neutros e ligações glicosídicas. Para validar as conclusões obtidas com os compostos modelo, foram também analisadas amostras de polissacarídeos do café obtidas a partir de resíduo de café e café instantâneo. Os resultados obtidos a partir dos oligossacarídeos modelo quando submetidos a tratamento térmico (seco), assim como à oxidação induzida por HO• (em solução), indicam a ocorrência de despolimerização, o que está de acordo com estudos anteriores que reportam a despolimerização das galactomananas e arabinogalactanas do café durante a torra. Foram ainda identificados outros compostos resultantes da quebra do anel de açúcares formados durante o tratamento térmico e oxidativo da Ara3. Por outro lado, o tratamento térmico a seco dos oligossacarídeos modelo (individualmente ou quando misturados) promoveu a formação de oligossacarídeos com um maior grau de polimerização, e também polissacarídeos com novos tipos de ligações glicosídicas, evidenciando a ocorrência de polimerização através reações de transglicosilação não enzimática induzidas por tratamento térmico a seco. As reações de transglicosilação induzidas por tratamento térmico a seco podem ocorrer entre resíduos de açúcares provenientes da mesma origem, mas também de origens diferentes com formação de estruturas híbridas, contendo arabinose e manose como observado nos casos dos compostos modelo usados. Os resultados obtidos a partir de amostras do resíduo de café e de café instantâneo sugerem a presença de polissacarídeos híbridos nestas amostras de café processado, corroborando a ocorrência de transglicosilação durante o processo de torra. Além disso, o estudo de misturas contendo diferentes proporções de cada oligossacarídeo modelo, mimetizando regiões do grão de café com composição distinta em polissacarídeos, sujeitos a diferentes períodos de tratamento térmico, permitiu inferir que diferentes estruturas híbridas e não híbridas podem ser formadas a partir das arabinogalactanas e galactomananas, dependendo da sua distribuição nas paredes celulares do grão e das condições de torra. Estes resultados podem explicar a heterogeneidade de estruturas de melanoidinas formadas durante a torra do café. Os resultados obtidos a partir de misturas modelo contendo um oligossacarídeo (Ara3 ou Man3) e 5-CQA sujeitas a tratamento térmico a seco, assim como de amostras provenientes do resíduo de café, mostraram a formação de compostos híbridos compostos por moléculas de CQA ligadas covalentemente a um número variável de resíduos de açúcar. Além disso, os resultados obtidos a partir da mistura contendo Man3 e 5-CQA mostraram que o CQA atua como catalisador das reações de transglicosilação. Por outro lado, nas misturas modelo contendo um péptido, mesmo contendo também 5-CQA e sujeitas ao mesmo tratamento, observou-se uma diminuição na extensão das reações transglicosilação. Este resultado pode explicar a baixa extensão das reações de transglicosilação não enzimáticas durante a torra nas regiões do grão de café mais ricas em proteínas, apesar dos polissacarídeos serem os componentes maioritários dos grãos de café. A diminuição das reações de transglicosilação na presença de péptidos/proteínas pode dever-se ao facto de os resíduos de açúcares redutores reagirem preferencialmente com os grupos amina de péptidos/proteínas por reação de Maillard, diminuindo o número de resíduos de açúcares redutores disponíveis para as reações de transglicosilação. Além dos compostos já descritos, uma diversidade de outros compostos foram formados a partir dos sistemas modelo, nomeadamente derivados de desidratação formados durante o tratamento térmico a seco. Em conclusão, a tipificação das modificações estruturais promovidas pela torra nos polissacarídeos do café abre o caminho para a compreensão dos mecanismos de formação das melanoidinas e da relação estrutura-atividade destes compostos.
Polysaccharides are the major components of green and roasted coffee beans, and coffee brew. The most abundant ones are galactomannans, followed by arabinogalactans. During the roasting process, galactomannans and arabinogalactans undergo structural modifications that are far to be completely elucidated due to their diversity and complexity of the compounds formed. During the roasting process, galactomannans and arabinogalactans react with proteins, chlorogenic acids, and sucrose, originating high molecular weight brown compounds containing nitrogen, known as melanoidins. Several biological activities and beneficial health effects have been attributed to coffee melanoidins. However, their exact structures and the mechanisms involved in their formation remain unknown, as well as the structure-biological activity relationship. The use of model systems and mass spectrometry analysis allow to obtain an overall view and, simultaneously, detailed, of the structural modifications in coffee polysaccharides promoted by roasting, contributing to the elucidation of the structures and formation mechanisms of melanoidins. Based on this thesis, oligosaccharides structurally related to the backbone of galactomannans, (β1→4)-D-mannotriose, and the side chains of arabinogalactans, (α1→5)-Larabinotriose, alone or in mixtures with 5-O-caffeoylquinic acid, the most abundant chlorogenic acid in green coffee beans, and dipeptides composed by tyrosine and leucine, used as models of proteins, were submitted to dry thermal treatments, mimicking the coffee roasting process. The oxidation induced by hydroxyl radicals (HO•) was also studied, since these radicals seem to be involved in the modification of the polysaccharides during roasting. The identification of the structural modifications induced by thermal and oxidative treatment of the model compounds was performed mostly by mass spectrometry-based analytical strategies, but also using liquid chromatography. Gas chromatography was used in the analysis of neutral sugars and glycosidic linkages. To validate the conclusions achieved with the model compounds, coffee polysaccharide samples obtained from spent coffee grounds and instant coffee were also analysed. The results obtained from the model oligosaccharides when submitted to thermal treatment (dry) or oxidation induced by HO• (in solution) indicate the occurrence of depolymerization, which is in line with previous studies reporting the depolymerization of coffee galactomannans and arabinogalactans during roasting. Compounds resulting from sugar ring cleavage were also formed during thermal treatment and oxidative treatment of Ara3. On the other hand, the dry thermal treatment of the model oligosaccharides (alone or when mixed) promoted the formation of oligosaccharides with a higher degree of polymerization, and also polysaccharides with new type of glycosidic linkages, evidencing the occurrence of polymerization via non-enzymatic transglycosylation reactions induced by dry thermal treatment. The transglycosylation reactions induced by dry thermal treatment can occur between sugar residues from the same origin, but also of different origins, with formation of hybrid structures, containing arabinose and mannose in the case of the model compounds used. The results obtained from spent coffee grounds and instant coffee samples suggest the presence of hybrid polysaccharides in these processed coffee samples, corroborating the occurrence of transglycosylation during the roasting process. Furthermore, the study of mixtures containing different proportions of each model oligosaccharide, mimicking coffee bean regions with distinct polysaccharide composition, subjected to different periods of thermal treatment, allowed to infer that different hybrid and non-hybrid structures may be formed from arabinogalactans and galactomannans, depending on their distribution in the bean cell walls and on roasting conditions. These results may explain the heterogeneity of melanoidins structures formed during coffee roasting. The results obtained from model mixtures containing an oligosaccharide (Ara3 or Man3) and 5-CQA and subjected to dry thermal treatment, as well as samples derived from spent coffee grounds, showed the formation of hybrid compounds composed by CQA molecules covalently linked to a variable number of sugar residues. Moreover, the results obtained from the mixture containing Man3 and 5-CQA showed that CQA acts as catalyst of transglycosylation reactions. On the other hand, in the model mixtures containing a peptide, even if containing 5-CQA and subjected to the same treatment, it was observed a decrease in the extent of transglycosylation reactions. This outcome can explain the low extent of non-enzymatic transglycosylation reactions during roasting in coffee bean regions enriched in proteins, although polysaccharides are the major components of the coffee beans. The decrease of transglycosylation reactions in the presence of peptides/proteins can be related with the preferential reactivity of reducing residues with the amino groups of peptides/proteins by Maillard reaction, decreasing the number of reducing residues available to be directly involved in the transglycosylation reactions. In addition to the compounds already described, a diversity of other compounds were formed from model systems, namely dehydrated derivatives formed during dry thermal treatment. In conclusion, the identification of the structural modifications in coffee polysaccharides promoted by roasting pave the way to the understanding of the mechanisms of formation of melanoidins and structure-activity relationship of these compounds.

This thesis describes strategies for and examples ofcellulose fiber modification.The ability of an engineered biocatalyst, acellulose-binding module fused to theCandida antarcticalipase B, to catalyze ring-openingpolymerization of e-caprolactone in close proximity tocellulose fiber surfaces was explored. The water content in thesystem was found to regulate the polymer molecular weight,whereas the temperature primarily influenced the reaction rate.The hydrophobicity of the cellulose sample increased as aresult of the presence of surface-deposited polyester.

A two-step enzymatic method was also investigated. Here,Candida antarctica lipase B catalyzed the acylation ofxyloglucan oligosaccharides.The modified carbohydrates werethen incorporated into longer xyloglucan molecules through theaction of a xyloglucan endotransglycosylase. The modifiedxyloglucan chains were finally deposited on a cellulosesubstrate.

The action ofCandida antarcticalipase B was further investigated inthe copolymerization of e-caprolactone and D,L-lactide.Copolymerizations with different e-caprolactone-to-D,L-lactideratios were carried out. Initially, the polymerization wasslowed by the presence of D,L-lactide. During this stage,D,L-lactide was consumed more rapidly than ε-caprolactoneand the incorporation occurred dimer-wise with regard to thelactic acid units.

Morphological studies on wood fibers were conducted using asol-gel mineralization method. The replicas produced werestudied, without additional sample preparation, by electronmicroscopy and nitrogen adsorption. Information concerning thestructure and accessibility of the porous fiber wall wasobtained. Studies of never-dried kraft pulp casts revealedmicro-cavities and cellulose fibrils with mean widths of 4.7(±2) and 3.6 (±1) nm, respectively.

Finally, cationic catalysis by simple carboxylic acids wasstudied. L-Lactic acid was shown to catalyze the ring-openingpolymerization of ε-caprolactone in bulk at 120 °C.The reaction was initiated with methylß-D-glucopyranoside, sucrose or raffinose, which resultedin carbohydrate-functionalized polyesters. The regioselectivityof the acylation was well in agreement with the correspondinglipase-catalyzed reaction. The polymerization was alsoinitiated with a hexahydroxy-functional compound, whichresulted in a dendrimer-like star polymer. The L-lactic acidwas readily recycled, which made consecutive reactions usingthe same catalyst possible.

Keywords:Candida antarcticalipase B, cationic catalysis,cellulose-binding module, dendrimer, enzymatic polymerization,fiber modification, silica-cast replica, sol-gelmineralization, organocatalysis, xyloglucanendotransglycosylase

Tip60 is a 60 kDa nuclear protein which exists in three isoforms, belongs to the MYST/HAT family of proteins and was discovered after its interaction with the Human HIV-1 Tat. As a nuclear protein, Tip60 can act as a coactivator or repressor. To understand the HAT action of Tip60, two possible catalytic models exist; the ping-pong and the ternary complex formation models. In correlation with the exploration of HAT catalytic action, mutations of a Cys to Ala and a Glu to Gln on Esa1 (yeast homolog of Tip60 and MYST/HAT prototype), was reported to show wild type-like and decreased acetylating properties, respectively. In this work, Tip60 HAT action was explored. In Tip60, the Cys in the active site is important for acetylation of the H4(1-20) substrate and the Glu showed semi loss in acetylating the H4(1-20) peptide substrate. These data highlight a unique mechanism of Tip60 catalysis.

Cobalamin, also known as vitamin B12, is an essential nutrient for many different organisms including mammals, fish, birds, nematodes, and a variety of bacteria. However, cobalamin is only synthesised by a few bacteria and archaea. Organisms that cannot synthesise cobalamin de novo must obtain it from their diet. In humans, the cobalamin uptake mechanism has been studied in detail, but in many organisms, such as Caenorhabditis elegans, no method of transport has been defined, and their need for cobalamin is recognised by a cobalamin deficiency phenotype. Corrin ring modified fluorescent analogues of cobyric acid and ribose conjugated fluorescent analogues of cobalamin were synthesised in order to follow the uptake and localisation of these corrinoids in a variety of organisms. Both the C5 corrin-ring modified and the ribose conjugated analogues were absorbed by Salmonella enterica, using the B12 uptake system (Btu) and could be converted into active coenzyme forms. The imaging of these fluorescent analogues enabled the identification of the coelomocytes in C. elegans as a possible storage cell for cobalamin. However, the C5 cobyric acid analogue was not recognised which suggests that the C. elegans cobalamin transport mechanism is specific for complete corrinoid molecules. Lepidium sativum, garden cress, was shown to take up both cobalamin analogues from the roots and store it in the vacuoles of the cotyledons in seedlings, even though plants have no cobalamin requirement. In contrast, Arabidopsis thaliana did not transport any of the cobalamin analogues. Cobalamin deficiency has been implicated in impeding disease progression in a number of diseases, such as tuberculosis. The Mycobacterium tuberculosis cobalamin uptake protein, BacA, has only recently been identified, and there is still much to learn about the relationship between M. tuberculosis and cobalamin. Incubations of a cobalamin dependent strain of M. tuberculosis, ΔmetE, with a selection of cobalamin biosynthesis intermediates showed that cobyric acid is the earliest intermediate to be taken up and converted into the cofactor form. The C5 corrin ring modified cobyric acid fluorescent analogue is also capable of rescuing this ΔmetE strain, and is taken up faster than the ribose conjugated cobalamin analogue. Overall, the research outlined in this thesis demonstrates that fluorescent corrinoid analogues can be used to follow the journey of cobalamin in a broad range of different organisms and systems.

The employment of enzymes and whole cells has been important in many industries for centuries. However, it is only in the last 30 years that the use of enzymes for the synthesis of high-value fine chemicals has enjoyed increasing popularity. In fact, esterases and lipases are used almost routinely these days to provide optically active building blocks for the construction of imaginative new routes to chiral target molecules. The major topic of this work describes the utilization of enzymes (namely lipases) in the synthesis and modification of natural and non-natural compounds. Chapter 1 outlines the strengths and weaknesses of the most widely used enzyme systems and a description of a brief summary on the state of the art of biotransformations with special emphasis on the general applicability and reliability of various reaction types is described. Chapter 2 describes the enzymatic resolution of various 3-acetoxy-4-aryl-substituted azetidin-2-ones. Following screening of enzymes, such as Novozym-435, PS-30, PPL and AYS the best conditions were a phosphate buffer with PS-30 as the enzyme. The resulting products were the (3S, 4R)-3-hydroxy-4-aryl-substituted azetidin-2-ones and the unreacted (3R, 4S)-3-acetoxy-4-aryl-substituted azetidin-2-ones. Reactions generally occurred with high conversion and high selectivity. In Chapter 3, the regioselective transesterifications and hydrolysis of peracylated sophorolipid (SL) derivatives catalyzed by lipases was investigated. It was confirmed from the detailed spectral analysis of the products that transesterification failed to furnish any free hydroxyls on the sophorose ring. Instead, transesterification took place on the methyl ester located at the carboxylic end of the 17-hydroxyoctadecenoic acid chain attached to the C-1' position of the sophorose ring. In Chapter 4, the chemo-enzymatic syntheses of enantiomerically pure R and S imperanene from vanillin are described. The key step entails the asymmetrization of a prochiral diol using lipase PS-30. The resulting monoacetate has enantiomeric excesses of >97%. Biocatalysts represent a new class of chiral catalysts useful for a broad range of selective organic transformations. It is stating the obvious to say that biocatalysis is not a panacea for synthetic organic chemistry. However, advances over the past thirty years mean that it would be a serious mistake not to consider the employment of a biocatalyst, in, perhaps, the key step in a sequence of transformations that turn a cheap starting material into an expensive fine chemical.

La valorisation de la biomasse saccharidique pour la production de dérivés biosourcés d'intérêt est un enjeu important. La cellulose est le polysaccharide le plus abondant sur Terre et représente une source de matière première considérable. Dans ce travail, de nouveaux procédés de dépolymérisation de la cellulose pour l'obtention contrôlée de cellodextrines sont décrits. Ils proposent une approche alternative plus douce aux procédés de production actuels en privilégiant l'utilisation d'enzymes, et de liquides ioniques comme solvants alternatifs. Ce travail rapporte l'élaboration de deux méthodes d'obtention contrôlée d'oligosaccharides à partir de cellulose et de cellulose acétate par combinaisons successives d'hydrolyses acide et enzymatique. Ces procédés ont permis l'obtention de cellodextrines de tailles ciblées avec de bons rendements, et constituent une voie prometteuse pour la valorisation de la cellulose en dérivés biosourcés. La deuxième partie de ce travail consiste en la modification chimio-enzymatique des oligosaccharides de cellulose produits pour leur valorisation en biomolécules d'intérêt, plus particulièrement dans le domaine de l'agrochimie. Les cellodextrines sont utilisées en tant que base saccharidique pour la synthèse d'analogues de lipo-chitooligosaccharides comme potentiels fertilisants verts. Deux méthodes de préparation ont été élaborées à l'aide des glycoside-hydrolases comme outils de synthèse. Les stratégies développées permettent un accès efficace à la synthèse d'analogues et peuvent être adaptées pour la production d'autres molécules.

La cellulose est le biopolymere le plus abondant sur terre, et l'etude de sa degradation presente une importance ecologique et industrielle croissante. Trois aspects fonctionnels et structuraux des cellulases ont ete abordes au cours de ce travail: l'adsorption, les interactions avec la cellulose cristalline et l'organisation des differents domaines constitutifs des cellulases. Les observations faites en microscopie electronique sur la morphologie de la degradation de fibres de coton, ont permis de mieux cerner le mode d'action d'une endoglucanase, eg v de humicola insolens, sur un substrat cellulosique industriel. Grace a un immunomarquage a l'or colloidal, nous avons pu visualiser les sites de fixation de eg v a la surface des fibres de coton. L'etude de la degradation enzymatique de microcristaux de cellulose de valonia natifs et modifies par trois cellulases de humicola insolens, met en evidence que l'ultrastructure du substrat est le facteur determinant de la reactivite enzymatique. Nos travaux demontrent qu'une diminution du degre de cristallinite et une augmentation de la surface accessible entraine un accroissement important de la reactivite du substrat. Les etudes en diffusion de la lumiere ont fourni des donnees precises sur les coefficients de diffusion de trois cellulases de humicola insolens ainsi qu'une estimation de la taille hydrodynamique de ces enzymes. De plus, cette technique represente un outil interessant pour analyser les differents variants produits lors d'une approche d'ingenierie des proteines. Elle permet, en effet, de suivre le comportement en solution d'un type de proteine en fonction de differents parametres tels que la temperature, le ph et la concentration en proteines

Les exopolysaccharides (EPS) synthétisés par des bactéries possèdent une grande diversité de structures et constituent une source importante de molécules aux propriétés nouvelles. Parmi ceux-ci, l’EPS HYD 657 ou deepsane est produit par une bactérie marine : Alteromonas macleodii subsp. Fijiensis biovar deepsane, collectée dans une zone de sources hydrothermales profondes. Déjà valorisé dans le domaine de la cosmétique mais de structure non élucidée, la première partie de cette étude a consisté à caractériser une partie de la structure de cet EPS complexe de poids moléculaire supérieur â 106 g/mol. Son unité de répétition est ramifiée et constituée de 16 à 18 oses, dont 7 types de monosaccharides différents (neutres et acides) avec 3 types dc substituants (sulfate, lactate et pyruvate). L’étude de l’EPS natif et de fractions de bas poids moléculaires obtenues par dégradation de Smith a permis d’identifier la structure de deux oligosaccharides constitutifs de cette unité répétitive et de positionner deux substituants. La seconde partie du travail est consacrée à l’étude de deux procédés de dépolymérisation en vue d’obtenir des EPS de bas poids moléculaires pour élargir le champ d’applications du FIYD 657. Après comparaison d’un procédé connu (dépolymérisation radicalaire) et d’un procédé développé au cours de cette étude (broyage mécanique), deux EPS de bas poids moléculaires, dont l’un sur-sulfaté, ont été préparés en vue de tester leurs propriétés biologiques : des activités biologiques intéressantes ont ainsi été mises en évidence dans le domaine de l’immunomodulation. Afin de compléter la recherche d’outils de dépolymérisation de cet EPS, la troisième partie se focalise sur la recherche d’activités enzymatiques à partir de la souche productrice de cet EPS. Une culture de la souche en conditions de production d’EPS a permis de générer un extrait enzymatique actif sur cet EPS
Bacteria are known to produce exopolysaccharides (EPS) with a great diversity of structures and are an important source of polysaccharides with new properties. Among those, the EPS HYD 657 or deepsane is produced by a marine bacteria: Alteromonas macleodii subsp. Fijiensis biovar deepsane, collected around deep-sea hydrothermal vents. This high molecular weigh EPS (>106 g/mol) is already used in cosmetics but its structure remained unknown so that the first aim of this study consists in elucidating its repeating unit. The data show a very complex branched repeating unit of 16-18 sugars with 7 different types of monosaccharides (neutral and acidic) and 3 types of substituents (sulphate, lactyl and pyruvyl groups). Analyses of native and oligomeric fragments from Smith degradation allow us to identify two oligosaccharides of this repeating unit and the position of two substituents. In order to enlarge the application field of this EPS, two depolymerization processes were studied. After comparison of the first one know process (free-radical depolymerization) and development of a second one (ball-milling), two low molecular weigh EPS were prepared and sulphate groups were added: they show interesting properties in modulating a way of the immune system. To enlarge depolymerization tools of this EPS, the research of enzymatical activities s developed in the third part. Protein extracts were generated by cultivating the strain producing J IN L 657 under EPS-producing conditions. One of those extracts was shown to be active to depolymerize this EPS

Der Actinomycet T. fusca KW3, isoliert aus Kompost, bildete während der Kultivierung im Mineralsalz-Spurenelement-Vitamin-Minimalmedium nach Zusatz von PET-Fasern eine 52 kDa Carboxylesterase (TfCa), welche effizient zyklische PET Trimere (CTR) hydrolysiert. Die TfCa besitzt einen pI von 4,8, eine Substratspezifität gegenüber kurzkettigen p-Nitrophenyl-Estern und wird durch Phenylmethylsulfonylfluorid (PMSF) und Tosyl-L-Phenylalanin-Chloromethylketon (TPCK) in der Aktivität gehemmt. Die Carboxylesterase hydrolysiert kein Cutin oder Poly-ε-caprolacton (PCL). CTR hingegen wurden durch die TfCa mit einem Km von 0,5 mM und einer Vmax von 9,3 μmol/min/mg bei optimalen Bedingungen (60°C, pH 6) hydrolysiert. Das aktive Zentrum der Carboxylesterase besteht aus den Aminosäuren Ser185, Glu319 und His415, wobei das Serin in das katalytische Motiv G-E-S-A-G eingebettet ist. Während der Reaktion setzte die TfCa auch Hydrolyseprodukte aus PET-Fasern und -Filmen frei. Der Nachweis der Hydrolyse erfolgte durch Umkehrphasen-Hochleistungsflüssigkeitschromatographie der Abbauprodukte und bei den PET-Filmen zusätzlich mittels Rasterelektronenmikroskopie. Dabei zeigte die Carboxylesterase verglichen mit anderen PET-Hydrolasen eine geringere Effizienz, was durch die Lage des aktiven Zentrums in einer Bindungstasche und der daraus folgenden schlechten Zugänglichkeit für polymere Substrate begründet werden kann. Bei der Hydrolyse der viel kleineren CTR war die TfCa deutlich effektiver, was auf eine höhere Spezifität gegenüber kurzkettigen PET Substraten hinweist.

The activity of protein kinases is heavily dependent on the phosphorylation state of the protein. Kinase phosphorylation states have been prepared through biological or enzymatic means for biochemical evaluation, but the use of protein chemical modification as an investigative tool has not been addressed. By chemically reacting a genetically encoded cysteine, phosphocysteine was installed via dehydroalanine as a reactive intermediate. The installed phosphocysteine was intended as a surrogate to the naturally occurring phosphothreonine or phosphoserine of a phosphorylated protein kinase. Two model protein kinases were investigated on: MEK1 and p38α. The development of suitable protein variants and suitable reaction conditions on these two proteins is discussed in turn and in detail, resulting in p38α-pCys180 and MEK1-pCys222. Designed to be mimics of the naturally occurring p38α-pThr180 and MEK1-pSer222, these two chemically modified proteins were studied for their biological function. The core biological studies entailed the determination of enzymatic activity of both modified proteins, and included the necessary controls against their active counterparts. In addition, the studies on p38α-pCys180 also included a more detailed quantification of enzymatic activity, and the behaviour of this modified protein against known inhibitors of p38α was also investigated. Both modified proteins were shown to be enzymatically active and behave similarly to corresponding active species. The adaptation of mass spectrometry methods to handle the majority of project's analytical requirements, from monitoring chemical transformations to following enzyme kinetics was instrumental in making these studies feasible. The details of these technical developments are interwoven into the scientific discussion. Also included in this thesis is an introduction to the mechanism and function of protein kinases, and on the protein chemistry methods employed. The work is concluded with a projection of implications that this protein chemical modification technique has on kinase biomedical research.

Les polymères en solution peuvent s’auto-assembler pour former différents types de complexes (coacervats, agrégats, etc.). Ces objets, en plus de régir l’organisation cellulaire peuvent être détournés pour encapsuler des molécules d’intérêt. Cependant, avant de pouvoir les utiliser en tant que tel, la compréhension des mécanismes d’auto-assemblage est indispensable pour pouvoir les contrôler et ainsi former des objets à façon. Ce travail de thèse porte sur l’auto-assemblage entre la gomme d’Acacia et le chitosane. Les interactions mises en jeu lors de la séparation de phases associatives reposent principalement sur des interactions électrostatiques. Dans un premier temps, la formation de ce complexe a été analysée d’un point de vue thermodynamique par titration calorimétrique isotherme, en fonction des paramètres physico-chimiques, en particulier du pH, de la température et du ratio molaire. Il a ainsi été démontré qu’une augmentation de température ou de pH favorisait l’enthalpie au dépend de l’entropie et qu’il était possible de former des coacervats dans toutes les conditions étudiées en jouant sur le couple pH/température. Pour changer le nombre et la nature des interactions entre les polysaccharides, ces derniers ont été modifiés par voie enzymatique. Un procédé développé au laboratoire reposant sur l’utilisation d’une laccase pour oxyder l’acide férulique a été mis en œuvre. Dans un premier temps, la modification de la gomme d’Acacia a été démontrée, notamment grâce à des outils spectroscopiques (FTIR, RMN). De plus, la structure des nombreux produits d’oxydation a été étudiée (RMN, LCMS). Les produits obtenus sont majoritairement des dimères d’acide férulique et une structure complète a été élucidée. Les produits greffés sur la gomme étant de nature phénolique, leur greffage a un impact sur les propriétés techno-fonctionnelles de cette dernière (solubilité dans l’eau, comportements thermique et rhéologique, tension de surface, propriétés antioxydantes, etc.). Enfin, le greffage de composés phénoliques modifiant l’hydrophobie et les charges des polysaccharides, des auto-assemblages entre les différents polymères ont été réalisés pour déterminer leur impact sur les interactions mises en jeu et la nature des complexes formés. Dans des conditions données et en fonction des polysaccharides mis en présence, il est possible de former des coacervats, des agrégats voire un mélange des deux. La formation de ces objets a été corrélée avec une étude des paramètres thermodynamiques mis en jeu. Ces résultats ouvrent de nouvelles voies dans la compréhension et le contrôle de la complexation entre polysaccharides qui, à plus long terme, déboucheront sur des applications dans le domaine de l’encapsulation
Polymers in solution can self-assemble to form different types of complexes (coacervates, aggregates, etc.). These objects, in addition to being part of the cellular organization, can be repurposed to encapsulate molecules of interest. However, before being able to use them as such, the understanding of the self-assembly mechanisms is essential to be able to control them and thus form targeted objects. This thesis work focuses on the self-assembly between gum Arabic and chitosan. The interactions involved in associative phase separation are mainly based on electrostatic interactions. Initially, the formation of this complex was analyzed from a thermodynamic point of view by isothermal calorimetric titration, depending on the physicochemical parameters, in particular the pH, the temperature and the molar ratio. It was thus demonstrated that an increase in temperature or pH favored enthalpy and disfavored entropy and that it was possible to form coacervates under all studied conditions by controlling the pH/temperature combination. To change the number and nature of the interactions between polysaccharides, they were modified by enzymatic pathway. A process developed at the laboratory, based on the use of a laccase to oxidize ferulic acid, has been implemented. First, the modification of gum Arabic was demonstrated, in particular with the support of spectroscopic tools (IR-FT, NMR). In addition, the structure of the numerous oxidation products has been studied (NMR, LCMS). The products obtained are mainly ferulic acid dimers and a complete structure has been elucidated. The products grafted on the gum are of phenolic nature so their grafting has an impact on its techno-functional properties (water solubility, thermal and rheological behavior, surface tension, antioxidant properties, etc.). Finally, the grafting of phenolic compounds modified the polysaccharides hydrophobia and charges, so they were mixed in order to determine the impact of these new groups on the interactions involved in the self-assemblies and the nature of the complexes formed. Under given conditions and depending on the polysaccharides used, it is possible to form coacervates, aggregates or even a mixture of both. The formation of these objects was correlated with a study of the thermodynamic parameters involved. These results paves the way for understanding and controlling complexation between polysaccharides that, in the longer term, will lead to applications in the field of encapsulation

Untersuchungen zur Reaktion von Proteinen während einer Hochdruckbehandlung (HD) ermöglichen ein besseres Verständnis der Reaktivität und Struktur auf molekularer Ebene. In der vorliegenden Arbeit wurde die enzymatische Oligomerisierung von Hühnereiweißlysozym (HEWL) mithilfe der druckstabilen mikrobiellen Transglutaminase (mTGase) unter HD untersucht. Die resultierenden Oligomere wurden anschließend hinsichtlich ihrer strukturellen und funktionellen Eigenschaften charakterisiert. Vergleichende Untersuchungen wurden mit dem evolutionsbiologisch verwandten Protein, dem α-Lactalbumin durchgeführt. Abschließend erfolgten orientierende Studien zur nicht-enzymatischen Vernetzung von HEWL und ausgewählten Milchproteinen, bei welchen eine kovalente Verknüpfung über vergleichbare Isopeptide nachgewiesen werden konnte. Kompakte, globuläre Proteine, wie das untersuchte HEWL stellten unter Normaldruck keine Substrate für die mTGase dar. Auch war eine enzymatische Vernetzung nach erfolgter Hochdruckbehandlung aufgrund der Reversibilität der druckinduzierten Auffaltung nicht möglich. So wurde HEWL nur bei simultaner Behandlung mit mTGase und hohem hydrostatischem Druck zu Homooligomeren vernetzt. Neben einem geeigneten Puffersystem wurden der pH-Wert, die Inkubationszeit, die Temperatur, der hydrostatische Druck, die Enzymaktivität der mTGase und die Proteinkonzentration des Lysozyms verändert. Abhängig von den Reaktionsbedingungen wurden Produkte mit stark variierenden Vernetzungsgraden erhalten, wobei eine maximale Oligomerisierung von zirka 75% aus einer 3%igen HEWL-Probe in Tris-HCl-Puffer bei pH 7,5 mit 160 U mTGase/g Protein über 30 min, 600 MPa und 40°C erreicht wurde. Zudem erfolgte eine Kategorisierung aller resultierenden Proben anhand ihres mittels Gelelektrophorese bestimmten Vernetzungsgrades in drei Untergruppen: LMW (niedrig vernetzt, 0 - 30%), MMW (mittel vernetzt, 30 - 60%) und HMW (hoch vernetzt, 60 - 100%). In den so vernetzten Proben wurden das reaktionsspezifisch gebildete Isopeptid N ε (γ L Glutamyl)-L-Lysin (Glu_Lys) nachgewiesen und die beteiligten reaktiven Aminosäuren identifiziert. Die Bestimmung von Glu_Lys, welches für die kovalenten Verknüpfungen verantwortlich ist, erfolgte nach enzymatischer Hydrolyse am Aminosäureanalysator mit Ninhydrin-Nachsäulen-Derivatisierung. Eine erste Abschätzung des Isopeptid¬gehaltes zeigte zudem, dass es bei der Oligomerisierung sowohl zu inter- als auch intra¬molekularer Vernetzung kam. Der minimal notwendige Gehalt an Cross-Link-Aminosäuren, [CLAA]min lag zum Teil um den Faktor zwei unter dem Gehalt des quantifizierten Glu_Lys. Anschließend konnte nach tryptischem Verdau über die RP-HPLC/ESI-TOF-MS für die gering vernetzten Proben (LMW) genau eine definierte kovalente Verknüpfungsstelle ermittelt werden. Für die MMW- und HMW-Proben wurden fünf bzw. sechs Peptidfragmente detektiert. Bei den LMW-Proben wurde Lys1 mit Gln121 vernetzt. Den höher oligomerisierten Proben konnten die Lysinreste Lys1, Lys13, Lys116 und die Glutaminreste Gln41, Gln57, Gln121 zugeordnet werden. Somit gelang eine erste strukturelle Aufklärung der Vernetzungsprodukte. Der Aufbau der Oligomere läuft demnach zuerst gerichtet und linear ab. Insbesondere bei höheren Temperaturen und Enzymaktivitäten werden jedoch ungeordnete Strukturen gebildet. Die einzelnen Vernetzungsprodukte scheinen aufgrund der Lage der reaktiven Aminosäuren im HEWL-Molekül über mehrere intermolekulare Bindungen eine variierende Struktur auszubilden. Eine Quantifizierung der einzelnen Isopeptide erfolgte nicht, orientierende MS-Untersuchungen lassen aber vermuten, dass auch hier bevorzugte Reaktionsorte existieren. Die vernetzten Proben wurden nachfolgend über Ammoniumsulfatfällung konzentriert und mittels Gelpermeationschromatographie (GPC) fraktioniert. Die Ausbeuten der GPC waren sehr gering. Eine Fraktionierung in einzelne, selektiv verknüpfte Oligomere wurde nicht erreicht. Die enzymatisch oligomerisierten Proben sowie ausgewählte GPC-Fraktionen mit höheren Oligomeren wurden hinsichtlich funktioneller und struktureller Konsequenzen untersucht. Begonnen wurde dabei mit der lytischen Enzymaktivität des HEWL gegen Zellwände des Micrococcus lysodeikticus. Eine abnehmende bzw. verbleibende Lyseaktivität korrelierte mit einer zunehmenden Oberflächen¬hydrophobität der Oligomerengemische. Beide Größen verhielten sich indirekt proportional zueinander. Während der hydrophobe Kern des Moleküls mit steigender Oligomerisierungsrate freigelegt wurde, senkte sich die Lyseaktivität bis auf null ab. Eine räumliche Deformation oder Barriere entstand mutmaßlich im oder in der Nähe des reaktiven Zentrums (Glu35 und Asp52) des Lysozyms, so dass der Enzym-Substrat-Komplex nicht mehr ausgebildet werden konnte. Die Untersuchung der Veränderung sekundärer und tertiärer Strukturbestandteilte erfolgte mithilfe der Zirkular-Dichroismus-Spektroskopie. Gleichwohl für die Tertiärstruktur keine großen Veränderungen aufgezeigt wurden, ist für die Sekundärstruktur mit zunehmendem Vernetzungsgrad eine Abnahme der α-Helices und eine Zunahme von ungeordneten und β Faltblatt-Bereichen detektiert worden. Es konnte daher die unter Hochdruck bekannte Auffaltung des HEWL über die enzymatische Vernetzung derart stabilisiert werden, dass eine vollständige Rückfaltung nicht mehr gegeben war. Das Fibrillierungsverhalten der oligomerisierten Proben im Sauren im Vergleich zum unbehandelten HEWL stellte eine weitere Charakterisierungsmöglichkeit dar. Die Analyse der inkubierten Proben erfolgte mithilfe dreier photometrischer Methoden (Umsetzung mit den Reagenzien 8-Anilino-1-naphtalinsulfonsäure, Kongorot oder Thioflavin T). Die fibrillierten Proben wurden zudem transmissionselektronenmikroskopisch (TEM) untersucht. Mit zunehmender Vernetzung war dabei eine abnehmende Fibrillierungsneigung zu beobachten, welche gut strukturell zu erklären ist, da die zusätzlichen, kovalenten Isopeptidbindungen die Proteinmoleküle gegen eine saure Auffaltung stabilisieren. Eine Auffaltung ist jedoch die Grundvoraussetzung für eine Assoziation und Bildung in-vitro-induzierter, amyloider Strukturen. Ferner wurde das antimikrobielle Verhalten der Präparate gegen grampositive und -negative Mikroorganismen getestet. Unbehandeltes Lysozym zeigt grundsätzlich gegenüber grampositiven Mikroorganismen eine gute antimikrobielle Aktivität. Eingesetzt wurden der Agardiffusions- und der bakterielle Hemmtest (Trübungsassay). Hierbei zeigten alle geprüften Proben keine Wirkung gegenüber gramnegativen Bakterien. Die antimikrobielle Wirkung gegenüber den grampositiven Mikroorganismen variierte stark. Das Phänomen der erhöhten Sensibilität gegenüber ausgewählten Bakterienstämmen im niederkonzentrierten Bereich wurde für Bacillus subtilis (grampositiv) und die mittel- bzw. hochvernetzten Proben im Vergleich zu unbehandelten HEWL (je 0,00625% Probe, w/v) reproduzierbar nachgewiesen. Auf die umfassende Charakterisierung der enzymatisch vernetzten HEWL-Proben folgten orientierende Vergleichsstudien mit dem evolutionsbiologisch verwandten α Lactalbumin (α-LA). Die enzymatische Oligomerisierung konnte für das Molkenprotein dabei im Gegensatz zum HEWL bereits unter Atmosphärendruck erzielt werden. Die Vernetzungsraten betrugen, unabhängig von den untersuchten Rahmenparametern aber abhängig vom Calciumgehalt, zirka 35% (mit Ca) bis 72% (ohne Ca). Das α-LA als Calcium-bindendes Protein wurde somit durch die Abwesenheit des Metallions derart destabilisiert, dass es für die mTGase besser umsetzbar wurde. Die im Vergleich zum Lysozym vermehrt enthaltenen potentiell reaktiven Aminosäuren (doppelt so viel Lys und Gln) trugen ebenfalls zu einer stärkeren Oligomerisierung bei. Abschließend erfolgten Studien zu nicht-enzymatischen, vakuuminduzierten Kondensations-reaktionen. Dabei wurde trockenes HEWL im Vakuum thermisch induziert vernetzt. Die Methode ist in der Literatur als Zero-Length-Cross-Linking (ZLCL) beschrieben. Die Untersuchung der Parameter Vakuum, Temperatur, pH-Wert und Zyklenzahl erfolgte an dem globulären Protein. Dieses konnte unter nicht denaturierenden Bedingungen bis zum Di- und Trimer vernetzt werden. Weitere Milchproteinproben (ein Molkenproteinisolat und β-Casein) wurden nur exemplarisch unter Standardbedingungen untersucht. Hierbei wurde das Molkenproteinisolat deutlich besser als HEWL und das β-Casein bei 85°C über je 24 h und Einsatz von Vakuum am stärksten oligomerisiert. Die gute Umsetzung des β-Caseins ist dabei auf die fehlende Tertiär- und Sekundärstruktur zurückzuführen. Zum Teil entstanden auch Casein-Polymere, welche nicht mehr elektrophoresegängig waren. Die beteiligten Isopeptide wurden analog zu den enzymatisch vernetzten Proben über die Aminosäureanalytik nachgewiesen. Es konnte das Isopeptid N-ε-(β-Aspartyl-)Lysin (Asp_Lys) neben Lysinoalanin (LAL), aber kein Glu_Lys in HEWL nachgewiesen werden. Beide Isopeptide (Asp_Lys und Glu_Lys) sowie LAL sind dagegen im β Casein gebildet worden. Der Einfluss struktureller Gegebenheiten auf die Reaktionsfähigkeit der Proteine konnte folglich eindeutig belegt werden.

La résistance à la chimiothérapie constitue un frein majeur à son efficacité. Notre équipe a récemment pu montrer que le masitinib, un nouvel inhibiteur de protéines tyrosine kinases, possède une activité de resensibilisation des cellules tumorales résistantes à la chimiothérapie lorsqu'il est combiné à certaines chimio-drogues. L'objectif des travaux de cette thèse est de déterminer les voies de signalisation, modulées par l'action du masitinib, qui sont impliquées dans la resensibilisation aux chimiothérapies et amélioration de l'activité anti-tumorale.Dans la première partie de la thèse, nous avons pu identifier la nucléoside kinase dCK (désoxycytidine kinase), protéine activatrice d'un grand nombre de chimiothérapies, comme nouvelle cible du masitinib. Cette première étude nous a permis de mettre en évidence un nouveau concept thérapeutique: le masitinib, un composé chimique de type inhibiteur de protéines tyrosine kinases, peut jouer en même temps le rôle d'activateur de nucléoside kinase.Nous avons pu mettre en évidence dans la deuxième partie de la thèse que le traitement combiné entre l'épi-drogue décitabine et le masitinib peut être plus efficace pour la réexpression de certains gènes non ou peu induits par la décitabine seule.En conclusion, ces travaux nous ont permis de mettre en évidence l'interaction entre un inhibiteur de protéine tyrosine kinases et une nucléoside kinase, dans un concept d'activation enzymatique qui pourra certainement servir de base pour l'élaboration de nouvelles petites molécules chimiques spécifiques de l'activation de dCK ou d'autres nucléosides kinases nécessaires à l'activation des drogues de chimiothérapie
Resistance to chemotherapy is considered as one of the major blockers of its efficacy. Recently, our team demonstrated that masitinib, a new tyrosine kinases inhibitor, possesse a resensitization activity of cell lines resistant to chemotherapy when associated with chemodrugs.The aim of this work is to determine signaling pathways, modulated by masitinib action, that could explain the resensitization to chemotherapy and improvement of anti-tumoral activity.In the first part of this work, we identified the nucleoside kinase dCK (deoxycytidine kinase), a chemotherapy activating protein, as a new target of masitinib. In summary, this first part of the work allowed us to describe a new and never described concept: masitinib, a small molecule belonging to tyrosine kinases group, can also play a role as nucleoside kinase activator.We were able to demonstrate through the second part of the work that the combined treatment of the epidrug decitabine and masitinib can be more effective than decitabine treatment for the re-expression of some genes non or weakly induced by decitabine when used alone.In conclusion, These data allowed us to introduce an interaction between a tyrosine kinases inhibitor and a nucleoside kinase, as an enzymatic activation new concept. This could be used as a base for the design of new small chemical molecules specific for dCK or other nucleoside kinases essential for the activation of chemodrugs. This concept will obviously help to imagine and evaluate more potential therapeutic combinations of chemodrugs and small chemical molecules to overcome the resistance to chemotherapy dependent on nucleoside kinases

In biosensors, printing involves the transfer of materials, proteins or cells to a substrate. It offers many capabilities thatcan be utilized in many applications, including rapid deposition and patterning of proteins or other biomolecules.However, issues such as stability when using biomaterials are very common. Using proteins, enzymes, as biomaterialink require immobilizations and modifications due to changing in the structural conformation of the enzymes, whichleads to changes in the properties of the enzyme such as enzymatic activity, during the printing procedures andrequirements such as solvent solutions. In this project, an innovative approach for the fabrication of proteinmicroparticles based on cross-linking interchange reaction is presented to increase the stability in different solvents.The idea is to decrease the contact area between the enzymes and the surrounding environment and also preventconformation changes by using protein microparticles as an immobilization technique for the enzymes. The theory isbased on using a cross-linking reagent trigging the formation of intermolecular bonds between adjacent proteinmolecules leading to assembly of protein molecules within a CaCO3 template into a microparticle structure. TheCaCO3 template is removed by changing the solution pH to 5.0, leaving behind pure highly homogenous proteinmicroparticles with a size of 2.4 ± 0.2 μm, according to SEM images, regardless of the incubation solvents. Theenzyme model used is Horse Radish Peroxidase (HRP) with Bovine Serum Albumin (BSA) and Glutaraldehyde (GL)as a cross-linking reagent. Furthermore, a comparison between the enzymatic activity of the free HRP and the BSAHRPprotein microparticles in buffer and different solvents are obtained using Michaelis-Menten Kinetics bymeasuring the absorption of the blue product produced by the enzyme-substrate interaction using a multichannelspectrophotometer with a wavelength of 355 nm. 3,3’,5,5’-tetramethylbenzidine (TMB) was used as substrate. As aresult, the free HRP show an enzymatic activity variation up to ± 50 % after the incubation in the different solventswhile the protein microparticles show much less variation which indicate a stability improvement. Moreover, printingthe microparticles require high microparticle concentration due to contact area decreasing. However, usingmicroparticles as a bioink material prevent leakage/diffusion problem that occurs when using free protein instead.

A cellulase and a xylanase enzyme preparation were assessed for their potential to enhance the fiber characteristics of both mechanical and kraft pulps derived from Douglas-fir wood chips. The effects of cellulase treatments on the pulp properties were dependent on enzyme dosage and resulted in improvements in handsheet density and smoothness, pulp freeness and fiber coarseness. However, this was achieved at the expense of both strength and yield loss. Enzymatic treatments of individual fiber length fractions indicated that, in general, all fiber length fractions demonstrated similar trends to those observed with the cellulase treated unfractionated pulp. In contrast, the individual fiber length fractions responded differently to xylanase treatments, as indicated by the solubilization of highmolecular- mass, UV-absorbing material released during enzyme treatments. Xylanase treatments enhanced the handsheet density and smoothness as well as some strength properties. However, the response of the different fiber length fractions to xylanase treatments was not uniform, indicating that fiber composition plays a role in determining the efficacy of the treatments. The application of hydrolytic enzymes to the pulp fibers resulted in changes in both fiber and paper properties. Monitoring pore volume, degree of polymerization, crystallinity, FT-IR spectra, and scanning electron microscopy helped elucidate changes in fiber composition and morphology. There was strong evidence that the reduction in paper strength resulted from the collective effects of decreased intrinsic fiber strength and the reduction in the degree of polymerization of a large portion of the hemicellulose component of the fibers. Other contributing factors included fiber defibrillation and fines hydrolysis. Since the traditional hydrolases (cellulases/xylanases) appeared to modify the fibers by changes to the fiber surface, cellobiose dehydrogenase. (CDH), purified from Phanerochaete chrysosporium was assayed to see if its oxidoreductase activity could further enhance access of the enzymes to a Douglas-fir kraft pulp. Although the addition of cellobiose dehydrogenase alone had little effect, supplementation with cellobiose and iron resulted in a substantial reduction in the degree of polymerization of the pulp cellulose. This indicated that cellobiose dehydrogenase generated hydroxyl radicals via Fenton's chemistry, which subsequently resulted in the depolymerization of the cellulose. In this way a substantial reduction in the degree of polymerization of the cellulose could be achieved without a significant release of sugar or yield loss. Having established that cellulase enzymes could cause the greatest alterations in fiber morphology and that their attack was most noticeable on smaller, thinner fibers, further studies were carried out on the selective treatment of the larger coarser fibers. These cellulase treated fibers were then recombined with the untreated fibers and refined or, alternatively, first refined and then recombined with the untreated fibers. Laboratory scale fractionation treatments resulted in significant improvements in both the tensile (17 %) and burst indexes (24 %) (at 100 PFI revolutions) with minimal enzyme addition and little yield loss. A subsequent study was carried out to determine if this combined approach, using industrial scale fractionation, could also provide such positive effects. Improvements in both tensile and burst indexes were observed, however, not to the same extent as was observed when the fibers were separated by laboratory fractionation.

Thesis (M.S.)--University of Georgia, 2002.
Directed by Louise Wicker. Includes articles submitted to Journal of agricultural and food chemitry, and Food hydrocolloids. Includes bibliographical references.

Thesis (M.S.)--University of Wisconsin--Madison, 1992.
Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 113-124).

The objective of this study was to improve canola protein gelation properties with the use of enzymes. Both cross-linking and limited proteolysis were explored. Enzyme treatments were performed prior to heat induced gelation. A texture analyzer, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and scanning electron microscopy were used to characterize the resulting networks. Enzymatic cross-linking with transglutaminase was shown to improve the gelation of canola protein isolate (CPI). To the contrary, proteolysis with trypsin, ficin and bromelin, did not enhance the gelation properties of CPI.
October 2006

Carboxyl esterases, particularly arylesterases, were predicted from 16 microbial genomes, and then expressed in E. coli. Of the more than 175 cloned genes, 86 were expressed in soluble form. These were screened for activity using a range of both commercial and natural substrates. Forty-eight proteins were active on pNP-acetate at pH 8 whereas 38 proteins did not exhibit any activity towards any substrates. Among the 48 active proteins, 20 proteins showed arylesterase activity. To date, 8 bacterial esterases and 2 archaeal arylesterases were characterized in terms of pH stability and optima, thermal inactivation, solvent stability, and kinetics. To our knowledge there is only one other published report of arylesterases from archaea. The synthetic capability of arylesterases can transform phenolic acids to value-added chemicals. Accordingly, this project provides an arsenal of industrially significant activities that can extend the antioxidant properties of lignin-derived molecules in a broader range of renewable products.

The bonding of fibres in paper is influenced by environmental changes (e.g. moisture) that may cause unstable fibres to move. These movements include cell-wall swelling, fibre lifting and/or puffing that break inter-fibre bonds and lead to reduced strength and surface roughness. Fibre puffing is defined as the expansion of the lumen area as result of changes in the environment. Puffing was investigated through image analysis of scanning electron micrographs. Detailed images were obtained with samples that were embedded in resin and then etched. Puffing of fibres was then quantified by calculating the ratio of lumen area to fibre area. Stability of softwood and hardwood fibres was studied in this way, and to simulate printing, handsheets were calendered and rewetted. This method was later validated against commercial sheets. Compared to softwood, hardwood fibres were more stable and most of the handsheet properties were retained after rewetting. Mannanase and/or endoglucanase treatments resulted in improved fibre stability by increasing fibre bonding, fibrillation or fibre collapse. Mannanase improved handsheet smoothness and strength as well as fibre stability, but endoglucanase was less effective. The effect of the enzymes was more difficult to observe on hardwood fibres, because even untreated fibres were more stable under moist conditions. Thin-walled fibres such as earlywood were less stable than latewood fibres, but it responded better to mannanase treatment. Thick-walled fibres (latewood), on the other hand, were more difficult to improve with enzymes. The potential of enzymes to improve fibre stability of commercial pulp was tested on chemi-thermo-mechanical pulp (CTMP) and bleached CTMP. Enzyme treatment improved fibrillation and reduced beating energy of bleached CTMP. Mannanase again resulted in the most improved fibre stability. On rejects, a lack of response to enzymes was overcome by pre-treating the pulp with alkaline peroxide. This study provided new insights into the stability of fibres with different morphology. It was also demonstrated that fibre stability can be improved with enzyme treatment and it is expected that this knowledge could have significant commercial value.
Dissertation (PhD)--University of Pretoria, 2010.
Microbiology and Plant Pathology
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