No description available.

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / Hydrogels prepared from photopolymerization have been widely used in many biomedical applications. Ultraviolet (200-400 nm) or visible (400-800 nm) light can interact with light-sensitive compounds called photoinitiators to form radical species that trigger photopolylmerization. Since UV light has potential to cause cell damage, visible light-mediated photopolymerization has attracted much attention. The conventional method to fabricate hydrogels under visible light exposure requires usage of co-initiator triethanolamine (TEA) at high concentration (∼200 mM), which reduces cell viability. Therefore, the first objective of this thesis was to develop a new method to form poly(ethylene glycol)-diacrylate (PEGDA) hydrogel without using TEA. Specifically, thiol-containing molecules (e.g. dithiothreitol or cysteine-containing peptides) were used to replace TEA as both co-initiator and crosslinker. Co-monomer 1-vinyl-2-pyrrolidinone (NVP) was used to accelerate gelation kinetics. The gelation rate could be tuned by changing the concentration of eosinY or NVP. Variation of thiol concentration affected degradation rate of hydrogels. Many bioactive motifs have been immobilized into hydrogels to enhance cell attachment and adhesion in previous studies. In this thesis, pendant peptide RGDS was incorporated via two methods with high incorporation efficiency. The stiffness of hydrogels decreased when incorporating RGDS. The second objective of this thesis was to fabricate hydrogels using poly(ethylene glycol)-tetra-acrylate (PEG4A) macromer instead of PEGDA via the same step-and-chain-growth mixed mode mechanism. Formation of hydrogels using PEGDA in this thesis required high concentration of macromer (∼10 wt.%). Since PEG4A had two more functional acrylate groups than PEGDA, hydrogels could be fabricated using lower concentration of PEG4A (∼4 wt.%). The effects of NVP concentration and thiol content on hydrogel properties were similar to those on PEGDA hydrogels. In addition, the functionality and chemistry of thiol could also affect hydrogel properties.

Giardia intestinalis is a unicellular protozoan parasite responsible for 280 million gastrointestinal infections every year. When colonizing its host, Giardia interacts closely with the small intestine epithelium by attaching to enterocytes and releasing multiple proteins to the extracellular environment. Some of the released proteins have been shown to aid the parasite’s survival in the intestine by disrupting various host defense mechanisms. Here, we attempt to characterize the specific localization of five proteins after their secretion by Giardia. In parallel we aim to produce and identify parasite’s molecules potentially working as triggers of the immune response built during infection. To study the localization of specific secreted proteins during in vitro interactions with differentiated Caco-2 cells, we started by creating transgenic parasites expressing the ADI, EF1α and G3PD proteins with a downstream detectable tag. To identify candidate proteins from Giardia, thought by our lab to be involved in immune system activation, we established a mammalian expression system for the production of recombinant versions of the selected candidate giardial PAMPs. We achieved the expression of the VSP1267 protein, natively present on the parasite’s surface. However, we found that this protein was not secreted after expression, thus complicating its purification and later use in TLR-activation experiments. In the future, we aim to localize the tagged proteins, expressed by the produced transgenic trophozoites, and optimize the mammalian expression system in order to identify candidate immune triggers during giardiasis.

Problématique : Durant la période fœtale, le métabolisme global du fœtus fonctionne en hypoxie, ce qui limite la phosphorylation oxydative dans la mitochondrie, et par conséquent la production d’adénosine triphosphate (ATP). Ces conditions sont nécessaires pour le développement intra-utérin. Lors de la naissance, l’augmentation des concentrations d’oxygène et un stress oxydatif permettent une transition métabolique. Une charge oxydative supplémentaire en période néonatale pourrait perturber cette transition métabolique et causer des complications. La nutrition parentérale (NP) administrée aux nouveau-nés prématurés apporte un triple fardeau oxydatif : une exposition à des peroxydes oxydants autogénérés par l’interaction des composants de la NP, une carence en vitamine C (instable en solution), et une déficience en glutathion, vu la charge oxydative élevée. Cette charge oxydative excessive affecte l’homéostasie redox au foie et aux poumons, ainsi que le métabolisme énergétique hépatique, et ce, par des effets immédiats et à long-terme. La méthylation de l’ADN est un possible mécanisme qui explique les effets à long terme. Le but de ce travail était de caractériser l’impact à court- et long-terme de la NP néonatale sur l’homéostasie redox, la méthylation de l’ADN, et le métabolisme des glucides et lipides, en isolant chacun des facteurs nutritionnels. Méthodes : Des cochons d’Inde ont été divisés dans les groupes suivants 1) NP : nutrition intraveineuse complète ; 2) NP+ glutathion disulfure (GSSG) (6 ou 12µM- substrat pour la synthèse intra-cellulaire de glutathion); 3) Diète complète : nutrition orale complète 4) Diète déficiente en Vitamine C; 5) Diète déficiente en Cystéine; 6) Diète double déficiente; ou. À 1 semaine de vie, la moitié des animaux était sacrifié et l’autre moitié a commencé à manger une diète complète jusqu’à l’âge adulte. Résultats et discussion : Les animaux ayant reçu une NP néonatale ont un métabolisme énergétique permettant la synthèse de nicotinamide adénine dinucléotide phosphate (NADPH) par l’augmentation de l’activité de la glucokinase (captation de glucose), et diminution de celles de la phosphofructokinase-1 (PFK-1) (glycolyse) et acétyl-CoA-carboxylase-1 (ACC)(lipogenèse). À l’âge adulte, les animaux ont une diminution des niveaux de GSSG, indiquant un débalancement de l’homéostasie redox vers le côté réducteur programmé par la NP néonatale. L’activité augmentée de l’ACC suggère une tendance à accumuler les lipides au foie à la suite d’une diète riche en glucides. L’ajout de glutathion à la NP ne prévient pas ces perturbations, car les déficiences en glutathion et vitamine C jouent un rôle sur la modulation des niveaux protéiques de l’ACC. Les diètes néonatales déficientes en vitamine C et cystéine augmentent l’activité de la PFK-1. Cette augmentation se maintient jusqu’à l’âge adulte chez les mâles, mais pas chez les femelles. Les niveaux protéiques de la glucokinase et ACC sont diminués à 1 semaine, et ceux de l’ACC sont élevés à 3 mois dans les groupes ayant reçu une des diètes déficientes. Ces effets sont similaires à ceux trouvés dans les animaux nourris avec la NP, suggérant que la déficience de la NP en ces nutriments et non les peroxydes cause ces effets. Dans tous les groupes, un stress oxydatif a été démontré à 1 semaine de vie, soit par l’augmentation des niveaux de GSSG, ou la diminution du GSH. Cet effet est vrai pour le foie et le poumon. Une réponse de Nrf2 est observée aussi au foie, ce qui caractérise un niveau bas de stress oxydatif. La baisse de GSH pulmonaire chez les animaux déficients est secondaire à l’inhibition oxydative de la voie de transméthylation au foie. Une diminution des niveaux d’ARNm de glutathion réductase et glutarédoxine sont observées, ce qui favorise encore le stress oxydatif pulmonaire. À long terme, les effets sont les opposés, soit débalancement de l’homéostasie redox vers le côté réducteur au foie et poumon. La méthylation de l’ADN était diminuée au foie des animaux nouveau-nés recevant les diètes déficientes, mais aucun changement n’a été observé aux poumons. Cette diminution est en accord avec les hauts niveaux d’ARNm des gènes de la protéine régulatrice de la glucokinase, et AMPK. À long-terme, l’effet inverse est observé pour la méthylation de l’ADN Conclusion : La NP modifie le flot d’énergie au foie à 1 semaine visant favoriser le métabolisme redox en détriment du métabolisme énergétique. Cet effet semble créer une déficience énergétique fonctionnelle, qui se développe en une lipogenèse accrue en âge adulte. Cela peut représenter un exemple de la plasticité développementale. Bien qu’un stress oxydatif en âge néonatal ne soit pas létal, il affecte le métabolisme énergétique et redox à long-terme, probablement par la méthylation de l’ADN. Les résultats de ce travail démontrent que ces animaux adultes ont une capacité accrue d’entreposer de l’énergie, soit par une lipogenèse plus élevée, soit par une accumulation d’énergie redox (glutathion). Aucune maladie métabolique n’était observée chez les animaux, mais il est attendu à ce que ces animaux développent ces maladies plus facilement suite à l’exposition à des insultes (habitudes de vie malsaines, tabagisme, etc.). / Problematic: During the fetal period, the general metabolism works under hypoxia, limiting oxidative phosphorylation in mitochondria and adenine triphosphate (ATP) synthesis. These conditions are necessary for intrauterine development. After birth, the increasing oxygen concentrations and the associated oxidative stress induce a metabolic transition. An excessive oxidative load during the neonatal period could perturb this transition. Parenteral nutrition (PN) administered to premature newborns comes with a triple oxidative burden: contaminating peroxides generated in solution, vitamin C deficiency (unstable in solution), and glutathione deficiency (caused by the high oxidative load). This oxidative load affects redox homoeostasis in the liver and lungs, as well as energy metabolism in the liver. These effects are not only immediate, but they are also delayed. DNA methylation is a candidate mechanism explaining the long-term effects. The objective of this work was to characterize the short- and long-term impacts of neonatal PN over redox homoeostasis, DNA methylation and carbohydrate and lipid metabolism by isolating each of these factors. Methods: Six groups of three-day-old guinea pigs received for 4 days either: 1) Total PN; 2) PN+glutathione disulfide (GSSG) (6 or 12µM-anti-peroxide);3) Vitamin C deficient; 4) Cysteine deficient; 5) Double deficient; or 6) Complete diets. At 1 week of life, half of the animals were sacrificed, and the other half started eating nutritionally complete diets until adulthood. Results and discussion: NP animals had energy metabolism shifted favouring nicotinamide adenine dinucleotide phosphate (NADPH) synthesis, as evidenced by the increase in glucokinase activity (glucose trapping in hepatocytes) and decrease in phosphfuctokinase-1 (PFK-1) (glycolysis) and acetyl-CoA-carboxyalase-1 (ACC) (lipogenesis) activities. Adding GSSG to parenteral nutrition prevents these changes. During adulthood, ACC activity is increased, suggesting a tendency to accumulate lipids after a diet rich in carbohydrates. Adding GSSG to PN does not prevent these changes as they seem to be caused by the nutritional deficiencies in vitamin C and cysteine. Neonatal diets deficient in vitamin C and cysteine increase PFK-1 activity. This increase is maintained until adulthood in males but not in females. Protein levels of glucokinase and ACC are decreased at 1 week of life and ACC levels are increased at adulthood in deficient groups. These effects are like the ones observed in PN animals. In all groups, oxidative stress is demonstrated in 1-week-old animals, either by an increase in GSSG levels, or a decrease in GSH. This is true for the liver and lungs. An Nrf2 response is also observed in the liver, suggesting a low level of oxidative stress. The decrease in lung GSH is secondary to the oxidative inhibition of the transmethylation pathway in the liver. Decreased levels of glutathione reductase and glutaredoxin mRNA levels are observed in lungs, favouring pulmonary oxidative stress. At adulthood, an imbalance in redox homeostasis towards a reducing state is observed in lungs and liver. DNA methylation was decreased in the liver of deficient animals at 1-week, but no changes were observed in lungs. This decrease is in accordance with the decrease in mRNA levels of glucokinase regulatory protein and AMPK. At adulthood, the opposite effect was observed for DNA methylation. Conclusion: Parenteral nutrition alters the energy flow in the liver of 1-week-old animals, favouring redox metabolism over energy metabolism. This effect seems to create a phenotype of functional energy deficiency which translates into an increased lipogenesis at adult age. This may be an example of developmental plasticity. Although neonatal oxidative stress is not lethal, it affects energy and redox metabolism at adulthood, probably through DNA methylation. The presented results demonstrate these animals have an increased capacity of storing energy, either through increased lipogenesis, or by an increase in redox energy accumulation (glutathione). No metabolic disease was observed. Although it would be expected that these animals would develop these diseases more easily after exposure to insults, such as unhealthy lifestyle habits, smoking, and others.

In dieser Arbeit wurden ungesättigte Vinyl- und Ethynylphosphonothiolate hergestellt und als Linker für Cystein-selektive Proteinmodifikationen verwendet. Zunächst wurde, ausgehend von ungesättigten Phosphoniten und elektrophilen Disulfiden als Startmaterialien, eine Syntheseroute zur Herstellung von ungesättigten Phosphonothiolaten entwickelt. Die hohe Chemoselektivität dieser Reaktion ermöglichte die Einführung von Vinylphosphonothiolaten auf ungeschützten Modellpeptiden und dem Protein Ubiquitin. Es konnte gezeigt werden, dass ungesättigte Phosphonothiolate unter neutralen bis leicht basischen Bedingungen selektiv mit Thiolen reagieren und sich daher als Linker für Cystein-selektive Proteinmodifikationen eignen. Die Vielseitigkeit der hier entwickelten Biokonjugationsmethode wurde in drei Anwendungen demonstriert. Ausgehend von dem Vinylphoshonothiolat-modifizierten Ubiquitin konnten homogene Ubiquitin-Protein-Konjugate erzeugt werden; zum einen ein nicht hydrolysierbares Diubiquitin-Konjugat und zum anderen ein Ubiquitin-α–Synuclein-Konjugat. Des Weiteren wurden ungesättigte Phosphonothiolate als Linker in Antikörper-Wirkstoff-Konjugaten getestet. Hier zeigte sich, dass insbesondere Vinylphosphonothiolat-Linker Potential zur Herstellung von stabilen Antikörper-Konjugaten aufweisen. Schließlich wurden Vinylphosphonothiolate als Linker verwendet, um sowohl Chaperon-bindende Antikörper als auch Deubiquitinasen (DUBs) mit photoreaktiven Crosslinkern auszustatten um damit dynamische Protein-Interaktionen zu untersuchen. Insgesamt ermöglicht das hier entwickelte Verfahren die chemoselektive Umwandlung von elektrophilen Disulfiden in elektrophile Vinyl- und Ethynylphosphonothiolate, wodurch Reaktivität für eine Thioladdition induziert wird. Dadurch können zwei komplexe, thiolhaltige Moleküle selektiv konjugiert werden, was insbesondere für die Herstellung von homogen modifizierten Peptid- und Proteinkonjugaten von Bedeutung ist. / In this work, unsaturated vinyl- and ethynylphosphonothiolates were synthesised and used as linkers for cysteine-selective protein modifications. First, a synthetic route for the generation of unsaturated phosphonothiolates was developed, using unsaturated phosphonites and electrophilic disulfides as starting materials. The high chemoselectivity of this reaction enabled the introduction of vinylphosphonothiolates on unprotected model peptides and the protein ubiquitin. It could then be shown that unsaturated phosphonothiolates react selectively with thiols under neutral to slightly basic conditions and are therefore suitable as linkers for cysteine-selective protein modifications. The versatility of the herein developed bioconjugation method was demonstrated in three applications. First, starting from the vinylphosphonothiolate-modified ubiquitin, homogeneous ubiquitin-protein conjugates could be generated, in particular a non-hydrolyzable diubiquitin conjugate and a ubiquitin-α-synuclein conjugate. Second, the suitability of unsaturated phosphonothiolates as linkers for the generation of stable antibody-drug conjugates was tested. Vinylphosphonothiolate linkers thereby showed potential to produce stable antibody conjugates. Finally, vinylphosphonothiolates were used as linkers to conjugate both chaperone-binding antibodies and deubiquitinases (DUBs) to photo-reactive crosslinkers in order to investigate dynamic protein interactions. Overall, the herein developed methodology enables the chemoselective conversion of electrophilic disulfides into electrophilic vinyl- and ethynylphosphonothiolates, which in turn react selectively with thiols. As a result, two complex, thiol-containing molecules can be selectively conjugated, which is particularly important for the production of homogeneously modified peptide and protein conjugates.

Chemical modification of proteins is critical for many areas of biochemistry and medicine. Several methods for site-selective protein modification are reported in this Thesis that are useful in accessing both natural and artificial protein architectures. Multiple, complementary methods for the conversion of cysteine to dehydroalanine are described. Dehydroalanine is used as a general precursor to several post-translational modifications and glycosylation, polyprenylation, phosphorylation, and lysine methylation and acetylation are all accessible. These modifications and their mimics were explored on multiple proteins, including histone proteins. Unnatural modifications were also explored. The first examples of olefin metathesis and Suzuki-Miyaura cross-coupling on protein substrates are reported. Allyl sulfides were discovered to be remarkably reactive substrates in olefin metathesis, allowing use of this reaction in water and on proteins. For Suzuki-Miyaura cross-coupling, a new catalyst is described that is fully compatible with proteins. Both olefin metathesis and cross-coupling allow the formation of carbon-carbon bonds on proteins. The prospects of these transformations in chemical biology are discussed. Finally, a novel strategy is reported for the installation of natural, unnatural, and post-translationally modified amino acid residues on proteins. This technology relies on addition of carbon radicals to dehydroalanine. This method of "chemical mutagenesis" is anticipated to complement standard genetic manipulation of protein structure.

Strikt anaerobe Bakterien wie Clostridium difficile und C. scatologenes verwenden GRE, um die chemisch ungünstige Decarboxylierung von 4-Hydroxyphenylacetat zu p-Cresol zu katalysieren. Das Enzymsystem besteht aus einer Decarboxylase und dem zugehörigen Aktivierungsenzym. Die 4-Hydroxyphenylacetat-Decarboxylase (4Hpad) besitzt zusätzlich zum Protein-basierten Glycinradikal eine weitere Untereinheit mit bis zu zwei [4Fe-4S] Clustern und repräsentiert hierdurch eine neue Klasse von Fe/S-Cluster-haltigen GREs, die aromatische Verbindungen umsetzen. Das Aktivierungsenzym (4Hpad-AE) weicht vom Standardtypus ab, indem es zusätzlich zum S-Adenosylmethionin(SAM)-bindenden [4Fe-4S]-Cluster (RS-Cluster) mindestens einen weiteren [4Fe-4S]-Cluster bindet. In dieser Studie wurden heterologe Expressions- und Reinigungsprotokolle für 4Hpad und 4Hpad-AE entwickelt. Kristallstrukturen von 4Hpad cokristallisiert mit den Substraten (4-Hydroxyphenylacetat, 3,4-Dihydroxyphenylacetat) und dem Inhibitor (4-Hydroxyphenylacetamid) zeigten geringe strukturelle Änderungen im aktiven Zentrum des Proteins. Die Radikalbildung am 4Hpad-AE wurde durch die Überprüfung einer klassischen reduktiven Spaltung von SAM zu den Reaktionsprodukten 5’-Deoxyadenosin und Methionin bestätigt. EPR- und Mössbauer-Spektroskopische Analysen zeigten, dass 4Hpad-AE mindestens einen zusätzlichen [4Fe-4S] Cluster neben dem einzelnen RS-Cluster enthält. Die katalytische Notwendigkeit eines zusätzlichen Clusters wurde durch eine Mutationsanalyse untersucht, wobei eine verkürzte Version des Enzyms ohne die zusätzliche Cystein-reiche Insertion konstruiert wurde. Das verkürzte Mutante ohne die Bindungsmotive für die zusätzlichen Cluster gekennzeichnet, die Konfiguration, Stöchiometrie und die Funktion der zusätzlichen Cluster diagnostizieren. / 4-hydroxyphenylacetate decarboxylase (4Hpad) is a two [4Fe-4S] cluster containing glycyl radical enzyme proposed to use a glycyl/thiyl radical dyad to catalyze the last step of tyrosine fermentation in Clostridium difficile and C. scatologenes by a Kolbe-type decarboxylation. The decarboxylation product p-cresol is a virulence factor of the human pathogen C. difficile. The small subunit of 4Hpad may have a regulatory function with the Fe/S clusters involved in complex formation and radical dissipation in the absence of substrate. The respective activating enzyme (4Hpad-AE) has one or two [4Fe-4S] cluster(s) in addition to the SAM-binding [4Fe-4S] cluster (RS cluster). The role of these auxiliary clusters is still under debate with proposed functions including structural integrity and conduit for electron transfer to the RS cluster. This study shows the optimized expression and purification protocols for the decarboxylase and the co-crystallization experiments and binding studies with 4-hydroxy-phenylacetate and 3,4-dihydroxyphenylacetate and with the inhibitor 4-hydroxy-phenylacetamide. The purification and characterization of active site mutants of decarboxylase are also done. Concerning 4-HPAD-AE, we report on the purification of code-optimized variants, and on spectroscopic and kinetic studies to characterize the respective i) SAM binding enthalpies, ii) rates for reductive cleavage of SAM and iii) putative functions of the additional Fe/S clusters. The truncated mutant lacking the binding motifs for the auxiliary clusters is characterized to diagnose the configuration, stoichiometry and function of the auxiliary clusters.

No description available.

Tripanossomas de mamíferos constituem um dos grupos mais complexos da família Trypanosomatidae, abrangendo parasitas com ciclos de vida e estruturas populacionais heterogêneos. De acordo com a diversidade, filogenias baseadas em genes SSUrDNA e gGAPDH segregaram estes parasitas em 4 Clados principais: T. brucei, T. cruzi, T. theileri e T. lewisi. Catepsinas L e B (CATL e CATB), as principais atividades proteolíticas dos tripanossomas, participam não apenas na degradação de proteínas como também em eventos biológicos como diferenciação, invasão celular, virulência e evasão do sistema imune. Comparamos os perfis proteolíticos de enzimas CATL em tripanossomas patogênicos e não patogênicos e também isolamos e sequenciamos os domínios catalíticos dos genes CATL e CATB em diversas espécies dos principais clados. Os resultados provaram a utilidade destes marcadores no diagnóstico e genotipagem de T. cruzi, T. rangeli, T. theileri e T. congolense, assim como na construção de filogenias robustas da família Trypanosomatidae, congruentes com os marcadores tradicionais. / Trypanosomes of mammals comprise one of the most complex groups of the family Trypanosomatidae, including parasites with heterogeneous life cycles and population structures. According to such diversity, phylogenetic analyzes based on SSUrDNA and gGAPDH genes segregate these parasites in 4 major clades: T. brucei, T. cruzi, T. lewisi and T. theileri. Cathepsins L and B (CATL and CATB), the main proteolytic activities of trypanosomes, are not only involved in protein degradation but also in biological events such as cell differentiation, cell invasion, virulence, and evasion from the immune system. We comparatively analysed the CATL proteolytic profiles in pathogenic and non-pathogenic trypanosomes, and isolated and sequenced the catalytic domains of CATB and CATL genes in several species of the major clades. Our results demonstrated the usefulness of both markers in the diagnosis and genotyping of T. cruzi, T. rangeli, T. congolense and T. theileri as well as in the construction of robust phylogenies of the family Trypanosomatidae, congruent with traditional markers.