1) Geminiviruses are a group of plant viruses which contain circular single stranded DNA molecules as their genomes and the capsid consists of two icosahedra fused together to form twinned or geminate particles. The largest genus in the family Geminiviridae is that of begomoviruses which are of two kinds; the monopartite begomoviruses which contain only one circular single stranded DNA molecule as their genome and the bipartite begomoviruses which contain two circular single stranded DNA molecules (designated DNA-A and DNA-B) as their genomes. In bipartite viruses, the two DNA molecules are enclosed in separate geminate capsids. 2) In bipartite begomoviruses, the DNA-A encodes the proteins essential for replication and encapsidation of the viral genome while the DNA-B encodes the proteins involved in movement. The DNA-B encodes two proteins: the BV1 or the nuclear shuttle protein (NSP) and BC1 or the cell-to-cell movement protein. Geminiviruses have DNA genomes which replicate inside the host cell nucleus. The NSP, which contains nuclear localization signal, brings the viral DNA from nucleus to the cytoplasm while the BC1 serves to take the viral genome to the cell periphery for movement to the neighbouring cell through the plasmodesmata. 3) The monopartite begomoviruses do not contain DNA-B (which, in bipartite begomoviruses, encodes the proteins involved in movement) and it has been suggested that some of the proteins encoded by DNA-A take up the movement function. Based on studies on TYLCV and CLCuV, a model has been proposed for the movement of monopartite begomoviruses according to which the coat protein (CP) of monopartite begomoviruses serves as the functional equivalent of the NSP of bipartite begomoviruses 4) The present thesis deals with the biochemical characterization of the C4 protein of the monopartite begomovirus CLCuKV-Dab. As stated in statement (3) above, the V2 and C4 proteins of monopartite begomoviruses have been implicated to be involved in cell-to¬cell movement of the viral genome. In TYLCV, both the proteins were shown to be localized to the cell periphery and could move from one cell to another through the plasmodesmata. Further, the V2 protein of CLCuKV-Dab was shown to interact with the coat protein and bind to single stranded DNA. The biochemical properties of the C4 protein needed to be elucidated in order to strengthen the proposal of its probable involvement in movement. 5) The objectives of the present study were: i) Bioinformatic analysis of the C4 protein of CLCuKV-Dab ii) Biochemical characterization of ATPase and pyrophosphatase activities of the C4 protein. iii) Studies on the effect of V2-C4 interaction on the enzymatic properties of C4. iv) Functional characterization of C4 in planta. 6) The FoldIndex© and PONDR analyses predicted the C4 protein of CLCuKV-Dab to be natively unfolded. Similarly, in PSIpred analysis, most of the C4 protein was predicted to be a random coil without any well-defined secondary structure. Further, the protein sequence was analyzed using the motifscan server. However, no motif for any specific function was predicted in the C4 Protein. 7) The C4 gene was initially cloned into pRSET-C vector and overexpressed as histidine tagged protein and the solubility of the protein was tested in various conditions including low temperature (18° C) after inducing the expression of the protein, buffers of various pH and different salt concentrations but the protein remained insoluble. Subsequently, the protein was purified under denaturing conditions and attempts were made to refold the protein but the protein precipitated during refolding. In order to get the C4 protein in soluble form, the C4 gene was subcloned into pGEX-5X2 vector and overexpressed as a GST-tagged fusion protein (GST-C4). Some of the GST-C4 protein was soluble which was purified by using GST-bind resin. The purified fusion protein was observed as a 37 kDa band on SDS-PAGE gel. The purified protein was accompanied by a degraded product of approximately 30 kDa size. Both the intact GST-C4 protein and the degraded product were detected in western blot analysis using anti-GST antibody. 8) Because C4 has been implicated to be involved in movement of monopartite begomoviruses and movement is an energy requiring process, it was of interest to determine if GST-C4 possesses ATPase activity. The purified GST-C4 protein was incubated with γ-[32P]-ATP, the product of the reaction was separated by thin layer chromatography and the chromatography plate was analyzed by phosphorimager. The hydrolysis of ATP by GST-C4 and the release of inorganic phosphate was clearly observed, suggesting that GST-C4 might possess ATPase activity. 9) The reaction conditions for the ATPase activity of GST-C4 were standardized. The activity increased linearly upto 2.60μM of the protein. The optimum temperature and pH for the ATPase activity were found to be 30 C and 6.0 respectively. The activity was inhibited by EDTA, suggesting that it is dependent on divalent metal ions. The activity was stimulated by Mg+2, Mn+2 and Zn+2 but inhibited by Ca+2ions. Further, in the time course experiment, it was observed that the ATPase activity increased linearly upto one hour. 10) The Km, Vmax and kcat for the ATPase activity of GST-C4 were found to be 51.72 ± 2.5 µM, 7.2 ± 0.54 nmoles/min/mg of the protein and 0.27 min-1 respectively. Some of the other virally encoded ATPases have been found to exhibit kcat similar to that found for GST-C4 but it is much lower than those of most of the prokaryotic and eukaryotic ATPases (as mentioned in Table 3.3, page 100, chapter 3). Further, the presence of the degraded product did not affect the kinetic constants as described in chapter 3, pages 95¬-98. It is possible that the enzymatic activity might increase upon interaction with some ligand. 11) In the absence of any putative ATP binding motifs, systematic deletions from N-and C-termini were made to delineate the regions of C4 important for the ATPase activity. GST-N∆15-C4 and GST-N∆30-C4 exhibited approximately 70 % reduction in the ATPase activity while all the C-terminal deletion mutants (GST-C∆10-C4, GST-C∆20¬C4 and GST-C∆30-C4) retained the activity similar to the full length GST-C4 protein. This suggested that the N-terminal region of C4 may contain the residues important for the ATPase activity of GST-C4. 12) In the N-terminal region of C4, there is a sequence CSSSSR which closely resembles the sequence present at the active site of phosphotyrosine phosphatases (CXXXXXR). However, GST-C4 did not catalyze the hydrolysis of p-Nitrophenyl phosphate, a substrate analogue commonly used to assay phosphotyrosine phosphatase activity. It was of interest to determine if the cysteine and arginine in this sequence are important for the ATPase activity of GST-C4. GST-R13A-C4 exhibited an approximately two fold reduction in Vmax suggesting that R13 in C4 may be catalytically important for the ATPase activity of GST-C4. On the other hand, the C8A mutation did not affect the ATPase activity of GST-C4. 13) The GST-C4 protein was tested for its ability to hydrolyze several other phosphate containing compounds as mentioned chapter 2, pages 53-55. Among these compounds, GST-C4 catalyzed the hydrolysis of sodium pyrophosphate, that is, GST-C4 exhibited an inorganic pyrophosphatase activity. 14) The reaction conditions for the inorganic pyrophosphatase activity of GST-C4 were initially standardized. The pyrophosphatase activity of GST-C4 increased linearly upto 3.38 µM of the protein. The optimum temperature and pH for the pyrophosphatase activity were found to be 37° C and 7.0 respectively. The pyrophosphatase activity was inhibited by EDTA, suggesting that it is dependent on divalent metal ions. The activity was most efficiently stimulated by Mg+2, although it was also stimulated by Mn+2and Zn+2but inhibited by Ca+2ions. Thus, the pyrophosphatase activity of GST-C4 resembles the family I inorganic pyrophosphatases in metal ion requirements. Further, the pyrophosphatase activity increased linearly upto 1 hour 30 minutes. 15) The Km, Vmax and Kcat for the pyrophosphatase activity of GST-C4 were found to be 0.76 ± 0.04 mM, 141.16 ± 20 nmoles/min/mg of the protein and 5.2 minrespectively. The kcat for the pyrophosphatase activity was approximately 20 fold higher than that for the ATPase activity (0.27 min-1). 16) GST-N∆15-C4 and GST-N∆30-C4 exhibited >70 % reduction in the pyrophosphatase activity, a finding similar to that for the ATPase activity. On the other hand, while GST-C∆10-C4 retained the activity similar to the full length GST-C4 protein, GST-C∆20-C4 and GST-C∆30-C4 exhibited 20 % and 60 % reduction in the pyrophosphatase activity, respectively, as compared to the full length GST-C4 protein. This suggested that the C-terminal region of C4 may also contain the residues important for the pyrophosphatase activity of GST-C4. However, the C-terminal deletion mutants retained the ATPase activity similar to the full length protein. 17) The pyrophosphatase activity of GST-C4 was stimulated more than three fold by several reducing agents. The C4 protein contains only one cysteine (at position 8 in the C4 sequence). This was the first clue that the cysteine may be important for the pyrophosphatase activity of the GST-C4 protein. Further, the pyrophosphatase activity of GST-C4 did not exhibit preference for a particular kind of reducing agent like that of the pyrophosphatase activity in Streptococcus faecalis. 18) GST-C8A-C4 exhibited more than two fold reduction in Vmax, suggesting that the C8 may be catalytically important for the pyrophosphatase activity of GST-C4. On the other hand, the R13A mutation did not affect the pyrophosphatase activity of the GST-C4 protein. Thus, it is possible that during catalysis, the cysteine thiolate of C4 makes a 19) The pyrophosphatase activity of GST-C4 was inhibited by vanadate and fluoride. Vanadate was found to be a competitive inhibitor with Ki 0.33 mM while fluoride was a non-competitive inhibitor with Ki 2.82 mM. A comparative account of the two enzymatic activities of GST-C4 is presented in table 6.1

No description available.

L’athérosclérose est une maladie vasculaire inflammatoire chronique qui se développe progressivement au cours de la vie. Les mécanismes impliqués sont complexes et la recherche de nouveaux candidats impliqués dans l'athérogénèse est toujours d'actualité. L’Angiopoietine-like 2 (Angptl2) est une protéine relativement peu connue, aux propriétés pro-angiogéniques et pro-inflammatoires, qui appartient par homologie à la grande famille des angiopoietines, mais dont le récepteur n'est pas encore clairement identifié. Les situations pathologiques dans lesquelles l’Angptl2 jouerait un rôle crucial sont diverses, mais sa contribution moléculaire dans le développement de l’athérosclérose est inconnue. Par differential display, nous avons initialement identifié l'Angptl2 comme étant surexprimée dans des cellules endothéliales sénescentes, isolées et cultivées à partir d'artères mammaires internes de patients athérosclérotiques ayant subi un pontage coronarien. Cette découverte a été la à base de mon projet, et mes objectifs ont été 1) de déterminer l'implication de l’Angptl2 vasculaire en présence de facteurs de risques tels que le tabagisme et la dyslipidémie, 2) de produire et de purifier une protéine recombinante fonctionnelle de l’Angptl2 afin d'identifier in vitro de nouvelles propriétés cellulaires de l'Angptl2 et 3) d'étudier in vivo le potentiel pro-athérogénique de l'Angptl2 recombinante dans un modèle murin de dyslipidémie sévère. Nous avons montré que l’Angptl2 est sécrétée préférentiellement dans des conditions pro-oxydantes et pro-inflammatoires, avec une augmentation de son expression endothéliale de l’ordre de 6 fois chez des patients coronariens fumeurs atteints de maladie pulmonaire obstructive chronique. Suite à ces résultats, nous avons émis l’hypothèse que l’Angptl2, en plus de ses fonctions pro-inflammatoires connues, possède des propriétés pro-oxydantes. Nous avons démontré que l’Angptl2 recombinante stimule en effet la production de radicaux libres dans des HUVEC en culture, via l’inhibition partielle de la voie cytoprotectrice antioxydante Nrf2/HO-1 et potentiellement via l'activation de kinase intracellulaire de type p38. A l'aide de souris dyslipidémiques LDLr-/-; hApoB-100+/+, nous avons démontré que le niveau d’Angptl2 plasmatique, vasculaire et dans les plaques athéromateuses, augmente parallèlement avec le développement de l’athérosclérose. De plus, une stimulation avec l’Angptl2 recombinante engendre chez ces souris une réponse inflammatoire évaluée par l’expression endothéliale de cytokines et de molécules d'adhésion et par l’infiltration de leucocytes sur l’endothélium vasculaire. Finalement, l’administration intraveineuse de la protéine recombinante d’Angptl2 pendant quatre semaines à des souris LDLr-/-; hApoB-100+/+ augmente de 10 fois l'expansion de la plaque athérosclérotique et double leur taux de cholestérol circulant. Nous avons aussi montré que chez des patients athérosclérotiques, l'Angptl2 plasmatique est 6 fois plus élevée que chez des sujets sains du même âge. Nos études semblent donc définir l’Angptl2 comme un facteur contribuant directement au développement de l'athérosclérose en favorisant la sénescence, l’inflammation et l’oxydation des cellules endothéliales. Ces propriétés pourraient globalement définir l'Angptl2, non seulement comme un nouveau biomarqueur circulant de l’athérosclérose, mais également comme l'un de ses promoteurs. / Atherosclerosis is a chronic vascular inflammatory disease that develops gradually during life. While the control mechanisms of this disease are complex and variable, research continues to identify new protein candidates involved in atherogenesis. Angiopoietin-like2 (Angptl2) is a relatively unknown protein, recently shown to display angiogenic and pro-inflammatory properties. Based upon structural homology, Angptl2 is a member of the angiopoietin family; however, the Angptl2 receptor has not yet been clearly identified. The reported pathological situations in which Angptl2 may play a crucial role are multiple, but its molecular contribution in the development of atherosclerosis remains unknown. By differential display, we initially identified Angptl2 as being overexpressed in senescent endothelial cells, isolated and cultivated from internal mammary arteries of atherosclerotic patients undergoing coronary bypass. This observation was at the basis of my project. My specific objectives were 1) to determine the abundance of vascular Angptl2 in the presence of risk factors such as smoking and dyslipidemia, 2) to produce and purify a functional recombinant human Angptl2 protein in order to examine its effects on cellular function in vitro, and 3) to study the pro-atherogenic potential of Angptl2 in vivo using a mouse model of severe dyslipidemia. We showed that Angptl2 is preferentially secreted under pro-oxidant and pro-inflammatory conditions, with a 6-fold increase in endothelial Angptl2 expression in smoker coronary patients with chronic obstructive pulmonary disease. Based on these results, we hypothesized that, in addition to its known pro-inflammatory functions, Angptl2 has pro-oxidant properties. Accordingly, we demonstrated that recombinant Angptl2 stimulates the production of free radicals by HUVEC, an action exerted, at least in part, by the inhibition of the cytoprotective antioxidant pathway, Nrf2/HO-1, and potentially via the activation of the intracellular p38 MAPK pathway. In dyslipidemic LDLr-/-; hApoB-100+/+ mice, we showed that the levels of endogenous Angptl2 in plasma, vascular tissue and atherosclerotic lesions increase in parallel with the development of atherosclerosis. In addition, stimulation with recombinant Angptl2 induces an inflammatory response, as assessed by the expression of cytokines and adhesion molecules and by infiltration of leukocytes into the vascular endothelium. Furthermore, intravenous infusion of purified recombinant Angptl2 for four weeks promoted a 10-fold increase in the formation of atherosclerotic plaques in LDLr-/-; hApoB-100+/+ mice and doubled their circulating cholesterol levels. Finally, we also demonstrated that plasma Angptl2 is 6-fold higher in atherosclerotic patients than in age-matched healthy subjects. These studies therefore strongly suggest that Angptl2 could directly contribute to the development of atherosclerosis by promoting senescence, inflammation and oxidation in endothelial cells. Such properties indicate that Angptl2 may be both a new biomarker of atherosclerosis, as well as one of its contributors.

L’athérosclérose est une maladie vasculaire inflammatoire chronique qui se développe progressivement au cours de la vie. Les mécanismes impliqués sont complexes et la recherche de nouveaux candidats impliqués dans l'athérogénèse est toujours d'actualité. L’Angiopoietine-like 2 (Angptl2) est une protéine relativement peu connue, aux propriétés pro-angiogéniques et pro-inflammatoires, qui appartient par homologie à la grande famille des angiopoietines, mais dont le récepteur n'est pas encore clairement identifié. Les situations pathologiques dans lesquelles l’Angptl2 jouerait un rôle crucial sont diverses, mais sa contribution moléculaire dans le développement de l’athérosclérose est inconnue. Par differential display, nous avons initialement identifié l'Angptl2 comme étant surexprimée dans des cellules endothéliales sénescentes, isolées et cultivées à partir d'artères mammaires internes de patients athérosclérotiques ayant subi un pontage coronarien. Cette découverte a été la à base de mon projet, et mes objectifs ont été 1) de déterminer l'implication de l’Angptl2 vasculaire en présence de facteurs de risques tels que le tabagisme et la dyslipidémie, 2) de produire et de purifier une protéine recombinante fonctionnelle de l’Angptl2 afin d'identifier in vitro de nouvelles propriétés cellulaires de l'Angptl2 et 3) d'étudier in vivo le potentiel pro-athérogénique de l'Angptl2 recombinante dans un modèle murin de dyslipidémie sévère. Nous avons montré que l’Angptl2 est sécrétée préférentiellement dans des conditions pro-oxydantes et pro-inflammatoires, avec une augmentation de son expression endothéliale de l’ordre de 6 fois chez des patients coronariens fumeurs atteints de maladie pulmonaire obstructive chronique. Suite à ces résultats, nous avons émis l’hypothèse que l’Angptl2, en plus de ses fonctions pro-inflammatoires connues, possède des propriétés pro-oxydantes. Nous avons démontré que l’Angptl2 recombinante stimule en effet la production de radicaux libres dans des HUVEC en culture, via l’inhibition partielle de la voie cytoprotectrice antioxydante Nrf2/HO-1 et potentiellement via l'activation de kinase intracellulaire de type p38. A l'aide de souris dyslipidémiques LDLr-/-; hApoB-100+/+, nous avons démontré que le niveau d’Angptl2 plasmatique, vasculaire et dans les plaques athéromateuses, augmente parallèlement avec le développement de l’athérosclérose. De plus, une stimulation avec l’Angptl2 recombinante engendre chez ces souris une réponse inflammatoire évaluée par l’expression endothéliale de cytokines et de molécules d'adhésion et par l’infiltration de leucocytes sur l’endothélium vasculaire. Finalement, l’administration intraveineuse de la protéine recombinante d’Angptl2 pendant quatre semaines à des souris LDLr-/-; hApoB-100+/+ augmente de 10 fois l'expansion de la plaque athérosclérotique et double leur taux de cholestérol circulant. Nous avons aussi montré que chez des patients athérosclérotiques, l'Angptl2 plasmatique est 6 fois plus élevée que chez des sujets sains du même âge. Nos études semblent donc définir l’Angptl2 comme un facteur contribuant directement au développement de l'athérosclérose en favorisant la sénescence, l’inflammation et l’oxydation des cellules endothéliales. Ces propriétés pourraient globalement définir l'Angptl2, non seulement comme un nouveau biomarqueur circulant de l’athérosclérose, mais également comme l'un de ses promoteurs. / Atherosclerosis is a chronic vascular inflammatory disease that develops gradually during life. While the control mechanisms of this disease are complex and variable, research continues to identify new protein candidates involved in atherogenesis. Angiopoietin-like2 (Angptl2) is a relatively unknown protein, recently shown to display angiogenic and pro-inflammatory properties. Based upon structural homology, Angptl2 is a member of the angiopoietin family; however, the Angptl2 receptor has not yet been clearly identified. The reported pathological situations in which Angptl2 may play a crucial role are multiple, but its molecular contribution in the development of atherosclerosis remains unknown. By differential display, we initially identified Angptl2 as being overexpressed in senescent endothelial cells, isolated and cultivated from internal mammary arteries of atherosclerotic patients undergoing coronary bypass. This observation was at the basis of my project. My specific objectives were 1) to determine the abundance of vascular Angptl2 in the presence of risk factors such as smoking and dyslipidemia, 2) to produce and purify a functional recombinant human Angptl2 protein in order to examine its effects on cellular function in vitro, and 3) to study the pro-atherogenic potential of Angptl2 in vivo using a mouse model of severe dyslipidemia. We showed that Angptl2 is preferentially secreted under pro-oxidant and pro-inflammatory conditions, with a 6-fold increase in endothelial Angptl2 expression in smoker coronary patients with chronic obstructive pulmonary disease. Based on these results, we hypothesized that, in addition to its known pro-inflammatory functions, Angptl2 has pro-oxidant properties. Accordingly, we demonstrated that recombinant Angptl2 stimulates the production of free radicals by HUVEC, an action exerted, at least in part, by the inhibition of the cytoprotective antioxidant pathway, Nrf2/HO-1, and potentially via the activation of the intracellular p38 MAPK pathway. In dyslipidemic LDLr-/-; hApoB-100+/+ mice, we showed that the levels of endogenous Angptl2 in plasma, vascular tissue and atherosclerotic lesions increase in parallel with the development of atherosclerosis. In addition, stimulation with recombinant Angptl2 induces an inflammatory response, as assessed by the expression of cytokines and adhesion molecules and by infiltration of leukocytes into the vascular endothelium. Furthermore, intravenous infusion of purified recombinant Angptl2 for four weeks promoted a 10-fold increase in the formation of atherosclerotic plaques in LDLr-/-; hApoB-100+/+ mice and doubled their circulating cholesterol levels. Finally, we also demonstrated that plasma Angptl2 is 6-fold higher in atherosclerotic patients than in age-matched healthy subjects. These studies therefore strongly suggest that Angptl2 could directly contribute to the development of atherosclerosis by promoting senescence, inflammation and oxidation in endothelial cells. Such properties indicate that Angptl2 may be both a new biomarker of atherosclerosis, as well as one of its contributors.

La protéine kinase activée par AMP (AMPK) est un senseur et régulateur central de l'état énergétique cellulaire, mais ces voies de signalisation ne sont pour le moment que partiellement comprises. Deux criblages non-biaisés pour la recherche de partenaires d'interaction et de substrats d'AMPK ont précédemment été réalisés dans le laboratoire. Ces derniers ont permis l'identification de plusieurs candidats (protéines), mais leur rôle fonctionnel et physiologique n'était pas encore établi. Ici nous avons caractérisé la fonction de la relation entre AMPK et quatre partenaires d'interaction : gluthation S-transferases (GSTP1 and GSTM1), fumarate hydratase (FH), l'E3 ubiquitine-ligase (NRDP1), et les protéines associées à la membrane (VAMP2 and VAMP3). Chacune de ces interactions parait avoir un rôle différent dans la signalisation AMPK, agissant en amont ou en aval de la protéine AMPK. GSTP1 et GSTM1 contribueraient à l'activation d'AMPK en facilitant la S-glutathionylation d'AMPK en conditions oxydatives moyennes. Cette régulation non-canonique suggère que l'AMPK peut être un senseur de l'état redox cellulaire. FH mitochondrial est l'unique substrat AMPK clairement identifié. Etonnamment le site de phosphorylation se trouve dans le peptide signal mitochondrial, ce qui pourrait affecter l'import mitochondrial. NRDP1, protéine pour laquelle nous avons pour la première fois développé un protocole de production de la protéine soluble, est faiblement phosphorylée par l'AMPK. L'interaction ne sert pas à l'ubiquitination d'AMPK, mais affecte le renouvellement de NRDP1. Finalement, l'interaction de VAMP2/3 avec AMPK n'implique pas d'évènement de phosphorylation ou d'activation d'un des partenaires. Nous proposons un mécanisme de recrutement d'AMPK par VAMP2/3 (" scaffold ") au niveau des vésicules en exocytose. Ce recrutement favoriserait la phosphorylation de substrats de l'AMPK à la surface des vésicules en exocytoses. Une fois mis en commun, nos résultats enrichissent les connaissances sur les voies de signalisation AMPK, et suggèrent une grande complexité de ces dernières. Plus que les kinases en amont et des substrats en aval, la régulation de la signalisation d'AMPK se fait via des modifications secondaires autres que la phosphorylation, via des effets sur le renouvellement de protéines, et probablement via un recrutement spécifique de l'AMPK dans certains compartiments cellulaires.

Oxygen homeostasis is essential to the life of aerobes, which is regulated in humans by Hypoxia Inducible Factor-1α (HIF-1α). Under hypoxic conditions, HIF-1α transactivates over a hundred genes related angiogenesis, erythropoiesis, etc. HIF-1α level and function is regulated by four HIF hydroxylase enzymes: three isoforms of prolyl hydroxylase domain (PHD1, PHD2 and PHD3) and factor inhibiting HIF-1α (FIH). PHD2 is the focus of this research. PHD2 is a non-heme Fe(II) 2-oxoglutarate dependent dioxygenase, which controls HIF-1α levels by hydroxylating two proline residues within the ODD domain of HIF-1α, then the hydroxylated prolines are recognized by pVHL, which targets HIF-1α for proteasomal degradation. Under hypoxic conditions PHD2 cannot hydroxylate HIF-1α and its level rises in cells. The aims of this research include understanding how PHD2 chooses its substrate, how the O2 activation occurs, and how certain transition metals inhibit PHD2. Our results revealed that electrostatics play a role in substrate selectivity of PHD2 by provoking a change in the opening and closing rate of β2β3 loop for NODD and CODD substrates. Mutational studies of second coordination sphere residues combined with kinetic studies indicated that decarboxylation of 2OG is the slow step in the chemical mechanism. The removal of a hydrogen-bond by the Thr387aAla mutation revealed a rate 15 times faster than WT-PHD2 by making O2 a better nucleophile. Our results indicate that this hydrogen bonding is essential for proper O2 activation. Previous reports show that certain metals increase HIF-1α levels by inhibiting PHD2. However there are conflicts about how this inhibition occurs, either through metal replacement from the active site or metals binding to a different site causing inhibition. Our competitive and non-competitive kinetic assays showed different inhibition profiles. Under competitive conditions Zn2+, Co2+, Mn2+, and Cu2+ can bind to the enzyme active site and lead to inhibition but under non-competitive conditions Zn2+, Co2+, and Mn2+ partially inhibit PHD2 suggesting that these metals cannot displace the Fe2+ from the active site. XAS experiments with Zn2+ and Fe3+ indicate that Zn2+ binds to the surface of PHD2 in a six-coordinate manner composed of two Cys201, 208, His205, Tyr197 and two water ligands.

No description available.

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

Les quinze dernières années ont été marquées par une croissance exponentielle du domaine du Web tant dans le nombre de sites Web disponibles que dans le nombre d'utilisateurs de ces sites. Cette croissance a généré de très grandes masses de données relatives aux traces d'usage duWeb par les internautes, celles-ci enregistrées dans des fichiers logs Web. De plus, les propriétaires de ces sites ont exprimé le besoin de mieux comprendre leurs visiteurs afin de mieux répondre à leurs attentes. Le Web Usage Mining (WUM), domaine de recherche assez récent, correspond justement au processus d'extraction des connaissances à partir des données (ECD) appliqué aux données d'usage sur le Web. Il comporte trois étapes principales : le prétraitement des données, la découverte des schémas et l'analyse (ou l'interprétation) des résultats. Un processus WUM extrait des patrons de comportement à partir des données d'usage et, éventuellement, à partir d'informations sur le site (structure et contenu) et sur les utilisateurs du site (profils). La quantité des données d'usage à analyser ainsi que leur faible qualité (en particulier l'absence de structuration) sont les principaux problèmes en WUM. Les algorithmes classiques de fouille de données appliqués sur ces données donnent généralement des résultats décevants en termes de pratiques des internautes (par exemple des patrons séquentiels évidents, dénués d'intérêt). Dans cette thèse, nous apportons deux contributions importantes pour un processus WUM, implémentées dans notre bo^³te à outils AxisLogMiner. Nous proposons une méthodologie générale de prétraitement des logs Web et une méthodologie générale divisive avec trois approches (ainsi que des méthodes concrètes associées) pour la découverte des motifs séquentiels ayant un faible support. Notre première contribution concerne le prétraitement des données d'usage Web, domaine encore très peu abordé dans la littérature. L'originalité de la méthodologie de prétraitement proposée consiste dans le fait qu'elle prend en compte l'aspect multi-sites du WUM, indispensable pour appréhender les pratiques des internautes qui naviguent de fa»con transparente, par exemple, sur plusieurs sites Web d'une même organisation. Outre l'intégration des principaux travaux existants sur ce thème, nous proposons dans notre méthodologie quatre étapes distinctes : la fusion des fichiers logs, le nettoyage, la structuration et l'agrégation des données. En particulier, nous proposons plusieurs heuristiques pour le nettoyage des robots Web, des variables agrégées décrivant les sessions et les visites, ainsi que l'enregistrement de ces données dans un modèle relationnel. Plusieurs expérimentations ont été réalisées, montrant que notre méthodologie permet une forte réduction (jusqu'à 10 fois) du nombre des requêtes initiales et offre des logs structurés plus riches pour l'étape suivante de fouille de données. Notre deuxième contribution vise la découverte à partir d'un fichier log prétraité de grande taille, des comportements minoritaires correspondant à des motifs séquentiels de très faible support. Pour cela, nous proposons une méthodologie générale visant à diviser le fichier log prétraité en sous-logs, se déclinant selon trois approches d'extraction de motifs séquentiels au support faible (Séquentielle, Itérative et Hiérarchique). Celles-ci ont été implémentées dans des méthodes concrètes hybrides mettant en jeu des algorithmes de classification et d'extraction de motifs séquentiels. Plusieurs expérimentations, réalisées sur des logs issus de sites académiques, nous ont permis de découvrir des motifs séquentiels intéressants ayant un support très faible, dont la découverte par un algorithme classique de type Apriori était impossible. Enfin, nous proposons une boite à outils appelée AxisLogMiner, qui supporte notre méthodologie de prétraitement et, actuellement, deux méthodes concrètes hybrides pour la découverte des motifs séquentiels en WUM. Cette boite à outils a donné lieu à de nombreux prétraitements de fichiers logs et aussi à des expérimentations avec nos méthodes implémentées.

GeTe and Ge2Sb2Te5 alloys are potential candidates for non-volatile phase change random access memories (PCRAM). For electrical data storage applications the materials should have stable amorphous and crystalline phases, fast crystallization time, low power to switch, and high crystallization activation energy (to be stable at normal operating temperatures). Phase change memories can be tuned through compositional variations to achieve sufficient phase change contrast and thermal stability for data retention. Selenium is one of the attractive choices to use as an additive material owing to its flexible amorphous structure and a variety of possible applications in optoelectronics and solar cells. GeSb2Te3Se alloy, in which 25 at.% of Se substituted for Te, show a higher room temperature resistance with respect to parent GeSb2Te4 alloy, but the transition temperature is lowered which will affect the thermal stability. The RESET current observed for Sb65Se35 alloys were reduced and the crystallization speed increased 25 % faster with respect to Ge2Sb2Te5. Alloys of Ga-Sb-Se possess advantages such as higher crystallization temperatures, better data retention, higher switching speed, lower thermal conductivity and lower melting point than the GST, but the resistance ratio is limited to about two orders of magnitude. This affects the resistance contrast and data readability. It is with this background a study has been carried out in GeTe and GeSbTe system with Se doping. Studies on structural, thermal and optical properties of these materials all through the phase transition temperatures would be helpful to explore the feasibility of phase change memory uses. Thin films along with their bulk counterparts such as (GeTe)1-x Sex ( 0 < x ≤ 0.50) and (GST)1-xSex (0 < x ≤ 0.50), including GeTe and GST alloys, have been prepared. The results are presented in four chapters apart from the Introduction and Experimental techniques chapters. The final chapter summarizes the results. Chapter 1 provides an introduction to chalcogenide glasses, phase change memory materials and their applications. The fundamental properties of amorphous solids, basic phase change properties of Ge2Sb2Te5 and GeTe alloys and their applications are presented in detail. Various doping studies on GeTe and Ge2Sb2Te5 reported in literatures are reviewed. The limitations, challenges, future and scope of the present work are presented. In chapter 2, the experimental techniques used for thin film preparation, electrical characterizations, optical characterization and surface characterizations etc. are explained. Chapter 3 deals entirely on Ge2Sb2Te5 films studied throughout the phase transition, by annealing at different temperatures. Changes in sheet resistance, optical transmission, morphology and surface bonding characteristics are analyzed. The crystallization leads to an increase of roughness and the resistance changes to three orders of magnitude at 125 oC. Optical studies show distinct changes in transmittance during phase transitions and the optical parameters are calculated. Band gap contrast and disorder variation with annealing temperatures are explained. The surface bonding characteristics studied by XPS show Ge-Te, Sb-Te bonds are present in both amorphous and crystalline phases. The temperature dependent modifications of the band structure of amorphous GST films at low temperatures have been little explored. The band gap increment of around 0.2 eV is observed at low temperature (4.2 K) compared to room temperature 300 K. Other optical parameters like Urbach energy and B1/2 are studied at different temperatures and are evaluated. The observed changes in optical band gap (Eopt) are fitted to Fan’s one phonon approximation, from which a phonon energy (ћω) corresponding to a frequency of 3.59 THz resulted. The frequency of 3.66 THz optical phonons has already been reported by coherent phonon spectroscopy experiment in amorphous GST. This opens up an indirect method of calculating the phonon frequency of the amorphous phase change materials. Chapter 4 constitutes comparison of optical, electrical and structural investigation of GST and (GST)1-xSex films. It is well known that GST alloys have vacancy in their structure, which leads to the possibility of switching between the amorphous and crystalline states with minimum damage. Added Se may occupy the vacancy or change the bonding characteristics which intern may manifest in the possibility of change in optical and electrical parameters. The structural studies show a direct amorphous to hexagonal transition in (GST)1-xSex, where x ≥ 0.10 at.%. Raman spectra of the as deposited and annealed (GST)1-xSex films show structural modifications. The infrared transmission spectra indicate a shift in absorption edges from low to high photon energy when Se concentration increases in GST. Band gap values calculated from Tauc plot show the band gap increment with Se doping. It is noted that a small amount of Se doping increases the resistance of the amorphous and crystalline phases and maintains the same orders of resistance contrast. This will be beneficial as it improves the thermal stability and reduces the write current in a device. Switching studies show an increasing threshold voltage as the Se doping concentration increases. Chapter 5 comprises compositional dependent investigations of the bulk GeTe chalcogenides alloys added with different selenium concentrations. The XRD investigations on bulk (GeTe)1-xSex (x = 0.0, 0.02, 0.10, 0.20 and 0.50 at.%) alloys show that the crystalline structure of GeTe alloys does not affect ≤ 0.20 at.% of Se concentration. With increasing amount of Se concentration the alloys gets modified in to a homogeneous amorphous structure. This result has been verified from the XRD, Raman, XPS, SEM and DSC measurements. The possibility that Se occupying the Ge vacancy sites in GeTe structure is explained. Since Se is an easy glass former, the amorphousness increases in the alloys due to new amorphous phases formed by the Se with other elements. It is shown from Raman and XPS analysis that the Ge-Te bonds exists up to Se 0.20 at.% alloys. Ge-Se and GeTe2 bonds are increasing with increasing Se at.%. Melting temperature has found decreases and the reduction in melting point may reduces the RESET current. Further studies on switching behavior may bring out its usefulness. Chapter 6 deals with studies on (GeTe)1-xSex films for phase change memory applications based on the insight received from their bulk study. Even at low at.% addition of Se makes the as prepared (GeTe)1-xSex film amorphous. At 200 oC, GeTe crystalline structure is evolved and the intensity of the peaks reduces in the alloys with increase of Se content. At 300 oC, more evolved GeTe crystalline structure is seen compared to 200 oC annealed films whereas 0.20 at.% Se alloy remain amorphous. Resistance and thermal studies shows increase in crystallization temperature. It is expected that Se sits in the vacancies of the GeTe crystalline structural formation. This may also account for the increased threshold voltages with increasing Se doping. The band gap increase with increase of Se at.% signifying the possibility of band gap tuning in the material. Possible explanation for the increased order in GeTe due to Se doping is presented. The modifications in the alloy with Se addition can be explained with the help of chemical bond energy approach. Those bonds having higher energy leads to increased average bond energy of the system and hence the band gap. The XPS core level spectra and Raman spectra investigation clearly shows the GeTe bonds are replaced by Ge-Se bonds and GeTe2 bonds. The 0.10 at.% Se alloy is found to have a higher thermal stability in the amorphous state and maintains a gigantic resistance contrast compared to other Se concentration alloys. This alloy can be considered as an ideal candidate for multilevel PCM applications. Chapter 7 summarizes the major findings from this work and the scope for future work.