Cyclic AMP (cAMP) is a second messenger that translates extracellular signals into tightly regulated biological responses. The cAMP binding domain (CBD) is a conserved regulatory switch that binds to cAMP and allosterically controls multiple cellular functions. All CBDs share a common architecture comprised of α- and β-subdomains. cAMP binds to the phosphate binding cassette (PBC) nested within the β-subdomain. In mammals the main cAMP receptors are protein kinase A (PKA), guanine exchange factors (EPAC) and ion channel proteins, including both the hyperpolarization-activated cyclic nucleotide-dependent channels (HCN channels) and the cyclic nucleotide-gated channels (CNG channels). Impaired activities of these proteins are associated with diabetes, cardiovascular diseases, cancer and Alzheimer's disease. Therefore, these proteins represent promising therapeutical targets. However, the mechanism of their cAMP-dependent allosteric control is not completely understood. In the present thesis we have studied the allosteric mechanism of activation in PKA and EPAC using an NMR-based approach and we have proposed a model explaining how cAMP allosterically controls the activity of PKA and EPAC. Binding of cAMP to the Regulatory (R) subunit of PKA facilitates the release of the Catalytic (C) subunit. According to our model, binding of cAMP triggers long range perturbations that propagate from the PBC to the R:C interface through both direct and indirect pathways. The indirect pathway involves two key relay sites located at the C-terminus of β2 (1163) and at the N-terminus of β3 (D170). D170 functions as an electrostatic switch that mediates the communication between the PBC and the helical subdomain, whereas 1163 controls the global unfolding. Hence, removal of cAMP uncouples the α- and β-subdomains by breaking the circuitry of cooperative interactions radiating from the PBC. The proposed model was further validated by the cAMP agonist Sp-cAMPS and the cAMP antagonist Rp-cAMPS. It was observed that Rp-cAMPS, in which the equatorial exocylic oxygen is replaced by sulphur, does not activate a necessary indirect allosteric pathway, while its diastereoisomer (Sp-cAMPS) with opposite phosphorus chirality behaves similarly to cAMP activating all allosteric pathways. Our data also showed that the cAMP-antagonist stabilizes a ternary inhibitory complex between the effector ligand and both the regulatory and the catalytic subunits of PKA. At this point it is still not understood how the proposed model of cAMP allostery is conserved in other cAMP binding proteins such as EPAC. EPAC is a multidomain guanine nucleotide exchange factor specific for small GTP-binding proteins and is directly activated by cAMP. We have probed how cAMP docks into the EPAC1 CBD and how its signal allosterically propagates from the cAMP binding site to the helical subdomain, which mediates the inhibitory interactions between the regulatory and catalytic regions of EPAC. Our comparative NMR investigation of cAMP signalling in PKA and EPAC revealed key functionally significant differences between these two systems that will facilitate the design of EPAC-selective therapeutics. / Thesis / Doctor of Philosophy (PhD)

Thesis (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2005. / Vita. Bibliography: References located at the end of each chapter.

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Les organismes unicellulaires sont très vulnérables aux changements rapides de leur environnement puisqu’ils sont en contact direct avec celui-ci. Les organismes unicellulaires utilisent plusieurs stratagèmes pour réguler l’expression génique et par conséquent, les diverses voies métaboliques nécessaires aux différentes conditions environnementales auxquelles ils sont confrontés. On sait maintenant que certains ARN, dont les riborégulateurs, ont également un grand rôle à jouer dans les processus de régulation de l’expression du génome. En général, les riborégulateurs sont des éléments génétiques situés dans les régions 5’ non traduites (5’ UTR) de l’ARN messager bactérien. Ces éléments possèdent une structure tertiaire bien définie qui est conservée à travers l'évolution. Les riborégulateurs subissent un changement de conformation en s’associant à un ligand spécifique et modulent l’expression des gènes qu’ils contrôlent en aval. Le rôle des riborégulateurs en relation avec le métabolisme des eubactéries peut être d’une grande importance. C’est le cas de Clostridium difficile qui voit son génome régulé par au moins une quarantaine de riborégulateurs. Étant un pathogène nosocomial, causant des infections contractées dans le milieu hospitalier, bien connu pour engendrer des complications au niveau de l’intestin, il est intéressant d’étudier la relation gène-riborégulateur-métabolisme chez C. difficile. De plus, les riborégulateurs ont montré un potentiel intéressant comme cible antibiotique pour combattre certaines infections. C. difficile possède quatre riborégulateurs guanine transcriptionnels qui contrôlent quatre gènes intervenant dans la voie de biosynthèse de la guanosine monophosphate (GMP). Deux de ces gènes interviennent directement dans la voie de synthèse du GMP soit une guanosine-monophosphate synthase (guaA) et une xanthine phosphoribosyltransférase (XPRTase) (xpt) ainsi que deux transporteurs de précurseur nommés CD630_21070 codant pour une perméase uracile/xanthine et CD630_ 27040 une perméase putative. Bien que quelques études ont démontré l’importance que pourrait avoir le gène guaA chez d’autres espèces bactériennes (Staphylococcus aureus, Escherichia coli, Streptococcus suis et, Salmonella thyphimurium), aucune étude de C. difficile n'a élucidé la relation entre les quatre riborégulateurs guanine et les gènes qu’ils contrôlent, de même que leur rôle au sein du métabolisme du GMP dans un contexte in vivo. Le présent mémoire porte sur l’étude de ces quatre riborégulateurs guanine chez C. difficile, les gènes régulés par ces riborégulateurs et leurs effets sur la biologie de C. difficile. Une fois que les recherches bio-informatiques ont été entreprises, le projet s’est divisé en deux grandes parties soit l’efficacité de régulation des riborégulateurs guanine et l’importance des quatre gènes qui sont sous le contrôle de ces riborégulateurs chez C. difficile 630. Afin de vérifier si les riborégulateurs guanine avaient une affinité acceptable pour leur ligand (guanine), des essais de cartographies chimiques ont été faits et des Kd ont été déterminés. Ces Kd se retrouvent tous dans le bas nanomolaire (nM) de 2,61 ± 1,29 nM pour le riborégulateur guaA et des Kd de 1,78 ± 0,95 nM, de 3,06 ± 0,29 nM et de 4,44 ± 2,75 nM pour les riborégulateurs xpt, CD_21070 et CD_27040 respectivement. Pour la deuxième partie du projet, quatre mutants d’inactivation de gène par insertion ont été conçus grâce à l’utilisation du système ClosTron. Ces quatre mutants, correspondant aux gènes guaA, xpt, CD630_21070 et CD630_27040, ont ensuite été analysés lors d’essais de croissance afin de vérifier les phénotypes associés aux inactivations de gènes. À la suite des résultats d’essais de croissance des divers mutants d’inactivation, une emphase a été mise sur le gène guaA et son riborégulateur puisque ce dernier montrait un phénotype d’inhibition de croissance. L’efficacité avec laquelle le riborégulateur guaA pouvait réprimer l’expression génique a été déterminée lors des essais de gène rapporteur gusA et de PCR quantitative en temps réel. Une baisse de l’expression ligand-dépendante a été observée dans des conditions variant en concentration de guanine. Le mutant de délétion par inactivation du gène guaA a aussi démontré une baisse dans sa capacité d’infecter un modèle murin. En effet, lors d’une étude d’infection en compétition avec le type sauvage, les décomptes cellulaires du mutant guaA étaient diminués de 4 logs. Ces résultats indiquent un rôle fondamental du gène guaA sur le pouvoir infectieux de C. difficile 630 et mettent en évidence l’importance du riborégulateur qui contrôle l’expression de ce gène. Toutes les expériences faites dans le cadre du projet ont été entreprises chez C. difficile 630 afin de garder un contexte plus naturel au cours des analyses. Les résultats présentés ici mettent en évidence le potentiel des riborégulateurs comme cibles antibiotiques. Des travaux futurs devront être effectués afin de vérifier l’effet que pourraient avoir certains analogues de ligands qui ciblent les riborégulateurs guanine sur la viabilité de C. difficile.

Glioblastomas are an incurable type of brain tumor with a mean survival time of 9-12 months following diagnosis. One of the reasons for this poor prognosis is the ability of tumor cells to invade the surrounding normal brain tissue. Enzymes responsible for this invasive nature include the matrix metalloproteinase family. MMP-1 is a member of this family which has been well studied in many types of invasive tumors, with gliomas being an exception. We studied a single nucleotide polymorphism (SNP) in the MMP-1 promoter that may influence glioma biology. This SNP consists of the presence (2G) or absence (1G) of a guanine nucleotide at position -1607. The additional guanine nucleotide creates a binding site for ETS transcription factors and combined with the AP-1 binding site at position -1602 creates a Ras Responsive Element. We determined that the distribution of the MMP-1 genotype differed significantly between the healthy population and the glioblastoma patient population, with the 2G/2G genotype more prevalent in the glioblastoma patients. In addition, MMP-1 mRNA and protein examined in a select group of patient tissue had significantly higher levels when compared to normal brain controls, however, there was no correlation with genotype. Promoter reporter assays indicated that the 2G promoter was approximately three times more active than the 1G promoter in three different glioma cell lines.We investigated potential signaling mechanisms responsible for increases in MMP-1 transcription due to the presence of the RAS responsive element. Treatment of glioma cell lines with hepatocyte growth factor/scatter factor (HGF/SF) led to significant increases in MMP-1 transcription, via the MAP kinase ERK pathway. AP-1 transcription factor proteins, cJun and cFos were increased in response to HGF treatment but not Ets-1 and ETV-1. HGF/SF treatment of glioma cell lines differing in their MMP-1 genotype affected binding of ETS and AP-1 proteins to the endogenous MMP-1 distal promoter. Using chromatin immunoprecipitation assays, we identified these differentially DNA-bound AP-1 and ETS proteins. The data presented indicate that the MMP-1 SNP (-1607) is important in glioma biology and may contribute to tumor function and future investigations into its role in glioma biology is warranted.

It has been proven that platinum complexes are active in anticancer treatment as well as several other transition metals complexes. There is an effort in recent medicine to replace cisplatin complexes by drugs with smaller side effects. This work focuses on the reaction of 5'-dGMP (2'-deoxyguanosine-5'˗monophosphate) and cGMP (cyclic 2'-deoxyguanosine- monophosphate) with a platinum complex PtIV (dach)Cl4 (dach=diaminocyclohexane). In these two cases the Pt(IV) complex is only reduced in the presence of 5'-dGMP. The first part of the explored mechanism is the substitution reaction where a coordinate-covalent bond between platinum and nitrogen N7 of guanine is formed. In the next step oxygen of phosphate group is transferred to the C8 site. Subsequently the Pt(IV) complex is reduced. The final products represent 8˗oxo˗GMP and PtII (dach)Cl2, which are active in anticancer treatment in comparison with the kineticly inert reactant. The substitution of a chloride anion ends the reaction path for cGMP forming PtIV (dach)Cl3(N7-cGMP) complex. The structures were optimized at the DFT level with B3LYP functional in the basis set 6-31G(d) and PCM/UA0 solvation model. The energy parameters were computed at the B3LYP/6˗311++G(2df,2pd) level in the IEFPCM/sUAKS solvation model. Finally, the rate constants were...

Parts of human telomere sequences containing at least 4 guanine subsequences show the ability to form intrastrand quadruplexes of remarkable conformational diversity. Former studies using conventional Raman spectroscopy have revealed that the sequence G3(TTAG3)3 at milimolar concentrations in phosphate buffer solution doped with Na+ ions (ionic strength 150 mM) adopts antiparallel conformation regardless of the length of standing at room temperature or annealing, whereas K+ ions cause gradual transition to "3+1" or even parallel conformation. On the other hand, measurements carried out upon sequence AG3(TTAG3)3 at similar concentrations using Photonic Crystal Fibre-enhanced Raman Spectroscopy (PCFRS) suggest that in the respective presence of both Na+ and K+ (ionic strength 100 mM), a parallel structure is adopted. The hereby presented work employs conventional Raman spectroscopy and Drop Coating Deposition Raman spectroscopy to examine the sequence AG3(TTAG3)3 at concentrations ranging from units to hundreds of milimoles in strands. It concludes that the structure adopted in the presence of Na+, resp. K+ ions is antiparallel, resp. "3+1", and doesn't change over time despite both long standing and annealing. Two hypotheses about the cause of the differences between the results obtained by PCFRS and...

O trabalho apresentado nesta Dissertação de Mestrado descreve o desenvolvimento e aplicação de eletrodos de pasta de carbono modificados eletroquimicamente em soluções de guanina e de eletrodos de grafite pirolítico modificados em soluções de dopamina. Estes eletrodos foram empregados na detecção e, a quantificação, por voltametria de pulso diferencial (VPD), de alguns compostos de importância biológicas tais como NADH, NADPH, 8-oxo-guanina, ácido úrico (AU), ácido ascórbico (AA), dopamina (DA) e xantina (XA). No primeiro caso, os eletrodos de pasta de carbono foram modificados em solução de guanina por aplicação de um potencial de 1,1 V (vs Ag/AgCl, KClsat) ao eletrodo de trabalho por 12 minutos sob sat agitação constante. Com estes eletrodos detectaram-se NADH, NADPH, 8-oxo-guanina e AU, com limites de detecção de 3,3, 3,7, 2,0 e 6,6 x 10-6 mol L-1 respectivamente, na faixa de concentração de 7,5 x 10-6 a 8,1 x 10-4 mol L-1 . No segundo caso, eletrodos de grafite pirolítico, previamente tratados em solução de NaOH, foram modificados eletroquimicamente em solução de DA por aplicação de um potencial 1,5 V (vs Ag/AgCl, KClsat ) ao eletrodo de trabalho durante 2 minutos. Com estes eletrodos foi possível a determinação simultânea de AA, AU e DA. Para obtenção das curvas analíticas variou- se a concentração do analito de interesse, mantendo-se constante a concentração dos possíveis interferentes nos valores de 1,0 x 10-4 mol L-1 (DA), 5,0 x 10-5 mol L-1 (AU) e 1,0 x 10-3 mol L-1 (AA). Os limites de detecção calculados para AU, AA e DA foram respectivamente de 1,4 x 10-6 mol l-1 , 2,5 x 10-5 mol l-1 e 1,1 x 10-7 mol l-1 . Ácido úrico foi determinado em amostras de urina, sangue e soro humano com 92 a 103 % de recuperação, sem a necessidade de tratamento prévio das amostras. / Chemically Modified Carbon Paste and Pyrolitic Graphite Electrodes were prepared via electrochemical deposition from guanine and dopamine solutions. Carbon paste electrodes were modified in guanine solutions under an applied potential of 1.1 V (vs Ag/AgCl, KClsat ) during 12 minutes under constant stirring. They were used for sat electrochemical detection of NADH, NADPH, uric acid and 8-oxoguanine. Detection limits were 3.3, 3.7, 6.6 and 2.0 10-6 mol L-1 respectively, with sensitivity of 0.13, 0.10, 0.26 and 0.40 A mol-1 L cm-2 , respectively. The electrodes showed high reproducibility and absence of surface poisoning effects. Good analytical performance was attributed to the formation of superficial dimer or trimers species of guanine during the modification process. Pyrolitic graphite electrodes, previously submitted an electrochemical treatment in NaOH solution, were modified in dopamine solution (phosphate buffer, pH 10) under an applied potential of 1.5 V (vs Ag/AgCl, KClsat ) during 2 minutes under constant sat stirring and, further used for the simultaneous determination of ascorbic acid (AA), uric acid (AU) and dopamine (DA). The analytical curves were obtained changing the concentration of the wished analyte, at constant concentration levels of the interferences: 1.0 x 10-4 mol L-1 (DA), 5.0 x 10-5 mol L-1 (UA) and 1.0 x 10-3 mol L-1 (AA). Detection limits were 1.4 x 10-6 mol L-1 , 2.5 x 10-5 mol L-1 and 1.1 x 10-7 mol L-1 for UA, AA and DA, respectively. Uric acid was determined in human urine, blood and serum samples without any previous treatment. Recovering percentages of 92 to 103 % were obtained.

An estimated 1,735,350 new cancer diagnosis and 609,640 cancer related deaths are predicted to occur in the United States in 2018. To improve patient prognosis, biomarkers are needed to identify cancer in early stages. When diagnosed at an early stage, cancer is more likely to respond to treatments and patients have a higher survival rate. Consequently, there is an ever-present need to identify biomarkers that can aid in the detection of cancer. Additionally, there is a paradigm shift in the field of cancer treatment towards immunotherapy. Traditional cancer treatments include chemotherapy, radiation, and hormone therapy and are not cancer-specific, which leads to bystander effects on the patient<&trade>s normal organs that often harm the patient and create unnecessary hardship. To alleviate this, immunotherapy utilizes a patient<&trade>s own immune cells to attack and destroy cancer cells via cancer-specific biomarkers. These biomarkers are ideally on the surface of cancer cells and absent from the patient<&trade>s normal cells to avoid healthy tissue destruction. With this new therapy, there is a recent push to find surface antigens for immunotherapy techniques.This dissertation describes the characterization of HPRT as a diagnostic and therapeutic biomarker for the detection and possible treatment of hematological and solid malignancies. We describe the general upregulation of HPRT upon malignancy and show that this elevation in protein expression is independent of stage, which indicates that it would be useful as an early stage diagnostic companion tool. We have preliminarily linked the elevation in HPRT to a mutation in one of its prime transcription factors, p53. Specific mutation in p53 called Gain of Function mutations have shown to influence salvage pathway enzyme expression, and we have shown that mutations in p53 are relevant to the elevated levels of HPRT within several cancer types. In addition, we also found that HPRT associates significantly with the membrane of several cancer cell lines as well as patient samples. We found that HPRT has insignificant expression on normal cells, which suggests it may be useful as a targetable biomarker for immunotherapy. Throughout our analysis, we also determined that HPRT might have a role in immune regulation as an elevation of the protein correlates to the decrease of several pro-inflammatory genes involved in immune activation. The knowledge gained from the data presented in this dissertation have opened up new functions for HPRT outside of simple nucleotide production and have confirmed that HPRT has a unique role in cancer that has not been previously reported.

The present thesis investigates the electronic and structural properties of adenine, cytosine, and guanine layers on hydrogen passivated silicon (111)(7x7). The (7x7) reconstruction of the silicon surface was achieved by direct current heating of the samples in UHV conditions. After in situ hydrogen passivation layers of the DNA bases were prepared in different thicknesses by means of organic molecular beam deposition, all samples were characterized employing valence band and core level photoemission spectroscopy. Additionally the near edge x-ray absorption fine structure of the DNA base layers was investigated. A detailed and consistent picture of structural and electronic properties of the nucleotide bases in the solid state could be developed by comparison of measurements and DFT/B3LYP calculations.