A Adenina Fosforibosiltransferase (APRT E.C. 2.4.2.7) pertence à família de enzimas Fosforibosil Transferases (PRTase) do Tipo I , que catalisa a conversão reversível de Adenina e 5-fosfo-α-D-ribose-1-difosfato (PRPP) em difosfato e adenosina monofosfato, um importante precursor energético da célula. A APRT integra a via de salvação de purinas, única forma de suprir o balanço de purinas em Schistosoma mansoni. Este trabalho apresenta o isolamento, clonagem, expressão heteróloga e purificação da APRT de S. mansoni a fim de caracterizá-la quanto seus parâmetros físico-químicos. Não se obtendo cristais de proteína, foram elaborados modelos tridimensionais por homologia para estudos de dinâmica molecular e avaliação conformacional via tCONCOORD. A estrutura de APRT humana foi usada como controle nas simulações. Os dados computacionais e de biologia molecular foram comparados entre si para validação mútua e, verificou-se que a análise cuidadosa de dados computacionais é capaz de fornecer informações críticas sobre a APRT, auxiliando e guiando os estudos experimentais. Ainda, as simulações de dinâmica molecular foram capazes de evidenciar a abertura de loops do sítio ativo, explicitar a importância da análise de rotâmeros em modelos, permitindo, então, rearranjar da forma correta resíduos erroneamente modelados. Por fim, um estudo envolvendo mecanismo catalítico sugere a participação de uma molécula de água abstraindo o próton ligado ao N9 da adenina e, para efeito de comparação, um mecanismo alternativo independente desta participação também foi descrito. Ambas as observações expandem a corrente visão sobre o mecanismo catalítico de APRTs. / The Adenine Phoshoribosyltransferase (APRT E.C.2.4.2.7) belongs to the Phosphoribosyltransferase enzyme family (PRTase) of type I which catalyzes the reversible conversion of adenine and 5-phospho-α-D-ribose-1-diphosphate (PRPP) in diphosphate and adenosine monophosphate, an important source of this compound for the cell. APRT is involved in the purine salvage pathway, the only way that Schistosoma mansoni has to supply its purine demands. This work shows the isolation, cloning, heterologous expression and the purification of APRT from S. mansoni in order to establish its physical chemical and kinetics parameters. Since crystallographic structure was not obtained, we built homology models to perform molecular dynamics experiments and conformational evaluation via tCONCOORD. The human APRT structure was used as control in the simulation experiments. The computational and molecular biology data were compared for consistency and the detailed analysis of the former allowed us to improve experimental manipulation of APRT. The molecular dynamics experiments showed the opening of the loops of the catalytic binding site and the key function of rotamers. Finally, we were able to suggest that a water molecule may catch the proton of adenine N9. Both observations improve the current view of APRT catalytic mechanism.

No description available.

The adsorption of biologically active molecules, such as the DNA bases, amino acids, on solid surfaces has been the subject of a number of experimental and theoretical studies in the past years. The understanding of the self-assembly mechanism of bioactive molecules on surfaces not only is fundamentally important in the preparation of bioactive surfaces, but also provides us insight into the origins of life and homo-chirality in nature. In this thesis, the adsorption behaviour of adenine and phenylglycine molecules on the Cu(110) surface has been investigated in order to understand the effect of experimental parameters like coverage, annealing temperature etc. on the molecular orientation and the ordering of the adlayer structures. The thesis is organised in six parts: Chapter I gives an introduction to the relevance of surface sciences studies, describing the phenomena of surface chirality and molecular adsorption behaviours on surfaces. Chapter II gives an overview of the experimental techniques and introduces basic concepts of theoretical calculation. Chapter III investigates the effect of experimental parameters, e.g. surface coverage, annealing temperature and substrate temperature on molecular diffusion, molecular orientation and ordering of the adlayer structures. LT-STM examination of the contrast variations of adenine chains and isolated adsorbate as a function of the tip-sample bias voltage is also presented with the aim to understand the tunnelling mechanism. Chapter IV shows RAIR spectra studies of the evolution of phenylglycine molecular orientation as a function of surface coverage at room temperature. The adsorption geometry and binding nature of phenylglycine is discussed. Chapter V concerns with the adsorption behaviours of phenylglycine and adenine on Cu(110) surface pre-covered with oxygen. Chapter VI summarises the conclusions and describes the outlook of some future work.

Poly(ADP-ribosyl)ation is a reversible post-translational modification of histones and nuclear proteins rapidly stimulated by DNA damage. Its homeostasis is a dynamic process regulated by the synthesizing enzymes poly(ADP-ribose) polymerases (PARPs) and the degrading enzyme poly(ADP-ribose) glycohydrolase (PARG). PARP-1, the first-discovered and major PARP, has been the focus of many studies aimed at clarifying the biological function of poly(ADP-ribose) (PAR). This abundant nuclear enzyme plays key roles in a variety of cellular processes, including the regulation of chromatin structure, transcription and genomic integrity. Its multifunctionality has made it an attractive and potential target for therapy, as evidenced by the numerous PARP-1 inhibitors currently undergoing clinical trials. The transient nature of PAR, explained by the close coordination between PARP-1 and PARG, has also highlighted the potential of targeting PARG for diseases of inappropriate cell death. A number of obstacles, however, have prevented PARG from being studied as extensively as PARP-1. The extreme sensitivity of PARG to proteases and its insolubility at high concentrations have limited structure-activity relationship analyses and structural studies of PARG, and the unavailability of high-throughput activity assays has stalled the discovery and development of specific and cell permeable PARG inhibitors, subsequently slowing down the validation of PARG as a therapeutic target. The work presented in this dissertation describes in detail strategies devised to overcome these difficulties. First, a novel colorimetric high-throughput assay for PARG was evaluated and its sensitivity and precision were compared to a widely-used radiolabelling assay. Second, several expression and purification systems were constructed in order to obtain high quantities of soluble human PARG protein adequate for in vitrostructural studies. The efficacy of these strategies was demonstrated in structure-activity analyses of PARG which led to the identification of a regulatory segment far removed linearly from the catalytic site of PARG. This region, necessary for catalytic activity, corresponds with a recently identified mitochondrial targeting sequence (MTS) and was thus named the ‘regulatory segment/MTS’ (REG/MTS). Finally, based on structural data obtained, secondary structure predictions were made to provide insight into the molecular composition of the different domains of PARG, whose structures still remain to be determined.

Novel Ca²⁺ signalling pathways in both endothelial cells and smooth muscle cells of rat small resistance arteries were investigated using a combination of confocal imaging, isometric tension recordings, and electrophysiology to study freshly isolated arteries and cells. We first examined the hypothesis that hyperpolarization could alter endothelial cell Ca²⁺ events. Hyperpolarization evoked by direct opening of K_ATP channels in the smooth muscle with levcromakalim triggered an increase in the frequency of Ca²⁺ events in the endothelium of rat cremaster arterioles. These Ca²⁺ events were discrete in nature, requiring subcellular regions of interest to reliably identify them. Opening of K_ATP channels indirectly through β-adrenoceptor stimulation with isoprenaline, caused a similar increase in the frequency of endothelial cell Ca²⁺ events in rat mesenteric third order arteries. These events also had a similar, focal profile. Pharmacological investigation suggested that the response to isoprenaline was receptor-mediated, and dependent on Ca²⁺ influx and opening of K_ATP channels. The presence of β-adrenoceptors on endothelial cells was confirmed using fluorescently-tagged β-adrenoceptor ligands, which showed punctate labelling in smooth muscle and endothelial cells of rat mesenteric arteries. Freshly isolated endothelial cells also showed Ca²⁺ increases to isoprenaline, although this was not consistently observed. Following on from the observed endothelial cell Ca²⁺ response to hyperpolarization, we tested the hypothesized involvement of hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels using the channel inhibitor, ZD7288. Pre-treatment with ZD7288 (1 μM) reduced both the endothelial cell Ca²⁺ response to isoprenaline (in mesenteric arteries) and levcromakalim (in cremaster arterioles). HCN channel subtypes were identified in cremaster arterioles through immunolabelling. We also observed an interesting effect of higher concentrations of ZD7288 to potentially inhibit K⁺ channels, including endothelial cell KCa channels, since hyperpolarization to isoprenaline, levcromakalim or acetylcholine (ACh) was reduced by 10 μM ZD7288, and relaxation to ACh was partially inhibited. ACh-mediated relaxation was also partially inhibited by the clinically used HCN channel blocker, ivabradine (0.3-30 μM). Finally, we identified an interaction of the Ca²⁺-releasing second messenger nicotinic acid adenine dinucleotide phosphate (NAADP) with BKCa channels in the smooth muscle. NAADP-mobilised Ca²⁺ has been reported to interact with ryanodine receptors hence we hypothesized an interaction with BK_Ca channels via Ca²⁺ sparks. We found that NAADP-AM relaxed and hyperpolarized rat mesenteric arteries, which was blocked by iberiotoxin (BK_Ca channel inhibitor) and high extracellular [K⁺] (45 mM). Furthermore, NAADP increased paxilline-sensitive K⁺ currents and the frequency and amplitude of spontaneous transient outward currents (STOCs) in freshly isolated vascular smooth muscle cells patched in the whole-cell configuration, further supporting an action at BK_Ca channels. All together these data identify novel Ca²⁺ signalling pathways in resistance arteries that are both activated by and promote hyperpolarization, which is a key determinant of vascular tone.

Les composés organophosphorés sont des molécules importantes aussi bien dans le domaine de l'industrie nucléaire que pour les systèmes vivants. En effet, plusieurs extractants à la base de procédés du cycle de retraitement du combustible sont des molécules organophosphorées (TBP, HDEHP par exemple) et dans le domaine biologique les nucléotides sont des organophosphates qui jouent un rôle très important dans différents processus métaboliques.Si la littérature concernant les interactions des phosphates inorganiques avec les actinides est abondante, les études publiées avec des composés organophosphates se limitent généralement à des approches macroscopiques et/ou physiologiques. L'objectif de cette thèse est d'étudier la structure des plusieurs molécules organophosphorées avec des actinides pour affiner la compréhension et développer de nouveaux édifices spécifiques. La famille de molécules retenue pour cette approche est composée de 3 nucléotides d'adénine mono, bi et triphosphate (AMP, adénosine monophosphate – ADP, adénosine diphosphate - ATP, adénosine triphosphate) et d'un aminoalkylphosphate (AEP, O-phosphoryléthanolamine). La synthèse en milieu aqueux et faiblement acide (2,8-4) de plusieurs lanthanides représentants des actinides(III) (Lu, Yb, Eu) et d'actinides (U(VI), Th(IV) et Am(III)) a été réalisée. Plusieurs techniques analytiques et spectroscopiques ont été employées pour décrire la structure des complexes obtenus: les analyses spectrométriques réalisées par FTIR et RMN ont permis d'identifier les groupes fonctionnels impliqués dans la complexation, les analyses par ESI-MS et par titrage pH-métrique ont permis d'affiner la spéciation en solution et les analyses par EXAFS réalisées sur la ligne MARS du synchrotron SOLEIL, ont permis de décrire l'environnement proche des cations, tant pour des composés solides que pour des solutions. Quelques approches théoriques par DFT pour identifier des structures stables ont complété les approches expérimentales.Tous les complexes solides (AMP, ADP, ATP et AEP) présentent des organisations polynucléaires, alors que les complexes d'ATP en solution sont mononucléaires. Dans tous les complexes synthétisés, l'interaction prépondérante entre les cations et les groupes phosphates des ligands a été démontrée. Les complexes avec les ligands monophosphatés (Lu-AMP, Lu-AEP et Th-AMP) s'organisent de manière identique avec des phosphates pontants indiquant que la partie organique n'a pas un effet important sur leurs structures.Les complexes solides d'ADP et d'ATP (avec les deux ions métalliques sphéroïdes Lu et Th) présentent beaucoup de similitudes au niveau de l'environnement local indiquant que la présence d'un troisième groupe phosphate n'a pas d'effet important sur l'organisation des complexes au niveau local. La structure fine de ces complexes n'a cependant pas pu être déterminée précisément, malgré les approches théoriques qui ont été menées.Les complexes de lanthanides et d'actinides avec l'ATP ont un comportement similaire au niveau macroscopique suggérant une structure identique au niveau moléculaire.Avec l'uranyle, le complexe U-AMP à pH acide montre une organisation moléculaire différente de celui préparée à pH basique mais avec les mêmes sites de coordination: phosphates et hydroxyles du sucre. / Organophosphorus compounds are important molecules in both nuclear industry and living systems fields. Indeed, several extractants of organophosphorus compounds (such as TBP, HDEHP) are used in the nuclear fuel cycle reprocessing and in the biological field, the nucleotides are organophosphates which play a very important role in various metabolic processes. If the literature on the interactions of actinides with inorganic phosphate is abundant, published studies with organophosphate compounds are generally limited to macroscopic and / or physiological approaches. The objective of this thesis is to study the structure of several organophosphorus compounds with actinides to refine a better understanding and develop new specific buildings blocks. The family of the chosen molecules for this approach consists of three adenine nucleotides mono, bi and triphosphate (AMP, adenosine monophosphate - ADP, adenosine diphosphate - ATP, adenosine triphosphate) and an aminoalkylphosphate (AEP O-phosphorylethanolamine). Complexes Synthesis was conducted in aqueous medium and weakly acidic (2.8-4) for several representatives of lanthanides considered as actinides (III) (Lu, Yb, Eu) and actinides (U (VI), Th (IV) and Am (III)). Several analytical and spectroscopic techniques have been used to describe the organization of the synthesized complexes: spectrometric analysis performed by FTIR and NMR were used to identify the functional groups involved in the complexation, analysis by ESI-MS and pH-metric titration were used to determine the solution speciation and EXAFS analyzes were performed on Mars beamline of the SOLEIL synchrotron, have described the local cation environment, for both solution and solid compounds. Some theoretical approaches of DFT were conducted to identify stable structures in purpose of completing the experimental approaches. All solid complexes (AMP, ADP, ATP and AEP) have polynuclear structures, while soluble ATP complexes are mononuclear. For all synthesized complexes, it has been demonstrated that the dominant interaction is between the cations and the phosphate groups of the ligands. Complexes with monophosphate ligands (AMP-Lu, Lu-Th-AEP and AMP) show similar organizations with bridging phosphates indicating that the organic part does not have a significant effect on their structures. ADP and ATP solid state complexes (with two spheroid metal ions: Lu and Th) show several similarities in terms of local environment indicating that the occurrence of a third phosphate group has no significant effect on the local organization of the complex. However, despite the theoretical approaches that have been conducted, the fine structure of these complexes has not been accurately determined, Complexes of lanthanides and actinides with ATP behave similarly at macroscopic level suggesting an identical structure at the molecular level for these complexes.With uranyl, U-AMP complexe synthesized at acidic pH show different behavior at molecular level than that observed at alkaline pH but the same coordination sites (phosphates and hydroxyls ribose groups) have been demonstrated for both complexes.

In our studies we found that stabilized expression of HIF-1α in heart led to better recovery of function and less tissue death after 30 minutes of global ischemia, via mechanisms that preserve the mitochondrial polarization. Our group previously showed that HIF-1α conferred ischemic tolerance by allowing cardiomyocytes to use fumarate as an alternative terminal electron acceptor to sustain anaerobic mitochondrial polarization. The source of fumarate was identified as the purine nucleotide cycle (PNC). Here we discovered that HIF-1α upregulates AMP deaminase 2 (AMPD2), the entry point to the PNC. The combination of glycolysis and the PNC may protect the heart's nucleotide resources. We subsequently examined the effects that HIF-1α exerts on nucleotide metabolism in the ischemic heart. We found that HIF-1α expression reduces adenosine accumulation in the ischemic heart. As ATP is depleted during ischemia, AMP accumulates. Our results suggest that AMP metabolism is shunted towards AMPD2 rather than the adenosine producing 5'-nucleotidase pathway. Subsequently, we treated hearts with the PNC inhibitor hadacidin followed by 30 minutes of global ischemia. Inclusion of hadacidin reduced ATP and adenylate energy charge in the hearts. These findings allow us to propose that activity of the PNC prevents the F0F1 ATP synthase from consuming glycolytic ATP in order to maintain mitochondrial polarization during ischemia. Thus, the PNC provides ATP sparing effects and preserves the energy charge in the ischemic heart. The fact that ATP and adenylate energy charge is better preserved during the initial 20 minutes of ischemia in HIF-1α expressing hearts is supportive of our observation that HIF-1α upregulates the PNC. HIF-1α also upregulates adenosine deaminase, which degrades adenosine. The limitation of adenosine accumulation may help HIF-1α expressing hearts avoid toxicity due to chronic adenosine exposure. Finally, we found that HIF-1α induces the expression of the nucleotide salvage enzyme hypoxanthine phosphoribosyl transferase (HPRT). Upon reperfusion HPRT serves to reincorporate the nucleotide degradation product, hypoxanthine, into the adenylate pool and may prevent the production of reactive oxygen species. Collectively, HIF-1α robustly protects the heart from ischemic stress and it upregulates several pathways whose cardioprotective role may extend beyond the remodeling of nucleotide metabolism.

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.

Šilumos taikymas įvairioms ligoms gydyti jau buvo naudojamas senovės Egipto, Graikijos, Romos civilizacijose daugiau kaip prieš 2000 m. pr. Šiuo metu hipertermija plačiai taikoma visame pasaulyje gydant vėžį, nes tai pigus ir patogus metodas turintis mažą šalutinį poveikį. Mokslininkai nustatė, kad vėžinės ląstelės greičiau žūsta esant aukštesnei už fiziologinę (41-45°C) temperatūrai, todėl hipertermija, derinama su kitais vėžio gydymo metodais (radioterapija, chemoterapija, imunoterapija ir chirurgija), tampa efektyvesniu metodu. Kadangi yra mažai žinoma apie hipertermijos poveikio mechanizmą sveiko audinio ląstelėms karščiavimo, hiperterminio vėžio gydymo ar gydymo termoabliacija metu, todėl yra svarbu nustatyti hipertermijos paveiktų ląstelių gyvybingumą bei hipertermijos poveikį adenino ir piridino nukleotidų koncentracijoms. Šio darbo tikslas buvo įvertinti hipertermijos, būdingos nutolusioms nuo termozondo audinio sritims poveikį, adenino ir piridino nukleotidų koncentracijoms žiurkės kepenų ląstelėse bei audinyje. Buvo naudojamas jonų porų efektyviosios skysčių chromatografijos metodas, leidžiantis vienoje chromatografinėje analizėje išskirstyti labai skirtingo hidrofobiškumo junginius. Taip pat buvo vertintas gyvų ir negyvų ląstelių skaičius gautoje hepatocitų suspensijoje panaudojant tripano mėlio metodą bei NAD(P)H fluorescencijos pokyčiai kepenų audinyje termoabliacijos metu. Gauti rezultatai parodė, kad išskirti hepatocitai pasižymėjo dideliu gyvybingumu (8... [toliau žr. visą tekstą] / The application of heat in the treatment of disease was first recorded in the ancient civilizations of Egypt, Greece, and Rome from as early as 2000 BC. Nowadays hiperthermia is widely using in cancer diseases in all the world. It was determined by many scientists that cancer cells are more sensitive for supraphysiological temperature (41-45°C) killing compared to normal cells. There are numerous evidences that hyperthermia can increase the effectiveness of other cancer therapies: radiotherapy, chemotherapy, immunotherapy and surgery. There is little known about the mechanisms of hyperthermia effects on healthy tissue, which are important in fever, in hyperthermic treatment of neighboring tumour and in thermoablation. Therefore it is very important to determinate the vability of cells during different hyperthermic treatment and hyperthermic effects of adenine ir pyridine nucleotides concentrations.The aim of study was to value the effect of hyperthermia,which is typical remote from thermoprobe tissue areas, on the concentration of adenine and pyridine nucleotides in hepatocytes and liver tissue. It was used ion-pair high-performance liquid chromatography method, which allows to disperse different combinations of hydrophobicity. Also were evaluated live and dead cells quantity in the suspension through tripan blue method and NAD(P)H fluorescence changes in liver tissue during the ablation. The results showed that isolated hepatocytes exhibited with high viability (80%)... [to full text]

Improved sequencing technologies have created an explosion of sequence information that is analyzed and proteins are annotated automatically. Annotations are made based on similarity scores to previously annotated sequences, so one misannotation is propagated throughout databases and the number of misannotated proteins grows with the number of sequenced genomes. A systematic approach to correctly identify the function of proteins in the amidohydrolase superfamily is described in this work using Clusters of Orthologous Groups of proteins as defined by NCBI. The focus of this work is COG1816, which contains proteins annotated, often incorrectly, as adenosine deaminase enzymes. Sequence similarity networks were used to evaluate the relationship between proteins. Proteins previously annotated as adenosine deaminases: Pa0148 (Pseudomonas aeruginosa PAO1), AAur_1117 (Arthrobacter aurescens TC1), Sgx9403e and Sgx9403g, were purified and their substrate profiles revealed that adenine and not adenosine was a substrate for these enzymes. All of these proteins will deaminate adenine with values of kcat/Km that exceed 105 M-1s-1. A small group of enzymes similar to Pa0148 was discovered to catalyze the hydrolysis of N-6-substituted adenine derivatives, several of which are cytokinins, a common type of plant hormone. Patl2390, from Pseudoalteromonas atlantica T6c, was shown to hydrolytically deaminate N-6-isopentenyladenine to hypoxanthine and isopentenylamine with a kcat/Km of 1.2 x 107 M^-1 s^-1. This enzyme does not catalyze the deamination of adenine or adenosine. Two small groups of proteins from COG1816 were found to have 6-aminodeoxyfutalosine as their true substrate. This function is shared with 2 small groups of proteins closely related to guanine and cytosine deaminase from COG0402. The deamination of 6-aminofutalosine is part of the alternative menaquinone biosynthetic pathway that involves the formation of futalosine. 6-Aminofutalosine is deaminated with a catalytic effeciency of 105 M-1s-1 or greater, Km’s of 0.9 to 6.0 µM and kcat’s of 1.2 to 8.6 s-1. Another group of proteins was shown to deaminate cyclic- 3’, 5’ -adenosine monophosphate (cAMP) to produce cyclic-3’, 5’-inosine monophosphate, but will not deaminate adenosine, adenine or adenosine monophosphate. This protein was cloned from a human pathogen, Leptospira interrogans. Deamination may function in regulating the signaling activities of cAMP.