Poly(ADP-ribose) polymerase-1 (PARP-1) is an abundant nuclear protein that catalyzes the cleavage of NAD⁺ into nicotinamide and ADP-ribose moiety, the latter of which may be covalently attached as a branched polymer of poly(ADP-ribose) to PARP-1 itself (automodification) or to other nuclear acceptor proteins (transmodification). PARP-1 plays pivotal roles in many fundamental biological processes, including DNA repair, gene expression, cell death and cell cycle regulation. The multiple functions of PARP-1 in various cellular events correlate well to its roles in carcinogenesis, inflammatory response, neural function, and aging. PARP-1 has a modular organization comprising six independent domains (domain A-F). Each domain has its own characteristic function in PARP-1 enzymatic catalysis. In this dissertation, the solution structure of domain C was determined by multi-dimensional NMR spectroscopy. To complement the structural results, the requirement of domain C for PARP-1 catalysis was demonstrated using activity assays. This structure-function relationship study will help to unveil the mechanism of the PARP-1 reaction, and should provide valuable information for the design of more potent and selective PARP-1 inhibitors. The determination of poly(ADP-ribosyl)ation sites is critical for understanding the biological roles of this modification. However, the identification of poly(ADPribosyl)ation sites has countered some daunting technical limitations due to the difficulties resulting from the heterogenous nature of this modification. In this dissertation, a methodology based on mass spectrometry is developed and used to identify ADP-ribosylation sites within the automodification domain (domain D) of PARP-1. Using this method, we were able to unambiguously localize three ADPribosylation sites on domain D. This method can be readily applied to study the transmodification of other substrates as well as PARP-1 automodification. As many as seventeen PARP homologues exist in the human proteome. The functional redundancy of the multiple PARP proteins has complicated the analysis of mammalian PARP-1 function in vivo. We have probed the biological roles of PARP-1 using an artificial PARP-1 pathway in yeast, an organism lacking the endogenous PARP-1. Our data suggest the heterologously expressed human PARP-1 in yeast retains some similar functions as it does in mammalian cells. Furthermore, a new function of PARP-1 in ribosome biogenesis was proposed. / text

Phosphate esters and their hydrolysis reactions underpin many of the most important reactions in biology and have therefore been the focus of continued research. In this thesis, a range of theoretical studies on two phosphate ester hydrolysis reactions is presented. Particular attention is paid to the role of solvent in these reactions. The first reaction studied is the hydrolysis of dimethyl phosphate. A study using density functional theory examines three possible mechanisms for this reaction in the gas phase and the presence of solvent is also considered through the use of reaction field methods. The base-catalysed mechanism for this reaction receives further attention and the reaction energy profile in solution is adiabatically mapped using two different hybrid QM/MM potentials. The use of a QM/MM potential facilitates an atomistic representation of the solvent. Another study determines the potential of mean force for this reaction by simulating the reaction using QM/MM molecular dynamics simulations in conjunction with umbrella sampling methods. Both QM/MM studies demonstrate that, in solution, the rate-determining step for the base-catalysed reaction is the cleavage of the bond between the phosphorous and the leaving group. The QM/MM studies also established that the reaction proceeds via the formation of a short-lived pentacoordinated intermediate species. The second reaction studied was the base-catalysed hydrolysis of methyl ribose phosphate, a realistic model of the nonenzymatic hydrolysis of RNA. Since the hydrolysis of thio-substituted analogues of RNA have been the study of many experimental studies probing the mechanism of RNA hydrolysis, theoretical studies of the hydrolysis of two thio analogues of methyl ribose phosphate are also presented. The results of these studies provide valuable insight into the mechanism of RNA hydrolysis and concludes that the cleavage of P-O5' bond corresponds to the reaction transition state.

Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1959. / Typescript. Abstracted in Dissertation abstracts, v. 19 (1959) no. 12, p. 3105. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 152-159).

Thèse (Ph. D.) -- Université Laval, 1998. / Bibliogr.: f. 195-232. Publié aussi en version électronique.

Thèse (M.Sc.) -- Universoté Laval, 1997. / Bibliogr.: f. 79-85. Publié aussi en version électronique.

NÓBREGA, Raphael Batista da. Estruturas cristalográficas da lectina de canavalia brasiliensis complexadas com adenina e ribose: analise estrutural e perspectivas. 2016. 100 f. Tese (Doutorado em Bioquímica)-Universidade Federal do Ceará, Fortaleza, 2017. / Submitted by Coordenação PGBioquímica (pg@bioquimica.ufc.br) on 2017-08-11T17:17:13Z No. of bitstreams: 1 2016_tese_rbdanobrega.pdf: 1747142 bytes, checksum: 2fc1ddf9766df7742629554dc08e08d0 (MD5) / Approved for entry into archive by Jairo Viana (jairo@ufc.br) on 2017-08-22T21:09:24Z (GMT) No. of bitstreams: 1 2016_tese_rbdanobrega.pdf: 1747142 bytes, checksum: 2fc1ddf9766df7742629554dc08e08d0 (MD5) / Made available in DSpace on 2017-08-22T21:09:24Z (GMT). No. of bitstreams: 1 2016_tese_rbdanobrega.pdf: 1747142 bytes, checksum: 2fc1ddf9766df7742629554dc08e08d0 (MD5) Previous issue date: 2016 / Legume lectins (e.g ConA) are the most studied plant lectin family. The physiological and biological activities attribute to them, such as plant defense and antidepressant function, take into account their interactions with mono- and oligosaccharides in a specific and reversible manner. However, several studies show that these proteins can bind other biomolecules, such as hydrophobic compounds (e.g. adenine and indole acetic acid) and non protein amino acids (e.g. α-aminobutyric acid, AABA), although the structure-function relationship of these interactions remained poorly understood. In this study, we described two crystallographic structures of ConBr lectin isolated from the seeds of C. brasiliensis, complexed with two different ligands: a complex of the lectin with β-D-ribofuranose and another with adenine, both compounds found in the Carbohydrate-Recognition Domain (CRD). Based on the location of these binders, it is suggested by the docking ConBr can bind to adenosine. In addition, this study shows that AABA can take different provisions in its binding site. Taken together, these results reveal new insights into the physiological and biological activities legume lectins. / A família de lectinas vegetais mais estudadas é a das plantas leguminosas como a Concanavalina A (ConA) – Canavalia ensiformes. As atividades fisiológicas e biológicas atribuídas, tais como defesa da planta e ação antidepressiva, leva em consideração as suas interações com mono e oligossacarídeos de uma maneira específica e reversível. Embora lectinas da subtribo Diocleinae, como a ConA, sejam consideradas específicas para glicose e manose, estudos comparativos mostram que lectinas de diferentes espécies apresentam desempenhos diferenciados frente a um determinado modelo de atividade biológica, algo que parece estar relacionado à arquitetura do Domínio de Reconhecimento a Carboidrato (CRD) e à capacidade (ou não) de ligação a determinados mono- e oligossacarídeos. Além disso, tais atividades parecem não depender apenas da interação com carboidratos, haja vista que diversos estudos mostram que estas proteínas podem se ligar a outras biomoléculas, como compostos hidrofóbicos (a exemplo de adenina e ácido indolacético) e aminoácidos não protéicos (a exemplo do ácido α-aminobutírico – AABA). Neste trabalho, foram descritas duas estruturas cristalográficas da lectina ConBr, isolada de sementes da Canavalia brasiliensis (feijão-bravo-do-Ceará), complexada com dois diferentes ligantes: um complexo da lectina com a β-D-ribofuranose e outro com a adenina, ambos compostos localizados no CRD. Baseado na localização desses ligantes, sugere-se, por Docking que a ConBr pode se ligar à adenosina. Além disso, esse estudo mostra que o AABA pode assumir diferentes disposições em seu sítio de ligação. Tomados em conjunto, estes resultados revelam novas perspectivas para as atividades fisiológicas e biológicas de lectinas de leguminosas.

Changes in the synthesis and activity of matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) are associated with myocardial remodeling. Here we measured the expression and activity of MMPs and TIMPs, and tested the hypothesis that increased MMP activity plays a proapoptotic role in β-adrenergic receptor (β-AR)-stimulated apoptosis of adult rat ventricular myocytes (ARVMs). β-AR stimulation (isoproterenol, 24 h) increased mRNA levels of MMP-2 and TIMP-1 while it decreased TIMP-2 mRNA levels as analyzed by real-time PCR. Western blot analysis, immunocytochemical analysis, in-gel zymography, and MMP-2 activity assay confirmed β-AR-stimulated increases in MMP-2 protein-levels and activity. Inhibition of MMPs using GM-6001 (a broad-spectrum inhibitor of MMPs), SB3CT (inhibitor of MMP-2), and purified TIMP-2 inhibited β-AR-stimulated apoptosis as determined by TdT-mediated dUTP nick end labeling staining. Treatment with active MMP-2 alone increased the number of apoptotic cells. This increase in MMP-2-mediated apoptosis was inhibited by GM-6001 and SB3CT pretreatment. Coimmunoprecipitation studies indicated increased physical association of MMP-2 with β1-integrins after β-AR stimulation. Inhibition of MMP-2 using SB3CT or stimulation of β1-integrin signaling using laminin inhibited the increased association of MMP-2 with β1- integrins. β-AR stimulation increased poly-ADP-ribose-polymerase cleavage, which was inhibited by inhibition of MMP-2. These data suggest the following: 1) β-AR stimulation increases MMP-2 expression and activity and inhibits TIMP-2 expression; 2) inhibition of MMPs, most likely MMP-2, inhibits β-AR-stimulated apoptosis; and 3) the apoptotic effects of MMP-2 may be mediated, at least in part, via its interaction with β1 integrins and poly-ADP-ribose-polymerase cleavage.

Enzymatic activity has been identified in cultured cells which catalyzes the removal of intact mono(ADP-ribose) residues which are bound to protein at arginine. Other activities have been detected which catalyze the removal of ADP-ribose via the sequential removal of AMP and ribose-5-phosphate.

Les dommages directs induits à l'ADN par les radiations ultraviolettes (UV) sont éliminés grâce à la réparation par excision de nucleotides (NER). La poly(ADP-ribose) polymerase-1 (PARP-1) est une enzyme impliquée dans différentes voies de réparation de l'ADN. Notre laboratoire a montré que la PARP-1 était activée par les dommages directs dus aux UV et que son absence retarde significativement la réparation de ces dommages dans un gène rapporteur viral. Le but de ce projet était de déterminer si la PARP-1 affectait le NER de l'ADN génomique des cellules eucaryotes. Nous avons observé un délai dans la réparation des dommages directs à l'ADN causés par les UV dans les cellules eucaryotes n'exprimant pas la PARP-1. De plus, la PARP-1 immunoprécipite in vivo avec des protéines impliquées dans la phase de reconnaissance de ces dommages. Nos résultats montrent donc que la PARP-1 joue aussi un rôle dans le NER.