Les glycosyltransferases sont les enzymes responsables de la synthèse d'oligosaccharides, de polysaccharides et de glycoconjugués. Elles catalysent le transfert d'un saccharide à partir d'un substrat donneur, en général un nucléotide sucre, vers un substrat accepteur. Le mécanisme de réaction des glycosyltransférases peut avoir lieu avec une inversion ou une rétention de l'anomérie de liaison du sucre transféré. De nombreuses incertitudes subsistent au sujet du mécanisme des glycosyltransférases transférant avec rétention de l'anomérie. L'élucidation de ce mécanisme aiderait à la conception d'inhibiteurs ciblés afin de soigner des maladies allant des infections virales et bactériennes au cancer. De nombreuses protéines sont actives à l'état cristallin, ce qui fait de la cristallographie aus rayons X un outil de choix pour étudier le mécanisme d'enzymes. La « cristallographie cinétique » est un terme qui regroupe l'ensemble des techniques permettant d'initier une activité biologique in crystallo pour générer et piéger une quantité significative d'un état intermédiaire de réaction, afin de résoudre sa structure par cristallogrpahie aux rayons X. Le but de mon projet était d'étudier le mécanisme catalytique d'une glycosyltransférase transférant avec rétention de l'anomérie, par cristallographie cinétique. De cette façon, j'ai étudié une enzyme du groupe sanguin responsable du transfert d'un galactose à partir d'UDP-Gal vers l'antigène H. J'ai étudié les effets de la cryoprotection sur la structure de la protéine, et j'ai effectué les études préalables nécessaires à l'application de deux techniques issues de la cristallographie cinétique à l'étude de ces enzymes : « Déclencher-tremper »et « Tremper-déclencher ». / Glycosyltransferases are a large class of enzymes responsible for the synthesis of oligosaccharides, polysaccharides and glycoconjugates. They catalyze the transfer of a saccharide from a donor substrate, usually a nucleotide sugar, to an acceptor. Glycosyltransferase reactions can occur with either retention or inversion of the anomeric configuration of the transferred sugar. Many uncertainties remain concerning the catalytic mechanisms of retaining glycosyltransferases even though the elucidation of this mechanism would help in the rationale design of potent inhibitors to treat diseases ranging from viral and bacterial infections to cancer. Many proteins function in the crystalline state which makes X-ray crystallography a potential powerful tool for studying enzymatic mechanisms. ‘Kinetic crystallography' is a term coined to name the ensemble of techniques to initiate a biological turnover in crystallo in order to generate and trap a significant amount of a given intermediate reaction state, and then solve its X-ray structure. The aim of my project was to investigate the catalytic mechanism of a retaining glycosyltransferase, by kinetic crystallography methods. In this way, I studied a human blood group synthase responsible for the transfer of a galactose from UDP-Gal to the H antigen. I investigated the effects of the cryoprotectant on the structure of the protein, and I made preliminary studies to apply two kinetic crystallography techniques to the enzyme: freeze-trigger and trigger freeze experiments.

Les NO-synthases sont des flavohémoprotéines responsables de la production de NO• chez les mammifères (mNOS). Elles se composent d’un domaine réductase, qui lie les cofacteurs FMN et FAD et le co-substrat NADPH, et d’un domaine oxygénase qui lie l’hème, le substrat L-arginine et le cofacteur redox essentiel tétrahydrobioptérine H4B. Ces quinze dernières années, plusieurs NOS d’origine bactérienne (bacNOS) ont été caractérisées et il a été montré qu’elles étaient semblables au domaine oxygénase de leurs homologues mammifères. Il existe cependant des différences significatives entre mNOS et bacNOS, la plus importante étant l’absence de domaine réductase chez les NOS d’origine bactérienne. De plus, le(s) mécanisme(s) catalytique(s) de ces dernières ainsi que leur(s) fonction(s) in vivo restent actuellement à déterminer. Plusieurs études publiées montrent que la substitution Val/Ile à proximité du site actif, conservée entre mNOS et bacNOS, est partiellement responsable des différences observées au niveau catalytique entre ces deux groupes. Dans le cadre de cette thèse, j’ai utilisé les spectroscopies d’absorption UV-visible et RPE, ainsi que des techniques de cinétiques rapides comme le stopped-flow et le freeze-quench, pour caractériser les deux mutants complémentaires bsNOS I224V et iNOS V346I afin de mieux comprendre l’influence de cette mutation. J’ai ainsi montré qu’il existait des différences fondamentales entre bacNOS et mNOS qui ne sont pas liées à la substitution Val/Ile et que ces deux familles d’enzymes suivent probablement des mécanismes catalytiques différents pour l’étape d’oxydation du NOHA. Ces résultats sont confirmés par l’étude de la NOS thermostable issue de Geobacillus stearothermophilus. Lorsqu’on s’intéresse au fonctionnement in vivo des bacNOS, se pose également la question de la nature du cofacteur redox puisque de nombreuses bactéries possédant une NOS n’ont pas la machinerie nécessaire à la synthèse de H4B ; c’est par exemple le cas de Deinococcus radiodurans pour qui l’utilisation du tétrahydrofolate H4F a été proposée. J’ai donc étudié et caractérisé deiNOS de manière approfondie en présence de différents cofacteurs afin de mieux comprendre leurs rôles redox et structural. Ceci a notamment permis de proposer un mécanisme catalytique légèrement différent de celui suivi par bsNOS ce qui suggère que ces enzymes pourraient avoir différentes fonctions in vivo. Enfin, la première caractérisation in vitro d’une NOS de plante, issue de l’algue verte unicellulaire Ostreococcus tauri est présentée dans ce manuscrit. Les résultats suggèrent que celle-ci aurait effectivement une activité NO-synthase in vivo. / NO-synthases are flavohemoproteins responsible for NO• production in mammals (mNOS). They are comprised of a reductase domain, that binds FMN, FAD and NADPH, and an oxygenase domain, that binds heme, the substrate L-arginine and the essential redox active tetrahydrobiopterin cofactor H4B. In the last 15 years, several bacterial NOS (bacNOS) have been characterized and shown to resemble the oxygenase domain of their mammalian counterpart. However bacNOS exhibit significant differences from mNOS, the most striking one being the lack of a reductase domain, and their catalytic mechanism(s) and in vivo function(s) are currently poorly understood. Previously published studies suggest that a conserved Val to Ile substitution near the active site is at least partially responsible for the differences in catalysis observed between mNOS and bacNOS. During my PhD I characterized the mutants on this particular position, bsNOS I224V and iNOS V346I, using UV-visible and EPR spectroscopies as well as rapid-kinetic technics such as stopped-flow spectrophotometry and rapid-freeze quench, to better understand the influence of this substitution. This showed that mammalian and bacterial enzymes are fundamentally different and probably follow different mechanisms for NOHA oxidation. Results from studying the thermostable NOS from Geobacillus stearothermophilus further confirm these observations. Another important issue regarding bacNOS functioning in vivo concerns the nature of the redox active cofactor since many NOS-containing bacteria do not have the machinery for H4B biosynthesis; this is for instance the case of Deinococcus radiodurans for which the use of tetrahydrofolate H4F has been proposed. I therefore performed an extensive characterization of deiNOS in the presence of various cofactors to better understand their redox and structural roles. This allowed proposing a slightly different mechanism for deiNOS, compared to bsNOS, suggesting different function(s) in vivo. Finally, the first in vitro characterization of a plant NOS from the unicellular green alga Ostreococcus tauri is reported in this manuscript. The results suggest that this NOS-like protein is indeed a genuine NO-synthase.

No description available.

Microbial degradation of aromatic hydrocarbons is imperative for maintaining the global carbon cycle and removing potentially toxic aromatic xenobiotics. This thesis focuses on the characterization of a pyruvate-specific class II aldolase (BphI) and acetaldehyde dehydrogenase (BphJ), the final two enzymes of the bph meta-cleavage pathway in Burkholderia xenovorans LB400. This pathway is responsible for the degradation of the industrial pollutant polychlorinated biphenyls (PCB) and therefore mechanistic characterization of these enzymes can be applied to improve pollutant degradation. BphI catalyzes the aldol cleavage of 4-hydroxy-2-oxoacids to pyruvate and an aldehyde while BphJ transforms aldehydes to acyl-CoA, using NAD+ and CoASH as cofactors. Size-exclusion chromatography was used to determine that the oligomeric unit of the BphI-BphJ complex is a heterotetramer. The aldolase BphI was shown to exhibit a compulsory order mechanism and utilize 4-hydroxy-2-oxoacids with an S configuration at C4. The generation of BphI active site variants allowed for the proposal of a catalytic mechanism and a greater understanding as to how stereospecificity occurs. Using steady-state kinetic assays, Arg-16 was demonstrated to be essential for catalysis. Molecular modeling of the substrate and pH dependency (wild-type pKa of ~7, lost in H20A and H20S variants) were used to identify His-20 as the catalytic base. Tyr-290 was originally proposed to be the catalytic acid. However, this was refuted as a Tyr-290 (Y290F) variant did not affect the catalytic efficiency of the enzyme. Instead, the variant was observed to exhibit a loss of stereochemical control. From the crystal structure of an orthologous aldolase-dehydrogenase complex, solvent isotope effect studies, and a proton inventory, a water molecule was implicated as the catalytic acid. Based on their position within the crystal structure, Leu-87 and Leu-89 were implicated in substrate specificity. Replacement of Leu-89 with alanine effectively increased the length of the active site, allowing for the accommodation of longer aldehyde substrates. In contrast, Leu-87 was responsible for hydrophobic stabilization of the C4-methyl of the substrate. Double variants L87N;Y290F and L87W;Y290F were constructed to enable the binding of 4(R)-hydroxy-2-oxoacids. Polarimetric analysis confirmed that the double variants were able to synthesize 4-hydroxy-2-oxoacids of up to 8 carbons in lengths, which were of the opposite stereoisomer to those produced by the wild-type enzyme. Cys-131 was identified as the catalytic thiol that forms an acyl-enzyme intermediate in the dehydrogenase, BphJ. This enzyme was shown to exhibit similar specificity constants for acetaldehyde and propionaldehyde and utilize aliphatic aldehydes from two to five carbons in length as substrates. The enzyme was able to use either NAD+ or NADP+ as the cofactor. Finally, we demonstrated that aldehydes produced in the aldolase reaction are not released into the bulk solvent but are channeled directly to the dehydrogenase, providing the first biochemical determination of substrate channeling in any aldolase-dehydrogenase complex. / Chapter 3 - Reprinted (adapted) with permission from Baker, P., Carere, J., and Seah, S. Y. (2011) Probing the Molecular Basis of Substrate Specificity, Stereospecificity, and Catalysis in the Class II Pyruvate Aldolase, BphI, Biochemistry 50: 3559-3569. Copyright (2011) American Chemical Society. Chapter 4 - Reprinted (adapted) with permission from Baker, P., and Seah, S. Y. (2012) Rational design of stereoselectivity in the class II pyruvate aldolase BphI, J Am Chem Soc 134: 507-513. Copyright (2012) American Chemical Society. Chapter 6 - Reprinted (adapted) with permission from Baker, P., Hillis, C., Carere, J., and Seah, S. Y. (2012) Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes, Biochemistry 51: 1942-1952. Copyright (2012) American Chemical Society. / National Science and Engineering Research Council of Canada (NSERC), Ontario Graduate Scholarship in Science and Technology

No description available.

Les Méthionine sulfoxyde réductases (Msr) catalysent la réduction spécifique des méthionine sulfoxydes (Met-O) en méthionines (Met). Elles sont impliquées dans la résistance des cellules à un stress oxydant et dans la virulence des bactéries pathogènes du genre Neisseria. Cette famille d'enzyme se compose de trois classes, les MsrA et B, structuralement distinctes, et présentant une stéréosléctivité respectivement pour l'isomère S et R de la fonction sulfoxyde du substrat. Une troisième classe, découverte récemment, et appelée fRMsr, catalyse la réduction spécifique de la forme libre de l'isomère R de la fonction sulfoxyde. La fRMsr appartient à la famille des domaines GAF, généralement impliqués dans la signalisation cellulaire, et les fRMsr représentent le premier domaine GAF présentant une activité enzymatique. Les études réalisées au cours de ma thèse sur la fRMsr de Neisseria meningitidis ont permis de montrer que : 1) fRMsr de N. meningitidis présente un mécanisme catalytique identique à MsrA/B avec la formation d'au moins un pont disulfure intramoléculaire Cys84-Cys118 réduit par la thiorédoxine (Trx) ; 2) La Cys118 est le résidu catalytique sur lequel l'intermédiaire acide sulfénique doit se former ; 3) L'étape réductase est l'étape cinétiquement déterminante du mécanisme à deux étapes conduisant à la formation du pont disulfure Cys84-Cys118. La combinaison de l'analyse des résultats cinétiques, et de la structure tridimensionnelle de la fRMsr de N. meningitidis en complexe avec le substrat ont permis de montrer : 1) L'existence d'un site de reconnaissance oxyanion impliqué dans la stabilisation de la fonction carboxylate ; 2) Un rôle de la fonction carboxylate du résidu Asp143 dans la catalyse de l'étape réductase ; 3) Le résidu Glu125 est impliqué dans la reconnaissance et/ou le positionnement du substrat Met-O probablement via la stabilisation du groupement NH3+ ; 4) Un rôle du résidu Asp141 dans le positionnement des résidus Asp143 et Glu125 ; 5) le noyau indole du Trp62 est impliqué dans la stabilisation du groupe méthyle-[epsilon] / Methionine sulfoxide reductases (Msr) catalyze the specific reduction of methionine sulfoxides (Met-O) into methionine (Met). They are involved in cell defences against oxidative stress and virulence of pathogenic bacteria of Neisseria genius. This family of enzymes consists of three classes, MsrA and MsrB, structurally-unrelated, Specific for the S and the R epimer of the sulfoxide function of the substrate, respectively. A third class, recently discovered and called fRMsr, selectively reduce the free form of the R epimer of the sulfoxide function. The fRMsr belongs to the family of GAF domains, they are usually involved in cell signaling, and fRMsr represent the first GAF domain to show enzymatic activity. The studies of the Neisseria meningitidis fRMsr have shown that: 1) The Neisseria meningitidis fRMsr have a identical catalytic mechanism to MsrA and MsrB with the formation of at least one intramolecular disulfide bond, Cys84-Cys118 reduced by thioredoxin (Trx) ; 2) The Cys118 is demonstrated to be the catalytic Cys on which a sulfenic acid is formed ; 3) The Reductase step is the rate determining step of the mechanism leading to the formation of the disulfide bond Cys84-Cys118. The combination of the biochemical and kinetics data, and the examination of the 3D structure of the N. meningitidis fRMsr in complex with its substrate shown: 1) an oxyanion hole involved in the accommodation of the carboxylate group ; 2) the carboxylate group of the Asp143 residue involved in the catalysis of step reductase, and 3) The Glu125 residue involved in the recognition and/or positioning of the Met-O probably by the stabilization of the NH3+; 4) the Asp141 residue involved in the positioning of Asp143 and Glu125 residues ; 5) the indole ring of the Trp62 residue involved in stabilizing of the epsilon-methyl group

A enzima Glucosamina-6-fosfato desaminase (GlcN6P desaminase) é envolvida na conversão reversível da D-glucosamina-6-fosfato (GlcN6P) em Fru6P e amônia, como parte do caminho metabólico de aminoaçúcares como fonte de energia celular. A enzima hexamérica (peso mol. 178200) exibe uma cooperatividade homotrópica intensa em direção à GlcN6P a qual é modulada alostericamente pelo ativador N-acetil-D-glucosamina 6-fosfato (GlcNAc6P). A GlcN6P desaminase foi cristalizada no grupo espacial R32, com parâmetros de rede a = b = 125.9 &#197 e c = 223.2 &#197 e um conjunto de dados à 2.1 &#197 de resolução foi coletado usando radiação de luz síncrotron (Horjales et ai., 1992). A procura no banco de dados de seqüências OWL não mostrou homologia significante com qualquer outra família de proteína, desta maneira a determinação da estrutura foi feita pela técnica de substituição isomórfica múltipla (MIR) a partir de dois derivados, um composto de platina, o K2PtCl4 e um complexo de mercúrio, o ácido mersálico. O mapa MIR a 3 &#197 de resolução mostrou contornos claros e utilizando técnicas de nivelamento de solvente (solvent flattening) estendeu-se as fases até 2.5 &#197. A enzima cristaliza-se com dois monômeros na unidade assimétrica. A densidade eletrônica final foi interpretada com o auxílio do programa gráfico \'O\', sendo possível determinar sem ambigüidade 230 dos 266 resíduos de cada monômero; a partir daí foram usados subseqüentes mapas de Fourier diferença para a localização de todos os outros resíduos. O refinamento do modelo foi feito utilizando o programa X-PLOR (Brünger, 1993), usando a rotina simulated annealing, obtendo o fator R final de 17.4% com 348 moléculas de água e quatro íons inorgânicos de fosfato. O enovelamento do monômero tem uma estrutura do tipo &#945/&#946 com uma folha-&#946 pregueada paralela central com sete fitas com topologia 4x, 1x, 1x, -3x, -1x, -1x, envolvida por ambos os lados por oito hélices-&#945 e uma hélice 310 com duas voltas. A sexta fita da folha-&#946 central tem um prolongamento no C-terminal que faz parte de uma segunda folha-&#946 antiparalela de três fitas com topologia 2, -1. O hexâmero tem uma simetria local 32, com dois trímeros empacotados frente-a-frente com uma rotação relativa de 15&#176 em tomo do eixo de ordem 3 e ligados por pontes salinas e algumas interações hidrofóbicas em tomo do eixo não cristalográfico de ordem 2. As moléculas de cada trímero formam um contato não usual de três resíduos Cis 219 próximo ao eixo de ordem três. Os complexos com ativador alostérico (GlcNAc6P) e inibidor competitivo (2-desoxi 2-amino glucitol 6-fosfato) foram co-cristalizados isomorficamente com a estrutura nativa. Os mapas Fourier diferença mostram claramente densidades para os ligantes, definindo sem ambigüidade o sítio ativo e alostérico. O refinamento dos complexos produziu a mesma conformação da proteína nativa, na margem de erro experimental. Os sítios alostéricos (seis) estão localizados na interface adjacente dos monômeros de cada trímero e os sítios ativos (ou catalíticos) no lado externo de cada monômero, no C-terminal da folha-&#946 central. O monômero tem uma topologia com enovelamento similar a um domínio de ligação de NAD, excluindo os segmentos de aminoácidos 1-35, 145-188 e 243-266. As estruturas dos complexos e da nativa estão em um estado alostérico R em concordância com o modelo MWC para um sistema do tipo K (Monod et al, 1965). Um mecanismo alostérico similar ao da GlcN6P desaminase é encontrado na enzima fosfofrutoquinase (Evans, 1981). Um mecanismo catalítico é proposto para a reação de isomerisação-desaminação da enzima GlcN6P desaminase a partir do mecanismo geral para aldose-cetona isomerases. / The enzyme Glucosamine-6-phosphate deaminase (GlcN6P deaminase) is involved in the reversible conversion of D-glucosamine-6-phosphate (GlcN6P) into Fru6P and ammonia. The hexameric enzyme (mol.wt.=178200) exhibits an intense homotropic co-operativity towards GlcN6P which is allosterically modulated by the activator N-acetyl-D-glucosamine 6-phosphate (GlcNAc6P). The GlcN6P deaminase was crystallized in space group R32, with cell parameters a=b= 125.9 &#197 and c = 223.2 &#197 and a native dataset was collected to 2.1 &#197 resolution at a synchrotron source (Horjales et al, 1992). A search of the OWL sequences database has shown no significant homology with any other known protein family. Therefore, the structure determination will have to be achieved through the Multiple Isomorphous Replacement technique from two isomorphous derivatives, a platinum compound K2PtCl4 and a mercury complex, mersalyl acid. The MIR map at 3 &#197 resolution showed clear molecular boundaries and solvent flattening techniques (Wang, 1985) were used to extend the phase set to 2.5 &#197. The final electron density map was interpreted with the aid of the graphic program \'O\'. The enzyme crystallizes with a dimmer in the asymmetric unit and 230 out of the total 266 residues of each crystallographically independent monomer could be unambiguously identified in the map. The remaining residues were located after subsequent difference Fourier maps. The refinement was made with program X-PLOR (Brunger, 1993), using the simulated annealing routine, obtained R=17.4 % with 348 water molecules and four inorganic phosphate ions. The monomer fold shows an &#945/&#946 structure with a central 7-stranded &#946-sheet with topology 4x, 1x, 1x, -3x, -1x, -1x, surrounded on both sides by eight &#945-helices and 2-turn 310 -helix. The sixth strand of the central &#946-sheet is common to a second 3-stranded anti-parallel &#946-sheet with topology 2, -1. The hexamer has local 32 symmetry, with two trimmers packed in a face-to-face arrangement with a relative rotation of 15&#176 around the 3-fold axis, and linked together by salt-bridge and some hydrophobic contacts. The molecules of each trimmer have extensive contacts and show an unusual feature of the three Cys219 residues closely clustered around the 3-fold axis. The complexes with allosteric activator (GlcNAc6P) and inhibitor (2-deoxy-2-amino glucitol 6-phosphate) were co-crystallized isomorphously with the native structure. The difference Fourier maps shows clear density for the ligands, unambiguously defining the active and allosteric sites. The complexes refinement produced the same conformation of the native, within experimental error. The allosteric sites are located at the interfaces of adjacent monomers from each trimer and the active sites (or catalytic) lie at the external side of each monomer, at the C-terminal end of the central parallel &#946-sheet. The monomer has a similar folding topology as a typical NAD binding domain, excluding the segments of aminoacids 135, 145-188 and 243-266. The native and complexes structures are at the allosteric state R concerted with MWC model for a K-system (Monod et al, 1965). A similar allosteric mechanism is found in the enzyme phosphofructokinase (Evans, 1981). A catalytic mechanism is proposed for the isomerisation-deamination reaction of the enzyme from general mechanism for aldo-keto isomerases.

In light of its rapidly growing energy demand, human society has an urgent need to become much more strongly reliant on renewable and sustainable energy carriers. Molecular hydrogen made from water with solar energy could provide an ideal case. The development of inexpensive, robust and rare element free catalysts is crucial for this technology to succeed. Enzymes in nature can give us ideas about what such catalysts could look like, but for the directed adjustment of any natural or synthetic catalyst to the requirements of large scale catalysis, its capabilities and limitations need to be understood on the level of individual reaction steps. This thesis deals with kinetic and mechanistic investigations of photo- and electrocatalytic hydrogen production with natural and synthetic molecular catalysts. Photochemical hydrogen production can be achieved with both E. coli Hyd-2 [NiFe] hydrogenase and a synthetic dinuclear [FeFe] hydrogenase active site model by ruthenium polypyridyl photosensitization. The overall quantum yields are on the order of several percent. Transient UV-Vis absorption experiments reveal that these yields are strongly controlled by the competition of charge recombination reactions with catalysis. With the hydrogenase major electron losses occur at the stage of enzyme reduction by the reduced photosensitizer. In contrast, catalyst reduction is very efficient in case of the synthetic dinuclear active site model. Here, losses presumably occur at the stage of reduced catalyst intermediates. Moreover, the synthetic catalyst is prone to structural changes induced by competing ligands such as secondary amines or DMF, which lead to catalytically active, potentially mononuclear, species. Investigations of electrocatalytic hydrogen production with a mononuclear catalyst by cyclic voltammetry provide detailed kinetic and mechanistic information on the catalyst itself. By extension of existing theory, it is possible to distinguish between alternative catalytic pathways and to extract rate constants for individual steps of catalysis. The equilibrium constant for catalyst protonation can be determined, and limits can be set on both the protonation and deprotonation rate constant. Hydrogen bond formation likely involves two catalyst molecules, and even the second order rate constant characterizing hydrogen bond formation and/or release can be determined.

Nitric oxide (NO) overproduction is correlated with numerous human diseases, such as arthritis, asthma, diabetes, inflammation and septic shock. The enzyme activities of both NO synthase (NOS) and dimethylarginine dimethylaminohydrolase-1 (DDAH-1) promote NO production. DDAH-1 mainly colocalizes in the same tissues as the neuronal isoform of NOS and catabolizes the endogenously-produced competitive inhibitors of NOS, N[omega]-monomethyl-L-arginine (NMMA) and asymmetric N[omega], N[omega]-dimethyl-L-arginine (ADMA). Inhibition of DDAH-1 leads to elevated concentrations of NMMA and ADMA, which subsequently inhibit NOS. To better understand DDAH-1, I first characterized the catalytic mechanism of human DDAH-1, where Cys274, His173, Asp79 and Asp127 form a catalytic center. Particularly, Cys274 is an active site nucleophile and His173 plays a dual role in acid/base catalysis. I also studied an unusual mechanism for covalent inhibition of DDAH-1 by S-nitroso-L-homocysteine (HcyNO), where an N-thiosulfoximide adduct is formed at Cys274. Using a combination of site directed mutagenesis and mass spectrometry, we found that many residues that participate in catalysis also participate in HcyNO mediated inactivation. Following these studies, I then screened a small set of known NOS inhibitors as potential inhibitors of DDAH-1. The most potent of these, an alkylamidine, was selected as a scaffold for homologation. Stepwise lengthening of the alkyl substituent changes an NOS-selective inhibitor into a dual-targeted NOS/DDAH-1 inhibitor then into a DDAH-1 selective inhibitor, as seen in the inhibition constants of N5-(1-iminoethyl)-, N5-(1-iminopropyl)-, N5-(1-iminopentyl)- and N5-(1-iminohexyl)-L-ornithine for neuronal NOS (1.7, 3, 20, >1,900 [mu]M, respectively) and DDAH-1 (990, 52, 7.5, 110 [mu]M, respectively). X-ray crystal structures suggest that this selectivity is likely due to active site size differences. To rank the inhibitors' in vivo potency, we constructed a click-chemistry based activity probe to detect inhibition of DDAH-1 in live mammalian cell culture. In vivo IC50 values for representative alkylamidine based inhibitors were measured in living HEK293T cells. Future application of this probe will address the regulation of DDAH-1 activity in pathophysiological states. In summary, this work identifies a versatile scaffold for developing DDAH targeted inhibitors to control NO overproduction and provides useful biochemical tools to better understand the etiology of endothelial dysfunction. / text

A enzima Glucosamina-6-fosfato desaminase (GlcN6P desaminase) é envolvida na conversão reversível da D-glucosamina-6-fosfato (GlcN6P) em Fru6P e amônia, como parte do caminho metabólico de aminoaçúcares como fonte de energia celular. A enzima hexamérica (peso mol. 178200) exibe uma cooperatividade homotrópica intensa em direção à GlcN6P a qual é modulada alostericamente pelo ativador N-acetil-D-glucosamina 6-fosfato (GlcNAc6P). A GlcN6P desaminase foi cristalizada no grupo espacial R32, com parâmetros de rede a = b = 125.9 &#197 e c = 223.2 &#197 e um conjunto de dados à 2.1 &#197 de resolução foi coletado usando radiação de luz síncrotron (Horjales et ai., 1992). A procura no banco de dados de seqüências OWL não mostrou homologia significante com qualquer outra família de proteína, desta maneira a determinação da estrutura foi feita pela técnica de substituição isomórfica múltipla (MIR) a partir de dois derivados, um composto de platina, o K2PtCl4 e um complexo de mercúrio, o ácido mersálico. O mapa MIR a 3 &#197 de resolução mostrou contornos claros e utilizando técnicas de nivelamento de solvente (solvent flattening) estendeu-se as fases até 2.5 &#197. A enzima cristaliza-se com dois monômeros na unidade assimétrica. A densidade eletrônica final foi interpretada com o auxílio do programa gráfico \'O\', sendo possível determinar sem ambigüidade 230 dos 266 resíduos de cada monômero; a partir daí foram usados subseqüentes mapas de Fourier diferença para a localização de todos os outros resíduos. O refinamento do modelo foi feito utilizando o programa X-PLOR (Brünger, 1993), usando a rotina simulated annealing, obtendo o fator R final de 17.4% com 348 moléculas de água e quatro íons inorgânicos de fosfato. O enovelamento do monômero tem uma estrutura do tipo &#945/&#946 com uma folha-&#946 pregueada paralela central com sete fitas com topologia 4x, 1x, 1x, -3x, -1x, -1x, envolvida por ambos os lados por oito hélices-&#945 e uma hélice 310 com duas voltas. A sexta fita da folha-&#946 central tem um prolongamento no C-terminal que faz parte de uma segunda folha-&#946 antiparalela de três fitas com topologia 2, -1. O hexâmero tem uma simetria local 32, com dois trímeros empacotados frente-a-frente com uma rotação relativa de 15&#176 em tomo do eixo de ordem 3 e ligados por pontes salinas e algumas interações hidrofóbicas em tomo do eixo não cristalográfico de ordem 2. As moléculas de cada trímero formam um contato não usual de três resíduos Cis 219 próximo ao eixo de ordem três. Os complexos com ativador alostérico (GlcNAc6P) e inibidor competitivo (2-desoxi 2-amino glucitol 6-fosfato) foram co-cristalizados isomorficamente com a estrutura nativa. Os mapas Fourier diferença mostram claramente densidades para os ligantes, definindo sem ambigüidade o sítio ativo e alostérico. O refinamento dos complexos produziu a mesma conformação da proteína nativa, na margem de erro experimental. Os sítios alostéricos (seis) estão localizados na interface adjacente dos monômeros de cada trímero e os sítios ativos (ou catalíticos) no lado externo de cada monômero, no C-terminal da folha-&#946 central. O monômero tem uma topologia com enovelamento similar a um domínio de ligação de NAD, excluindo os segmentos de aminoácidos 1-35, 145-188 e 243-266. As estruturas dos complexos e da nativa estão em um estado alostérico R em concordância com o modelo MWC para um sistema do tipo K (Monod et al, 1965). Um mecanismo alostérico similar ao da GlcN6P desaminase é encontrado na enzima fosfofrutoquinase (Evans, 1981). Um mecanismo catalítico é proposto para a reação de isomerisação-desaminação da enzima GlcN6P desaminase a partir do mecanismo geral para aldose-cetona isomerases. / The enzyme Glucosamine-6-phosphate deaminase (GlcN6P deaminase) is involved in the reversible conversion of D-glucosamine-6-phosphate (GlcN6P) into Fru6P and ammonia. The hexameric enzyme (mol.wt.=178200) exhibits an intense homotropic co-operativity towards GlcN6P which is allosterically modulated by the activator N-acetyl-D-glucosamine 6-phosphate (GlcNAc6P). The GlcN6P deaminase was crystallized in space group R32, with cell parameters a=b= 125.9 &#197 and c = 223.2 &#197 and a native dataset was collected to 2.1 &#197 resolution at a synchrotron source (Horjales et al, 1992). A search of the OWL sequences database has shown no significant homology with any other known protein family. Therefore, the structure determination will have to be achieved through the Multiple Isomorphous Replacement technique from two isomorphous derivatives, a platinum compound K2PtCl4 and a mercury complex, mersalyl acid. The MIR map at 3 &#197 resolution showed clear molecular boundaries and solvent flattening techniques (Wang, 1985) were used to extend the phase set to 2.5 &#197. The final electron density map was interpreted with the aid of the graphic program \'O\'. The enzyme crystallizes with a dimmer in the asymmetric unit and 230 out of the total 266 residues of each crystallographically independent monomer could be unambiguously identified in the map. The remaining residues were located after subsequent difference Fourier maps. The refinement was made with program X-PLOR (Brunger, 1993), using the simulated annealing routine, obtained R=17.4 % with 348 water molecules and four inorganic phosphate ions. The monomer fold shows an &#945/&#946 structure with a central 7-stranded &#946-sheet with topology 4x, 1x, 1x, -3x, -1x, -1x, surrounded on both sides by eight &#945-helices and 2-turn 310 -helix. The sixth strand of the central &#946-sheet is common to a second 3-stranded anti-parallel &#946-sheet with topology 2, -1. The hexamer has local 32 symmetry, with two trimmers packed in a face-to-face arrangement with a relative rotation of 15&#176 around the 3-fold axis, and linked together by salt-bridge and some hydrophobic contacts. The molecules of each trimmer have extensive contacts and show an unusual feature of the three Cys219 residues closely clustered around the 3-fold axis. The complexes with allosteric activator (GlcNAc6P) and inhibitor (2-deoxy-2-amino glucitol 6-phosphate) were co-crystallized isomorphously with the native structure. The difference Fourier maps shows clear density for the ligands, unambiguously defining the active and allosteric sites. The complexes refinement produced the same conformation of the native, within experimental error. The allosteric sites are located at the interfaces of adjacent monomers from each trimer and the active sites (or catalytic) lie at the external side of each monomer, at the C-terminal end of the central parallel &#946-sheet. The monomer has a similar folding topology as a typical NAD binding domain, excluding the segments of aminoacids 135, 145-188 and 243-266. The native and complexes structures are at the allosteric state R concerted with MWC model for a K-system (Monod et al, 1965). A similar allosteric mechanism is found in the enzyme phosphofructokinase (Evans, 1981). A catalytic mechanism is proposed for the isomerisation-deamination reaction of the enzyme from general mechanism for aldo-keto isomerases.