The serine hydrolase (SH) enzyme superfamily is one of the largest and most diverse enzyme classes in eukaryotes and prokaryotes. The most virulent human malaria parasite Plasmodium falciparum has over 40 predicted serine hydrolases (SH). Prior investigation on a few of these have suggested their critical role in parasite biology. The majority of the SHs in P. falciparum have not been functionally characterized. Investigation of these uncharacterized SHs will provide new insights into essential features of parasite metabolism and possibly lead to new antimalarial targets. In this study, we have employed activity-based protein profiling (ABPP) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to functionally characterize SHs. In our effort to profile plasmodial SHs using ABPP, we have identified a human erythrocyte SH, acylpeptide hydrolase (APEH) in the developing parasites. This finding is the first report of internalization of host hydrolytic enzyme by the parasite. Treatment of parasites with an APEH specific triazole urea inhibitor, AA74-1, caused growth inhibition in parasites with poor potency in the first replication cycle, however, the potency dramatically increased in the second cycle. We show that this unique growth inhibition profile is due to the inability of AA74-1 to inhibit parasite-internalized APEH in vivo. These findings suggest that internalization of active APEH by the parasite is essential for parasite survival. Lipases catalyze the hydrolysis of ester bonds of lipid species such as neutral lipids and phospholipids. Although roles of lipases in propagation, as well as virulence in various organisms, have been acknowledged, in P. falciparum lipases remain understudied. We combined LC-MS/MS with the SH-directed ABPP to identify lipases of SH superfamily in P. falciparum. We have identified 16 plasmodial SHs with putative lipase activity. Bioinformatics analysis of our identified lipases is consistent with our findings. We have screened a panel of various classes of SH inhibitors in a competitive ABPP. A plasmodial putative lipase was potently and specifically inhibited by human monoacylglycerol lipase inhibitor. This inhibition profile suggests it as a monoacylglycerol lipase which plays a role in releasing fatty acids from neutral lipid. This finding shows that how inhibitor screening can aid in building hypotheses on biological roles of an enzyme. Altogether, in this dissertation, we have presented a robust strategy of identifying and functionally characterizing SHs in P. falciparum, which opens the door to the discovery of new biological processes. / Doctor of Philosophy / Malaria contributed to nearly a half a million deaths in 2017. The vast majority of malaria-related deaths are due to the parasite Plasmodium falciparum. This parasite resides inside human red blood cells (erythrocytes) and grows rapidly during a 48 hour cycle. There are over 40 serine hydrolase (SH) superfamily proteins in the parasite. Biological functions of the majority of SHs in the parasite remains unknown. Study on these SHs will provide new insights into parasite biology, and possibly present new antimalarial drug targets. We used chemical biology techniques to identify and functionally characterize parasite SHs. In one study, we show the parasite intenalized a human erythrocyte SH, acylpeptide hydrolase (APEH). We used an APEH-specific inhibitor to investigate the biological significance of internalized APEH in parasite biology. Treatment of the parasite with the inhibitor resulted in parasite growth inhibition suggesting internalization of APEH is essential for parasite survival. Lipases are enzymes that aid in break down of lipids and have shown to be crucial for growth and pathogenicity in various organisms. Lipases and lipid catabolism remain understudied in the malaria parasite. We used mass spectrometry in our approach to identify 16 lipases in asexual parasites. We have also shown that screening with highly specific inhibitors can help in predicting biological function of a particular enzyme. In summary, in this body of work, we have presented an approach of studying SHs in the malaria parasite, which will provide new insights into parasite biology.

Plant aromatic amino acid decarboxylases (AAADs) are a group of economically important enzymes categorically joined through their pyridoxal 5'-phosphate (PLP) dependence and sequence homology. Extensive evolutionary divergence of this enzyme family has resulted in a selection of enzymes with stringent aromatic amino acid substrate specificities. Variations in substrate specificities enable individual enzymes to catalyze key reactions in a diverse set of pathways impacting the synthesis of monoterpenoid indole alkaloids (including the pharmacologically active vinblastine and quinine), benzylisoquinoline alkaloids (including the pharmacologically active papaverine, codeine, morphine, and sanguinarine), and antioxidant and chemotherapeutic amides. Recent studies of plant AAAD proteins demonstrated that in addition to the typical decarboxylation enzymes, some annotated plant AAAD proteins are actually aromatic acetaldehyde synthases (AASs). These AASs catalyze a decarboxylation-oxidative deamination process of aromatic amino acids, leading to the production of aromatic acetaldehydes rather than the AAAD derived arylalkylamines. Research has implicated that plant AAS enzymes are involved in the production of volatile flower scents, floral attractants, and defensive phenolic acetaldehyde secondary metabolites. Historically, the structural elements responsible for differentiating plant AAAD substrate specificity and activity have been difficult to identify due to strong AAAD and AAS inter-enzyme homology. Through extensive bioinformatic analysis and experimental verification of plant AAADs, we have determined some structural elements unique to given types of AAADs. This document highlights structural components apparently responsible for the differentiation of activity and substrate specificity. In addition to producing primary sequence identifiers capable of AAAD activity and substrate specificity differentiation, this work has also demonstrated applications of AAAD enzyme engineering and novel activity identification. / Ph. D.

I evaluated the potential of isomers of the low molecular weight phosphomonoester naphthyl phosphate as general diagnostic substrates for differentiating between two families of protein phosphatases: the protein-tyrosine phosphatases [PTPs] and the dual-specificity protein phosphatases [DSPs]. Three PTPs, PTP-1B, Tc-PTPa, and PTP-H1, and three DSPs, Cdc-14, VHR, and IphP, were challenged in vitro with alpha-naphthyl phosphate and beta-naphthyl phosphate. Both the DSPs and PTPs readily hydrolyzed beta-naphthyl phosphate. As expected, the DSPs also hydrolyzed alpha-naphthyl phosphate at rates comparable to beta-naphthyl phosphate and two of the PTPs, PTP-1B and Tc-PTPa, hydrolyzed alpha-naphthyl phosphate at a rate one-tenth that of beta-naphthyl phosphate. However, PTP-H1 hydrolyzed both alpha- and beta- naphthyl phosphate at nearly equal rates. Intriguingly, when challenged with radiolabeled phosphoproteins, PTP-H1 was markedly less stringent, by a factor of 40- to 200- fold, than PTP-1B or Tc-PTPa in its selectivity for [32P]phosphotyrosyl- over [32P]phosphoseryl- proteins in vitro. The DSPs and PTPs listed above also were challenged in vitro with free phosphoserine. Each displayed little or no activity towards free phosphoserine. However, the addition of a hydrophobic "handle" to form N-(cyclohexane carboxyl)-O-phospho-L-serine produced a derivative that was hydrolyzed by IphP at rates comparable to that of the avid substrates p-nitrophenyl phosphate and beta-naphthyl phosphate. VHR also hydrolyzed N-(cyclohexane carboxyl)-O-phospho-L-serine, though at a lower rate than IphP. Cdc14 displayed little activity towards N-(cyclohexane carboxyl)-O-phospho-L-serine. The active site of VHR was mapped and amino acid residues potentially involved in binding N-(cyclohexane carboxyl)-O-phospho-L-serine were identified. The amino acid sequence of VHR was aligned with the amino acid sequences of IphP and Cdc14 to identify the nature of the corresponding residues in IphP and Cdcd14. Low molecular weight phosphomonoesters have proven to be effective in vitro indicators of protein phosphatase activity. They also have shown potential as diagnostic substrates for specific subclasses of protein phosphatases. However, neither alpha- and beta- naphthyl phosphate nor N-(cyclohexane carboxyl)-O-phospho-L-serine proved to be universal discriminatory substrates for the functional subgroups within the family of protein-tyrosine phosphatases. Indeed, the probability of identifying such a substrate would appear to be relatively low. / Master of Science

No description available.

京都大学 / 新制・課程博士 / 博士(医学) / 甲第25176号 / 医博第5062号 / 新制||医||1071(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 武藤 学, 教授 萩原 正敏, 教授 永井 純正 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

La NADPH oxydase du phagocyte est une enzyme impliquée dans la défense immunitaire contre les pathogènes. Après activation du phagocyte, cette enzyme produit des ions superoxyde par réduction du dioxygène par le NADPH. Elle est constituée de quatre sous- unités cytosolubles (p47phox ; p67phox ; p40phox et Rac), et deux membranaires (gp91 ; p22phox). Son activation fait intervenir un processus complexe qui met en jeu des changements d’interaction entre les protéines la constituant et qui permet l’assemblage des six sous- unités. Afin d’obtenir des informations sur les processus d’assemblage et d’activation, j’ai reconstitué le complexe dans un système cell free à l’aide de protéines recombinantes pour pouvoir contrôler tous les paramètres. Dans ce travail nous avons comparé les modes d’activation de p47phox par phosphorylation, par mutation substitutionelle sérine - aspartate en position S303,S304 et S328 pour mimer la phosphorylation et enfin par addition d’acide arachidonique (AA) activateur connu de l’enzyme in vitro mais aussi in vivo. Bien qu’il ai été montré que ces trois méthodes ouvrent la protéine vers une conformation ayant des propriétés similaires, nous avons trouvé que les effets de ces méthodes d’activation sont significativement différents. Ainsi, les changement de conformation observés par dichroisme circulaire, sont dissemblables. Pour p47phox, l’addition de AA déstructure la protéine. La phosphorylation induit un déplacement bathochrome des bandes de CD qualitativement similaire, alors que les mutations S-D de p47phox provoquent un déplacement opposé. Pour le complexe p47phox-p67phox l’addition d’AA destructure le mélange tandis que la mutation induit relativement peu de changement. Nous avons mesuré les constantes de dissociation Kd du complexe p47phox-p67phox. Alors que pour les protéines « sauvages », le Kd est faible (4±2 nM), les mutations de p47phox ainsi que l’addition d’AA augmentent cette valeur jusqu’à environ 50 nM, montrant une diminution de l’affinité entre p47phox-p67phox. De même, sur le complexe entier, l’effet de la phosphorylation de p47phox est différent de la mutation. Nous avons mesuré les valeurs de EC50 relatives à p67phox pour les différentes formes de p47phox. L’activation de p47phox par phosphorylation diminue l’EC₅₀, alors que les doubles ou triple mutations augmentent sa valeur. Nous avons confirmé que la phosphorylation et la mutation sont insuffisantes pour activer l’enzyme. La présence de AA est indispensable pour le fonctionnement du complexe. L’ordre de fixation des sous unités cytosoliques semble indifférent mais il faut que tous les composants soient présents lors de l’ajout de AA. Enfin, la délétion de p47phox dans la partie C-terminale (aa 343 à 390, domaine d’interaction avec p67phox) il n’y a plus de formation du dimère mais l’enzyme fonctionne normalement. Ces résultats apportent des éléments nouveaux sur le rôle de la dimérisation p47 phox-p67 phox, non indispensable à l’activité du système et sur le rôle mineur de la phosphorylation dans l’activation de la NADPH oxydase in vitro. / The NADPH oxidase of phagocytes is an enzyme involved in the innate defense of organisms against pathogens. After phagocyte activation, this enzyme produces superoxide ions by reduction of dioxygen by NADPH. It is constituted of four cytosolic sub-units (p47phox ; p67phox ; p40phox et Rac) and two membrane proteins (gp91 ; p22phox). Its activation takes place through a complex process that involves protein-protein interaction changes leading to assembly and functionning of the catalytic core. In order to obtain information on this process, I have reconstituted the enzyme in a cell free systeme using recombinant proteins, to be able to fully control all the measurement conditions. In this work, we have compared different activation modes of p47phox i) phosphorylation; ii) substitution serine - aspartate by mutations at positions S303, S304 and S328 to mimic phosphorylation; iii) addition of arachidonic acid (AA), a well known activator molecule in vitro. It has been shown that these three activating methods transform p47phox to an open configuration with similar characteristics. However, we have found that the effects of these methods are significantly different. Indeed, the conformational changes observed by circular dichroism are different. For p47phox, the addition of AA destructures the protein. Its phosphorylation induces a bathochromic displacement of the bands, whereas the mutations S-D lead to an opposite displacement. For the dimer p47phox-p67phox , the addition of AA destructures the proteins while mutations induce hardly no changes. We have measured the dissociation constant Kd of the complex p47phox-p67phox. For wild type proteins, Kd value is low (4±2 nM), while mutations of p47phox as well as addition of AA increase its value up to 50 nM, showing a decrease of affinity between p47phox and p67phox. Moreover, on the whole complex, the effect of phosphorylation of p47phox is different from mutations. We have shown that the EC50 values relative to p67phox are sensitive to the various modifications of p47phox. Phosphorylation of p47phox decreases EC₅₀, while double or triple mutations increase its value. We have confirmed that phosphorylation and mutation are not sufficient to activate the enzyme. The presence of AA is a prerequisite for the functionning of the complex, i.e. production of superoxide. The binding order of the cytosolic proteins seems random but it is necessary that all the components be present during the activation by AA. Finally, deletion of the C terminal part of p47phox (aa 343 to 390, interaction domain with p67phox) leads to the absence of dimer formation but does not affect the enzyme activity. These results bring new information on the role of dimerisation of p47-p67 and on that of phosphorylation in the activation of NADPH oxidase in vitro.

Chez la drosophile, l’activation du récepteur Toll menant à une réponse antimicrobienne peut se faire par deux voies différentes. Ces deux voies sont activées soit par des récepteurs dédiés, les Pattern Recognition Receptors (PRRs) reconnaissant des motifs moléculaires microbiens, soit par la coupure d’une molécule circulante appelée Perséphone par des protéases microbiennes extrêmement diverses sécrétées pendant une infection. Cependant, le mécanisme par lequel Perséphone est activée demeurait ambigu. Nous avons identifié une région unique dans Perséphone fonctionnant comme un appât pour les protéases exogènes indépendamment de leur origine, type ou spécificité. Une coupure dans cette région constitue la première étape d’une activation séquentielle de Perséphone ; elle permet de recruter la cathepsine circulante 26-29-p, qui va générer la forme active de Perséphone.Ces travaux montrent comment un récepteur de l’immunité innée, Perséphone, peut être activé par un signal de danger, en l’occurrence des enzymes microbiennes, et non par la détection de motifs moléculaires qui peuvent être présents dans la flore microbienne hébergée par les animaux. / In Drosophila, the antimicrobial response against infections can be triggered by two different extracellular mechanisms that both lead to the activation of the Toll receptor. These two mechanisms are activated either by the recognition of specific microbial determinants by Pattern Recognition Receptors (PRRs), or by the cleavage of the circulating serine protease Persephone by a wide range of microbial proteases secreted during infections. However, the molecular mechanism underlying Persephone activation remained ambiguous. We identified a unique region in Persephone pro-domain that functions as a bait for exogenous proteases independently of their origin, type or specificity. Cleavage of Persephone in this bait region constitutes the first step of a sequential activation and licenses the subsequent maturation of Persephone to the endogenous circulating cysteine cathepsin 26-29-p. Our data establish Persephone itself as an immune receptor able to sense a broad spectrum of microbes through the recognition of danger signals rather than molecular patterns.

Thesis (Ph. D.)--University of Virginia, 2008. / Title from title page. Includes bibliographical references. Also available online through Digital Dissertations.

Chirality is the property of objects, including molecules, which are not superimposable on their materialized mirror image. Chiral molecules are omnipresent in living organisms and the constituents of biological macromolecules (proteins and nucleic acids) are chiral. Amino-acids (constituting proteins), ribose and 2-deoxy-ribose (the only chiral constituent of RNA and DNA nucleotides respectively) are furthermore generally present in living organisms only under one of their enantiomeric forms. This is referred to as the homochirality of the living world. The origin of this homochirality is still unexplained, even if many partial scenarios have been proposed in the literature. All scenarios involve the creation of a small enantiomeric excess for certain molecules, amplification of this excess and chirality transfer to other chiral molecules. The origin of homochirality on Earth is closely related to the origin of life, and is currently supposed to have preceded life. As no-one will ever be able to directly observe the phenomena which lead to homochirality, and life, on our planet, the only scientific approach to try and help explain how this occurred is to build scenarios, and test them taking into account all available information on the physical and chemical conditions on the primitive Earth (Earth before life appeared). In our work, we investigated three scenarios related to the origin of homochirality on Earth. One of these scenarios also relates to a very precise step of the origin of life: the selection of beta-d-ribofuranose as component of RNA nucleotides.<p><p>Enantiomeric excesses (up to 15 %) of alpha-methylated alpha-amino-acids have been detected in meteorites which fell on Earth during the 20th century. No enantiomeric excess is detected for the corresponding alpha-hydroxy-acids in the same meteoritic samples and small (2% at most) or no enantiomeric excesses have been measured for non-methylated alpha-amino-acids. In the first part of our work, we investigated if photolysis by circularly polarized light (CPL) in space could be at the origin of the presence (or absence) of an enantiomeric excess for these compounds. Experiments to reproduce UV-CPL photolysis are difficult to undertake: they require high-energy circularly polarized photons, hence the use of a synchrotron. In our work, we used quantum mechanical calculations to obtain the electronic circular dichroïsm (ECD) spectra of two -methylated -amino-acids, their corresponding alpha-hydroxy-acids and one non-methylated alpha-amino-acid. Differences are observed between these spectra, and we propose a scenario to explain the experimental measurements reported here above: the enantioselective photolysis, in the gas phase at low temperatures (20K at most), of the alpha-amino-acids by UV-CPL with lambda>210 nm. Under these conditions no photolysis of the alpha-hydroxy-acids would occur. This scenario concerns the first step in the origin of homochirality on Earth: the creation of a small enantiomeric excess for some chiral molecules.<p><p>The second scenario that we investigated relates to the enantiomeric amplification step of the origin of homochirality on Earth, for which the role of the alpha-amino-acid serine has been suggested in the literature. Serine clusters have been observed in the gas phase by mass spectrometry. Among these clusters the octamer has been shown to be a magic number cluster and to have a preference for homochirality. An enantiomeric amplification via cycles of formation and dissociation of the octamer has been suggested. No complete scenario has however been proposed in the literature to explain how this could have occurred on the primitive Earth, but any scenario would most probably include an aqueous phase. We aimed at determining if the homochiral preference of serine octamers also exists in solution and therefore we first investigated if serine octamers exist in solution. For this study, we used nuclear magnetic resonance and infrared spectroscopies, which are well-adapted to the study of molecular assemblies in solution. We were able to demonstrate that most probably serine clusters are not present in solution, and if they are it could only be in extremely low concentration. The scenario suggested in the literature is discussed in the light of our results and of literature data on serine clusters.<p><p>As last hypothesis, we investigated a possible scenario for the selection of beta-d-ribofuranose as component of RNA nucleotides. The currently known prebiotic synthesis pathways to ribose also lead to the formation of many other carbohydrates, and ribose is only a minor product of these syntheses. Our hypothesis is that beta-d-ribofuranose could have been selected through favorable interactions with alpha-amino-acids already present on the primitive Earth under one enantiomeric form. Indeed, it is plausible that a peptidic world emerged before the presence of RNA and that homochiral alpha-amino-acids were present on Earth when RNA was synthesized. Under this hypothesis, we investigated the role that alpha-l-amino-acids could have played in the selection of alpha-d-ribofuranose as component of RNA nucleotides. This work is related to the last step of the origin of homochirality: chirality transfer. Our scenario was investigated via nuclear magnetic resonance studies of the interaction between alpha-amino-acids and carbohydrates. We were able to show that, in the systems that we studied, when an interaction occurs it is very weak (affinity constant less than 1M−1) and non enantioselective. Our results most probably discard the role that alpha-amino-acids alone could have played in the selection of beta-d-ribofuranose as component of RNA nucleotides, but does not discard the role that peptides could have played in this selection. / Doctorat en Sciences de l'ingénieur / info:eu-repo/semantics/nonPublished

Le récepteur du glutamate de type N-méthyl-D-aspartate (NMDAR) est un transducteur clef dans la physiologie du système nerveux et dans nombre de ses pathologies, selon qu’il est localisé à la synapse ou en position extra-synaptique respectivement. Son activité est sous le contrôle étroit du ‘site-glycine’, dont l’activation est gouvernée par la disponibilité en coagoniste. Pourtant, on ignore encore largement les règles qui régissent cette étape limitante de l’activation des NMDARs in situ. Par ailleurs, l’ensemble des onnaissances actuelles suggère que les astrocytes pourraient contrôler les NMDARs dans le contexte des interactions entre cellules gliales et neurones, en particulier via la libération du gliotransmetteur D-sérine. Le principal objectif de ce travail de thèse a été de comprendre les modalités du contrôle endogène des NMDARs par leur site co-agoniste, dans la région CA1 de l’hippocampe. Nous avons porté notre attention, avant tout, sur les acteurs de ce contrôle : la glycine et la D-sérine, qui sont les ligands endogènes du site-co-agoniste. Nous nous sommes intéressés à leur contribution respective dans le contrôle des NMDARs, aux dynamiques de ce contrôle en fonction de l’activité neuronale, à ses variations en fonction de la localisation des NMDARs, ainsi qu’à ses modifications développementales. Nous montrons par des approches d’électrophysiologie que la D-sérine, et non la glycine, est le co-agoniste endogène des NMDARs à la synapse CA3-CA1 chez l’adulte. Elle est délivrée par les prolongements astrocytaires environnants, d’une manière qui est influencée par l’activité synaptique. Sa libération répond à un mécanisme vésiculaire et est dépendante de la signalisation calcique intra-astrocytaire. De cette manière, les astrocytes exercent un contrôle étroit et dynamique des NMDARs à l’état basal et au cours de phénomènes de plasticité synaptique. En contre partie, à l’inverse de leurs homologues localisés à la synapse, les NMDARs extrasynaptiques sont contrôlés par la glycine à l’âge adulte. Cette compartimentation spatiale est dictée par une disponibilité différentielle des deux co-agonistes aux différents sites. Elle est également favorisée par une composition en sous-unités des NMDARs synaptiques et extra-synaptiques différente qui leur confère une affinité distincte pour la glycine et la D-sérine. Enfin, le contrôle des NMDARs par la D-sérine astrocytaire observé à l’âge adulte n’est pas opérationnel à la naissance. En effet, il ne se met en place qu’au cours du premier mois post-natal, de façon concomitante au changement de composition en sous-unités des NMDARs. / N-methyl D-aspartate receptors (NMDARs) are central to many aspects of brain physiology and pathology, which they impact differently depending on their synaptic or extrasynaptic location, respectively. In addition to glutamate, they are gated by the necessary binding of a co-agonist on the so-called ‘glycine-binding site’. However, very little is known about the rules that govern the control of NMDARs through this site, in situ. Evidence now suggests that astrocytes could play a critical role in controlling NMDARs activity, in particular through the release of the gliotransmitter D-serine. In the present work, we aimed at understanding how NMDARs are endogenously controlled through their co-agonist binding site, in the CA1 region of rat hippocampus. We primarily focused on the role of two endogenous ligands of this site: glycine and D-serine. We investigated their relative contribution in the control of NMDARs at the different subcellular locations, the dynamics of such control according to synaptic activity, as well as possible changes during post-natal development. Using elecrophysiological approaches, we demonstrate that NMDARs are gated by Dserine, but not glycine, at CA3-CA1 synapses in adults. D-serine is supplied at least in part by surrounding astrocytes in an activity-dependant manner. Its release occurs in response to calcium signalling within the astrocyte and in a vesicular way. Correspondingly, we found astrocytic supply of D-serine to be essential for NMDARs-dependant functions such as synaptic plasticity. In contrast with their synaptic counterparts, extrasynaptic NMDARs are gated by endogenous glycine and not by D-serine. We provide evidence that this compartmentation relies on the differential availability of the two co-agonists at synaptic and extrasynaptic sites. Besides, due to differences in their subunit composition, synaptic and extrasynaptic NMDARs may have preferential affinity for D-serine and glycine respectively. Finally, we show that the control of the NMDAR co-agonist site is developmentally regulated. Early after birth, glycine is the endogenous co-agonist of synaptic NMDARs. The control exerted by D-serine only progressively appears during the first post-natal month, as the switch in NMDARs subunit composition occurs, suggesting a maturation of cellular interactions at the tripartite synapse.