An in vitro method was developed for measuring aromatase, based on binding of competitive aromatase inhibitor [11C]vorozole to the active site of the enzyme. [11C]Vorozole displayed high, specific binding in vitro to human placenta and human granulosa cells (GC), both fresh and frozen/thawed cells, provided correct procedures were used. High, specific binding was also observed in pig and rat ovaries, whereas binding in other tissues was unspecific and usually low. Aromatase concentrations measured by [11C]vorozole binding correlated well to aromatase activity measured by [3H]water release from 1β[3H]androstenedione. In human GC in vitro, low concentrations of 5α-dihydrotestosterone (DHT), but not of other androgens, stimulated aromatase activity measured by [3H]water release but had no effects on aromatase concentration measured by [11C]vorozole binding. DHT may interact with aromatase differently than other androgens, perhaps by changing aromatase affinity to precursor. In the rat estrous cycle, aromatase activity in ovarian homogenate, measured by [3H]water release, together with serum androstenedione and estradiol-17β, peaked between 6 and 13 h after onset of the light period of proestrus, the former activity being independent of radioactive substrate concentration. [11C]Vorozole binding characteristics changed more rapidly than de novo synthesis of the enzyme. [11C]Vorozole binding Kd showed close inverse correlation to aromatase activity in ovarian homogenate and to serum estradiol-17β. Rapid changes in substrate affinity rather than changes in substrate concentration or de novo synthesis of the enzyme may thus be important for regulation of ovarian aromatase. The [11C]vorozole in vivo technique yields additional information compared with traditional in vitro techniques.

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.

Degradation of the mRNA 3'-end located poly(A) tail is an important step for mRNA decay in mammalian cells. Thus, to understand mRNA decay in detail, it is important to identify the catalytic activities involved in degrading poly(A). We identified and purified a 54-kDa polypeptide responsible for poly(A)-specific 3' exonuclease activity in calf thymus extracts. The 54-kDa polypeptide is a proteolytic fragment of the poly(A)-specific ribonuclease (PARN) 74-kDa polypeptide. PARN is a divalent metal ion dependent, poly(A)-specific, oligomeric, processive and cap interacting 3' exonuclease. An active deadenylation complex, consisting of the poly(A)-tailed RNA substrate and PARN, has been identified. The interaction with the 5'-end cap structure stimulates PARN activity and also amplifies the processivity of the deadenylation reaction. Furthermore, the cap binding site and the active site of PARN are separate from each other. To characterise the active site of PARN, we per-formed side-directed mutagenesis, Fe2+-mediated hydroxyl radical cleavage and metal ion switch experiments. We have demonstrated that the conserved acidic amino acid residues D28, E30, D292 and D382 of human PARN are essential for PARN activity and that these amino acid residues are directly involved in the co-ordination of at least two metal ions in the active site of PARN. Phosphorothioate modification on RNA substrates revealed that the pro-R oxygen atom of the scissile phosphate group interacts directly with the metal ion(s). Based on our studies, we propose a model for the action of PARN. Similarly to what has been observed for ribozymes, aminoglycoside antibiotics inhibit PARN activity, most likely by the displacement of catalytically important divalent metal ions. Among the aminoglycoside antibiotics tested, neomycin B is the most potent inhibitor. We speculate that inhibition of enzymes using similar catalytic mechanisms as PARN could be a reason for the toxic side effects caused by aminoglycoside antibiotics in clinical practice.

La phase initiale (de quelque fractions de seconde à quelques minutes) de la polymérisation catalytique des oléfines est encore peu comprise. Elle est pourtant reconnue comme une étape cruciale pour contrôler la morphologie de la particule de polymère et pour garantir la performance optimale du catalyseur et une certaine stabilité thermique du procédé. Ce travail présente l'étude et l'optimisation d'un mini réacteur à lit fixe pour mener des polymérisations catalytiques en phase gaz avec des durées très faibles (minimum 0.1s) dans des conditions proches à celles utilisées industriellement. La possibilité de suivre la température du gaz et de récupérer les particules de polymère pour les caractériser permet de décrire d'une façon complète le comportement du catalyseur au début de la réaction. L'étude a été limitée à la polymérisation de l'éthylène (avec un catalyseur métallocène supporté sur silice) et l'attention a été particulièrement mise sur la relation entre transfert de chaleur de la particule et performance du catalyseur. Il a été montré que des températures trop élevées peuvent être responsable localement de la modification du comportement du site active et de l'altération des propriétés des polymères. Un choix adéquat des conditions de réaction permet de suivre indirectement l'évolution de la température des particules en mesurant celle de la phase gaz. Dans un deuxième temps différents métallocènes ont été utilisés pour étudier l'influence des conditions de réaction, de la préparation du catalyseur et des propriétés du support sur l'activité, les propriétés du polymère et la morphologie des particules au temps court. Une attention particulière a été portée sur l'évolution des sites actifs et sur la cristallisation des chaînes de polymère dans un support poreux en évolution. Une activité élevée a été mesurée dans les premières cinq secondes et les températures de fusion et cristallisation des polymères ont été utilisées comme sondes pour mesurer l'avancement de la fragmentation du support. Les résultats ainsi obtenus peuvent non seulement clarifier certains aspects clé du début de la polymérisation mais aussi être utilisés comme donnés de départ pour modéliser la particule en croissance et contribuer à réduire l'écart qui est actuellement présent entre comportement réel du catalyseur et prédictions des modèles / The early stages (from less than 1s to few minutes) of catalytic olefin polymerization are still fairly understood even if they are nowadays recognized to be crucial for the determination of the morphology of the polymer particle, the optimization of the whole catalyst performance and the thermal stability of the process. In this work we will present how we studied and optimized a specially conceived packed bed reactor to perform gas phase catalytic olefin polymerizations as short as 0.1s under industrially relevant conditions. The possibility to measure the reactor temperature and to recover unaltered the polymer particles allows to take a complete picture of the catalyst behavior at the reaction start-up. The study will be restrained to ethylene polymerization with silica supported metallocenes and special attention will be given to the relation between heat transfer from the growing particle and catalyst performance. It will be seen how particle temperature evolution can be followed indirectly by measuring the gas phase temperature .In the second part of this work different metallocene complexes will be used to study the influence of process conditions, catalyst preparation method and support properties on the evolution of reaction rate, and polymer MWD during the first reaction seconds. Special attention will be given to the active site evolution during the transient phase and it will be shown that temperature excursions can be responsible for a local variation in active site behavior thus altering the properties of the formed polymer. The last section will be dedicated to the study of the peculiar crystallization behavior of the polymer chains in an evolving inorganic support. It will be shown how the melting and crystallization temperatures of the polymers can be used as “sensors” to measure the degree of fragmentation of the support particle. The results obtained in this work allow to gain a deeper understanding of the key parameters for the polymerization start-up and can be used as input for single particle models thus allowing to reduce the gap actually present between real catalyst behavior and model predictions

Tato práce se zabývá vyhledáváním homologních enzymů v proteinových databázích, jejímž cílem je navrhnout nástroj poskytující takové vyhledávání. Čtenář se seznámí se základní teorií týkající se proteinů, enzymů, homologie, ale také s existujícími nástroji pro vyhledávání homologních proteinů a enzymů. Dále je popsáno ohodnocení nalezených existujících nástrojů pro vyhledávání homologních enzymů. Pro potřeby vyhodnocení byla vytvořena datová sada spolu s algoritmem pro vyhodnocení vyýsledků jednotlivých nástrojů. Další částí práce je návrh a implementace nové metody pro vyhledávání homologních enzymů společně s jejím vyhodnocením. Jsou popsány dva algoritmy (One-by-One a MSA) pro vyhledávání homologních enzymů, jejichž porovnání ukazuje, že MSA algoritmus je zanedbatelně lepší z hlediska přesnosti než One-by-One algoritmus zatímco z hlediska rychlosti vítězí One-by-One algoritmus.

A chemoselective catalyst is preferred in a chemical reaction where protecting groups otherwise are needed. The two lipases Candida antarctica lipase B and Rhizomucor miehei lipase showed large chemoselectivity ratios, defined as (kcat/KM)OH / (kcat/KM)SH, in a transacylation reaction with ethyl octanoate as acyl donor and hexanol or hexanethiol as acyl acceptor (paper I). The chemoselectivity ratio of the uncatalyzed reaction was 120 in favour of the alcohol. Compared to the uncatalyzed reaction, the chemoselectivity was 730 times higher for Candida antarctica lipase B and ten times higher for Rhizomucor miehei lipase. The KM towards the thiol was more than two orders of magnitude higher than the KM towards the corresponding alcohol. This was the dominating contribution to the high chemoselectivity displayed by the two lipases. In a novel approach, Candida antarctica lipase B was used as catalyst for enzymatic synthesis of thiol-functionalized polyesters in a one-pot reaction without using protecting groups (paper II). Poly(e-caprolactone) with a free thiol at one of the ends was synthesized in an enzymatic ring-opening polymerization initiated with mercaptoethanol or terminated with either 3-mercaptopropionic acid or g-thiobutyrolactone.

Higher alcohol synthesis (HAS) from syngas or biomass-derived syngas is an important process for the production of oxygenate fuels, fuel additives and other intermediates for valueded chemical feedstock to produce medicine, cosmetics, lubricants, detergents, and polyesters. Chapter I reviews biomass to liquid fuels technology, higher alcohols being used as alternative fuels and fuel additives, the historical perspective and commercial status of higher alcohols, the catalyst system and the reaction mechanism for HAS from syngas. Chapter II discusses the Zn-Mn promoted Cu-Fe based catalyst that was synthesized by the co-precipitation method. The reaction temperature has been tested to study the influence on the catalytic performance. The maximal CO conversion rate was 72%, and the yield of alcohol and hydrocarbon was also very high. Cu was the active site for alcohol synthesis, iron carbide was the active site for olefin and paraffin synthesis. The reaction mechanism of HAS from syngas over Zn-Mn promoted Cu-Fe based catalyst was proposed. Chapter III documents the three-dimensionally ordered macroporous (3DOM) Cu-Fe catalyst developed using a glyoxylate route colloidal crystal template method. The high intrinsic activity was ascribed to three factors. First, the unique ordered structure has a large pore size and interconnected macroporous tunnels of the catalyst with a large accessible surface area to improve the catalytic activity. Second, a high density of uniformly distributed defective Cu0 and Fe5C2 nanoparticles derived from the glyoxylate route helps to provide abundant, active, and stable dual sites. Third, atomic steps on the Cu surface, induced by planar defects and lattice strain, serve as high-activity oxygenation sites. Active Fe5C2 chain-growth sites intimately surround the defective and strained form of the Cu surface, which results in a synergetic effect between the active and stable Cu–FexCy dual site for HAS. In Chapter IV, in situ ambient pressure x-ray photoelectron spectroscopy and in situ synchrotron powder diffraction were applied to identify the active site of 3DOM Cu-Fe catalyst for HAS. The results show that after syngas pretreatment of the 3DOM Cu-Fe catalyst, Cu0 is the active oxygenation site for alcohol synthesis, and Fe5C2 is the active site for carbon chain growth.

No description available.

Zusammenfassung Das beta-Proteobakterium Ralstonia eutropha H16 besitzt zwei [NiFe]-Hydrogenasen, die dem Organismus das Wachstum mit H2 als alleiniger Energiequelle unter aeroben Bedingungen ermöglichen. Reguliert wird die Expression dieser [NiFe]-Hydrogenasen durch ein bakterielles Zweikomponentensystem. Die Signaltransduktionskette besteht aus einer H2-sensierenden, regulatorischen [NiFe]-Hydrogenase (RH), einer Histidin-Proteinkinase und einem Response-Regulator. Um Einblicke in die Struktur-Funktions-Beziehung der H2-sensierenden Komponente zu bekommen, wurden Aminosäure-Austausche in konservierten Bereichen nahe des NiFe-Zentrums der RH durchgeführt. Der Austausch des invarianten Glu13 (E13Q, E13L) resultierte im Verlust der regulatorischen, der H2-oxidierenden und der H/D-Austauschaktivitäten. Spektroskopische Daten wiesen auf ein vollständig assembliertes NiFe-Zentrum hin. Mit Hilfe der ortho-/para-Konversionsaktivität wurde gezeigt, dass dieses Zentrum nach wie vor H2 binden kann. Dies deutet darauf hin, dass eine H2-Bindung am aktiven Zentrum nicht für die regulatorische Funktion der RH ausreicht. Durch den Austausch des Asp15 in His wurde der Konsensus eines konservierten Motivs der Standard-Hydrogenasen hergestellt. Das entstandene RH-Mutantenprotein besaß nur noch eine sehr niedrige H2-oxidierende Aktivität, bei nahezu unveränderter H/D-Austauschrate sowie intakter regulatorischer Aktivität. Dies deutet darauf hin, dass der H2-Umsatz nicht entscheidend für die H2-Sensierung ist. Um Informationen über die Struktur des aktiven Zentrums der RH zu erhalten, war es notwendig, große Mengen RH zu isolieren. Hierfür wurde die Strep-tag-Technologie eingesetzt, die es ermöglichte, die RH als natives Doppeldimer und als homodimeres Protein zu reinigen. Röntgenabsorptionsspektroskopie ergab erstmals, dass sich die Koordination des Nickel-Atoms im aktiven Zentrum sowohl im oxidierten als auch im reduzierten Zustand der RH deutlich von der in Standard-Hydrogenasen unterscheidet. / The beta-proteobacterium Ralstonia eutropha H16 is capable of using H2 as a facultative energy source by means of two distinct, energy-converting [NiFe]-hydrogenases. Transcription of the hydrogenase genes is regulated in response to the availability of H2 via a histidyl-aspartyl phosphorelay comprising a heterodimeric, regulatory [NiFe]-hydrogenase (RH), a histidine protein kinase and a response regulator. In order to gain insights into the mechanism of H2-mediated signal transduction, conserved amino acid residues close to the NiFe active site of the RH were exchanged. Replacement of the strictly conserved Glu13 within the RH large subunit by glutamine and leucine resulted in the loss of the regulatory, H2-oxidizing and hydrogen/deuterium exchange activities. Infrared spectroscopic analysis revealed, that the RH E13Q and E13L derivatives contained a fully assembled NiFe active site and showed para-/ortho-H2 conversion activity. These results indicated that H2-binding at the active site is not sufficient for H2 sensing. Replacement of Asp15, a residue unique in H2 sensors, by histidine restored the consensus of energy-linked [NiFe]-hydrogenases. The resulting RH mutant protein showed only traces of H2-oxidizing activity, whereas the H/D-exchange activity and the regulatory activity were nearly unaffected. H2-dependent signal transduction in the respective mutant strain was less sensitive to O2 than in the wild type. These results suggest that the H2 sensing is independent of H2 turnover. To get insights into the structure of the RH it was necessary to isolate large amounts of RH. By establishing the Strep-tag technology, allowing a fast, mild and efficient purification, it was possible to isolate the native RH-double dimer as well as the modified monodimeric RHstop protein in sufficient amounts for spectroscopic analyses. X-ray absorption spectroscopy showed for the first time that the RH active site undergoes significant structural changes upon exposure to H2.

Les protéines à radical S-adénosyl-L-méthionine (SAM) utilisent un centre [Fe4S4] réduit pour initier le clivage réductive homolytique de la SAM et la formation d'une espèce hautement réactive - le radical 5'-déoxyadénosyl ou 5'-dA•. Dans la quasi-totalité de cas ce radical alkyl va arracher un atome d'hydrogène sur le substrat et déclencher ainsi sa conversion en produit. On trouve ces enzymes au niveau d'étapes clé de la synthèse de certaines vitamines, antibiotiques, précurseurs de l'ADN ou encore cofacteurs protéiques où elles sont souvent impliquées dans le clivage ou la formation des liaisons C-C, C-N, C-S ou encore C-P. Les travaux réalisés au cours de cette thèse ont été focalisés sur l'étude structurale et fonctionnelle de la protéine HydE ; une enzyme à radical SAM, qui intervient dans la biosynthèse du site actif organométallique de l'hydrogénase à [FeFe]. L'objectif principal était d'identifier le substrat de HydE et d'étudier les détails du fonctionnement d'une protéine à radical SAM. Nous avons réussi à identifier un groupe de molécules, dérivées de la cystéine, contentant un cycle thiazolidine avec un ou deux groupements carboxylates, qui ont une très bonne affinité pour le site actif de HydE. Certains de ces ligands se sont montrés d’être des substrats non physiologiques de l’enzyme. Grâce à ces substrats nous avons pu mettre en évidence un nouveau mécanisme d’attaque radicalaire dans les protéines à radical SAM. En effet, dans HydE nous avons observé une attaque directe du radical 5'-dA• sur l’atome soufre du thioéther appartenant au cycle thiazolidine. Cette réaction constitue un exemple pas comme les autres d’une insertion d’un atome de soufre (ou de sélénium) catalysée par une enzyme à radical SAM. Il s'agit également d'une première observation d'une réaction radicalaire dans les cristaux protéiques d'une enzyme à radical SAM et également un premier suivi en temps réel par la RMN du 13C et 1H de l'accumulation d'un des produits de la réaction catalysée par ces enzymes. Les résultats de calculs théoriques basés sur nos structures cristallographiques de haute résolution suggèrent que dans le cas de cette superfamille de protéines le radical 5'-dA• serait plutôt un état de transition et donc pas une espèce intermédiaire isolable. / Radical S-adenosyl-L-methionine (SAM) proteins use a reduced [Fe4S4] cluster to initiate homolytic reductive cleavage of SAM, which leads to the formation of highly reactive 5'-deoxyadenosyl radical species or 5'-dA•. In almost all cases this alkyl radical will abstract a hydrogen atom from the substrate and thus trigger its conversion into product. These enzymes are found in key steps of the synthesis of certain vitamins, antibiotics, DNA precursors or protein cofactors. They are often involved in the cleavage or formation of C-C, C-N, C-S or C-P bonds. The present thesis work has been focused on the structural and functional study of HydE protein; a radical SAM enzyme, involved in the biosynthesis of the organometallic active site of [FeFe]-hydrogenase. The main goal was to identify the substrate of HydE and to study details of how radical SAM proteins control the highly oxidizing 5'-dA• species. We managed to identify a group of molecules, derived from cysteine, containing a thiazolidine ring with one or two carboxylate groups, which have a very good affinity for the active site of HydE. We have demonstrated some of these ligands are non-physiological substrates of the enzyme. With these substrates we could highlight a new radical attack mechanism in radical SAM proteins. Indeed, in HydE we observed a direct attack on the 5'-dA • radical on the sulfur atom of the thioether belonging to the thiazolidine ring. This is an unprecedented reaction that contrasts with sulfur (or selenium) atom insertion reactions catalysed by some radical SAM enzymes. This is also the first observation of a radical reaction in the protein crystal of a radical SAM enzyme and also the first real-time monitoring by 1H- & 13C-NMR spectroscopy of the accumulation of products of the reaction catalysed by these enzymes. Theoretical calculations based on our high-resolution crystal structures suggest that in the case of this protein superfamily the 5'-dA• radical, which triggers the reaction in radical SAM enzymes, is a transition state and therefore not an isolable intermediate species.