Deuteration is the replacement of a hydrogen atom by deuterium atom in a molecule. The replacement begins at the most acidic hydrogen in the molecule. In ATP, the deshielded hydrogen is C8-H which is the first replaced during deuteration. During ATP deuteration some of the ATP is hydrolysed to ADP concurrently. Using kinetic analysis, it was confirmed that the ATP hydrolysis that occurs is 1st order in ATP concentration, while the hydrogen replacement is 2nd order. The ATP and its C8 deuterated analogue were tested against three enzymes shikimate kinase (SK), acetate kinase (AK) and glutamine synthetase (GS) to determine if a kinetic isotope effect (KIE) exists in these systems. With AK and GS, the KIED increased as the KIEH decreased, while with SK the KIED decreased as the KIEH increased as the concentration of the ATP or deuterated analogue increased. Deuteration of imidazole and purine compounds reduced the specific activity of AK or SK at low concentrations in an enzyme-catalysed reaction. From a library of imidazole-containing compounds that inhibited SK, three compounds were selected and their IC50 values were determined on the SK-catalysed reaction. These compounds show a differential potency and efficiency between their protonated and deuterated analogues when compared in a 1:1 mixture. Synthesized purines incorporating three different substituents at N-9 were tested against AK or SK for their ability to lower the specific activity of the enzymes used / Physics / M. Sc. (Physics)

This Ph.D. thesis addresses the structure-function relationship of the multimeric oxidoreductase WrbA with the principal aim being the explanation of the unusual kinetics of this enzyme in molecular terms, and thus getting an insight about its physiological role in bacteria. WrbA is a multimeric enzyme with FMN as a co-factor, catalyzing the oxidation of NADH by a two electrons transfer. Structure and function analysis of WrbA places this enzyme between bacterial flavodoxins and eukaryotic oxidoreductases in terms of its evolutionary relationship. The kinetic activity of WrbA was studied under varying conditions such as temperature, pH etc, and its kinetic mechanism was evaluated from parameters KM and Vmax and confirmed by product inhibition pattern experiments. Crystallization and proteolytic experiments also underpin the functional importance of the multimeric nature of WrbA and aid the understanding of the physiological role of this enzyme in molecular terms.

Global change phenomena, such as forest disturbance and land-use change significantly affect elemental balances as well as the structure and function of terrestrial ecosystems. Inappropriate land management often causes nutrient losses and finally soil degradation and loss of soil functioning. Especially in tropical ecoregions, soil degradation by nutrient losses is widely abundant. Soil microorganisms are the proximate agents of many processes performed in soils and are regarded as sensitive bio-indicators. However, the incorporation of microbial responses to the definition of critical soil conditions is not intensively developed. In the present thesis, several data analyses of the relationships between ecosystem disturbance and land-use change (natural forest, pastures of different ages, secondary succession) and a diverse set of soil ecological characteristics in the tropical mountain rainforest region of southern Ecuador were compiled. In particular, it was tested whether soil microbial biomass and community functioning were sensitive to land-use change effects. Furthermore, an information-theoretic approach was applied to find the factors that regulate soil microbial biomass and community function. Finally, in a nutrient enrichment experiment the above- and belowground responses to N and P additions were examined. The tested research questions and results were linked to the theory of ecological stoichiometry in order to connect the research to a sound and unifying scientific basis. Soil and microbial stoichiometry were affected by both land-use change and soil depth. After forest disturbance, significant decreases of soil C:N:P ratios at the pastures were fol-lowed by increases during secondary succession. Microbial C:N ratios varied slightly in response to land-use change, whereas no fixed microbial C:P and N:P ratios were observed. Shifts in microbial community composition were associated with soil and microbial stoichiometry. Strong positive relationships between PLFA-markers 18:2n6,9c (saprotrophic fungi) and 20:4 (animals) and negative associations between 20:4 and microbial N:P point to land-use change affecting the structure of soil food webs. Significant deviations from global soil and microbial C:N:P ratios indicated a major force of land-use change to alter stoichiometric relationships and to structure biological systems. Data analysis reveals a strong impact of land-use change on soil microbial biomass, C-mineralization, gross-NH4-consumption and –production rates. According to the results of the IT-approach, combined models better describe effects of land-use change on soil microorganisms than single explanation models. Microbial resources and soil chemical environment were important pre-dictors for soil microbial biomass and community functioning. Little is known about the environmental drivers of the catalytic properties of EHEs (e.g., pH, nutrients) and their functional link to the structure of soil microbial communities. The activities of the six hydrolytic enzymes were tested. Microbial production of AP responded to the low P status of the sites by a higher investment in the acquisition of P compared to C. Three major drivers of enzyme activities were found to be significant for enzyme production: 1.) Microbial demand for P regulated the production of AP, provided that N and C were available. At the natural forest site the two-fold higher specific activity of AP pointed to a high microbial P-demand, whereas the production of AP was constrained by the availability of N and DOC after pasture abandonment. 2.) Microbial biomass that was controlled by pH and resource availability was the main driver for CBH, BG and NAG activities. 3.) Substrate induction due to increased litter inputs of herbaceous plant species seemed to regulate AG and XYL activities during secondary succession. The enzymes’ affinity to substrate, as a potentially critically enzyme kinetic parameter is understudied. The data analysis suggests that microbial communities adapted to environmental changes, demonstrated high flexibility of extracellular enzyme systems and selected for enzymes with higher catalytic efficiency compared with pure cultures. Under in situ conditions, enzyme-specific environmental drivers of the Km, e.g., the pH for XYL, the C:N ratio for AP, and the C availability for NAG were found. The data demonstrated that the higher substrate affinity of XYL and AP was associated with more abundance of Gram(-) bacteria. The catalytic efficiency of enzymes decomposing cellulose, hemicellulose, and starch positively correlated with the relative abundance of Gram(-) bacteria. The turnover rate of the tested substrates was three to four times faster at the young pasture site compared with the longterm pasture and secondary succession sites. Nutrient inputs by atmospheric deposition are known to affect terrestrial ecosystems. However, little is known about how N and P co-limited ecosystems respond to single nutrient enrichment. In this work the susceptibility of above- and belowground ecosystem compo-nents and of their linkages in an N and P co-limited pasture to N- and P-enrichment was assessed. It was tested if the plants´responses can be explained by the concept of serially linked nutrients introduced by Ågren (2004). In this concept, the control of the growth rate by one nutrient is assumed to depend on the control of a different cellular process by another nutrient. The responses of shoot and root biomass and C:N:P stoichiometry of the grass Setaria sphacelata (Schumach.) to moderate N, P, and N+P application over five years were investigated. In addition, the effects of nutrient enrichment on soil nutrient pools, on arbuscular mycorrhizal fungi (AMF) as well as on microbial biomass, activity, and community structure were tested. In order to evaluate the importance of different factors explaining microbial responses, a likelihood-based information-theoretic approach was applied. The application of N+P increased aboveground grass biomass. Root biomass was stimulated by P-treatment. Grass C:N:P stoichiometry responded by altering the P-uptake or by translocating P from shoot to root. In particular, root C:N and C:P stoichiometry decreased in P- and in N-treatment. Extractable fractions of soil C, N, and P were significantly affected by nutrient enrichment. P application increased the biomass of Gram-positive bacteria and the abundance of AMF, however, results of the IT-approach suggested indirect effects of nutrient enrichment on microbes. The responses of the N and P co-limited pasture to particular nutrient enrichment support the concept of serially linked nutrients. The present study provides evidence for the fundamental importance of P for controlling resource allocation of plants in responses to nutrient enrichment. Resource allocation of the grass rather than direct effects of nutrient additions drives changes in AMF, microbial biomass, community structure, and activity. / Seit dem Übergang vom Holozän zum Anthropozän greift der Mensch immer stärker in globale und regionale Stoffkreisläufe ein. Durch die Zerstörung von Naturwäldern und Landnutzungswandel werden die Strukturen und die Funktionen der Ökosysteme stark verändert. Unangepasste Landnutzung führt zu Nährelementverlusten, die mittel- bis langfristige zur Bodendegradation und zur Reduktion von Bodenfunktionen führen. Solche Veränderungen sind insbesondere in den Tropen zu beobachten. Bodenmikroorganismen spielen in den Stoffkreisläufen eine zentrale Rolle. Zudem sind sie sensitive Bioindikatoren für den Zustand von Ökosystemen. Im Gegensatz dazu, werden die Bodenmikroorganismen noch nicht ausreichend für die Zustandsbewertung von Ökosystemen verwendet. In der vorliegenden Dissertation werden verschiedene Datenanalysen zu den Beziehungen von Landnutzungswandel (Naturwald, Weiden verschiedener Alter, sekundäre Sukzession) und den Eigenschaften der Bodenmikroorganismen in einer tropischen Bergregenwaldregion Süd-Ecuadors zusammengefasst. Ein besonderer Fokus lag darauf zu prüfen, ob die mikrobielle Biomasse und die Funktionen die von der mikrobiellen Gemeinschaft geleistet werden (z.B. Enzymaktivitäten) durch den Landnutzungswandel beeinflusst werden. Ein informations-theoretischer Ansatz wurde verwendet um verschiedene Erklärungsansätze der steuernden Faktoren vergleichend zu testen. Darüber hinaus wurden in einem Weidedüngungsexperiment die Reaktionen der ober- und der unterirdischen Ökosystemkomponenten auf die Anreicherung mit N und P getestet. Um die Ergebnisse auf eine breite wissenschaftliche Basis zu stellen wurde die Untersuchungen in den Kontext der Theorie die Ökologischen Stöchiometrie eingeordnet. Die C:N:P Stöchiometrie im Boden und in den Mikroorganismen veränderte sich durch den Landnutzungswandel und mit der Bodentiefe. Mit der Weideetablierung nahmen die C:N:P Verhältnisse im Boden deutlich ab, stiegen dann nach dem Verlassen der Weiden im Zuge der sekundären Sukzession wieder an. Das mikrobielle C:N Verhältnis variierte nur leicht, dagegen zeigten das C:P und N:P Verhältnis deutliche Veränderungen durch den Landnutzungswandel. Mit diesen Veränderungen in der Boden- und Organismenstöchiometrie waren auch Veränderungen in der Struktur der mikrobiellen Gemeinschaften verbunden. Deutliche positive Beziehungen existierten zwischen den saprotrophen Pilzen und den Protozoen. Die steigenden Mengen von Protozoen waren wiederrum mit sinkendem mikrobiellen N:P verbunden. Diese Muster weisen auf Veränderungen in den Bodennahrungsnetzten durch Landnutzungsänderungen hin. Sehr deutliche Abweichungen von globalen Mustern der C:N:P Stöchiometrie deuten darauf hin, dass der Landnutzungswandel signifikanten Einfluss auf die C:N:P Stöchiometrie ausübt. Der Landnutzungswandel beeinflusste auch die mikrobielle Biomasse, die Basalatmung, sowie die mikrobielle Aufnahme und Produktion von NH4-N im Boden. Dabei zeigten kombinierte Erklärungsansätze die adäquateren Beschreibungen der Muster. In den kombinierten Modellen zur Erklärung der mikrobiellen Biomasse und der mikrobiellen Leistungen überwogen Prädiktoren der mikrobiellen Ressourcen und der bodenchemischen Umwelt. Ein weiterer Schwerpunkt der Untersuchungen lag auf der Erfassung der Effekte des Land-nutzungswandels auf die Aktivität von extrazellulären Bodenenzymen. Bisher ist wenig darüber bekannt, welche Faktoren die katalytischen Eigenschaften steuern und beispielsweise, ob es Zusammenhänge zur mikrobiellen Gemeinschaftsstruktur gibt. Um diese Fragen näher zu beleuchten wurden sechs hydrolytische Enzyme basierend auf MUF-Substraten untersucht. Die mikrobielle Produktion von AP stand dabei in Zusammenhang mit dem niedrigen P-Status der untersuchten Böden. Das wurde besonders durch die hohe AP Produktion im Vergleich zu BG belegt. Im Allgemeinen konnten drei verschiedene Mechanismen festgestellt werden, die die Produktion der untersuchten EHEs vermutlich steuerten. 1.) Der P-Bedarf der Mikroorganismen regulierte die Produktion von AP, vorausgesetzt, dass ausreichend N und C zur Enzymsynthese zur Verfügung standen. 2.) Die Höhe der mikrobiellen Biomasse hat sich als wichtiger Faktor für die Produktion von CBH, BG und NAG gezeigt. Das deutet auf die konstitutive Produktion dieser Enzyme hin. 3.) Die substratinduzierte Produktion von Enzymen ist vermutlich entscheidend für die Aktivität von AG und XYL. Die Berücksichtigung der Enzymkinetiken, insbesondere der Michaelis-Menten-Konstante lieferte weitere Aufschlüsse über relevante Faktoren. Im Allgemeinen so scheint es, haben sich die mikrobiellen Gemeinschaften an die starken Umweltgradienten, die durch den Landnutzungswandel erzeugt worden angepasst. Im Vergleich zu den verfügbaren Daten aus Reinkulturen, wiesen die mikrobiellen Gemeinschaften der untersuchten Böden in der Regel eine deutlich höhere katalytische Effizienz auf. Auch für die Michaelis-Menten-Konstante sind die Faktoren enzymspezifisch. So ist für die Km von XYL der Boden-pH-Wert, für AP das C:N Verhältnis und für NAG die DOC-Menge entscheidend. Darüber hinaus haben sich deutliche Beziehungen zwischen der Menge an Gram(-)-Bakterien und der Substrataffinitäten von XYL und AP ergeben. Je höher die Gram(-)-Abundanz, desto höher war die Substrataffinität der Enzymsysteme. Gegenüber alter und degradierter Weiden, war der Umsatz der untersuchten Substrate im Oberboden der aktiv genutzten Weide drei- bis vierfach erhöht. In einem 5-jährigen Düngeexperiment in der Bergregenwaldregion der Anden Süd-Ecuadors wurden die Reaktionen des auf dieser Fläche N/P co-limitierten Grases (Setaria sphacelata), der Arbuskulären Mykorrhiza (AMF) sowie der Bodenmikroorganismen auf moderate N, P und N+P-Düngung untersucht. Die Zugabe von N+P erhöhte die oberirdische Biomasse (+61%) wohingegen die Wurzelbiomasse durch die Zugabe von P (+45%) anstieg. Die C:N:P Verhältnisse weisen auf veränderte P-Aufnahme oder Translokation von P in die Wurzeln hin. Im Besonderen verengte sich das Wurzel C:N and C:P in der P- und der N-Zugabe. Die aus dem Boden extrahierbaren C, N und P-Fraktionen wurden deutlich beeinflusst. Die Zugabe von P stimulierte die Biomasse Gram-(+)-Bakterien (+22%), die Abundanz der AMF (+46%) und die Brutto-N-Mineralisierung. Die Auswertungen deuten darauf hin, dass die Nährstoffanreicherung indirekt über die Veränderungen der Graswurzeln auf die Bodenorganismen wirkte. Die Ergebnisse bestätigen, dass N und P in den Reaktionen von co-limitierten Pflanzen eng miteinander verbunden sind. Vor allem aber steuert P grundlegend die Allokation von Ressourcen und wirkt damit auf andere Ökosystem-komponenten, z.B. auf die Struktur und Aktivität der Bodenmikroorganismen.

Three-dimensional structures of proteins provide insights into the mechanisms of macromolecular assembly, enzyme catalysis and mode of activation, substrate-specificity, ligand-binding properties, stability and dynamical features. X-ray crystallography has become the method of choice in structural biology due to the remarkable methodological advances made in the generation of intense X-ray beams with very low divergence, cryocooling methods to prolong useful life of irradiated crystals, sensitive methods of Xray diffraction data collection, automated and fast methods for data processing, advances and automation in methods of computational crystallography, comparative analysis of macromolecular structures along with parallel advances in biochemical and molecular biology methods that allow production of the desired biomolecule in quantities sufficient for X-ray diffraction studies. Advances in molecular biology techniques and genomic data have helped in identifying metabolic pathways responsible for metabolism of short-chain fatty acids (SCFAs). The primary objective of this thesis is application of crystallographic techniques for understanding the structure and function of enzymes involved in the metabolism of SCFAs in S. typhimurium. Pathways chosen for the present study are (i) propionate degradation to pyruvate and succinate by 2-methylcitrate pathway involving gene products of the prp operon, (ii) acetate activation to acetyl-CoA by AckA-Pta pathway involving gene products of the ack-pta operon, (iii) threonine degradation to propionate involving gene products of the tdc operon, (iv) 1,2-propanediol (1,2-PD) degradation to propionate involving gene products of the pdu operon. These metabolic pathways utilize a large number of enzymes with diverse catalytic mechanisms. The main objectives of the work include structural and functional studies on 2-methycitrate synthase (PrpC), acetate kinase (AckA), propionate kinase isoforms (PduW and TdcD) and propanol dehydrogenase (PduQ) from S. typhimurium. In the present work, these proteins were cloned, expressed, purified and characterized. The purified proteins were crystallized using standard methods. The crystals were placed in an X-ray beam and diffraction data were collected and used for the elucidation of structure of the proteins. The structures were subjected to rigorous comparative analysis and the results were complemented with suitable biochemical and biophysical experiments. The thesis begins with a review of the current literature on SCFAs metabolism in bacteria, emphasizing studies carried out on S. typhimurium and the closely related E. coli as well as organisms for which the structure of a homologue has been determined (Chapter 1). Metabolic pathways involving acetate utilization by activation to acetyl- CoA, propionate degradation to pyruvate and succinate, anaerobic degradation of Lthreonine to propionate and, 1,2-PD degradation to propionate are described in this chapter. Common experimental and computational methods used during the course of investigations are described in Chapter 2, as most of these are applicable to all structure determinations and analyses. Experimental procedures described here include cloning, overexpression, purification, crystallization and intensity data collection. Computational methods covered include details of various programs used during data processing, structure solution, refinement, model building, validation and structural analysis. In Chapter 3, X-ray crystal structure of S. typhimurium 2-methylcitrate synthase (StPrpC; EC 2.3.3.5) determined at 2.4 Å resolution and its functional characterization is reported. StPrpC catalyzes aldol-condensation of oxaloacetate and propionyl-CoA to 2- methylcitrate and CoA in the second step of 2-methylcitrate pathway. StPrpC forms a dimer in solution and utilizes propionyl-CoA more efficiently than acetyl-CoA or butyryl- CoA. The polypeptide fold and the catalytic residues of StPrpC are conserved in citrate synthases (CSs) suggesting similarities in their functional mechanisms. Tyr197 and Leu324 of StPrpC are structurally equivalent to the ligand binding residues His and Val, respectively, of CSs. These substitutions might be responsible for the specificities for acyl-CoAs of these enzymes. Structural comparison with the ligand free (open) and bound (closed) states of CSs showed that StPrpC represents the first apo structure among xvi CS homologs in a nearly closed conformation. StPrpC molecules were organized as decamers, composed of five identical dimer units, in the P1 crystal cell. Higher order oligomerization of StPrpC is likely to be due to high pH (9.0) of the crystallization condition. In gram-negative bacteria, a hexameric form, believed to be important for regulation of activity by NADH, is also observed. Structural comparisons with hexameric E. coli CS suggested that the key residues involved in NADH binding are not conserved in StPrpC. Structural and functional studies on S. typhimurium acetate kinase (StAckA; EC 2.7.2.1) are described in Chapter 4. Acetate kinase, an enzyme widely distributed in the bacteria and archaea domains, catalyzes the reversible phosphoryl transfer from ATP to acetate in the presence of a metal ion during acetate metabolism. StAckA catalyzes Mg2+ dependent phosphate transfer from ATP to acetate 10 times more efficiently when compared to propionate. Butyrate was found to inhibit the activity of the enzyme. Kinetic analysis showed that ATP and Mg2+ could be effectively substituted by other nucleoside 5′-triphosphates (GTP, UTP and CTP) and divalent cations (Mn2+ and Co2+), respectively. The X-ray crystal structure of StAckA was determined in two different forms at 2.70 Å (Form-I) and 1.90 Å (Form-II) resolutions, respectively. StAckA contains a fold with the topology βββαβαβα, similar to those of glycerol kinase, hexokinase, heat shock cognate 70 (Hsc70) and actin. StAckA consists of two domains with an active site cleft at the domain interface. Comparison of StAckA structure with those of ligand complexes of other acetokinase family proteins permitted the identification of residues essential for substrate binding and catalysis. Conservation of most of these residues points to both structural and mechanistic similarities between enzymes of this family. Examination of the active site pocket revealed a plausible structural rationale for the greater specificity of the enzyme towards acetate than propionate. Intriguingly, a major conformational reorganization and partial disorder in a large segment consisting of residues 230-297 of the polypeptide was observed in Form-II. Electron density corresponding to a plausible xvii citrate was observed at a novel binding pocket present at the dimeric interface. Citrate bound at this site might be responsible for the observed disorder in the Form-II structure. A similar ligand binding pocket and residues lining the pocket were also found to be conserved in other structurally known enzymes of acetokinase family. These observations and examination of enzymatic reaction in the presence of citrate and succinate (tricarboxylic acid cycle intermediates) suggested that binding of ligands at this pocket might be important for allosteric regulation in this family of enzymes. Propionate kinase (EC 2.7.2.15) catalyzes reversible conversion of propionylphosphate and ADP to propionate and ATP. S. typhimurium possess two isoforms of propionate kinase, PduW and TdcD, involved in 1,2-propanediol degradation to propionate and in L-threonine degradation to propionate, respectively. In Chapter 5, structural and functional analyses of PduW and TdcD, carried out to gain insights into the substrate-binding pocket and catalytic mechanism of these enzymes, are described. Both isoforms showed broad specificity for utilization of SCFAs (propionate > acetate), nucleotides (ATP ≈ GTP > UTP > CTP) and metal ions (Mg2+ ≈ Mn2+). Molecular modeling of StPduW indicated that the enzyme is likely to adopt a fold similar to other members of acetokinase family. The residues at the active site are well conserved. Differences in the size of hydrophobic pocket where the substrate binds, particularly the replacement of a valine residue in acetate kinases (StAckA: Val93) by an alanine in propionate kinases (StPduW: Ala92; StTdcD: Ala88), could account for the observed greater affinity towards their cognate SCFAs. Crystal structures of TdcD from S. typhimurium in complex with various nucleotides were determined using native StTdcD as the phasing model. Nucleotide complexes of StTdcD provide a structural rationale for the broad specificity of the enzyme for its cofactor. Binding of ethylene glycol close to the γ-phosphate of GTP might suggest a direct in-line transfer mechanism. The thesis concludes with a brief discussion on the future prospects of the work. xviii Projects carried out as part of Master of Science projects and as additional activity during the course of the thesis work are described in three appendices. Analysis of the genomic sequences of E. coli and S. typhimurium has revealed the presence of hpa operon essential for 4-hydroxyphenylacetate (4-HPA) catabolism. S. typhimurium hpaE gene encodes for a 55 kDa polypeptide (StHpaE; EC 1.2.1.60) which catalyzes conversion of 5-carboxymethyl-2-hydroxymuconic semialdehyde (CHMS) to 5-carboxymethyl-2-hydroxymuconic aldehyde (CHMA) in 4-HPA metabolism. Sequence analysis of StHpaE showed that it belongs to aldehyde dehydrogenase (ALDH) superfamily and possesses residues equivalent to the catalytic glutamate and cysteine residues of homologous enzymes (Appendix A). The gene was cloned in pRSET C expression vector and the recombinant protein was purified using Ni-NTA affinity chromatography. The enzyme forms a tetramer in solution and shows catalytic activity toward the substrate analog adipic semialdehyde. Crystal structure of StHpaE revealed that it contains three domains; two dinucleotide-binding domains, a Rossmann-fold type domain, and a small three-stranded β-sheet domain, which is involved in tetrameric interactions. NAD+-bound crystal of StHpaE permitted identification of active site pocket and residues important for ligand anchoring and catalysis. Mutarotases or aldose 1-epimerases (EC 5.1.3.3) play a key role in carbohydrate metabolism by catalyzing the interconversion of α- and β-anomers of sugars. S. typhimurium YeaD (StYeaD), annotated as aldose 1-epimerase, has very low sequence identity with other well characterized mutarotases. In Appendix B, the crystal structure of StYeaD determined in orthorhombic and monoclinic crystal forms at 1.9 Å and 2.5 Å resolutions, respectively are reported. StYeaD possesses a fold similar to those of galactose mutarotases (GalMs). Structural comparison of StYeaD with GalMs has permitted identification of residues involved in catalysis and substrate anchoring. In spite xix of the similar fold and conservation of catalytic residues, minor but significant differences in the substrate binding pocket were observed compared to GalMs. Therefore, the substrate specificity of YeaD like proteins seems to be distinct from those of GalMs. Pepper Vein Banding Virus (PVBV) is a member of the genus potyvirus and infects Solanaceae plants. PVBV is a single-stranded positive-sense RNA virus with a genome-linked viral protein (VPg) covalently attached at the 5'-terminus. In order to establish the role of VPg in the initiation of replication of the virus, recombinant PVBV VPg was over-expressed in E. coli and purified using Ni-NTA affinity chromatography (Appendix C). PVBV NIb was found to uridylylate Tyr66 of VPg in a templateindependent manner. Studies on N- and C-terminal deletion mutants of VPg revealed that N-terminal 21 and C-terminal 92 residues of PVBV VPg are dispensable for in vitro uridylylation by PVBV NIb.

La CO déshydrogénase (CODH) de Desulfovibrio vulgaris est une métalloenzyme qui catalyse la réduction réversible du CO2 en CO. C’est un homodimère composé de deux sites actifs Ni-4Fe-4S et de trois centres fer-soufre. Durant ma thèse, nous avons étudié la maturation de la CODH à nickel et les propriétés catalytiques de la CODH à nickel de D. vulgaris.Pour comprendre le mécanisme de maturation de la CODH à nickel, nous avons caractérisé deux formes de la CODH à nickel produites en présence ou en absence de CooC par des approches biochimiques, spectroscopiques, électrochimiques et cristallographiques. Notre caractérisation montre que la présence de CooC est nécessaire à l’obtention d’une CODH mature et activable. Nous avons également mis en évidence un processus d’activation en présence de nickel dans des conditions réductrices qui n’implique apparemment pas de changement structural du site actif.Notre étude de la CODH à nickel par électrochimie nous a permis de mettre en évidence plusieurs phénomènes d’activations/inactivations de l’enzyme dans des conditions aérobies et anaérobies, et l’existence d’une hétérogénéité fonctionnelle : plusieurs formes de l’enzyme qui montrent des propriétés catalytiques différentes peuvent être présentes simultanément. Cette observation pourrait éclairer d’une façon nouvelle l’hétérogénéité structurale observée par cristallographie et remettre en question les mécanismes proposés sur la base de ces structures. / The monoxide carbon dehydrogenase (CODH) from Desulfovibrio vulgaris is a metalloenzyme which catalyses the reversible reduction of CO2 into CO. It is a homodimer containing two active sites and three iron-sulfur clusters. During my thesis, we studied the maturation of CODH nickel and catalytic properties of Ni-CODH from D. vulgaris.In order to understand, the maturation mechanism of Ni-CODH, we have characterized two forms of Ni-CODH produced in the presence or absence of CooC by biochemical, spectroscopic, electrochemical and crystallographic approaches. Our characterisation shows that the presence of CooC is necessary to obtain a mature Ni-CODH which can be activated. We have also identified an activation process in the presence of nickel in reducing conditions that apparently involves no structural change in the active site.Our study of the Ni-CODH by electrochemistry has shown several phenomena of activation/inactivation of the enzyme under aerobic and anaerobic conditions, and the existence of a functional heterogeneity : several forms of the enzyme which show different catalytic properties may be present simultaneously. This observation could illuminate the structural heterogeneity observed by crystallography and question the proposed mechanisms on the basis of these structures.

Global change phenomena, such as forest disturbance and land-use change significantly affect elemental balances as well as the structure and function of terrestrial ecosystems. Inappropriate land management often causes nutrient losses and finally soil degradation and loss of soil functioning. Especially in tropical ecoregions, soil degradation by nutrient losses is widely abundant. Soil microorganisms are the proximate agents of many processes performed in soils and are regarded as sensitive bio-indicators. However, the incorporation of microbial responses to the definition of critical soil conditions is not intensively developed. In the present thesis, several data analyses of the relationships between ecosystem disturbance and land-use change (natural forest, pastures of different ages, secondary succession) and a diverse set of soil ecological characteristics in the tropical mountain rainforest region of southern Ecuador were compiled. In particular, it was tested whether soil microbial biomass and community functioning were sensitive to land-use change effects. Furthermore, an information-theoretic approach was applied to find the factors that regulate soil microbial biomass and community function. Finally, in a nutrient enrichment experiment the above- and belowground responses to N and P additions were examined. The tested research questions and results were linked to the theory of ecological stoichiometry in order to connect the research to a sound and unifying scientific basis. Soil and microbial stoichiometry were affected by both land-use change and soil depth. After forest disturbance, significant decreases of soil C:N:P ratios at the pastures were fol-lowed by increases during secondary succession. Microbial C:N ratios varied slightly in response to land-use change, whereas no fixed microbial C:P and N:P ratios were observed. Shifts in microbial community composition were associated with soil and microbial stoichiometry. Strong positive relationships between PLFA-markers 18:2n6,9c (saprotrophic fungi) and 20:4 (animals) and negative associations between 20:4 and microbial N:P point to land-use change affecting the structure of soil food webs. Significant deviations from global soil and microbial C:N:P ratios indicated a major force of land-use change to alter stoichiometric relationships and to structure biological systems. Data analysis reveals a strong impact of land-use change on soil microbial biomass, C-mineralization, gross-NH4-consumption and –production rates. According to the results of the IT-approach, combined models better describe effects of land-use change on soil microorganisms than single explanation models. Microbial resources and soil chemical environment were important pre-dictors for soil microbial biomass and community functioning. Little is known about the environmental drivers of the catalytic properties of EHEs (e.g., pH, nutrients) and their functional link to the structure of soil microbial communities. The activities of the six hydrolytic enzymes were tested. Microbial production of AP responded to the low P status of the sites by a higher investment in the acquisition of P compared to C. Three major drivers of enzyme activities were found to be significant for enzyme production: 1.) Microbial demand for P regulated the production of AP, provided that N and C were available. At the natural forest site the two-fold higher specific activity of AP pointed to a high microbial P-demand, whereas the production of AP was constrained by the availability of N and DOC after pasture abandonment. 2.) Microbial biomass that was controlled by pH and resource availability was the main driver for CBH, BG and NAG activities. 3.) Substrate induction due to increased litter inputs of herbaceous plant species seemed to regulate AG and XYL activities during secondary succession. The enzymes’ affinity to substrate, as a potentially critically enzyme kinetic parameter is understudied. The data analysis suggests that microbial communities adapted to environmental changes, demonstrated high flexibility of extracellular enzyme systems and selected for enzymes with higher catalytic efficiency compared with pure cultures. Under in situ conditions, enzyme-specific environmental drivers of the Km, e.g., the pH for XYL, the C:N ratio for AP, and the C availability for NAG were found. The data demonstrated that the higher substrate affinity of XYL and AP was associated with more abundance of Gram(-) bacteria. The catalytic efficiency of enzymes decomposing cellulose, hemicellulose, and starch positively correlated with the relative abundance of Gram(-) bacteria. The turnover rate of the tested substrates was three to four times faster at the young pasture site compared with the longterm pasture and secondary succession sites. Nutrient inputs by atmospheric deposition are known to affect terrestrial ecosystems. However, little is known about how N and P co-limited ecosystems respond to single nutrient enrichment. In this work the susceptibility of above- and belowground ecosystem compo-nents and of their linkages in an N and P co-limited pasture to N- and P-enrichment was assessed. It was tested if the plants´responses can be explained by the concept of serially linked nutrients introduced by Ågren (2004). In this concept, the control of the growth rate by one nutrient is assumed to depend on the control of a different cellular process by another nutrient. The responses of shoot and root biomass and C:N:P stoichiometry of the grass Setaria sphacelata (Schumach.) to moderate N, P, and N+P application over five years were investigated. In addition, the effects of nutrient enrichment on soil nutrient pools, on arbuscular mycorrhizal fungi (AMF) as well as on microbial biomass, activity, and community structure were tested. In order to evaluate the importance of different factors explaining microbial responses, a likelihood-based information-theoretic approach was applied. The application of N+P increased aboveground grass biomass. Root biomass was stimulated by P-treatment. Grass C:N:P stoichiometry responded by altering the P-uptake or by translocating P from shoot to root. In particular, root C:N and C:P stoichiometry decreased in P- and in N-treatment. Extractable fractions of soil C, N, and P were significantly affected by nutrient enrichment. P application increased the biomass of Gram-positive bacteria and the abundance of AMF, however, results of the IT-approach suggested indirect effects of nutrient enrichment on microbes. The responses of the N and P co-limited pasture to particular nutrient enrichment support the concept of serially linked nutrients. The present study provides evidence for the fundamental importance of P for controlling resource allocation of plants in responses to nutrient enrichment. Resource allocation of the grass rather than direct effects of nutrient additions drives changes in AMF, microbial biomass, community structure, and activity. / Seit dem Übergang vom Holozän zum Anthropozän greift der Mensch immer stärker in globale und regionale Stoffkreisläufe ein. Durch die Zerstörung von Naturwäldern und Landnutzungswandel werden die Strukturen und die Funktionen der Ökosysteme stark verändert. Unangepasste Landnutzung führt zu Nährelementverlusten, die mittel- bis langfristige zur Bodendegradation und zur Reduktion von Bodenfunktionen führen. Solche Veränderungen sind insbesondere in den Tropen zu beobachten. Bodenmikroorganismen spielen in den Stoffkreisläufen eine zentrale Rolle. Zudem sind sie sensitive Bioindikatoren für den Zustand von Ökosystemen. Im Gegensatz dazu, werden die Bodenmikroorganismen noch nicht ausreichend für die Zustandsbewertung von Ökosystemen verwendet. In der vorliegenden Dissertation werden verschiedene Datenanalysen zu den Beziehungen von Landnutzungswandel (Naturwald, Weiden verschiedener Alter, sekundäre Sukzession) und den Eigenschaften der Bodenmikroorganismen in einer tropischen Bergregenwaldregion Süd-Ecuadors zusammengefasst. Ein besonderer Fokus lag darauf zu prüfen, ob die mikrobielle Biomasse und die Funktionen die von der mikrobiellen Gemeinschaft geleistet werden (z.B. Enzymaktivitäten) durch den Landnutzungswandel beeinflusst werden. Ein informations-theoretischer Ansatz wurde verwendet um verschiedene Erklärungsansätze der steuernden Faktoren vergleichend zu testen. Darüber hinaus wurden in einem Weidedüngungsexperiment die Reaktionen der ober- und der unterirdischen Ökosystemkomponenten auf die Anreicherung mit N und P getestet. Um die Ergebnisse auf eine breite wissenschaftliche Basis zu stellen wurde die Untersuchungen in den Kontext der Theorie die Ökologischen Stöchiometrie eingeordnet. Die C:N:P Stöchiometrie im Boden und in den Mikroorganismen veränderte sich durch den Landnutzungswandel und mit der Bodentiefe. Mit der Weideetablierung nahmen die C:N:P Verhältnisse im Boden deutlich ab, stiegen dann nach dem Verlassen der Weiden im Zuge der sekundären Sukzession wieder an. Das mikrobielle C:N Verhältnis variierte nur leicht, dagegen zeigten das C:P und N:P Verhältnis deutliche Veränderungen durch den Landnutzungswandel. Mit diesen Veränderungen in der Boden- und Organismenstöchiometrie waren auch Veränderungen in der Struktur der mikrobiellen Gemeinschaften verbunden. Deutliche positive Beziehungen existierten zwischen den saprotrophen Pilzen und den Protozoen. Die steigenden Mengen von Protozoen waren wiederrum mit sinkendem mikrobiellen N:P verbunden. Diese Muster weisen auf Veränderungen in den Bodennahrungsnetzten durch Landnutzungsänderungen hin. Sehr deutliche Abweichungen von globalen Mustern der C:N:P Stöchiometrie deuten darauf hin, dass der Landnutzungswandel signifikanten Einfluss auf die C:N:P Stöchiometrie ausübt. Der Landnutzungswandel beeinflusste auch die mikrobielle Biomasse, die Basalatmung, sowie die mikrobielle Aufnahme und Produktion von NH4-N im Boden. Dabei zeigten kombinierte Erklärungsansätze die adäquateren Beschreibungen der Muster. In den kombinierten Modellen zur Erklärung der mikrobiellen Biomasse und der mikrobiellen Leistungen überwogen Prädiktoren der mikrobiellen Ressourcen und der bodenchemischen Umwelt. Ein weiterer Schwerpunkt der Untersuchungen lag auf der Erfassung der Effekte des Land-nutzungswandels auf die Aktivität von extrazellulären Bodenenzymen. Bisher ist wenig darüber bekannt, welche Faktoren die katalytischen Eigenschaften steuern und beispielsweise, ob es Zusammenhänge zur mikrobiellen Gemeinschaftsstruktur gibt. Um diese Fragen näher zu beleuchten wurden sechs hydrolytische Enzyme basierend auf MUF-Substraten untersucht. Die mikrobielle Produktion von AP stand dabei in Zusammenhang mit dem niedrigen P-Status der untersuchten Böden. Das wurde besonders durch die hohe AP Produktion im Vergleich zu BG belegt. Im Allgemeinen konnten drei verschiedene Mechanismen festgestellt werden, die die Produktion der untersuchten EHEs vermutlich steuerten. 1.) Der P-Bedarf der Mikroorganismen regulierte die Produktion von AP, vorausgesetzt, dass ausreichend N und C zur Enzymsynthese zur Verfügung standen. 2.) Die Höhe der mikrobiellen Biomasse hat sich als wichtiger Faktor für die Produktion von CBH, BG und NAG gezeigt. Das deutet auf die konstitutive Produktion dieser Enzyme hin. 3.) Die substratinduzierte Produktion von Enzymen ist vermutlich entscheidend für die Aktivität von AG und XYL. Die Berücksichtigung der Enzymkinetiken, insbesondere der Michaelis-Menten-Konstante lieferte weitere Aufschlüsse über relevante Faktoren. Im Allgemeinen so scheint es, haben sich die mikrobiellen Gemeinschaften an die starken Umweltgradienten, die durch den Landnutzungswandel erzeugt worden angepasst. Im Vergleich zu den verfügbaren Daten aus Reinkulturen, wiesen die mikrobiellen Gemeinschaften der untersuchten Böden in der Regel eine deutlich höhere katalytische Effizienz auf. Auch für die Michaelis-Menten-Konstante sind die Faktoren enzymspezifisch. So ist für die Km von XYL der Boden-pH-Wert, für AP das C:N Verhältnis und für NAG die DOC-Menge entscheidend. Darüber hinaus haben sich deutliche Beziehungen zwischen der Menge an Gram(-)-Bakterien und der Substrataffinitäten von XYL und AP ergeben. Je höher die Gram(-)-Abundanz, desto höher war die Substrataffinität der Enzymsysteme. Gegenüber alter und degradierter Weiden, war der Umsatz der untersuchten Substrate im Oberboden der aktiv genutzten Weide drei- bis vierfach erhöht. In einem 5-jährigen Düngeexperiment in der Bergregenwaldregion der Anden Süd-Ecuadors wurden die Reaktionen des auf dieser Fläche N/P co-limitierten Grases (Setaria sphacelata), der Arbuskulären Mykorrhiza (AMF) sowie der Bodenmikroorganismen auf moderate N, P und N+P-Düngung untersucht. Die Zugabe von N+P erhöhte die oberirdische Biomasse (+61%) wohingegen die Wurzelbiomasse durch die Zugabe von P (+45%) anstieg. Die C:N:P Verhältnisse weisen auf veränderte P-Aufnahme oder Translokation von P in die Wurzeln hin. Im Besonderen verengte sich das Wurzel C:N and C:P in der P- und der N-Zugabe. Die aus dem Boden extrahierbaren C, N und P-Fraktionen wurden deutlich beeinflusst. Die Zugabe von P stimulierte die Biomasse Gram-(+)-Bakterien (+22%), die Abundanz der AMF (+46%) und die Brutto-N-Mineralisierung. Die Auswertungen deuten darauf hin, dass die Nährstoffanreicherung indirekt über die Veränderungen der Graswurzeln auf die Bodenorganismen wirkte. Die Ergebnisse bestätigen, dass N und P in den Reaktionen von co-limitierten Pflanzen eng miteinander verbunden sind. Vor allem aber steuert P grundlegend die Allokation von Ressourcen und wirkt damit auf andere Ökosystem-komponenten, z.B. auf die Struktur und Aktivität der Bodenmikroorganismen.

<p>Coronaviruses (CoVs) are single-stranded, positive-sense RNA viruses in the Coronaviridae family. Within this family are four different genera, Alpha-, Beta-, Gamma-, and Deltacoronaviruses with human-infecting CoVs spanning the Alpha- and Beta-CoV genera. Most notably, Severe Acute Respiratory Syndrome Coronavirus-1 (SARS-CoV-1) and SARS-CoV-2 are Betacoronaviruses that spread worldwide in their outbreaks from 2002-2003 (SARS-CoV-1) and 2019-2020 (SARS-CoV-2). Human-infecting Alphacoronaviruses, NL63-CoV and 229E-CoV, have caused milder infections involving respiratory disease, gastroenteritis, and in more severe cases, death. Despite milder disease, Alphacoronaviruses are the cause of 15-30% of severe upper and lower respiratory tract infections each year. There have been recent efforts in the development of potent, small-molecule inhibitors to treat SARS-CoV-2 infection but there is an ongoing need to develop new and effective anti-coronavirus therapeutics to treat other human-infecting CoVs circulating society. Coronaviruses encode two essential proteases, the papain-like protease (PLP) and the 3C-like protease. PLPs are cysteine proteases located in non-structural protein 3 (nsp3). PLPs processes the viral polyprotein, releasing the first three nonstructural proteins encoded in the virus, and also are involved in evading the innate immune response through deubiquitinating (DUB) and deISGylating activity. </p> <p><br></p> <p>This study compares the substrate specificity and catalytic function of multiple human-infecting PLPs from both Alpha- and Beta-CoVs including NL63-CoV PLP2, 229E-CoV PLP2, Canine-CoV PLP2, FIPV-CoV PLP2, PEDV-CoV PLP2, SARS-CoV-1 PLpro, and SARS-CoV-2 PLpro. Interestingly, Alphacoronavirus PLP2s have a >400-fold greater catalytic efficiency for ubiquitin compared to Betacoronaviruses PLpro. This work also identifies a non-covalent scaffold of inhibitors that has pan-CoV inhibition; however, the IC50 values are >30-fold higher for NL63-CoV PLP2 than for SARS-CoV-1 PLpro. The X-ray structures of NL63 PLP2 and 229E PLP2 were determined to 2.1 Å and 1.8 Å, respectively, and provide structural information about the substrate and inhibitor binding region that could be the result in the differences in Alpha- and Betacoronavirus PLP function. Since PLP does not function as a single-domain in vivo, it is critical to understand the function of PLP when tethered to other domains of nsp3. This study also investigates nine different constructs of SARS-CoV-2 nsp3 with increasing domains, ranging from the single PLpro domain to Ubl1-Ydomain ΔTM1-TM2. Interestingly, the longer constructs of SARS-CoV-2 nsp3 show less catalytic efficiency for Ub-AMC and greater affinity for ISG15-AMC, with 8-fold lower Km values compared to PLpro alone. Lastly, each SARS-CoV-2 nsp3 construct was inhibited by a known PLpro inhibitor, GRL-0617, with reported IC50 values ranging from 0.91 μM to 1.9 μM. These data show that GRL-0617 still remains a lead compound to be optimized for cellular potency. </p> <p><br></p> <p>Overall, this dissertation advances the understanding of the kinetic and structural differences between Alphacoronavirus PLP2 and Betacoronavirus PLpro enzymes in the efforts of developing a pan-CoV inhibitor. Additionally, these data provide initial kinetic and biophysical characterization of PLpro within the larger context of nsp3 to elucidate the function of PLpro in its most native context during coronaviral infection.</p>

La dihydrofolate réductase humaine (DHFRh) est une enzyme essentielle à la prolifération cellulaire, ce qui en fait une cible de choix pour le traitement de différents cancers. À cet effet, plusieurs inhibiteurs spécifiques de la DHFRh, les antifolates, ont été mis au point : le méthotrexate (MTX) et le pemetrexed (PMTX) en sont de bons exemples. Malgré l’efficacité clinique certaine de ces antifolates, le développement de nouveaux traitements s’avère nécessaire afin de réduire les effets secondaires liés à leur utilisation. Enfin, dans l’optique d’orienter la synthèse de nouveaux composés inhibiteurs des DHFRh, une meilleure connaissance des interactions entre les antifolates et leur enzyme cible est primordiale. À l’aide de l’évolution dirigée, il a été possible d’identifier des mutants de la DHFRh pour lesquels l’affinité envers des antifolates cliniquement actifs se voyait modifiée. La mutagenèse dite ¬¬de saturation a été utilisée afin de générer des banques de mutants présentant une diversité génétique au niveau des résidus du site actif de l’enzyme d’intérêt. De plus, une nouvelle méthode de criblage a été mise au point, laquelle s’est avérée efficace pour départager les mutations ayant entrainé une résistance aux antifolates et/ou un maintient de l’activité enzymatique envers son substrat natif, soient les phénotypes d’activité. La méthode de criblage consiste dans un premier temps en une sélection bactérienne à haut débit, puis dans un second temps en un criblage sur plaques permettant d’identifier les meilleurs candidats. Plusieurs mutants actifs de la DHFRh, résistants aux antifolates, ont ainsi pu être identifiés et caractérisés lors d’études de cinétique enzymatique (kcat et IC50). Sur la base de ces résultats cinétiques, de la modélisation moléculaire et des données structurales de la littérature, une étude structure-activité a été effectuée. En regardant quelles mutations ont les effets les plus significatif sur la liaison, nous avons commencé à construire un carte moléculaire des contacts impliqués dans la liaison des ligands. Enfin, des connaissances supplémentaires sur les propriétés spécifiques de liaison ont put être acquises en variant l’inhibiteur testé, permettant ainsi une meilleure compréhension du phénomène de discrimination du ligand. / Human dihydrofolate reductase (hDHFR) is an essential enzyme for cellular proliferation and it has long been the target of antifolate drugs for the treatment of various types of cancer. Despite the clinical effectiveness of current antifolate treatments, new drugs are required to reduce the side-effects associated with their use. An essential requirement for design of new antifolates is a better understanding of how these drugs interact with their targets. We applied directed evolution to identify mutant hDHFR variants with modified binding to some clinically relevant antifolates. A saturation mutagenesis approach was used to create genetic diversity at active-site residues of hDHFR and a new, efficient screening strategy was developed to identify the amino acids that preserved native activity and/or conferred antifolate resistance. The screening method consists in a high-throughput first-tier bacterial selection coupled with a second-tier in vitro assay that allows for rapid detection of the best variants among the leads, according to user-defined parameters. Many active, antifolate-resistant mutants of hDHFR were identified. Moreover, the approach has proven efficient in rapidly assessing kinetic (kcat) and inhibition parameters of the hDHFR variants (IC50). Structure-function relationship analysis based on kinetic investigation, available structural and functional data as well as modeling were performed. By monitoring which mutations have the greatest effect on binding, we have begun to build a molecular picture of the contacts involved in drug binding. By varying the drugs we test against, we gain a better understanding of the specific binding properties that determine ligand discrimination.

Alzheimer’s disease (AD) is a chronic, progressive neurodegenerative disorder, characterized clinically by a progressive loss of memory, cognitive function, ability to care for oneself and psychiatric symptoms. First-line agents for the treatment of AD are ChE inhibitors (DON, GAL), whose modest clinical efficacy and the high incidence of dose-limiting toxicities limit their clinical utility. In addition to AD, ChE inhibitors (PYR) are used for other medical conditions, such as myasthenia gravis (MG). Furthermore, ChE inhibitors (PYR) are used by military personnel prophylactically if impending exposure to chemical warfare agents, e.g., soman, is suspected. The purpose of this research project was to understand the effect of age on the in-vitro sensitivity of ChE inhibitors in human RBCs and plasma. Understanding possible covariates, such as age and gender, may assist in optimizing dosing regimens of ChE inhibitors and/or developing newer ChE inhibitors with better adverse effect profiles. Plasma PHYS concentrations were measured by a validated HPLC-FD method. RBC AChE activity and plasma BuChE activity were measured by a modified Ellman’s colorimetric method using the model substrates, acetylthiocholine and butyrylthiocholine, respectively. The kinetics of RBC and plasma ChE activity followed Michaelis-Menten kinetics. Acetylthiocholine was found to be a nonselective substrate (RBC AChE Km = 73 μM; plasma BuChE Km = 117 μM); while butyrylthiocholine was a selective substrate for plasma BuChE (RBC AChE Km = 130,000 μM; plasma BuChE Km = 72 μM). For the following studies, RBC AChE activity was measured using acetylthiocholine as the substrate and plasma BuChE activity was measured using butyrylthiocholine as the substrate. This research project was performed in two parts: First, mechanistic studies of PHYS, PYR, DON and GAL, explored and determined the mechanism of in-vitro inhibition of RBC AChE and plasma BuChE inhibition, as well as the in-vitro degradation of PHYS in human whole blood, plasma and RBC. PHYS was rapidly degraded in human whole blood, RBC and plasma and followed Michaelis-Menten kinetics but its degradation clearance - scaled to whole blood clearance - was only predicted to account for 4-6% (i.e., 195-261 ml/min) of the reported total body clearance for PHYS (4500 ml/min). RBCs were responsible for 60% of the whole blood clearance while plasma accounted for 40% of the whole blood clearance. Inhibition results indicated that both PHYS and PYR were nonselective and rapid suicide ChE inactivators. PYR inactivated RBC AChE more rapidly at low concentrations and inactivated plasma BuChE more rapidly at high concentrations, but inactivated both more rapidly than PHYS. PHYS was a more potent inactivator than PYR with a Ki for RBC AChE of 0.011 μM and 0.063 μM, respectively, and 0.023 μM and 0.036 μM, respectively for plasma BuChE. DON was found to be a noncompetitive inhibitor for RBC AChE (Ki,noncomp = 114 μM), but a competitive inhibitor for plasma BuChE (Ki,comp = 213 μM). GAL was found to be a competitive inhibitor for both RBC AChE (Ki,comp = 66 μM) and plasma BuChE (Ki,comp = 358 μM). The second part involved a clinical study with ten young and nine elderly healthy subjects, balanced for gender, who donated blood for an in-vitro study in order to assess any age- and gender-related differences in in-vitro sensitivity to RBC AChE and plasma BuChE inhibition to all four ChE inhibitors. Elderly adults were found to be 2-3-fold less sensitive compared to the young adults for PHYS (BuChE Ki,pss; 0.010 and 0.015 μM, young and elderly, respectively) and PYR (AChE Ki,pss; 0.12 and 0.25 μM, young and elderly, respectively) only, while neither DON nor GAL showed any age-related differences in sensitivity. The observed differences for PHYS and PYR may be due to kinetic differences in ChE inactivation between young and aged adults, rather then a difference in binding affinities/potencies. These carbamate ChE inhibitors, presumably, have a slower decarbamoylation rate in younger adults than elderly adults, which leads to the observed difference in in-vitro sensitivity. The above in-vitro results were consistent with results of a meta-analysis: In a study by Knapp et al. (1991), young males (n=6), receiving 18 mg, 24 mg and 30 mg PHYS tablets, showed similar ex-vivo plasma BuChE sensitivity to (28 %/(ng/ml)) as the in-vitro sensitivity for young males in the current study (33 %/(ng/ml)). On the other hand, in the study by Men (2004), elderly males (n=8) and females (n=8), receiving 6.7 μg/kg PHYS as 30-minute infusion, showed similar ex-vivo RBC AChE sensitivity (12 %/(ng/ml)) as the in-vitro sensitivity for elderly subjects in the current study (9.7 %/(ng/ml)). This suggests that in-vitro measurement of ChE sensitivity is predictive of ex-vivo sensitivity in clinical studies. The study results suggest that elderly adults may require a 2-3-fold higher blood concentration than young adults to achieve the same ChE inhibition. This may explain why for epistigmine, an investigational carbamate ChE inhibitor for the treatment of AD, the maximum tolerated dose observed in young adults (40 mg single dose) was lower than for older adults (90 mg/day). Higher sensitivity in young adults prevented further dose escalation, while all elderly subjects tolerated higher doses. This research may have implications for other diseases and conditions, most notably MG and as a prophylaxis of nerve gases poisoning. As patients with MG age, they may become less sensitive to PYR, the most common symptomatic treatment for MG, and an increase in dose may be required. Further, older military personnel assigned to receive PYR, may require increased doses to achieve the targeted 10% RBC AChE inhibition, necessary to protect against nerve gas poisoning.

La dihydrofolate réductase humaine (DHFRh) est une enzyme essentielle à la prolifération cellulaire, ce qui en fait une cible de choix pour le traitement de différents cancers. À cet effet, plusieurs inhibiteurs spécifiques de la DHFRh, les antifolates, ont été mis au point : le méthotrexate (MTX) et le pemetrexed (PMTX) en sont de bons exemples. Malgré l’efficacité clinique certaine de ces antifolates, le développement de nouveaux traitements s’avère nécessaire afin de réduire les effets secondaires liés à leur utilisation. Enfin, dans l’optique d’orienter la synthèse de nouveaux composés inhibiteurs des DHFRh, une meilleure connaissance des interactions entre les antifolates et leur enzyme cible est primordiale. À l’aide de l’évolution dirigée, il a été possible d’identifier des mutants de la DHFRh pour lesquels l’affinité envers des antifolates cliniquement actifs se voyait modifiée. La mutagenèse dite ¬¬de saturation a été utilisée afin de générer des banques de mutants présentant une diversité génétique au niveau des résidus du site actif de l’enzyme d’intérêt. De plus, une nouvelle méthode de criblage a été mise au point, laquelle s’est avérée efficace pour départager les mutations ayant entrainé une résistance aux antifolates et/ou un maintient de l’activité enzymatique envers son substrat natif, soient les phénotypes d’activité. La méthode de criblage consiste dans un premier temps en une sélection bactérienne à haut débit, puis dans un second temps en un criblage sur plaques permettant d’identifier les meilleurs candidats. Plusieurs mutants actifs de la DHFRh, résistants aux antifolates, ont ainsi pu être identifiés et caractérisés lors d’études de cinétique enzymatique (kcat et IC50). Sur la base de ces résultats cinétiques, de la modélisation moléculaire et des données structurales de la littérature, une étude structure-activité a été effectuée. En regardant quelles mutations ont les effets les plus significatif sur la liaison, nous avons commencé à construire un carte moléculaire des contacts impliqués dans la liaison des ligands. Enfin, des connaissances supplémentaires sur les propriétés spécifiques de liaison ont put être acquises en variant l’inhibiteur testé, permettant ainsi une meilleure compréhension du phénomène de discrimination du ligand. / Human dihydrofolate reductase (hDHFR) is an essential enzyme for cellular proliferation and it has long been the target of antifolate drugs for the treatment of various types of cancer. Despite the clinical effectiveness of current antifolate treatments, new drugs are required to reduce the side-effects associated with their use. An essential requirement for design of new antifolates is a better understanding of how these drugs interact with their targets. We applied directed evolution to identify mutant hDHFR variants with modified binding to some clinically relevant antifolates. A saturation mutagenesis approach was used to create genetic diversity at active-site residues of hDHFR and a new, efficient screening strategy was developed to identify the amino acids that preserved native activity and/or conferred antifolate resistance. The screening method consists in a high-throughput first-tier bacterial selection coupled with a second-tier in vitro assay that allows for rapid detection of the best variants among the leads, according to user-defined parameters. Many active, antifolate-resistant mutants of hDHFR were identified. Moreover, the approach has proven efficient in rapidly assessing kinetic (kcat) and inhibition parameters of the hDHFR variants (IC50). Structure-function relationship analysis based on kinetic investigation, available structural and functional data as well as modeling were performed. By monitoring which mutations have the greatest effect on binding, we have begun to build a molecular picture of the contacts involved in drug binding. By varying the drugs we test against, we gain a better understanding of the specific binding properties that determine ligand discrimination.