In eukaryotes, the first step of interpreting the genetic information is the transcription of DNA into RNA. For protein-coding genes, such transcription is carried out by RNA polymerase II. A special domain of RNA polymerase II, called the C-terminal domain (CTD), functions as a master controller for the transcription process by providing a platform to recruit regulatory proteins to nascent mRNA (Chapter 1-2). The modifications and conformational states of the CTD, termed the 'CTD code', represent a critical regulatory checkpoint for transcription. The CTD, found only in eukaryotes, consists of 26--52 tandem heptapeptide repeats with the consensus sequence, Tyr₁Ser₂Pro₃Thr₄Ser₅Pro₆Ser₇. Phosphorylation of the serines and prolyl isomerization of the prolines represent two major regulatory mechanisms of the CTD. Interestingly, the phosphorylation sites are typically close to prolines, thus the conformation of the adjacent proline could impact the specificity of the corresponding kinases and phosphatases. Understanding how those modifying enzymes recognize and regulate the CTD is important for expanding our knowledge on the transcription regulation and deciphering the 'CTD code'. During my PhD study, I studied the function of CTD phosphatases and prolyl isomerase in the CTD regulation using Scp1, Ssu72 and Pin1 as model regulators. Scp1 and Ssu72 are both Ser5 phosphatases. However, Ssu72 is an essential protein and regulates the global transcription while Scp1 epigenetically silences the expression of specific neuronal genes. Pin1 is a highly conserved phosphorylation-specific prolyl isomerase that recognizes the phospho-Ser/Thr-Pro motif within the CTD as one of its primary substrates in vivo. Among these enzymes, Scp1 is the focal point of this dissertation, as it was studied from different angles, such as enzymatic mechanism (Chapter 3 describes the capture of phospho-aspartyl intermediate of Scp1 as a direct evidence for the proposed two-step mechanism), specific inhibition (Chapter 4 describes the identification and characterization of the first specific inhibitor of Scp1), and its non-active-site contact with the CTD (Chapter 5 describes the structural basis of this contact). These studies are of great importance towards understanding the molecular mechanism of the dephosphorylation process of the CTD by Scp1. / text

Previous work has shown that thrombin activatable fibrinolysis inhibitor (TAFI) was unable to prolong lysis of purified clots in the presence of Lys-plasminogen (Lys-Pg), indicating a possible mechanism for fibrinolysis to circumvent prolongation mediated by activated TAFI (TAFIa). Therefore, the effects of TAFIa on Lys-Pg activation and Lys-plasmin (Lys-Pn) inhibition by antiplasmin (AP) were quantitatively investigated using a fluorescently labeled recombinant Pg mutant which does not produce active Pn. High molecular weight fibrin degradation products (HMW-FDPs), a soluble fibrin surrogate that models Pn modified fibrin, treated with TAFIa decreased the catalytic efficiency (kcat/Km) of 5IAF-Glu-Pg cleavage by 417-fold and of 5IAF-Lys-Pg cleavage by 55-fold. A previously devised intact clot system was used to measure the apparent second order rate constant (k2) for Pn inhibition by AP over time. While TAFIa was able to abolish the protection associated with Pn modified fibrin in clots formed with Glu-Pg, it was not able to abolish the protection in clots formed with Lys-Pg. However, TAFIa was still able to prolong the lysis of clots formed with Lys-Pg. TAFIa prolongs clot lysis by removing the positive feedback loop for Pn generation. The effect of TAFIa modification of the HMW-FDPs on the rate of tissue type plasminogen activator (tPA) inhibition by plasminogen activator inhibitor type 1 (PAI-1) was investigated using a previously devised end point assay. HMW-FDPs decreased the k2 for tPA inhibition rate by 3-fold. Thus, HMW-FDPs protect tPA from PAI-1. TAFIa treatment of the HMW-FDPs resulted in no change in protection. Vitronectin also did not appreciably affect tPA inhibition by PAI-1. Pg, in conjunction with HMW-FDPs, decreased the k2 for tPA inhibition by 30-fold. Hence, Pg, when bound to HMW-FDPs, protects tPA by an additional 10-fold. TAFIa treatment of the HMW-FDPs completely removed this additional protection provided by Pg. In conclusion, an additional mechanism was identified whereby TAFIa can prolong clot lysis by increasing the rate of tPA inhibition by PAI-1 by eliminating the protective effects of Pn-modified fibrin and Pg. Because TAFIa can suppress Lys-Pg activation but cannot attenuate Lys-Pn inhibition by AP, the Glu- to Lys-Pg/Pn conversion is able to act as a fibrinolytic switch to ultimately lyse the clot. / Thesis (Master, Biochemistry) -- Queen's University, 2008-01-31 17:04:50.447

Thesis (Ph. D.)--West Virginia University, 2008. / Title from document title page. Document formatted into pages; contains vii, 143 p. : ill. (some col.). Includes abstract. Includes bibliographical references.

Made available in DSpace on 2016-04-04T12:26:00Z (GMT). No. of bitstreams: 2 14.pdf: 930696 bytes, checksum: 4334fa07716ed0ea4227a0d296d9310c (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2015 / Fundação Oswaldo Cruz. Instituto de Tecnologia em Fármacos/Farmanguinhos. Rio de Janeiro, RJ, Brasil. / A asparaginase de origem bacteriana é o principal medicamento para o tratamento da leucemia linfoblástica aguda, um câncer que afeta principalmente as crianças. Apesar de efetivo, o medicamento causa sérias reações imunológicas por ser produzido por um procarioto. Atualmente, o medicamento existente no mercado brasileiro é importado, o que acarreta dependência tecnológica, alto custo na obtenção do medicamento e dificuldade de abastecimento. As asparaginase II de Saccharomyces cerevisiae codificada pelo gene ASP3 apresenta, por suas características, potencial para uso como medicamento antileucêmico. Em trabalhos anteriores, este gene foi clonado e expresso em altos níveis na levedura Pichia pastoris. O presente trabalho teve como objetivo caracterizar as propriedades físico-químicas e bioquímicas da asparaginase periplásmica recombinante produzida por P. pastoris, tendo sido avaliados as melhores condições de estocagem da enzima após ressuspensão, o efeito de alguns íons e de alguns compostos na atividade asparaginásica, a afinidade da asparaginase pelos substratos D e L-asparagina e L-glutamina e os seus parâmetros cinéticos. Observou-se que a ressuspensão da asparaginase de levedura em água destilada e mantida a 4 °C reteve em torno de 98% da atividade original após 96 horas, na presença de sorbitol 0,1 M, mostrando ser esta a melhor condição de estocagem. Os valores do Km e da Vmáx foram determinados, obtendo-se 2,461 ± 0,170mM e 0,090 ± 0,0017mM min-1, respectivamente. A asparaginase de P.pastoris recombinante apresentou maior afinidade pela D-asparagina, de forma semelhante à asparaginase nativa de S. cerevisiae; e baixa atividade glutaminásica, o que favorece a sua utilização como medicamento pelo menor risco de efeitos tóxicos. O EDTA não apresentou efeito negativo sobre a asparaginase de levedura, indicando não ser a mesma uma metaloenzima. A influência negativa de agentes redutores sobre a atividade enzimática indica a presença de pontes de enxofre na estrutura proteica. Os resultados obtidos são de extrema importância para a continuidade dos estudos da utilização da asparaginase de Pichia pastoris recombinante como agente antileucêmico. / Bacterial asparaginase is the main medicament for the treatment of acute lymphoblastic leukemia, a cancer that primarily affects children. Although effective, the medicine causes serious immunological reactions due to its prokaryotic origin. Currently, the existing drug in the Brazilian market is imported, which carries a technological dependence, high cost and supply difficulties. The asparaginase II of Saccharomyces cerevisiae encoded by the ASP3 gene, given its characteristics, has potential to be used as an antileukemic drug. In previous work, this gene was cloned and expressed at high levels in the yeast Pichia pastoris. The present work aimed to characterize the physicochemical and biochemical properties of the recombinant periplasmic asparaginase produced by P. pastoris, having been assessed the best enzyme storage conditions after resuspension, the effect of some ions and some compounds in asparaginasic activity, asparaginase affinity for yhe substrates D- and L-asparagine and Lglutamine and its kinetic parameters. It was observed that the yeast asparaginase resuspension in distilled water and kept at 4 °C retained about 98% of the original activity after 96 hours in the presence of 0.1 M sorbitol, showing this to be the best storage condition. The values of Km and Vmax were determined to be 2,461 ± 0,170mM e 0,090 ± 0,0017mM min-1, respectively. The recombinant asparaginase showed higher affinity for D-asparagine, similarly to the native S. cerevisiae asparaginase; and low glutaminasic activity, which favors its use as a medicine due to the lower risk of toxic effects. EDTA showed no negative effect on the yeast asparaginase, indicating that it is not a metalloenzyme. The negative influence of reducing agents on the enzymatic activity indicates the presence of sulfur bridges in the protein structure. These results are extremely important for the further studies on the use of the recombinant Pichia pastoris asparaginase as antileukemic agent.

L'émergence de bactéries résistantes aux antibiotiques constitue un problème majeur de santé publique responsable d'un nombre croissant de décès, surtout dans les hôpitaux. La résistance aux aminoglycosides est principalement due à l'expression d'enzymes capables de les modifier, comme les aminoglycosides phosphotransférases (APH).Le premier volet de ce travail de thèse vise à mieux comprendre les bases moléculaires des interactions protéine-ligands et de la catalyse enzymatique d'une de ces enzymes, l'APH(2”)-IVa. La spécificité de substrats a été caractérisée en détails pour différents aminoglycosides par des méthodes thermodynamiques, de mesures cinétiques à l'état stationnaire et transitoire, par amarrage moléculaire et cristallographie aux rayons X. La seconde partie de cette étude consiste à développer et optimiser des inhibiteurs allostériques de ces enzymes capables de restaurer l'efficacité des aminoglycosides. Pour cela, une cavité, potentiellement impliquée dans la dynamique de l'APH(2”)-IVa, a été identifiée à partir de simulations de dynamique moléculaire. Celle-ci a servi de cible pour cribler, in silico, 12 000 composés issus de la banque de données Zinc. Ainsi, 14 composés ont été testés in vitro pour leur capacité à diminuer l'activité enzymatique d'APH. Parmi ces derniers, une molécule s'est révélée être un inhibiteur non-compétitif de l'APH(2”)-IVa. Une étude des relations structure-fonction a permis de déterminer les groupements les plus favorables à l'inhibition et d'identifier un composé plus efficace. L'utilisation de ces deux molécules permet de restaurer, par exemple, la sensibilité à la sisomicine d'une souche d'E. faecium exprimant cette enzyme. Cette étude fournit des bases au développement de thérapies combinant un aminoglycoside et un inhibiteur des enzymes d'inactivation constituant une stratégie pour lutter contre la résistance aux antibiotiques dans un contexte thérapeutique. / Emergence of multi-drug resistant bacteria leads to increasing fatal issues especially in hospitals. Resistance to aminoglycoside antibiotics is mainly due to the expression of modifying enzymes, such as aminoglycoside phosphotransferases (APH). The first aim of this project was to elucidate the molecular basis of protein-ligand interactions and catalysis of one of these enzymes, the APH(2”)-IVa. Promiscuity of aminoglycoside substrates has thus been characterized in details using thermodynamics, transient and steady state kinetics, molecular docking and X-ray crystallography techniques.The second part aimed to develop and optimize allosteric inhibitors of these enzymes able to counterbalance aminoglycoside resistance. For this purpose, a small cavity, potentially involved in APH dynamics, was identified from molecular dynamic simulations. This cavity was used as a target to virtually screen 12 000 compounds of the Zinc database. The efficiency of the 14 high-ranked molecules to inhibit APH was evaluated in vitro and lead to the identification of a non-competitive inhibitor of APH(2”)-IVa. Structure-activity relationships highlighted the most favourable substituents for APH inhibition and permitted to obtain a more potent compound. The two molecules were able to restore, for example, sisomicin susceptibility of an E. faecium strain, expressing this enzyme.This study provides a basis for the development of combined chemotherapies (antibiotic with enzyme inhibitor) which may overcome antibiotic resistance in a clinical context.

Magister Scientiae - MSc / This thesis deals with the design and implementation of some novel numerical methods for non-linear singular pertubations problems (NSPPs). It provide a survey of asymptotic and numerical methods for some NSPPs in the past decade. By considering two test problems, rigorous asymptotic analysis is carried out. Based on this analysis, suitable numerical methods are designed, analyzed and implemented in order to have some relevant results of physical importance. Since the asymptotic analysis provides only qualitative information, the focus is more on the numerical analysis of the problem which provides the quantitative information. / South Africa

Recently, there has been a growing drive towards the bottom-up development of synthetic cells that mimic key cellular features. A cellular feature ubiquitous amongst cells is that of compartmentalisation. Compartmentalisation enables the spatiotemporal control of biochemical reactions and is thus vital for the development of synthetic cells. To date, most synthetic cell models have utilised classical membrane bound containers as model compartments. However, recent advances in cell biology have highlighted the importance of membraneless compartments formed via liquid-liquid phase separation (LLPS) as organisation centres. It has been suggested that these organelles play a critical role in regulating cell biochemistry, yet very little is known about their interactions with enzymatic reactions. Thus, aiming to develop novel synthetic capabilities, the work presented in this thesis designs and characterises synthetic cells which include features of membraneless compartmentalisation. These systems utilise complex coacervates, a specific type of LLPS that is driven by the electrostatic attraction of oppositely charged polymers, as model membraneless compartments. These low complexity systems subsequently provide ideal platforms for systematic investigations of the interaction of membraneless coacervate compartments with enzymatic reactions. In Chapter 3 and 4, I focus on developing a responsive synthetic cell system that recapitulates features of membrane-bound and membraneless compartmentalisation. I generate a pH-responsive system by exploiting the intrinsic pKa of cationic polylysine to trigger coacervation within a liposome. This synthetic cell is then functionalised with the enzyme formate dehydrogenase (FDH). I show that coacervate properties can be utilized to locally concentrate and activate the FDH reaction at low enzyme concentrations, thus demonstrating that membraneless compartments can activate reactions via sequestration into coacervate reaction centres. In Chapter 5, I then proceed to characterise whether the diffusive exchange of molecules across a droplet phase boundary effects enzyme dynamics. Synthetic cells constructed from emulsion droplets with coacervate sub-compartments were used as model systems with diffusive exchange, while bulk coacervate and supernatant phases were used as uncoupled model systems without exchange. I studied the FDH reaction in both models and I conclude that coupling of the phases increases reaction rates compared to an uncoupled system. When coupled, the supernatant acts as a ’sink’ removing the product NADH from the coacervate droplets. This increases the apparent reaction rate in the supernatant, while the reduction of NADH concentration in the coacervate reduces product inhibition. This demonstrated that the open phase boundary tightly couples membraneless droplets to their surroundings, which can ultimately lead to increased reaction rates both inside and outside the compartments. Finally in Chapter 6, I scrutinize enzyme kinetics of the enzymes FDH and β -galactosidase in the unique coacervate physicochemical environment using Michaelis-Menten assays in CM-Dex/PDDA bulk phase. Results show that the KM and Vmax of FDH significantly increased compared to buffer, while those of β-galactosidase do not. I hypothesise that the negatively charged formate substrate of the FDH reaction interacts strongly with the positively charged PDDA, decreasing its affinity for the enzyme. Furthermore, I suggest that the coacervate environment facilitates the rate limiting hydride transfer of the reaction, thereby increasing the maximum rate. This data demonstrates that the coacervate environment itself can tune and control enzyme dynamics. In conclusion, my work establishes responsive, tunable and enzymatically active syn- thetic cellular systems with features of membraneless compartmentalisation. My results indicate that membraneless compartments can have significant impact on the dynamics of enzymatic reactions, opening up possible ways to control reaction rates in synthetic systems and suggesting plausible functions for membraneless organelles in vivo. Overall, I demonstrate that rationally designed synthetic cells provide biomimetic experimental platforms that offer insights into the influence of membraneless compartmentalisation on enzymatic reactions. Parts of the presented work have been published as two first author publications in peer-reviewed journals. / ‘Bottom-up'’ Modelle synthetischer Zellen, die Schlüsselmerkmale zellbasierten Lebens imitieren, rücken immer mehr in den Fokus. Von zentraler Bedeutung ist hier die Kompartmentbildung. Sie erst ermöglicht die räumliche und zeitliche Kontrolle biochemischer Abläufe und ist daher entscheidend bei der Entwicklung synthetischer Zellen. Bisher wurden in der Mehrzahl der synthetischen Zellmodelle klassische, membrangebundene Reaktionsräume als Modellkompartimente verwendet. Jüngste Fortschritte in der Zellbiologie belegen jedoch die Bedeutung von membranlosen Kompartimenten, die durch Flüssig-Flüssig-Phasentrennung (LLPS) gebildet werden. Es wird angenommen, dass diese membranlosen Kompartimente eine zentrale Rolle bei der Regulierung der Zellchemie spielen. Jedoch ist bisher nur sehr wenig über ihren Einfluss auf enzymatische Reaktionen bekannt und experimentell belegt. Mit dem Ziel, die Bandbreite und das Verständnis synthetischer Modelle zu erweitern, wurden in dieser Arbeit neue Methoden entwickelt und dargestellt, die membranlose Kompartmentbildung benutzen. Es wurden hierfür komplexe Koazervate eingesetzt, eine spezielle Art der LLPS, welche durch die elektrostatische Anziehung von entgegengesetzt geladenen Polymeren angetrieben wird. Diese verhältnismäßig einfachen Systeme bieten eine ideale Plattform für systematische Untersuchungen des Einflusses von membranlosen Koazervatkompartimenten auf enzymatische Reaktionen. In den Kapiteln 3 und 4 konzentrierte ich mich auf die Entwicklung eines reaktionsfähigen synthetischen Modellsystems, das die Phänomene sowohl membrangebundener als auch membranfreier Kompartmentbildung vereint. Zur Steuerung der Koazervierung innerhalb von Liposomen wurde ein pH-reaktives System verwendet, welches sich den intrinsischen pKa von kationischen Polylysin zunutze macht. Diese synthetis- che Zelle wurde im folgenden Schritt mit dem Enzym Formiat-Dehydrogenase (FDH) funktionalisiert. Ich konnte damit zeigen, dass es die Eigenschaften von Koazervaten ermöglichen, die FDH-Reaktion bei global sehr niedrigen Enzymkonzentrationen zu aktivieren. Hierbei wirken die membranlosen Koazervate in Folge einer lokal er- höhten Enzymkonzentration als Zentren gesteigerter Reaktivität. Dies geschieht durch die lokale Konzentrationserhöhung in Koazervaten, was bei LLPS auch durch den Verteilungskoeffizient beschrieben wird. Mit anderen Worten agieren diese membran- losen Kompartimente durch Sequestrierung als Reaktionszentren. Im Kapitel 5 charakterisierte ich den Einfluss von diffusivem Molekülaustausch auf die Enzymkinetik über die Koazervat-Phasengrenze hinweg. Hierbei wurden zwei Systeme miteinander verglichen. Einerseits wurde ein synthetisches Zellmodell, beste- hend aus mikrofluidisch hergestellten Wasser-in-Öl Emulsionstropfen, die Koazervate enthalten, als Modellsystem mit diffusivem Austausch zwischen den Phasen verwendet. Andererseits wurden separate, reine Koazervatphasen und reine Überstandsphasen als Modellsysteme ohne Austausch verwendet. Ich habe die FDH-Reaktion in beiden Modellsystemen untersucht und kam zu dem Schluss, dass die Kopplung der Phasen die Reaktionsgeschwindigkeiten im Vergleich zu den ungekoppelten Systemen erhöht. Bei der Kopplung wirkt die Überstandsphase als Senke, die das Produkt NADH aus den Koazervaten aufnimmt. Dies erhöht die scheinbare Reaktionsgeschwindigkeit im Überstand, während die Verringerung der NADH-Konzentration im Koazervat die Produkthemmung verringert. Dies zeigt, dass die offene Phasengrenze membranloser Kompartimente eng mit ihrer Umgebung gekoppelt ist, was als erhöhte Reaktionsraten sowohl innerhalb als auch außerhalb der Kompartimente gemessen werden kann. Schließlich untersuchte ich in Kapitel 6 die Enzymkinetik der Enzyme FDH und β- Galaktosidase in der physikalisch-chemischen Umgebung des Koazervats. Mit Hilfe von Michaelis-Menten-Experimenten in der CM-Dextran/PDDA-Bulkphase konnte gezeigt werden, dass KM und Vmax von FDH im Vergleich zum Überstand signifikant erhöht sind, wohingegen jene von β-Galaktosidase ein solches Verhalten nicht zeigen. Das führte mich zu der Hypothese, dass das negativ geladene Formiatsubstrat der FDH- Reaktion stark mit dem positiv geladenen PDDA interagiert, wodurch seine Affinität für das Enzym abnimmt. Darüber hinaus wird der ratenbegrenzende Hydridtransfer in der Umgebung des Koazervats erleichtert und es kann eine Erhöhung der Reaktionsrate beobachtet werden. Die Daten zeigen, dass abhängig vom Koazervat-Milieu die Enzymdynamik in verschiedene Richtungen gesteuert werden kann. Zusammenfassend lässt sich sagen, dass meine Arbeit reaktionsfähige, steuerbare und enzymatisch aktive synthetische Zellsysteme mit Eigenschaften membranloser Kompartmentbildung etabliert. Meine Ergebnisse deuten darauf hin, dass membranlose Kompartimente einen signifikanten Einfluss auf die Dynamik enzymatischer Reaktio- nen haben. Meine Untersuchungen eröffnen damit neuartige Wege zur Kontrolle der Reaktionsgeschwindigkeit in synthetischen Systemen und erweitern das Verständnis möglicher Funktionen membranloser Organellen in vivo. Insgesamt zeige ich, dass über- legt entworfene synthetische Zellen eine hervorragende biomimetische Plattform bieten, um Einblicke in den Einfluss von membranloser Kompartimentierung auf enzymatische Reaktionen zu gewinnen. Teile der vorgestellten Arbeit wurden als wissenschaftliche Beiträge in zwei begutachteten Journalen als Erstautor veröffentlicht.

>Magister Scientiae - MSc / This thesis deals with the design and implementation of some novel numerical methods for nonlinear singular perturbations problems (NSPPs). We provide a survey of asymptotic and numerical methods for some NSPPs in past decade. By considering two test problems, rigorous asymptotic analysis is carried out. Based on this analysis, suitable numerical methods are designed, analyzed and implemented in order to have some relevant results of physical importance. Since the asymptotic analysis provides only qualitative information, the focus is more on the numerical analysis of the problem which provides the quantitative information.

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