The relentless commercial drive for smaller, faster, and cheaper semi-conductor devices has pushed the existing patterning technologies to their limits. Photolithography, one of the crucial processes that determine the feature size in a microchip, is currently facing this challenge. The immaturity of next generation lithography (NGL) technology, particularly EUV, forces the semiconductor industry to explore new processing technologies that can extend the use of the existing lithographic method (i.e. ArF lithography) to enable production beyond the 32 nm node. Two new resolution enhancement techniques, double exposure lithography (DEL) and pitch division lithography (PDL), were proposed that could extend the resolution capability of the current lithography tools. This thesis describes the material and process development for these two techniques. DEL technique requires two exposure passes in a single lithographic cycle. The first exposure is performed with a mask that has a relaxed pitch, and the mask is then shifted by half pitch and re-used for the second exposure. The resolution of the resulting pattern on the wafer is doubled with respect to the features on the mask. This technique can be enabled with a type of material that functions as optical threshold layer (OTL). The key requirements for materials to be useful for OTL are a photoinduced isothermal phase transition and permeance modulation with reverse capabilities. A number of materials were designed and tested based on long alkyl side chain crystalline polymers that bear azobenzene pendant groups on the main chain. The target copolymers were synthesized and fully characterized. A proof-of-concept for the OTL design was successfully demonstrated with a series of customized analytical techniques. PDL technique doubles the line density of a grating mask with only a single exposure and is fully compatible with current lithography tools. Thus, this technique is capable of extending the resolution limit of the current ArF lithography without increasing the cost-of-ownership. Pitch division with a single exposure is accomplished by a dual-tone photoresist. This thesis presents a novel method to enable a dual-tone behavior by addition of a photobase generator (PBG) into a conventional resist formulation. The PBG was optimized to function as an exposure-dependent base quencher, which mainly neutralizes the acid generated in high dose regions but has only a minor influence in low dose regions. The resulting acid concentration profile is a parabola-like function of exposure dose, and only the medium exposure dose produces a sufficient amount of acid to switch the resist solubility. This acid response is exploited to produce pitch division patterns by creating a set of negative-tone lines in the overexposed regions in addition to the conventional positive-tone lines. A number of PBGs were synthesized and characterized, and their decomposition rate constants were studied using various techniques. Simulations were carried out to assess the feasibility of pitch division lithography. It was concluded that pitch division lithography is advantageous when the process aggressiveness factor k₁ is below 0.27. Finally, lithography evaluations of these dual-tone resists demonstrated a proof-of-concept for pitch division lithography with 45 nm pitch divided line and space patterns for a k₁ of 0.13. / text

Experimental observations indicate the presence of attached, gravity induced, horizontal buoyant currents above large area fires. Their driving mechanism is indirect and resembles the one observed above heated horizontal plates. Classic plume modelling is satisfactory for providing information for the flow far from the source. In dealing with large areas and directing attention to the flow close to the source, the classic plume theory should fail because the radial pressure gradient that is responsible for the driving of the flow is squeezed in the long and thin classic plume assumption. For this we propose a new plume structure for the description of the buoyant flow above a circular region of large radius L as “The flow field must be divided into three regions. A region where the flow is predominantly horizontal and attached to the surface, a transition region from horizontal to vertical where separation of the attached current takes place, and a region where vertical flow is established and classic plume theory can be applied”. A model for the description of the gross properties of the horizontal currents is developed under the term “horizontal plume”. The modified Richardson number for the horizontal plume a, being analogous to the radius of the large area, is studied asymptotically in the limit a → ∞ and second order uniformly valid semi-analytical solutions are obtained. The hot plate experiment was set up in order to test the model and facilitate its improvement. A chapter is dedicated to the data analysis coming from thermocouple readings and visualisation of the flow using particle image velocimetry.In the remainder of this thesis two classic problems of laminar natural convection are revisited. That of the first order laminar boundary layer above an isothermal circular plate of radius a and the first order laminar boundary layer above the semi- infinite plate inclined to horizontal. In both cases allowances to variable property effects were made through the introduction of a nondimensional parameter λT, with its value set to zero implying the assumption of the Boussinesq approximation. For the circular plate, fourth order series solutions were obtained valid at the edge of the plate where the effects of λT and Prandtl number Pr are studied. Furthermore a finite difference scheme for the numerical solution of the nonsimilar partial integro- differential equation was developed using the Keller Box method and compared with results obtained from the commercial finite element software COMSOL Multiphysics 3.5a. For the semi-infinite plate, fourth order series approximations valid at the edge of the plate were obtained, while an extensive analysis for the effect of λT, Pr and inclination parameter σ was performed on the flow. Positions of the separation points when the inclination is negative (σ < 0) as a function of Pr and λT were recovered.

En ökad utbredning av vankomycinresistenta enterokocker (VRE) har setts i Sverige sedan 2007. Bakteriemi orsakad av VRE är mycket svårbehandlad, varför snabbare tillförlitlig resistensdiagnostik är betydelsefullt för att minska dödlighet, vårdtider, vårdkostnader och belastning på sjukvårdssystemet. På mikrobiologilaboratoriet, Region Jönköpings län (RJL), tar idag identifiering av fenotypisk vankomycinresistens vid optimala förhållanden 6 timmar, räknat från att enterokocker konstaterats växa i blodet. Resistensgenerna vanA och vanB, som bland andra orsakar vankomycinresistens hos enterokocker, kan genetiskt verifieras med loop-mediated isothermal amplification men tar idag upp till ett dygn då bakteriekolonier används som analysmaterial i arbetsrutinen på molekylärbiologilaboratoriet, RJL. Syftet med studien var att utvärdera bakteriepellet som analysmaterial för genetisk identifiering av vanA och vanB, på Genie® II Mk2 med eazyplex® VRE basic, hos enterokocker från positiva blododlingar. För att utvärdera bakteriepellet som analysmaterial analyserades isolat av Enterococcus faecium (n=17) och Enterococcus faecalis (n=5) från bakteriepellets tillverkade från simulerade positiva blododlingar med eazyplex® VRE basic på Genie® II Mk2, varpå resultaten jämfördes mot isolatens faktiska närvaro/frånvaro av vanA/vanB. Samstämmigheten av de uppmätta- och de förväntade resultaten var fullständig, vilket indikerar att bakteriepellet med hög tillförlitlighet kan användas som analysmaterial till eazyplex® VRE basic för att påvisa vanA och vanB hos enterokocker i blododlingar. / An increased prevalence of vancomycin-resistant enterococci (VRE) has been observed in Sweden since 2007. Treating bacteremia caused by VRE is difficult, which is why faster, and reliable resistance diagnostics are important. At the Microbiology laboratory, Region Jönköping County, the identification of phenotypic vancomycin resistance under optimal conditions takes 6 hours from when growth of enterococci in blood is determined. The genes vanA and vanB, which among others cause vancomycin resistance, can be genetically verified by loop-mediated isothermal amplification, but takes up to one day since bacterial colonies are used as analysis material. The aim of the study was to evaluate bacterial pellet as an analytical material for genetic identification of vanA and vanB, on Genie® II Mk2 with eazyplex® VRE basic, in enterococci from positive blood cultures. To evaluate the bacterial pellet, isolates of Enterococcus faecium (n=17) and Enterococcus faecalis (n=5) from bacterial pellets made from simulated positive blood cultures were analyzed with eazyplex® VRE basic on the Genie® II Mk2, and the results were compared to the actual presence/absence of vanA/vanB in the isolates. The complete coherence between the expected and measured results indicates that the bacterial pellet can be used as an analytical material for eazyplex® VRE basic.

<p>The intricate interplay of biomolecules acting together, rather than alone, provides insight into the most basic of cellular functions, such as cell signaling, metabolism, defense, and, ultimately, the creation of life. Inherent in each of these processes is an evolutionary tendency towards increased efficiency by means of biolgocial synergy-- the ability of individual elements of a system to produce a combined effect that is different and often greater than the sum of the effects of the parts. Modern biochemists are challenged to find model systems to characterize biological synergy.</p><p>We discuss the multicomponent, enzyme complex the cellulosome as a model system of biological synergy. Native cellulosomes comprise numerous carbohydrate-active binding proteins and enzymes designed for the efficient degradation of plant cell wall matrix polysaccharides, namely cellulose. Cellulosomes are modular enzyme complexes, comparable to enzyme "legos" that may be readily constructed into multiple geometries by synthetic design. Cellulosomal enzymes provide means to measure protein efficiency with altered complex geometry through assay of enzymatic activity as a function of geometry.</p><p>Cellulosomes are known to be highly efficient at cellulose depolymerization, and current debates on the molecular origins of this efficiency suggest two related effects provide this efficiency: i) substrate targeting, which argues that the localization of the enzyme complex at the interface of insoluble cell wall polysaccharides facilitates substrate depolymerization; and ii) proximity effects, which describe the implicit benefit for co-localizing multiple enzymes with divergent substrate preferences on the activity of the whole complex.</p><p>Substrate targeting can be traced to the activity of a single protein, the cellulosomal scaffoldin cellulose binding module CBM3a that is thought to uniquely bind highly crystalline, insoluble cellulose. We introduce methods to develop a molecular understanding of the substrate preferences for CBM3a on soluble and insoluble cellulosic substrates. Using pivaloylysis of cellulose triacetate, we obtain multiple soluble cello-oligosaccharides with increasing degree of glucose polymerization (DP) from glucose (DP1) to cellodecaose (DP10) in high yield. Using calorimetry and centrifugal titrations, cello-oligosacharides were shown to not bind Clostridial cellulolyticum CMB3a. We developed AFM cantilever functionalization protocols to immobilize CBM3a and then probe the interfacial binding between CBM3a and a cellulose nanocrystal thin film using force spectroscopy. Specific binding at the interface was demonstrated in reference to a control protein that does not bind cellulose. The results indicate that i) CBM3a specifically binds nanocrystalline cellulose and ii) specific interfacial binding may be probed by force spectroscopy with the proper introduction of controls and blocking agents.</p><p>The question of enzyme proximity effects in the cellulosome must be answered by assaying the activity of cellulosomal cellulases in response to cellulosome geometry. The kinetic characterization of cellulases requires robust and reproducible assays to quantify functional cellulase content of from recombinant enzyme preparations. To facilitate the real-time routine assay of cellulase activity, we developed a custom synthesis of a fluorogenic cellulase substrate based on the cellohexaoside of Driguez and co-workers (vide infra). Two routes to synthesize a key thiophenyl glycoside building block were presented, with the more concise route providing the disaccharide in four steps from a commercial starting material. The disaccharide building blocks were coupled by chemical activation to yield the fully protected cellohexaoside over additional six steps. Future work will include the elaboration of this compound into an underivatized FRET-paired hexasaccharide and its subsequent use in cellulase activity assays.</p><p>This dissertation also covers an experimental system for the evaluation of methonium desolvation thermodynamics. Methonium (-N+Me3, Am) is an organic cation widely distributed in biological systems. The appearance of methonium in biological transmitters and receptors seems at odds with the large unfavorable desolvation free energy reported for tetramethylammonium (TMA+), a frequently utilized surrogate of methonium. We report an experimental system that facilitates incremental internalization of methonium within the molecular cavity of cucurbit[7]uril (CB[7]).</p><p>Using a combination of experimental and computational studies we show that the transfer of methonium from bulk water to the CB[7] cavity is accompanied by a remarkably small desolvation enthalpy of just 0.5±0.3 kcal*mol-1, a value significantly less endothermic than those values suggested from gas-phase model studies (+49.3 kcal*mol-1). More surprisingly, the incremental withdrawal of methonium surface from water produces a non- monotonic response in desolvation enthalpy. A partially desolvated state exists, in which a portion of the methonium group remains exposed to solvent. This structure incurs an increased enthalpic penalty of ~3 kcal*mol-1 compared to other solvation states. We attribute this observation to the pre- encapsulation de-wetting of the methonium surface. Together, our results offer a rationale for the wide biological distribution of methonium and suggest limitations to computational estimates of binding affinities based on simple parameterization of solvent-accessible surface area.</p> / Dissertation

CD2AP is a member of the CD2AP/CIN85 family of adaptors and involved in several cellular processes, such as kidney podocyte development, actin mediated membrane trafficking and T cell activation. It contains three SH3 domains whose binding properties and interaction partners remain largely unexplored. The CD2AP SH3 interaction with the novel partner Rab5-activating GEF RIN3 was studied extensively by isothermal titration calorimetry (ITC), peptide scanning arrays, mutagenesis and X-ray crystallography. Mapping of the interaction regions showed that human RIN3 contains two binding sites for the CD2AP SH3 domains. From these studies, the CD2AP SH3 recognition motif P-x-P/A-x-x-R emerged. Two crystal structures (1.65 &Aring; and 1.2 &Aring;) of the SH3 1 and SH3-2 domains in complex with RIN3 epitopes 1 and 2 respectively revealed that these residues serve as anchoring points. With the aid of bioinformatics tools, this motif was used to conduct a peptide array-based screen for additional signalling partner candidates. One of the hits was the Arf-GAP ARAP1. ITC data indicate that the three SH3 domains differentially recognise three ARAP1 epitopes, with the first ARAP1 epitope binding to SH3-2 in the nanomolar range. A crystal structure (1.6 &Aring;) of the SH3-2 domain in complex with the first ARAP1 epitope implicates two additional anchoring residues that extend beyond the PPII helical region of the canonical motif. The CD2AP/ARAP1 interaction was confirmed in podocytes and cancer cells at the endogenous protein level. Even though RIN3 and ARAP1 are involved in membrane trafficking, a direct link to CD2AP had not been reported before. Other candidates from the peptide array analyses were also investigated by ITC. In conclusion, this study led to the elucidation of the CD2AP SH3-1 and SH3-2 domain binding signatures and the identification of putative novel binding partners for all three SH3 domains. Lastly, insight was gained into the binding preferences of CD2AP SH3-3.

Dans cette thèse, une approche microcinétique expérimentale est utilisée pour caractériser des étapes élémentaires impliquées dans l’oxydation de CO par O2 sur des catalyseurs à base de Pd et d’Au supportés sur oxydes métalliques et identifier celles qui contrôlent la vitesse de réaction. Sur un catalyseur 1,4%Pd/Al2O3, l’évolution de la production de CO2 (RCO2(t)) par oxydation des espèces CO adsorbées (2 linéaires L et 2 pontées P) a été suivie lors de cycles successifs formation - oxydation des espèces. Une période d’induction est observée, donnant un pic de CO2 caractérisé partm et RCO2m. L’étude de l’impact de différents paramètres expérimentaux sur tm et RCO2m: le tempsde désorption avant oxydation, la pression partielle de O2, la température et le prétraitement ducatalyseur a permis de caractériser les étapes superficielles impliquées. Un modèle cinétique basé surl’oxydation des espèces CO P par une espèce oxygène faiblement adsorbée formée sur des sites libéréspar la désorption et/ou l’oxydation des espèces CO L a permis d’interpréter ces impacts. Ce modèle aégalement permis d’interpréter les différences d’activités du catalyseur vis-à-vis de la réaction CO/O2en fonction de son prétraitement après réduction sous H2 à 713 K : un refroidissement sous hydrogènepermet d’obtenir des conversions de CO proches de 100% à 300 K en excès de O2 alors qu’unedésorption préalable à 713 K donne de faibles conversions (< 4%). Ces différences sont attribuées àune reconstruction de la surface des particules de Pd par désorption de l’hydrogène à 713 K.Sur Au supporté sur Al2O3 et SiO2, l’étude a porté sur la première étape de l’oxydation du CO:l’adsorption du CO. Sous certaines conditions (température et pressions) l’adsorption de CO à 300 Kentraîne une reconstruction progressive des particules d’or modifiant significativement les propriétésdes espèces adsorbées. La cinétique de cette reconstruction à 300 K est étudiée et interprétée / The aim of this thesis is to use an experimental microkinetic approach to characterize elementary steps involved in the oxidation of CO by O2 over Pd and Au catalysts supported on Al2O3 and SiO2 and to identify those controlling the rate of the reaction. On 1.4% Pd/Al2O3, the evolution of the production of CO2 (RCO2(t)) by oxidation of the adsorbed CO species (2 linear L and 2 bridged B) was followed during successive formationoxidation cycles. An induction period is observed leading to a CO2 peak characterized by tm and RCO2m. The study of the impacts of different experimental parameters on tm and RCO2m such as the duration of a desorption before oxidation, the partial pressure of O2, the temperature and thepretreatment of the catalyst allows us to characterize the different surface elementary steps of thereaction. A kinetic model is proposed which is based on the oxidation of the B CO species by a weaklyadsorbed O species formed on Pd sites liberated by the desorption and the oxidation of the L COspecies. This model allows us to interpret the differences in the catalytic activity of the catalyst for theCO/O2 reaction according to the pretreatment procedure after reduction with H2 at 713 K: cooling thesolid in hydrogen permits obtaining a CO conversion of ��100% in excess O2 whereas a desorption at713 K provides CO conversions < 4%. These differences are ascribed to the reconstruction of thesurface of the Pd particles during the hydrogen desorption at 713 K. On Au/Al2O3 and Au/SiO2, the study concerns the first step of CO oxidation: the adsorption of CO. For a set of experimental conditions (Temperature and partial pressures), the adsorption of CO at 300 K leads to a progressive reconstruction of the Au particles modifying significantly the propertiesof the adsorbed species. The kinetic of this reconstruction is studied.

A doença de Chagas, causada pelo Trypanosoma cruzi, é uma doença tropical que aflige milhões de pessoas, gerando consequências sócio-econômicas devastadoras. Ela tem sido considerada uma doença tropical super-negligenciada, já que os únicos fármacos disponíveis para o seu tratamento apresentam baixa eficácia e causam vários efeitos colaterais. Além disso, os mesmos foram introduzidos há mais de três décadas. Com esse cenário, é evidente a necessidade da descoberta, desenvolvimento e introdução de novos fármacos para o tratamento eficiente e seguro da doença de Chagas. A enzima gliceraldeído-3-fosfato desidrogenase (GAPDH) é um alvo biomacromolecular atraente para a descoberta de novos fármacos contra os tripanossomatídeos, em virtude das enzimas da via glicolítica exercerem um papel fundamental no fornecimento de energia para a sobrevivência do parasito. Essa enzima foi selecionada neste trabalho de tese para a realização de estudos em química medicinal com base em quiminformática com o objetivo de identificar potenciais inibidores enzimáticos e do T. cruzi. Na primeira etapa desta tese, o ensaio virtual baseado na estrutura do alvo (SBVS) foi usado na identificação e seleção dos compostos. Como resultado do planejamento in silico, vinte compostos foram selecionados e avaliados experimentalmente na segunda etapa do trabalho empregando a técnica de calorimetria de titulação isotérmica (ITC). Destes, onze inibiram a GAPDH de T. cruzi resultando numa elevada taxa de acerto (>= 20%). Os novos inibidores apresentam excelente eficiência do ligante (LE), bem como mostram ligeira seletividade pela enzima do parasito. O ensaio dos inibidores contra a forma tripomastigota do T. cruzi identificou dois compostos capazes de inibir essa forma infectiva e um deles também mostrou ser um potente inibidor da forma amastigota do parasito, além de apresentar baixa toxidez. As duas melhores classes de inibidores da GAPDH e do parasito foram selecionadas para o estabelecimento de relações quantitativas entre a estrutura química e a atividade biológica (QSAR). Estudos de QSAR 2D (HQSAR) forneceram modelos com elevada capacidade preditiva e proporcionaram a identificação de características estruturais importantes para a otimização dos ligantes a compostos-matrizes. / Chagas disease, caused by Trypanosoma cruzi, is a tropical disease, which afflicts millions of people, thus generating devastating socio-economic consequences. It has been pointed out that it is a super-neglected tropical disease, based on available drugs with low efficacy and that give rise to many side effects. In addition, these drugs were introduced three decades ago. With this scenario, it is clear the necessity of the discovery, development and introduction of new efficient drugs to treat Chagas disease. The enzyme glyceraldehyde-3-phosphate dehydrogenase is a promising target for the development of new drugs against trypanosomatides, since the enzymes of the glycolytic pathway display a fundamental role in the energy supply to parasite survival. In this thesis, this enzyme was selected for medicinal chemistry within the cheminformatics framework aiming at the identification of potential enzymatic and parasite inhibitors. In the first part, structure-based virtual screening (SBVS) methods were employed in the selection and identification of compounds. Based on the in silico design, twenty compounds were selected and experimentally evaluated in the second part using the isothermal titration calorimetry (ITC) technique. Out of these, eleven compounds inhibited the T. cruzi GAPDH, resulting in high hit rates (>= 20 %). The new selected inhibitors display excellent ligand efficiency (LE), as well as some selectivity for the parasite enzyme. The inhibitors assay against the trypomastigote form of T. cruzi was used to identify two compounds able to inhibit this infective form, and one showed to be a strong amastigote parasite inhibitor, also disclosing low cytotoxicity profile. The best two classes of GAPDH and parasite inhibitors were selected for the establishment of a quantitative structure-activity relationship (QSAR). 2D QSAR (HQSAR) studies resulted in linear models with high predictive power, amenable for the identification of important structural features in the process of hit-to-lead optimization.

Mais de quarenta proteínas humanas estão envolvidas em doenças amilóides, sendo a transtirretina (TTR) uma dessas. A dissociação do tetrâmero da TTR é a etapa limitante para sua via de agregação. Esta etapa pode ser dificultada pela ligação de pequenas moléculas a dois sítios na interface tetramérica da TTR e facilitada em variantes mutantes. A mutante V30M é a variante amiloidogênica mais frequente da TTR e, apesar da mutação não se encontrar no sítio de ligação de pequenas moléculas, pode limitar a interação de inibidores com esta proteína. Desta forma, a busca de inibidores da agregação da TTR tipo selvagem (TTRwt) e mutantes amiloidogênicas vem sendo realizada. Na presente tese, flavonóides, freqüentemente encontrados em alimentos, e agonistas sintéticos do receptor do hormônio tireoidiano, seletivos para a isoforma beta deste receptor, foram selecionados para testes de inibição da agregação da TTRwt e mutante V30M. A interação dos melhores inibidores com a TTR foi também caracterizada em detalhes. Para isto, um ensaio de agregação in vitro da TTR foi utilizado para triagem dos compostos; e a assinatura termodinâmica da interação dos melhores inibidores com a TTR, bem como as estruturas cristalográficas TTR:inibidores foram determinadas por calorimetria de titulação isotérmica e cristalografia de proteínas, respectivamente. Os compostos sintéticos, GC-1 e GC-24, mostraram-se inibidores eficazes, porém com potência moderada. Já as flavonas luteolina (LUT), apigenina (API) e crisina (CHR), a flavanona naringenina (NAR), o flavonol kaenferol (KAE) e a isoflavona genisteína (GEN) apresentaram boa potência e eficácia de inibição da agregação da TTR in vitro. Os inibidores NAR, CHR, GEN e KAE não mostraram mesma capacidade de inibição da mutante V30M e apresentaram cooperatividade negativa para ligação aos dois sítios da TTR. A posição dos inibidores no sítio, bem como a variabilidade química/ estrutural dos compostos testados parecem influenciar os mecanismos de interação com os dois sítios da TTR e a ligação à mutante V30M. Modificações no sítio da mutante V30M foram identificadas e são apontadas como a principal causa para a seletividade de alguns inibidores à forma selvagem da TTR. De modo geral, a investigação detalhada da interação de pequenas moléculas com a TTR permitiu propor as bases moleculares da cooperatividade entre os sítios desta proteína e das diferenças de interação dos inibidores com a forma selvagem e mutante V30M da TTR. / More than forty human proteins are involved in human amyloid diseases, being transthyretin (TTR) one of these. TTR tetramer dissociation is a limiting step for its aggregation pathway. This step can be delayed by small molecules binding to two binding sites in the TTR tetramer interface and enhanced in TTR amyloidogenic variants. The V30M mutant is the most frequent TTR amyloidogenic variant and, eventhough the mutation is not situated in the TTR binding site, this mutation can limit small molecule interaction with the V30M mutant. Therefore, the search for wild type (TTRwt) and amyloidogenic TTR mutant inhibitors is under investigation. In the present thesis, flavonoids, frequently found in food, and synthetic thyroid hormone receptor beta-selective agonists were selected for evaluation of their inhibition ability on TTRwt and V30M mutant aggregation. The interaction of the best inhibitors with TTR was also characterized in details. For this, an in vitro TTR aggregation assay was used for inhibitor screening, and the thermodynamic signature of interaction, as well the TTR:inhibitors crystal complexes were determined by isothermal titration calorimetry and protein crystallography, respectively. The synthetic compounds, GC-1 and GC-24, displayed high efficacy, however moderated inhibition potency. The flavones luteolin (LUT), apigenin (API), chrisin (CHR), the flavanone naringenin (NAR), the flavonol kaenferol (KAE) and the isoflavone genistein (GEN) showed good potency and efficacy of TTR aggregation inhibition in vitro. The inhibitors, CHR, NAR, GEN and KAE, had lower inhibition capacity to the V30M mutant, and displayed negative cooperativity of binding to the two TTR binding sites. The inhibitor position in the binding site, as well as the chemical/ structural variability of the tested compounds seems to influence the interaction mechanism with the two TTR binding sites and the binding to the V30M mutant. Modifications on the V30M mutant binding sites were identified and pointed as the main reasons for the selectivity of some inhibitors to the wild type TTR. Overall, the detailed inspection of small molecule interaction with TTR suggests the molecular basis of the cooperativity between the two TTR binding sites and also of the differences between the inhibitors interaction with the wild type and with the V30M mutant TTR.

Apesar da incidência per capita da tuberculose (TB) ter se mantido estável em 2005, o número de novos casos que surgem a cada ano continua a aumentar no mundo todo. De acordo com a Organização Mundial de Saúde, foram estimados 9,4 milhões de novos casos de TB em 2008, dos quais 1,4 milhões eram HIV - positivos, e com 1,8 milhões de mortes - o equivalente a 4.500 mortes por dia. Fatores como migração, privação sócio-econômica, co-infecção TB-HIV e o aparecimento de cepas resistentes contribuíram para o aumento do número de casos de TB no mundo, principalmente nos países onde a TB já foi considerada erradicada, e criaram a necessidade do desenvolvimento de novas terapêuticas. Alvos moleculares específicos, que são essenciais para o patógeno, e ausentes no hospedeiro, como as enzimas da via do ácido chiquímico são alvos atraentes para o desenvolvimento de novas drogas antituberculose. Essa via leva à síntese de compostos aromáticos, como aminoácidos aromáticos, e é encontrada em plantas, fungos, bactérias e parasitas do phylum Apicomplexa, mas está ausente em humanos. No ano de 2000, foi comprovada a essencialidade dessa via para a viabilidade do bacilo, tornando todas essas enzimas alvos validados para estudo. A segunda enzima da via, deidroquinato sintase (DHQS), catalisa a conversão de 3-deoxi-D-arabino heptulosonato-7-fosfato em 3-deidroquinato, o primeiro composto cíclico. Neste trabalho, são descritos o requerimento de metais divalentes na reação e a determinação do mecanismo cinético da DHQS. Os parâmetros cinéticos verdadeiros foram determinados e, juntamente com os experimentos de ligação, o mecanismo rápido-equilíbrio aleatório foi proposto. O tratamento com EDTA aboliu completamente a atividade de DHQS, sendo que a adição de Co+2 e Zn+2 levam a recuperação total e parcial da atividade enzimática, respectivamente. O excesso de Zn+2 inibe a atividade DHQS, e os dados de ITC indicaram a presença de dois sítios seqüenciais de ligação, o que é consistente com a existência de um sítio secundário inibitório. O protocolo de cristalização foi estabelecido e experimentos em andamento proporcionarão a elucidação da estrutura tridimensional da DHQS, que irá beneficiar tanto o desenho de novos inibidores como uma análise detalhada dos rearranjos do domínio da proteína. Em conjunto, estes resultados representam um passo essencial para o desenho racional de inibidores específicos que podem fornecer uma alternativa promissora para um novo, eficaz, e mais curto de tratamento para TB. / Although the estimated per capita tuberculosis (TB) incidence was stable in 2005, the number of new cases arising each year is still increasing globally. According with World Health Organization, there were estimated 9.4 million new TB cases in 2008, from which 1.4 million were HIV-positive, with 1.8 million deaths total – equal to 4500 deaths a day. Migration, socio-economic deprivation, HIV co-infection and the emergence of extensively-resistance strains, have all contributed to the increasing number of TB cases worldwide, mainly in countries where it was once considered eradicated, and have created an urgent need for the development of new therapeutics against TB. Specific molecular targets, that are essential to the pathogen, and absent in the host, like the enzymes of the shikimate pathway, are attractive targets to development of new antitubercular drugs. This pathway leads to the biosynthesis of aromatic compounds, including aromatic amino acids and it is found in plant, fungi, bacteria and Apicomplexa parasites, but is absent in humans. In 2000, this pathway was proved to be essential to the viability of the pathogen, which validates all its enzymes as potential targets. The second enzyme of this pathway, dehydroquinate synthase (DHQS), catalyzes the conversion of 3-deoxy-D-arabinoheptulosonate 7-phosphate in 3-dehydroquinate, the first cyclic compound. In this work, we described the metal requirement and kinetic mechanism determination of the dehydroquinate synthase. The determination of the true kinetic parameters was performed, and, in addition to ligand binding experiments, the rapid-equilibrium random mechanism was determined. The treatment with EDTA abolished completely the activity of DHQS, and the addition of Co+2 and Zn+2 leads to full and partial recovery of enzyme activity, respectively. Excess of Zn+2 inhibits the DHQS activity, and the ITC data revealed two sequential binding sites, which is consistent with the existence of a secondary inhibitory site. The crystallization protocol was established and ongoing experiments will provide the three-dimensional structure of mtDHQS, which will benefit both the design of novel inhibitors as well as detailed analysis of domain rearrangements of protein. Taken together, these results represent an essential step for the rational design of specific inhibitors that can provide a promising alternative to a new, effective, and shorter treatment for TB.

Submitted by Sandra Pereira (srpereira@ufrrj.br) on 2016-10-17T10:53:24Z No. of bitstreams: 1 2016 - Monique Barreto Santos.pdf: 2356049 bytes, checksum: 8a379b47682a5e067746503ee59b6d27 (MD5) / Made available in DSpace on 2016-10-17T10:53:24Z (GMT). No. of bitstreams: 1 2016 - Monique Barreto Santos.pdf: 2356049 bytes, checksum: 8a379b47682a5e067746503ee59b6d27 (MD5) Previous issue date: 2016-02-29 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico - CNPq / Proteins are biopolymers of high nutritional and functional significance has been widely used as food ingredients. The interaction between two different proteins oppositely charged, and can give rise to complex coacervate currently used as an ingredient in food technology or as a microencapsulating agent. The formation of complex coacervates between Lysozyme and Ovalbumin and between Bovine serum albumin (BSA) and Lysozyme has been investigated as a function of pH, mass ratio of total and concentration of NaCl. For both interactions studied, complexing latched in a wide pH range which corresponds to the interval between the pI of proteins. Among Ovalbumin and Lysozyme interaction was more intense in the ratio r = 1 at pH 7.5 and BSA and Lysozyme most complex formation has occurred on the ratio r = 0.5 and pH 9.0. Changes in the ionic strength by adding NaCl negatively affected the interaction between Lysozyme and BSA already at a concentration of 0.01 mol / L and 0.03 mol / L abolished the interaction between Lysozyme and Ovalbumin. Through Potential - zeta can be seen that the formation of insoluble complexes was highest near the pI for all studied reasons, indicating that the interaction is given by neutralization of opposite charges. The Infrared spectra suggested that electrostatic interactions led interactions however, hydrogen bonds also had a hand in the coacervation process for the proteins under study. The micrographs showed that the insoluble complexes showed spherical structure and particle size showed the formation of structures with an average size around 2 ?m, much larger than the observable size for the isolated proteins. The isothermal titration calorimetry showed that the interaction between Lysozyme and Ovalbumin was exothermic and was performed in two steps, the first and second entropy directed enthalpy driven. The differential scanning calorimetry suggested the presence of a single point of denaturation, that the interaction between Lysozyme and BSA led to a new biopolymer with denaturation temperature 67 ? C differs from isolated proteins. These studies suggested that complex coacervates formed between Ovalbumin / Lysozyme and BSA / Lysozyme could be used as the encapsulating bioactive agent or as food ingredients in order to add nutritional value. / Prote?nas s?o biopol?meros de grande import?ncia nutricional e funcional tendo sido amplamente utilizadas como ingredientes alimentares. A intera??o entre duas prote?nas diferentes e opostamente carregadas pode dar origem aos complexo coacervado, atualmente utilizados como ingrediente na tecnologia de alimentos ou como agente de microencapsula??o. A forma??o de complexos coacervados entre Ovalbumina e Lisozima e entre Albumina s?rica bovina (BSA) e Lisozima foi investigada em fun??o do pH, raz?o de massa total e concentra??o de NaCl. Para as duas intera??es estudadas, a complexa??o acorreu em uma ampla faixa de pH, que corresponde ao intervalo entre os pI das prote?nas. Entre Ovalbumina e Lisozima a intera??o foi mais intensa na raz?o r=1 em pH 7,5 e para BSA e Lisozima a maior forma??o de complexos ocorreu na raz?o r=0,5 e pH 9,0. Altera??es na for?a i?nica por adi??o de NaCl influenciaram negativamente a intera??o entre Albumina BSA e Lisozima j? na concentra??o de 0,01 mol/L e a 0,03 mol/L suprimiu a intera??o entre Ovalbumina e Lisozima. Por meio do Potencial - zeta pode-se verificar que a forma??o de complexos insol?veis foi m?xima pr?ximo ao pI para todas as raz?es estudadas, indicando que a intera??o se deu por neutraliza??o de cargas opostas. Os espectros no infravermelho sugeriram que intera??es eletrost?ticas conduziram as intera??es no entanto, liga??es de hidrog?nio tamb?m tiveram participa??o no processo de coacerva??o para as prote?nas em estudo. As micrografias revelaram que os complexos insol?veis apresentavam estrutura esf?rica e o tamanho de part?cula demonstrou a forma??o de estruturas com tamanho m?dio em torno de 2 ?m, as quais s?o bem maiores do que o tamanho obervado para as prote?nas isoladas. A calorimetria de titula??o isot?rmica demonstrou que a intera??o entre Ovalbumina e Lisozima foi exot?rmica, a qual ocorreu em duas etapas, a primeira entropicamente dirigida e a segunda entalpicamente dirigida. A calorimetria diferencial de varredura sugeriu, pela presen?a de um ?nico ponto de desnatura??o, que a intera??o entre BSA e Lisozima deu origem a um novo biopol?mero com temperatura de desnatura??o a 67?C, diferente das prote?nas isoladas. Estes estudos sugeriram que complexos coacervados formados entre Ovalbumina / Lisozima e BSA / Lisozima poderiam ser utilizados como agente encapsulante de bioativos ou como ingredientes alimentares com o objetivo de agregar valor nutricional.