<p>The detection and quantitation of protein-ligand binding interactions is important not only for understanding biological functions but also for the characterization of novel protein ligands. Because protein ligands can range from small molecules to other proteins, general techniques that can detect and quantitate the many classes of protein-ligand interactions are especially attractive. Additionally, the ability to detect and quantify protein-ligand interactions in complex biological mixtures would more accurately represent the protein-ligand interactions that occur in vivo, where differential protein expression and protein complexes can significantly affect a protein's ability to bind to a ligand of interest.</p><p> The work in this dissertation is focused on the development of new methodologies for the detection and measurement of protein-ligand interactions in complex mixtures using multiplex analyses. Methodologies for two types of multiplexed analyses of protein-ligand binding interactions are investigated here. The first type of multiplex analysis involves characterizing the binding of one protein target to many potential ligands, and the second type involves characterizing the binding of one ligand to many proteins. The described methodologies are derived from the SUPREX (stability of unpurified proteins from rates of H/D exchange) and SPROX (stability of proteins from rates of oxidation) techniques, which are chemical modification strategies that measure thermodynamic stabilities of proteins using a relationship between a protein's folding equilibrium and the extent of chemical modification. These two techniques were utilized in the development and application of several different experimental strategies designed to multiplex the analysis of protein-ligand interactions.</p><p> The first strategy that was developed involved a pooled compound approach for making SUPREX-based measurements of multiple ligands binding to a target protein. Screening rates of 6 s/ligand were demonstrated in a high-throughput screening project that involved the screening of two chemical libraries against human cyclophilin A (CypA), a protein commonly overexpressed in types of cancer. This study identified eight novel ligands to CypA with micromolar dissociation constants. Second, an affinity-based protein purification strategy was developed for the detection and quantitation of specific protein-ligand binding interactions in the context of complex protein mixtures. It involved performing SPROX in cell lysates and selecting the protein of interest using immunoprecipitation or affinity tag purification. A third strategy developed here involved a SPROX-based stable isotope labeling method for measuring protein-ligand interactions in multi-protein mixtures. This strategy was used in a proof-of-principle experiment designed to detect and quantify the indirect binding between yeast cyclophilin and calcineurin in a multi-component protein mixture. Finally, a quantitative proteomics platform was developed for the detection and quantitation of protein-ligand binding interactions on the proteomic scale. The platform was used to profile interactions of the proteins in a yeast cell lysate to several ligands, including the bioactive small molecules resveratrol and manassantin A, the cofactor nicotinamide adenine dinucleotide (NAD+), and two proteins, phosphoglycerate kinase (Pgk1) and pyruvate kinase (Pyk1). The above approaches should have broad application for use as discovery tools in the development of new therapeutic agents.</p> / Dissertation

This thesis focuses on the construction and role of benchmark quality computations in the area of non-covalent interactions. We have provided a detailed error analysis of focal-point schemes commonly used in benchmark quality computations, as well as provide error and speedup analysis of commonly used approximations to these methods. An analysis of basis set effects on higher-order corrections to MP2/CBS has been carried out, providing the community error bounds on future benchmarks. We demonstrate how these high-level computations can elucidate a better understanding of non-bonded interactions in chemistry as well as provide high-quality reference data to refit existing methods against to increase the overall accuracy of the method.

Nitric oxide synthases (NOS) are responsible for the production of nitric oxide (NO), an essential cell-signaling molecule, in mammals. There are three isoforms of NOS with widely different tissue distribution. The overproduction of NO is marked in many human disease states and cancers, however due to the similarities of the enzyme isoforms, targeting NOS for inhibition has proven challenging. Endogenously, the methylated arginines, N[superscript ω]-monomethyl-L-arginine (NMMA) and asymmetric N[superscript ω], N[superscript ω]-dimethyl-L-arginine (ADMA), inhibit NOS. N[superscript ω], N[superscript ω]-Dimethylarginine dimethylaminohydrolase (DDAH1) metabolizes these methylated arginines and thus relieves NOS inhibition. The role of DDAH1 in the regulation of diseases such as cancer and septic shock is still being elucidated. It is thought that targeting DDAH1 for inhibition rather than NOS may circumvent many of the current problems with the treatment of NO overproduction such as isoform selectivity. My PhD studies focus on the synthesis of a series of irreversible inhibitors of DDAH1, an extensive study of their in vitro mode of inhibition, a comparison of analytical fitting methods, and the viability and efficacy of the inactivators in a human cell line. I also studied a potential endogenous inactivator of DDAH1, nitroxyl (HNO), a one-electron reduction product of NO. / text

Protein PEGylation (covalent attachment of poly(ethylene glycol) or PEG to proteins) is an excellent example of a drug delivery system that improves pharmacokinetics and pharmacodynamic properties of therapeutics. However, although PEGylation is clinically proven and attracts both scientific and commercial interest, the technique is associated with many process constraints, in particular related to controlling the number of conjugated PEG chains. A novel, solid-phase PEGylation methodology was attempted to overcome the drawbacks of the commonly used solution-phase methods for preparing PEGylated products. The solid-phase PEGylation methodology involved conjugating protein onto a tethered PEG derivative attached onto a solid matrix, followed by hydrolytic cleavage of the PEG chain from the solid matrix under mild conditions to yield PEGylated protein in free solution. PEGs with molecular weights (MWs) 2000 and 4000 Da were used and a heterobifunctional PEG derivative, α-(β-alanine)-ω-carboxy PEG, with a cleavable β-alanine ester terminal was prepared for surface grafting and protein conjugation. The amine terminal of this PEG derivative was used for grafting PEG onto carboxy functionalized hydrophilic Sephadex and hydrophobic polystyrene derivatives. The free carboxyl terminal was used for protein conjugation via amine coupling. A kinetic study of PEG-surface grafting was performed to understand the influence of a number of parameters on the PEG surface concentration and its conformation, including temperature, reaction time, nature of the matrix, solvent and base, and MW of PEG. PEG grafted matrices were characterized using various surface characterization tools including Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). Higher PEG grafting was observed with polystyrene matrices (up to 0.3 mmol/g) than either of the Sephadex derivatives (less than 0.15 mmol/g) using both molecular weights. Detailed surface characterization using XPS studies showed a layer thickness of 11.87 nm was achieved with polystyrene matrices using 4000 Da PEG derivatives after a grafting period of 72 hours at 40°C, indicating the presence of brush conformations for the grafted PEGs. In contrast, mushroom conformations were observed for PEG molecules grafted on both carboxymethyl and carboxypentyl Sephadex derivatives after the same reaction period, with a layer thickness of 2.62 nm and 4.14 nm respectively. Optimized PEG grafting and hydrolysis conditions were developed for solid-phase protein PEGylation using Cytochrome c as a model protein. The presence of PEGylated species were detected by size exclusion chromatography (SEC) from Sephadex derivatives but were absent when using polystyrene matrices. Both Sephadex derivatives gave mainly multi-PEGylated species with poor yields, in place of the expected mono-PEGylated products. A solution-phase PEGylation using the same PEG derivatives was performed successfully and various PEGylated species were identified and characterized using SEC and gel electrophoresis, based on their viscosity radius. An examination of the surface characteristics of the PEG-grafted was carried out by XPS, showing that protein conjugation was greatly influenced by surface force interactions, which depended on the PEG grafting densities and the nature of the solid matrices. Finally, fluorescent images obtained using confocal microscope with fluorescein isothiocyanate labelled Cytochrome c provided supporting evidence regarding the factors that constrained the solid-phase PEGylation process.

UCP1 is a member of the mitochondrial transmembrane anion carrier protein superfamily and is required to mediate adaptive thermogenesis in brown adipose tissue (BAT). Once activated, UCP1 uncouples mitochondrial respiration from ATP synthesis, thereby wasting the protonmotive force formed across the mitochondrial inner membrane as heat. It is hypothesized that proton leaks through UCP1 could be a molecular target to combat certain forms of obesity. Although it is well established that UCP1 is regulated by allosteric mechanisms, alternative methods such as post-translational modification still remain to be explored. The aims of the present study were to confirm the phosphorylation of UCP1 and the physiological relevance of this modification. Using isoelectric focusing, we confirmed that UCP1 displayed acidic shifts consistent with phosphorylation in BAT mitochondria isolated from cold exposed versus warm acclimated mice. A mouse model that ectopically expressed UCP1 in skeletal muscle was used to explore the link between the mitochondrial redox status and UCP1 function. Our results show that the expression of UCP1 in skeletal muscle led to decreases in body and tissues weights. In contrast, glucose uptake into skeletal muscle, food intake and energy expenditure was increased with the expression of UCP1. Finally, proton leaks through UCP1 were determined to be increased in isolated mitochondria from transgenic versus wild-type mice. Taken together these results indicate a complex interplay between mitochondrial redox status, post-translational modification and UCP1 function. Elucidation of novel mechanisms regulating UCP1 offers alternatives strategies that can be explored in order to modulate BAT thermogenesis.

En Science des colloïdes, il est fondamental de contrôler les interactions entre les particules et leur environnement pour obtenir les propriétés souhaitées. Dans ce travail de thèse, pour former des systèmes innovants, nous avons utilisé la chimie covalente réversible à l'interface particule/polymère dans deux domaines différents : les composites vitrimères et la nanocatalyse. Dans les composites, les liens réversibles permettent d'améliorer les propriétés mécaniques tout en limitant l'impact des charges sur les propriétés vitrimères des matériaux. Deux matrices vitrimères reposant sur des réactions d'échange de nature différente, la transestérification et la transimination, ont été étudiées. L'avantage du lien imine est d'être également dissociable dans certaines conditions douces, ce qui facilite le recyclage des matériaux. La réversibilité du lien imine peut aussi être exploitée pour contrôler la dispersion/agrégation de particules en solvant. Lorsqu'elles sont liées, les chaines polymères se déploient en bon solvant et confèrent aux particules une stabilisation stérique, stabilisation qui disparait lorsqu'elles sont détachées : les particules s'agrègent et peuvent être récupérées facilement. Ce concept a été développé sur un système catalytique composé de nanoparticules de palladium supportées sur des particules de silice. Les chaines greffées améliorent non seulement la dispersion des nanocatalyseurs et les taux de conversion du système catalytique, mais aussi stabilisent les nanoparticules de palladium à la surface de la silice, limitant leur lessivage et leur agrégation. L'efficacité catalytique du système est ainsi conservée sur plusieurs cycles. / The control of the interactions between particles and their environment is essential when dealing with colloids in order to reach desired properties. In this study, reversible covalent bonds were used as interfacial interactions in two systems: vitrimer composite materials and nanocatalysis in solution. The aim of this work was to develop materials which present original properties thanks to interfacial dynamic bonds. In composites, the introduction of dynamic covalent bonds between a vitrimer matrix and the fillers enables to improve mechanical properties while preserving vitrimer properties. Two vitrimer matrices based on two different exchange reactions, transesterification or transimination, have been studied. Imine bonds are reversible bonds that can dissociate in presence of water. We demonstrate that polyimine vitrimers can be reshaped and recycled under mild conditions. The reversibility of the imine bond can also be used to control the stability of a colloidal dispersion. Indeed, grafting of polymers on particles surface through reversible covalent bonds give them steric stabilization in good solvent of the chains. Dissocation of these bonds triggers detachment of the polymer chains and induces particle aggregation. This concept was applied to a catalytic system composed of palladium nanoparticles adsorbed onto silica particles. Polymer chains not only improve the dispersion of the whole catalytic system but also limit the leaching and aggregation of the palladium nanoparticles. As a consequence, the catalytic efficiency of the particles can be preserved over several cycles.

Dans l'optique de préparer des vitrimères à partir des thermoplastiques communément utilisés, tels le PMMA et le PS, des réactions d'échange dynamiques reposant les liens imine et esters boroniques ont été étudiées. Des paramètres importants comme la constante de dissociation de certaines molécules, la constante de vitesse et l'énergie d'activation ont été mesurées. Des monomères porteurs de liaisons échangeables ont été synthétisés et polymérisés. Des vitrimères, avec des liaisons C-C dans la chaine principale, ont été créés par différentes stratégies (PMMA et PS). Ces matériaux sont réticulés et insolubles avec un plateau caoutchouteux mais également façonnables et recyclables par moulage par compression ou par injection. Ces vitrimères peuvent relaxer les contraintes et couler à une température supérieure à celle de leur transition vitreuse. Des viscosités de 105-107 Pa.s ont été estimées pour les vitrimères PMMA reposant sur la chimie des esters boroniques. Des tests de traction montrent que leurs propriétés mécaniques de ces matériaux ne subissent pas de baisse significative après plusieurs cycles de recyclage par moulage par injection. Même après plusieurs cycles de moulage, les vitrimères basés sur la chimie des esters boroniques peuvent être complètement dé-réticulés, signe de leur stabilité à haute température lors du moulage. Ces vitrimères ont une résistance supérieure dans les conditions "d'environmental stress cracking" comme des réseaux polymères conventionnels. / With the aim to generate vitrimers from commonly used thermoplastics with carbon-carbon based backbones, such as PMMA and PS, dynamic covalent exchange reactions relying on Schiff’s bases and boronic esters were investigated. Two different approaches, i.e. crosslinking in solution or in extrusion, were used. These materials are processable via extrusion, compression and injection molding like their thermoplastic counterparts. The crosslinked nature of these systems was confirmed by solubility tests and DMA. Rheological measurements revealed the vitrimers ability to flow and viscosities between 105-107 Pa.s for boronic ester based PMMA vitrimers were measured. Consecutive tensile testing/reprocessing sequences proved the full recyclability of these vitrimers, and selective cleavage of the vitrimer networks followed by precise chemical analyses showed the thermal and chemical stabilities of vitrimers relying on boronic ester bonds. The stress cracking resistance of these vitrimers was significantly higher than that of parent thermoplastics, as can be expected for crosslinked systems.

The aim of this master thesis is to focus on a various methods of the conjugation of palladium nanoparticles of different shapes on the protein. The main point was to use both covalent and non-covalent conjugation of palladium nanoparticles on the protein and to use the functional conjugates to find out their stability in time.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / O objetivo deste trabalho foi estudar a imobilizaÃÃo da lipase de Candida antarctica tipo B (CalB) atravÃs de ligaÃÃo covalente utilizando a resina hidrofÃlica Toyopearl como suporte. Avaliaram-se vÃrios protocolos de ativaÃÃo, utilizando como agentes ativantes: glicidol, glutaraldeÃdo e etilenodiamina (EDA), e seu efeito na atividade hidrolÃtica do biocatalisador obtido. A atividade hidrolÃtica dos derivados foi avaliada pela hidrÃlise do butirato de para-nitrofenila (PNPB) e utilizou-se como reaÃÃo de esterificaÃÃo, a sÃntese do butirato de butila, empregando Ãcido butÃrico e butanol como substratos. O suporte foi previamente caracterizado pela obtenÃÃo de imagens por microscopia eletrÃnica de varredura (MEV), difratogramas de raio-X (DRX) e espectros de infravermelho (FTIR). A Ãrea superficial e a porosidade do suporte foram avaliadas pelo mÃtodo BET. Determinaram-se a concentraÃÃo de proteÃna e a atividade enzimÃtica do sobrenadante antes e apÃs os processos de imobilizaÃÃo. O melhor resultado de atividade hidrolÃtica da enzima imobilizada foi de 894,17  43,29 U/g de suporte, utilizando o suporte Toyopearl-Glioxil-EDA-GlutaraldeÃdo (Toyo-GEG). Este valor de atividade foi 1,56 vezes maior que o obtido para o derivado comercial Novozym 435. A influÃncia de diferentes concentraÃÃes de proteÃna foi avaliada e observou-se a saturaÃÃo do suporte com uma concentraÃÃo de 40 mg/g e 2238,25  27,33U/g de atividade. A influÃncia dos tempos de incubaÃÃo na imobilizaÃÃo indicou que longos tempos de imobilizaÃÃo acarretam na diminuiÃÃo da atividade hidrolÃtica dos biocatalisadores. Nos estudos de estabilidade tÃrmica a 60 C, conseguiu-se um elevado grau de estabilizaÃÃo para o derivado, com estabilidade tÃrmica superior a da enzima solÃvel. Para o derivado obtido com 72 horas de imobilizaÃÃo o fator de estabilizaÃÃo em relaÃÃo à enzima solÃvel e ao derivado comercial, respectivamente, foi de 694,56 e 12,74. Quanto à estabilidade operacional, apÃs o sÃtimo ciclo de sÃntese do butirato de butila, o derivado Toyo-GEG reteve em torno de 76 % de sua atividade inicial. / The objective of this work was to study the immobilization of Candida antarctica type B lipase (CalB) by covalent bond using hydrophilic resin named Toyopearl as a support. The influence of activation agents (glycidol, glutaraldehyde and ethylenediamine) in the hydrolytic activity of the biocatalyst was investigated. The enzyme preparations were tested in the hydrolysis of para-nitrophenyl butyrate (PNPB) and in an esterification reaction, butyl butyrate synthesis from butyric acid and butanol. The support was previously characterized by scanning electronic microscopy (SEM), Xray diffraction (DRX) and Fourier transform infra red (FTIR). Superficial area and porosity were evaluated using BET method. Protein concentration and enzymatic activity in the supernatant were determined before and after immobilization process. Best results of hydrolytic activity were obtained using the enzyme immobilized in Toyopearl-Glyoxyl-EDA-Glutaraldehyde (Toyo-GEG), 894.17  43.29 U/g of support, which is 1.56-fold higher than the hydrolytic activity of Novozym 435. The influence of different loadings of protein and the incubation time in the immobilization were also studied. The saturation of support was observed with a load of 40 mg/g of support with 2238.25  27.33 U/g. A decrease in the hydrolytic activity of enzyme preparations was observed for long incubation times. However, thermal stability studies at 60 C, showed that this parameter was important for enzyme stabilization. Thermal stabilization by immobilization was achieved and the immobilized enzyme was more thermal stable than the soluble enzyme. The immobilized lipase prepared at incubation time of 72 hours was 694.59-fold more stable than soluble enzyme and 12.74 -fold than Novozym 435. In organic medium, cycles of synthesis of butyl butyrate was chosen to quantify operational stability. After the seventh cycle, Toyo-GEG retained around 76 % of the initial activity.

L’hydroxyapatite phosphocalcique (HA) est largement utilisée en tant que substitut osseux. Sa composition chimique est proche de celle du minéral osseux ce qui en fait une céramique ostéoconductrice. Les hydroxyapatites silicatées (SiHA) sont actuellement étudiées. La présence de silicium au sein de la structure apatite pourrait accroître la bioactivité des implants. Cependant, ces substituts ne sont pas ostéoinducteurs. Ils n'ont pas la capacité d'induire la formation de tissus osseux, ce qui limite leur utilisation en chirurgie réparatrice. L'une des stratégies envisagées afin de les rendre ostéoinducteurs est de fonctionnaliser leur surface par des molécules biologiquement actives via des organosilanes. L’objectif de ce travail est d'étudier l’influence de l’incorporation du silicium dans l’hydroxyapatite et de la fonctionnalité (i.e. nombre de groupements hydrolysables) des amino-éthoxy-silanes sur le mode de greffage et la quantité de molécules à la surface des substrats. Les céramiques HA et SiHA silanisées ont été élaborés et caractérisées par spectroscopie de photoélectrons X et par analyse thermogravimétrique couplée à la spectrométrie de la masse. Les résultats ont confirmé un greffage covalent quelles que soient la nature du substrat et la fonctionnalité de l'organosilane. La quantité greffée augmente avec la fonctionnalité de l’organosilane. La présence de silicium au sein du substrat favorise le nombre de chaines éthoxyles impliquées dans la réaction d’hétérocondensation et diminue la quantité d’organosilanes greffée. Les organosilanes sont répartis d’une façon non homogène sur la surface mais sans formation d’une couche recouvrant celle-ci en totalité. / Calcium phosphate hydroxyapatite (HA) is widely used as bone substitute. Its chemical composition is close to the mineral part of bone which induces osteoconductive ceramics. Silicated hydroxyapatites (SiHA) are being studied. The incorporation of silicon in the hydroxyapatite structure would increase the bioactivity of the implant. However, these substitutes are not osteoinductive. They do not have the ability to induce bone formation which limits their use in reparative surgery. In order to obtain osteoinductive ceramics, it is possible to functionalize their surface by biologically active molecules via organosilanes. The present work studies the influence of silicon incorporation in the hydroxyapatite structure and the functionality (i.e. number of hydrolysable groups) of amino-ethoxy-silanes on the grafting mode and the quantity of molecules at the substrates surface. HA and SiHA silanised ceramics have been produced and characterized by means of X-ray photoelectron spectroscopy and thermogravimetric analysis coupled with mass spectrometry. The results confirmed the covalent grafting whatever the nature of the substrate and the functionality of the organosilane might be. The grafted amount increases with the functionality of organosilane. Moreover, the presence of silicon within the substrate promotes the number of ethoxyl chains involved in the heterocondensation reaction and decreases the grafted amount of organosilanes. The organosilanes are not homogeneously distributed on the surface but without formation of a layer covering the entire surface.