Cette thèse de doctorat s’inscrit dans le cadre de l’étude in silico des relations qui lient la séquence d’une protéine à sa structure, sa stabilité et sa fonction. Elle a pour objectif de permettre à terme la conception rationnelle de protéines modifiées qui restent actives dans des conditions physico chimiques non physiologiques. Nous nous sommes plus particulièrement penchés sur la stabilité thermique des protéines, qui est définie par leur température de fusion Tm au delà de laquelle leur structure n’est thermodynamiquement plus stable. Notre travail s’articule en trois grandes parties : la recherche de facteurs favorisant la thermostabilité des protéines parmi des familles de protéines homologues, la mise sur pied d’une base de données de protéines de structure et de Tm déterminées expérimentalement, de laquelle sont dérivés des potentiels statistiques dépendant de la température, et enfin la mise au point de deux outils bioinformatiques visant à prédire d’une part la Tm d’une protéine à partir de la Tm de protéines homologues et d’autre part les changements de thermostabilité d’une protéine (Tm) engendrés par l’introduction d’une mutation ponctuelle. La première partie a pour objectif l’identification des facteurs de séquence et de structure (e.g. fréquence de ponts salins, d’interactions cation-{pi}) responsables des différentes stabilités thermiques de protéines homologues au sein de huit familles (chapitre 2). La spécificité de chaque famille ne nous a pas permis de généraliser l’impact de ces différents facteurs sur la stabilité thermique des protéines. Cependant, cette approche nous a permis de constater la multitude de stratégies différentes suivies par les protéines pour atteindre une plus grande thermostabilité. La deuxième partie concerne le développement d’une approche originale pour évaluer l’influence de la température sur la contribution de différents types d’interactions à l’énergie libre de repliement des protéines (chapitres 3 et 4). Cette approche repose sur la dérivation de potentiels statistiques à partir d’ensembles de protéines de thermostabilité moyenne distincte. Nous avons d’une part collecté le plus grand nombre possible de protéines de structure et de Tm déterminées expérimentalement, et d’autre part développé des potentiels tenant compte de l’adaptation des protéines aux températures extrêmes au cours de leur évolution. Cette méthode originale a mis en évidence la dépendance en la température d’interactions protéiques tels les ponts salins, les interactions cation-{pi}, certains empilements hydrophobes ... Elle nous a en outre permis de mettre le doigt sur l’importance de considérer la dépendance en la température non seulement des interactions attractives mais également des interactions répulsives, ainsi que sur l’importance de décrire la résistance thermique par la Tm plutôt que la Tenv, température de l’environnement de l’organisme dont elle provient (chapitre 5). La dernière partie de cette thèse concerne l’utilisation des profils énergétiques dans un but prédictif. Tout d’abord, nous avons développé un logiciel bioinformatique pour prédire la thermostabilité d’une protéine sur la base de la thermostabilité de protéines homologues. Cet outil s’est avéré prometteur après l’avoir testé sur huit familles de protéines homologues. Nous avons également développé un deuxième outil bioinformatique pour prédire les changements de thermostabilité d’une protéine engendrés par l’introduction d’une mutation ponctuelle, en s’inspirant d’un logiciel de prédiction des changements de stabilité thermodynamique des protéines développé au sein de notre équipe de recherche. Ce deuxième algorithme de prédiction repose sur le développement d’une grande base de données de mutants caractérisés expérimentalement, d’une combinaison linéaire de potentiels pour évaluer la Tm, et d’un réseau de neurones pour identifier les coefficients de la combinaison. Les prédictions générées par notre logiciel ont été comparées à celles obtenues via la corrélation qui existe entre stabilités thermique et thermodynamique, et se sont avérées plus fiables. Les travaux décrits dans notre thèse, et en particulier le développement de potentiels statistiques dépendant de la température, constituent une nouvelle approche très prometteuse pour comprendre et prédire la thermostabilité des protéines. En outre, nos travaux de recherche ont permis de développer une méthodologie qui pourra être adaptée à l’étude et à la prédiction d’autres propriétés physico chimiques des protéines comme leur solubilité, leur stabilité vis à vis de l’acidité, de la pression, de la salinité ... lorsque suffisamment de données expérimentales seront disponibles.

Utilization of amorphous metallic alloy has received much attention for use in numerous microelectronic and electrochemical devices since they provide unique electrical, thermal conductivity, and magnetic properties. To develop these functional properties, it is essential to understand the amorphous structure and the property relationships. First principles calculations provide insight into the structure, thermodynamic stability, electronic and magnetic properties of amorphous alloys. For Ru- and Co-based alloys, the thermodynamic stability was examined by calculating the mixing energy along with those of crystalline counterparts. The amorphous RuP, CoP, RuB, and CoB alloys, become energetically more favorable than their crystalline counterparts at moderate P(B) content. The atomistic structures have well-defined local structures depending on the atomic size ratio and electronic interactions between constituent elements. Their local ordering is attributed to strong p-d hybridization, which contributes to stabilizing the Ru(Co)-P(B) alloys. Surface segregation of P(B) and interfacial adhesion with copper were also studied. Li-X (X: Si, Ge, and Sn) were examined when 1 or 2 Li atoms are inserted into the interstitial sites. Li insertion in the tetrahedral site, which is the most preferable site in the diamond matrix, causes outward displacement and charge localization around the X neighbors, thereby weakening of the covalent bonds leading to destabilization of the host matrix. We present the energetics, structure, electronic and mechanical properties of crystalline and amorphous Li-X (X: Si, Ge, Sn, and Si+Sn) alloys. Our calculations show that the incorporation of Li leads to disintegration of the tetrahedrally-bonded X network into small clusters of various shapes. Electronic structure analysis highlights that the charge transfer leads to weakening or breaking of X bonds with the growing splitting between s and p states, and consequently the Li-X alloys softens with increasing Li content. / text

No description available.

<p>While a number of different proteomic, genomic, and computational approaches exist for the characterization of drug action, each of the experimental approaches developed to date has both strengths and weaknesses. Currently, there is no one "perfect" assay for drug mode-of-action studies. A protocol that could assay all the proteins in the proteome for both direct and indirect binding interactions of drugs would greatly facilitate studies of drug action. Recently, the SPROX (stability of proteins from rates of oxidation) technique was developed as a chemical modification- and mass spectrometry-based strategy for detecting protein-ligand interactions by monitoring the change in thermodynamic stability of proteins upon ligand binding. This is accomplished by monitoring the denaturant dependent oxidation of globally protected methionine residues. The SPROX technique has been interfaced with bottom-up proteomics methods to allow for the proteome-wide analysis of protein-ligand interactions. However, the strategy has been limited by the need to detect and quantify methionine containing peptides in the bottom-up proteomics experiment. </p><p>The work in this dissertation is focused on evaluating the current SPROX protocol, developing modifications to improve proteome coverage, and applying the SPROX platform to two different drug mode-of-action studies. Three main strategies were employed to improve protein coverage. First, a chemo-selective isolation of un-oxidized methionine containing peptides was employed to enrich for methionine containing peptides, and it was found to produce a ~2-fold improvement in proteomic coverage. Second, a pre-fractionation strategy involving the use of isoelectric focusing was employed to decrease sample complexity prior to LC-MS/MS analysis and it was found to generate a ~2-3 fold improvement in proteomic coverage, however when combined with the methionine enrichment strategy the improvement was ~6-fold as the benefits of both were additive. Third, a tryptophan modification strategy was developed that could ultimately expand the number of useful peptides in proteome-wide SPROX experiments to include those that contain tryptophan. Also, investigated was the use of several different mass spectrometer systems (including a bench-top quadrupole and orbitrap system and two different quadrupole time-of-flight systems) in the SPROX protocol. The results of these studies indicate that there is a significant advantage in proteome coverage when faster mass spectrometers are used. The use of high energy collision dissociation (HCD) in the orbitrap system was also more advantageous than the use of collision induced dissociation (CID) in the Q-ToF systems. Regardless of the mass spectrometer used, the major source of error in the SPROX experiment was found to be the random error associated with the LC-MS/MS analysis of isobaric mass tagged peptides. This random error was found to yield a false discovery rate of between 3 and 10% for "hit" peptides in the SPROX experiment. </p><p>The above improvements in the SPROX protocol were used in two protein-ligand binding experiments. One set of experiments involved studies on two small molecules with a specific anti-cancer phenotype in human colon cancer cells. These studies identified 17 proteins as potential "hits" of these two small molecules. After preliminary validation of these proteins, approximately 50% were eliminated as false positives and one protein, p80/nucleophosim, showed consistent data indicating a destabilizing interaction with both small molecules. The destabilization is indicative of an indirect interaction with the small molecules that would be mediated through a protein-protein interaction network. In another set of experiments the breast cancer drug, tamoxifen, and its main, active metabolite, 4-hydroxy tamoxifen, were assayed for binding to the proteins in a yeast cell lysate to better understand its adverse effects on yeast cells. The results of these studies identified ~80 proteins as potential "hits" of these two drugs. After preliminary validation of these proteins, approximately 30% were eliminated as false positives and one protein, SIS1, type II Hsp40, showed consistent data indicative of a direct binding interaction.</p> / Dissertation

[pt] O presente trabalho visa dois objetivos. 0 primeiro, didático, é de apresentar algumas versões da Termodinâmica dos Meios Contínuos, elucidando suas semelhanças e diferenças várias formas da segunda lei são apresentadas, questionando-se em alguns casos as suas supostas generalidades. O segundo objetivo, de pesquisa, desenvolve na versão de Serrin os conceitos de Estabilidade Termodinâmica e Exergia, aplicando-os no estudo dos ciclos de Carnot e de Rankine. Através do conceito de função de acumulação introduz-se uma nova maneira de se determinar a eficiência dos referidos ciclos. Ainda na versão de Serrin, aplica-se a teoria de processos de transição no estudo do efeito Joule-Thomson. Os fluidos de trabalho são um gás ideal, caracterizado pela convexidade do seu espaço de estados, e um fluido de Van der Halls, que não possui a mesma característica. Finalmente, no contexto da Termodinâmica de Processos Irreversíveis é feita uma comparação entre as soluções de problemas de condução de calor em meios rígidos e elásticos lineares isotrópicos. / [en] The present work has two purposes. The first one is didactic. It intend to present many versions of the Continuun Thermodynamics discussing their resemblances and diferences. Many forms of the second law are presented and in some cases their supposed generalities are questioned. The second purpose lies on the basic research. It is carried out applying the Serrin s version the concepts of Thermodynamic Stability and Availability in the studied of the Carnot s and Rankine s cycles. By meaning of the accumulation function concept a newform to determine the efficience of the above cycles is introduced. On the other hand in the Serrin s version the theory of transition processes can be applied in the study of the Joule-Thomson effect. The working fluids are an ideal gas which is characterized by the convexity of it s state space and the Van der Waals fluid which is not provided of such characteristic. Finally in the context of the Irreversible Thermodynamics is made a comparison between the solutions of heat conduction problems in rigid and linear isotropic elastic continuum.

Ligand NOTPOEt was synthesized. Protonation constants and stability constants of Cu(II), Zn(II), Ni(II) and Ga(III) complexes were determined by potentiometric titrations. Cu(II) complex was characterized by UV-VIS spectroscopy and formation of Ga(III) complex was studied by NMR spectroscopy. The work was aimed at characterisation of the ligand with respect to potential application in biomedical imaging techniques.

The covalent attachment of poly(ethylene glycol) (PEG) to a protein surface (known as PEGylation), has been demonstrated to increase the serum half-life of therapeutic proteins by reducing kidney clearance and immunogenicity and by protecting against proteolysis. Theses beneficial effects could be further enhanced if PEGylation consistently increased protein conformational stability (i.e. the difference in free energy between the folded and unfolded states). However, the effects of PEGylation on protein conformational stability are unpredictable; PEGylation has been reported to increase, decrease, or have no effect on the conformational stability of medicinal proteins.This thesis details the results of two studies aimed at discovering the structural determinants which influence the thermodynamic impact of PEGylation on the WW domain, a small model protein. Chapter 1 is a brief introduction to protein therapeutics and protein PEGylation. Chapter 2 describes a study which demonstrates that the thermodynamic impact of PEGylation is strongly dependent on the site to which PEG is conjugated. The studies described in Chapter 3 elaborate on this site dependence, and demonstrate that PEG stabilizes the WW domain through interactions with the surface of the folded peptide, and that two factors – the orientation of the PEG chain (relative to the protein surface) and the identity of nearby side chains – play a critical role in determining the thermodynamic impact of PEGylation.

A laboratory scale study was carried out on a set of 6 borosilicate waste glasses made from simulated high-level nuclear waste. The test matrix was designed to explore the composition region suitable for the long-term geologic disposal of high-temperature-and high-waste-containing glasses. The glass compositions were selected to achieve maximum waste loading without a sacrifice in glass durability. The relationship between glass composition and chemical durability was examined. The qualitative effect of increasing B2O3 content on the overall waste glass leaching behavior has also been addressed. The glass composition matrix was designed by systematically varying the factors: %waste loading and (SiO2+Frit):B2O3 ratio, with (SiO2:Frit) ratio being held constant. In order to assess the chemical durability, the Product Consistency Test (ASTM C-1285) was performed. Under PCT protocol, crushed glass was allowed to react with ASTM type I water under static conditions. All leachate solutions were analyzed by the technique; Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES). A statistical regression technique was utilized to model the normalized release of the major soluble elements, Na, Si, and B, as a function of the individual as well as interactive chemical effects (B2O3, Al2O3, Fe2O3, MnO, SiO2, SrO, Na2O, B2O3*SiO2, B2O3*Al2O3, Fe2O3*Na2O, Al2O3*Na2O, and MnO*SiO2). Geochemical modeling was performed using the computer code EQ3/6 to: (1) determine the saturation states of the possible silicate minerals, a-cristobalite and chalcedony; and (2) predict the most stable mineral phase based on the mineral thermodynamic data. Mineral/water interactions were analyzed by representing the resultant glass data on a Na-Al-Si-O-H stability diagram.

Yes / The thermodynamic stability of caffeine (CA) cocrystals with dicarboxylic acids (DAs) as coformers was investigated in the presence of a range of structurally related dicarboxylic acids (SRDs). Two experimental conditions (slurry and dry-grinding) were studied for mixing the cocrystal and the SRD additive. The additives oxalic, malonic and glutaric acid led to the replacement of the acid coformer for certain cocrystals. Interestingly, a change in stoichiometry was observed for the CA:maleic acid system. A stability order among the cocrystals was established depending on their tendency to replace the coformer. To understand the factors controlling the relative stabilities, lattice energies were calculated using dispersion corrected Density Functional Theory (DFT). Gibbs free energy changes were calculated from experimental solubilities. The observed stability order corroborated well with lattice energy and Gibbs free energy computations.

<p>The identification and quantification of protein-protein interactions in large scale is critical to understanding biological processes at a systems level. Current approaches for the analysis of protein -protein interactions are generally not quantitative and largely limited to certain types of interactions such as binary and strong binding interactions. They also have high false-positive and false-negative rates. Described here is the development of and application of mass spectrometry-based proteomics metehods to detect and quantify the strength of protein-protein and protein-ligand interactions in the context of their interaction networks. Characterization of protein-protein and protein-ligand interactions can directly benefit diseased state analyses and drug discovery efforts. </p><p>The methodologies and protocols developed and applied in this work are all related to the Stability of Unpurified Proteins from Rates of amide H/D Exchange (SUPREX) and Stability of Protein from Rates of Oxidation (SPROX) techniques, which have been previously established for the thermodynamic analysis of protein folding reactions and protein-ligand binding interactions. The work in this thesis is comprised of four parts. Part I involves the development of a Histidine Slow H/D exchange protocol to facility SURPEX-like measurements on the proteomic scale. The Histidine Slow H/D exchange protocol is developed in the context of selected model protein systems and used to investigate the thermodynamic properties of proteins in a yeast cell lysate. </p><p>In Part II an isobaric mass tagging strategy is used in combination with SPROX (i.e., a so-called iTRAQ-SPROX protocol) is used to characterize the altered protein interactions networks associated with lung cancer. This work involved differential thermodynamic analyses on the proteins in two different cell lines, including ADLC-5M2 and ADLC-5M2-C2. </p><p>Parts III and IV of this thesis describe the development and application of a SPROX protocol for proteome-wide thermodynamic analyses that involves the use of Stable Isotope Labeling by Amino acid in cell Culture (SILAC) quantitation. A solution-based SILAC-SPROX protocol is described in Part III and a SILAC-SPROX protocol involving the use of cyanogen bromide and a gel-based fractionation step is described in Part IV. The SILAC-SPROX-Cyanogen bromide (SILAC-SPROX-CnBr) protocol is demonstrated to significantly improve the peptide and protein coverage in proteome-wide SPROX experiments. Both the SILAC-SPROX and SILAC-SPROX-CnBr porotocols were used to characterize the ATP binding properties of yeast proteins. Ultimately, the two protocols enabled 526 yeast proteins to be assayed for binding to AMP-PNP, an ATP mimic. A total of 140 proteins, including 37 known ATP-binding proteins, were found to have ATP binding interactions.</p> / Dissertation