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The need for cleaner and more efficient alternative energy sources is becoming urgent as concerns mount about climate change wrought by greenhouse gas emissions. Solid oxide fuel cells (SOFCs) are one of the most efficient options if the goal is to reduce emissions while still operating on fossil energy resources. One of the foremost problems in SOFCs that causes efficiency loss is the polarization resistance associated with the oxygen reduction reaction(ORR) at the cathodes. Hence, improving the cathode design will greatly enhance the overall performance of SOFCs. Lanthanum nickelate, La2NiO4+δ (LNO), is a mixed ionic and electronic conductor that has competitive surface oxygen exchange and transport properties and excellent electrical conductivity compared to perovskite-type oxides. This makes it an excellent candidate for solid oxide fuel cell (SOFC) applications. It has been previously shown that composites of LNO with Sm0.2Ce0.8O2-δ (SDC20) as cathode materials lead to higher performance than standalone LNO. However, in contact with lanthanide-doped ceria, LNO decomposes resulting in free NiO and ceria with higher lanthanide dopant concentration. In this study, the aforementioned instability of LNO has been addressed by compositional tailoring of LNO: lanthanide doped ceria (LnxCe1-xO2,LnDC)composite. By increasing the lanthanide dopant concentration in the ceria phase close to its solubility limit, the LNO phase has been stabilized in the LNO:LnDC composites. Electrical conductivity of the composites as a function of LNO volume fraction and temperature has been measured, and analyzed using a resistive network model which allows the identification of a percolation threshold for the LNO phase. The thermomechanical compatibility of these composites has been investigated with SOFC systems through measurement of the coefficients of thermal expansion. LNO:LDC40 composites containing LNO lower than 50 vol%and higher than 40 vol% were identified as being suitable to incorporate into full button cell configuration from the standpoint of thermomechanical stability and adequate electrical conductivity. Proof-of-concept performance comparison for SOFC button cells manufactured using LNO: La0.4Ce0.6O2-δ composite to the conventional composite cathode materials has also been provided. This thermodynamics-based phase stabilization strategy can be applied to a wider range of materials in the same crystallographic family, thus providing the SOFC community with alternate material options for high performance devices.

PEGylation of protein side-chains has been used for more than 30 years to enhance the pharmacokinetic properties of protein drugs, and has been enabled by the recent development of many chemoselective reactions for protein side-chain modification. However, there are no structure- or sequence-based guidelines for selecting sites that provide optimal PEG-based pharmacokinetic enhancement with minimal loss to biological activity. Chapter 1 is a brief introduction to protein PEGylation. In chapter 2 we use the WW domain of the human protein Pin 1 (WW) as a model system to probe the impact of PEG on protein conformational stability. Using a combination of experimental and theoretical approaches, we develop a structure-based method for predicting which sites within WW are most likely to experience PEG-based stabilization, and show that this method correctly predicts the location of a stabilizing PEGylation site within the chicken Src SH3 domain. PEG-based stabilization in WW is associated with enhanced resistance to proteolysis, is entropic in origin, and likely involves disruption by PEG of the network of hydrogen-bound solvent molecules that surround the protein. Chapter 3 shows that PEG-based stabilization of the WW domain depends strongly on the identity of the PEG-protein linker, with the most stabilizing linkers involving conjugation of PEG to an Asn side-chain amide nitrogen. Chapter 4 investigates the interplay between structure-based guidelines for PEG-base stabilization developed in chapter 2 and the different chemistries explored in chapter 3.

The current understanding of the mechanical properties and deformation behavior of some individual phases in titanium alloys is limited due to the fine scale at which these phases precipitate within the β-phase matrix. The α and ω phases represent the most widely observed phases in titanium alloys depending on the alloy composition and also the heat treatment procedure adopted during processing. The possibility of precipitating ω-phase depends on the content of the β-stabilizers within the system. Although a significant compositional partitioning occurs within ω-phase upon aging treatment, the knowledge of ω-phase mechanical properties as a function of composition is very limited. The initial part of the current work focuses on the effect of common β-stabilizers elements on the phase stability and mechanical properties of the ω-phase using first-principles calculations. A relation between the bonding nature, the phase stability, and elastic properties was proposed. Thereafter αʺ martensitic phase was investigated in Ti-Nb and Ti-Nb-O alloys. The phase stability and martensitic start temperature of αʺ-phase was studied as a function of Nb and oxygen content. Also, the effect of the lattice shear distortion induced by oxygen atom on stabilizing β-phase was investigated. Subsequently the effect of the β-stabilizers' elements on stacking faults energy and ductility in α-Ti alloys was studied. Both prismatic and basal slip system were investigated with different concentration of β-stabilizers at the slip plane. Lastly, while the Tadmor and Bernstein model was employed to predict the partial dislocation emission and twinning propensity, the Rice criterion was used to estimate the effect of different β-stabilizers on the ductility of α-Ti alloys.

<p>Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional calorimetric or spectroscopic approaches for measuring protein stability typically require large amounts of purified protein. This requirement has precluded their use in proteomic applications. Stability of Proteins from Rates of Oxidation (SPROX) is a recently developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new SPROX-like protocol was developed that measured protein folding free energies using the denaturant dependence of the rate at which globally protected tryptophan and methionine residues are modified with dimethyl (2-hydroxyl-5-nitrobenzyl) sulfonium bromide and hydrogen peroxide, respectively. This so-called Hybrid protocol was applied to proteins in yeast and MCF-7 cell lysates and achieved a ~50% increase in proteomic coverage compared to probing only methionine-containing peptides. Subsequently, the Hybrid protocol was successfully utilized to identify and quantify both known and novel protein-ligand interactions in cell lysates. The ligands under study included the well-known Hsp90 inhibitor geldanamycin and the less well-understood omeprazole sulfide that inhibits liver-stage malaria. In addition to protein-small molecule interactions, protein-protein interactions involving Puf6 were investigated using the SPROX technique in comparative thermodynamic analyses performed on wild-type and Puf6-deletion yeast strains. A total of 39 proteins were detected as Puf6 targets and 36 of these targets were previously unknown to interact with Puf6. Finally, to facilitate the SPROX/Hybrid data analysis process and minimize human errors, a Bayesian algorithm was developed for transition midpoint assignment. In summary, the work in this dissertation expanded the scope of SPROX and evaluated the use of SPROX/Hybrid protocols for characterizing protein-ligand interactions in complex biological mixtures.</p> / Dissertation

Title: Bifunctional ligands for copper(II) complexation Author: Bc. Martina Benešová Supervisor: doc. RNDr. Jan Kotek, Ph.D. Institution: Department of Inorganic Chemistry, Faculty of Science, CU in Prague Author's e-mail: EvaGlaser@seznam.cz ABSTRACT The main aim of this thesis was preparation of macrocyclic ligands based on 1,4,8,11- tetraazacyclotetradecane skeleton, which is suitable for selective complexation of divalent copper, and study of their properties. These ligands are suggested for potential utilization in nuclear medicine. Cyclam macrocycle was modified to bear one coordinating aminobenzylphospinate pendant arm (compound L1) or monophosphinate-bis(phosphonate) pendant arm (compound L2). During the synthesis, the skeleton was protected in positions 1, 4 and 8. In the frame of this work the synthesis of both targeted products was developed. Furthermore, a study of the thermodynamic, kinetic and coordination properties of ligand L2 was investigated by UV/VIS spectrophotometry and potentiometric titrations. A model bioconjugation of ligand L1 with primary amine was also studied. KEYWORDS Cyclam, phosphinates, phosphonates, nuclear medicine, copper(II) complexes, kinetic inertness, thermodynamic stability.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting the upper and lower motor neurons causing muscle atrophy and paralysis followed by death. Aggregates containing superoxide dismutase (SOD1) are found as pathological hallmark in diseased ALS patients. Consequently ALS is regarded as a protein misfolding disorder like Alzheimer’s disease and Parkinson’s disease. So far, little is known about the cause and mechanism behind SOD1 aggregation but the inherent property of all polypeptide chains to form stable aggregated structures indicates that the protein misfolding diseases share a common mechanism. Our results show that SOD1 aggregation starts from the globally unfolded state, since fibrillation is fastest at full occupancy of denatured protein induced either by chemical denaturation or mutation. Even so, the fibrillation rate shows a surprisingly weak dependence on the concentration of globally unfolded SOD1 indicating fibril fragmentation as the dominant mechanism for aggregate formation. This is further supported by the observation that the SOD1 sample has to be mechanically agitated for fibrillation to occur.  Interestingly, we observe a similar SOD1 aggregation behaviour in vivo, where the survival times of ALS transgenic mice correlates with mutant stability, and aggregate growth depends weekly on the concentration of unfolded monomer. Additionally, in-cell NMR measurements reveal that in live cells the thermodynamic equilibrium is shifted towards the unfolded state of SOD1, which is also more fully extended than in vitro. This suggests that the globally unfolded aggregation competent protein is more abundant in the crowded environment in vivo than dilute in vitro conditions. Finally, antibody analysis of aggregates from ALS transgenic mice reveals the existence of aggregate strains involving different parts of the protein depending on mutation, which may offer an explanation for the various disease phenotypes observed in ALS. Altogether these findings provide important clues for understanding SOD1 aggregation with implications for ALS, as well as other protein misfolding diseases.

The aim of this work was to synthesize and study acid-base and coordination properties of ligands bearing a neutral or negative charge on their pendant arms. Acid-base properties of two ligands and thermodynamic stability of their complexes with gallium, copper, and zinc ions were studied using potentiometry, UV-Vis and NMR. Solid state structure of one of the ligands and its complex with copper ion was studied using RTG structural analysis. Structure of complexes in solution was studied using methods of computational chemistry.

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