Este estudo enfocou a mediação por íons metálicos divalentes da solvólise da ligação éster formada entre peptídeos e resinas, método desenvolvido por nós para a preparação de peptídeos C-modificados. Os objetivos foram: i) adaptá-lo para a estratégia Fmoc de síntese, ii) buscar resinas adequadas para tal propósito, iii) verificar qual íon metálico é mais eficiente para mediar tal reação; iv) investigar o possível mecanismo pelo qual os íons metálicos mediam as reações estudadas. Para isso, foram testadas as resinas derivadas do ácido p-hidroximetilbenzóico (HMBA-AM, HMBA-PEGA, HMBA-TG) e do álcool p-benziloxibenzílico (Wang), os mediadores metálicos Ca2+ e Zn2+, condições reacionais determinadas em estudos anteriores do nosso grupo de pesquisa (50% nucleófilo/ DMF) e os solventes nucleófilos metanol, etanol, propan-1-ol, propan-2-ol, butan-1-ol, álcool benzílico, butilamina e hexilamina. O desligamento de aminoácidos e peptídeos esterificados das resinas ocorreu com altos rendimentos (72 - 98%). A resina HMBA-AM e o íon Zn2+ demonstraram ser a combinação mais eficiente. Análises de espectroscopia de infravermelho na presença e ausência do íon metálico indicaram um mecanismo de reação no qual a coordenação do íon Zn2+ com o álcool facilita a formação do íon alcóxido, o qual é um nucleófilo melhor que o álcool e com capacidade de atacar o carbono da carbonila da ligação éster entre o peptídeo e a resina. / The present study was focused on divalent metal ions-mediated solvolysis of the ester linkage formed between peptides and resins, a method developed by us for the preparation of C-modified peptides. The aims were: i) to adapt it for the Fmoc synthesis strategy; ii) to search resins suitable for such purpose; iii) to determine which divalent metal ion is the most efficient reaction mediator; iv) to investigate the mechanism by which the metal ion mediates the solvolysis reactions studied. Therefore, we employed the resins p-hydroxymethylbenzoic acid (HMBA-AM, HMBA-PEGA, HMBA-TG) and p-benzyloxybenzyl (Wang) alcohol, the metal ions Ca2+ and Zn2+, the optimized solvolysis conditions found in our previous studies (50% nucleophile/DMF) and the nucleophilic solvents methanol, ethanol, propan-1-ol, propan-2-ol, butan-1-ol, benzyl alcohol, butylamine and cyclohexylamine. Detachment of esterified amino acids or peptides from resins gave high yields (72-98%). HMBA-AM resin and Zn2+ ion showed to be the most effective combination of resin and metal ion. Infrared spectroscopy analysis of the peptide-resins in absence and presence of such metal ion suggested a mechanism of reaction where the coordination of Zn2+ ion with the alcohol promotes its deprotonation to give the alkoxide ion, which is a better nucleophile and can attack the carbonyl carbon of the ester linkage formed between the amino acid and the resin.

While protein therapeutics are indispensable in the treatment of a variety of diseases, including cancer, rheumatoid arthritis, and diabetes, key limitations including short half-lives, high immunogenicity, protein instability, and centralized production complicate long-term use and on-demand production. Site-specific polymer conjugation provides a method for mitigating these challenges while minimizing negative impacts on protein activity. However, the location-dependent effects of polymer conjugation are not well understood. Cell-free protein synthesis provides direct access to the synthesis environment and rapid synthesis times, enabling rapid evaluation of multiple conjugation sites on a target protein. Here, work is presented towards developing cell-free protein synthesis as a platform for both design and on-demand production of next generation polymer-protein therapeutics, including (1) eliminating endotoxin contamination in cell-free reagents for simplified therapeutic preparation, (2) improving shelf-stability of cell-free reagents via lyophilization for on-demand production, (3) coupling coarse-grain simulation with high-throughput cell-free protein synthesis to enable rapid identification of optimal polymer conjugation sites, and (4) optimizing cell-free protein synthesis for production of therapeutic proteins

Kirala aminer används idag både som aktiva substanser och som bindningsmedel i flertalet läkemedel, dock är dagens produktion med kinetic resolution ineffektiv vilket gör att mer effektiva och miljövänliga produktionssätt eftersträvas. Biotransformation har visat sig både vara miljövänligt och en effektiv metod för att producera kirala aminer. Aminosyror kan användas som aminodonatorer för att producera den kirala aminen 1-methyl-3-phenylpropylamine (MPPA) från prokirala ketonen bensylaceton (BA) med hjälp av aminetransaminas. I denna studie användes metaboliskt konstruerad Saccharomyces cerevisiae med enzymet CV-ωTA för att identifiera vilka aminosyror som var bäst lämpade för MPPA produktion. MPPA produktion kunde detekteras för alla testade aminosyror. Aminosyrans koncentration hade ingen tydlig påverkan på produktionen av MPPA. Alanin vara den aminosyra som gav högst produktionsutbyte följt av lysin. Ingen tydlig relation mellan produktion av MPPA och aminosyrornas koncentrationer kunde ses. Produktionen av MPPA var snabbare än förväntat och var klar redan dag tre för flera av aminosyrorna. Det fanns en antydan att BA kunde vara toxiskt för cellerna i högre koncentrationer och därmed påverka produktionen av MPPA. / Chiral amines are used in several types of pharmaceuticals as both active substrates and building blocks, and there is an endeavor to find new and more eco-efficient ways to produce them than today’s production with kinetic resolution. Biotransformation in yeast has shown great potential for production and is also seen as an eco-friendly way to produce chiral amines. Amino acids can be used as an amino donor for the production of chiral amines, e.g. 1-methyl-3-phenylpropylamine (MPPA) from prochiral ketones, e.g. benzylacetone (BA) with aminotransaminase. In this study the production was done with metabolically engineered Saccharomyces cerevisiae, with the gene for the enzyme CV-ωTA transformed. Ten different amino acids were screened in up to three different concentrations for each amino acid. Production of MPPA was observed for all amino acids, with alanine as the most efficient followed by lysine. No clear relationship was seen between amino acid concentration and MPPA production. The production of MPPA for several amino acids were quicker than expected and was completed at day three. Our data indicated a cytotoxic effect of BA at higher concentrations, that negatively affected the production of MPPA.

Plusieurs études ont montré que certaines kinases situées dans le foie, « mammalian target of rapamycin » (mTOR), « adenosine monophosphate-activated protein kinase » (AMPK) et « general control non-depressible kinase 2 » (GCN2) répondent à la disponibilité en acides aminés.L’objectif de nos études a été de préciser le rôle de deux de ces voies, l’AMPK et GCN2, dans les adaptations du métabolisme énergétique et de la synthèse protéique en réponse aux variations en protéines du régime. Pour cela, des souris de type sauvage et des souris KO n’exprimant plus la voie AMPK ou GCN2 dans le foie ont été nourries pendant trois semaines avec un régime faible, normal ou fort en protéines. Les analyses ont montré que les souris KO-AMPK foie spécifique et nourries sous régime normoprotéique adaptent leur métabolisme hépatique notamment en sécrétant le facteur fibroblastique FGF21 ce qui leur permet de compenser l’absence d’AMPK et de présenter des profils d’oxydation normaux.Au contraire, les souris KO-AMPK foie spécifique nourries avec des régimes faibles ou forts en protéines présentent des altérations des profils d’oxydation des lipides et des glucides liées à une absence de modification du métabolisme hépatique.La délétion de GCN2 dans le foie, quant à elle, n’a d’effet que sous régime faible en protéines : les souris KO-GCN2 foie spécifique présentent une plus faible oxydation lipidique et une plus forte oxydation glucidique que les souris sauvages en période postprandiale dû à l’absence d’induction de la sécrétion de FGF21.Concernant le métabolisme des protéines, les kinases GCN2 et AMPK ne semblent pas impliquées dans l’intensité du flux de synthèse protéique dans le foie et en périphérie dans le muscle en période postprandiale.En conclusion, ces travaux montrent que les délétions de l’AMPK et de GCN2 hépatiques affectent le métabolisme énergétique mais pas le métabolisme protéique et que les conséquences dépendent de la composition du régime. / Several studies have reported that some kinases located in the liver respond to the availability of amino acids. These kinases are mammalian target of rapamycin '(mTOR), "adenosine monophosphate-activated protein kinase" (AMPK) and "general control non-depressible kinase 2" (GCN2).The aim of our study was to clarify the role of two of these signaling pathways, AMPK and GCN2 in the adaptations of energy and protein metabolism in response to the modulation of dietary protein content. Wild-type and liver AMPK-deficient or liver GCN2-deficient mice were fed either a low, a normal or high protein diet during three weeks. Analyzes showed that liver AMPK-deficient mice fed under a normo-protein diet exhibit an adapatation of liver metabolism and secret FGF21 which enables them to have normal postprandial oxidation profiles.In contrast, liver AMPK-deficient mice fed a low or a high protein diet exhibit an alteration in postprandial oxidation profiles. The deletion of GCN2 in the liver only has an effect under low protein diet as liver GCN2 deficient mice have a lower lipid oxidation and a higher carbohydrate oxidation linked to the absence of FGF21 secretion. Concerning protein metabolism, AMPK and GCN2 do not seem to be involved in protein synthesis rate in the posrprandial period in the liver and periphery in the postprandial muscle. In conclusion, these studies show that hepatic AMPK and GCN2 deletions affect energy metabolism, but not protein metabolism and that the consequences depend on diet composition.

Le principal objectif de cette thèse a été d'exploiter des isoxazolidin-5-ones α-substituées aisément accessibles comme plateformes originales pour la synthèse d'acides β2,2-aminés énantiomériquement enrichis. Pour cela, nous avons montré que la catalyse par transfert de phase, avec l'utilisation de faibles quantités (2-3 mol%) d'un sel d'ammonium quaternaire énantiopur dédié, était l'outil adéquate pour la fonctionnalisation énantiosélective de la position α des isoxazolidin-5-ones et ainsi générer un centre quaternaire stéréogène. Cette stratégie organocatalytique a été appliquée à la création de liaison Carbone-Soufre, Carbone-Carbone et Carbone-Azote avec des excès énantiomériques de bons à excellents. Des réactions d'hydrogénolyse de la liaison N-O ou bien des réactions d'ouvertures via l'attaque de nucléophiles ont conduit à la formation des acides β2,2-aminés correspondants énantiomériquement enrichis. Enfin, de nouveaux sels d'ammonium quaternaires chiraux de type tropos, faciles d'accès, ont été conçus et évalués dans les réactions d'α-sulfanylation et d'addition conjuguée énantiosélectives dans les conditions de catalyse par transfert de phase mises en place. / The main purpose of this thesis was to use readily available α-substituted isoxazolidin-5-ones as original building blocks for the synthesis of enantioenriched β2,2-amino acids. Phase-transfer catalysis approach, with low loading of an appropriate quaternary ammonium salt, was found to be the most efficient tool for the enantioselective functionalization of the α-position of isoxazolidin-5-ones, allowed thereby to generate a stereogenic quaternary center. This organocatalytic strategy was applied to C-S, C-C and C-N bond formation with good to excellent enantiomeric excess. Hydrogenolysis reactions of the N-O bond or ring-opening reactions via nucleophilic addition reaction led to the corresponding enantioenriched β2,2-amino acids formation. Finally, new easily available chiral quaternary tropos-ammonium salts were designed and evaluated for both the enantioselective α-sulfanylation and conjuguated addition reactions.

Orientador: Luciano Hauschild / Resumo: Dois estudos foram conduzidos com objetivo de comparar a biodisponibilidade relativa de L-Met e DL-Met com base em ensaio de balanço de N e os efeitos promovidos por ambas as fontes na morfologia intestinal e no sistema antioxidante de suínos em fase inicial e final de creche. Em cada experimento foram utilizados 42 suínos machos castrados (Agroceres PIC, Rio Claro, SP, Brazil: CamboroughTM x AGPIC 337TM) com peso inicial de 10,7 ± 1,09 kg e 20,5 ± 1,55 kg, respectivamente para o experimento 1 e o experimento 2. Cada experimento foi dividido em dois períodos experimentais com 21 suínos. Cada período experimental correspondeu a um bloco. Três suínos foram distribuídos aleatoriamente em 7 dietas experimentais dentro de cada bloco, resultando em um total de 6 repetições por tratamento. As dietas basais (DB) foram formuladas com deficiência de 68% em metionina, porém adequadas para os demais aminoácidos. Três níveis graduados de DL-Met e L-Met (0,03, 0,06 e 0,09%) foram suplementados à dieta basal para criar as dietas 2-7 em ambos os estudos. No experimento 1, ambas as fontes de metionina reduziram linearmente o N excretado pela urina e aumentaram linearmente a retenção de N (% de absorvido) (P ≤ 0,03). A biodisponibilidade relativa estimada para L-Met em comparação a DL-Met foi de 106% (intervalo de confiança – IC de 95%: 39 a 173%) para retenção de N (% de absorvido) em uma base equi-molar. No experimento 2, a suplementação com ambas as fontes de Met diminuiu linearmente a excr... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Two studies were conducted to compare the relative bioavailability of L-Met and DL-Met based on N balance assay and the effects promoted by both sources on intestinal morphology and antioxidant system of weaned and growing pigs. In each experiment were used 42 barrows (Agroceres PIC, Rio Claro, SP, Brazil: CamboroughTM x AGPIC 337TM) with initial body weight of 10.7 ± 1.09 kg and 20.5 ± 1.55 kg, respectively for Experiment 1 and Experiment 2. Each experiment was divided into two batches with 21 pigs. Each batch corresponded to a block. Three pigs were randomly assigned to 7 experimental diets within each block, resulting in a total of 6 replicates per treatment. Basal diets (BD) were formulated with 68% methionine deficiency, but adequate for the other amino acids. Three graded levels of DL-Met and L-Met (0.03, 0.06 and 0.09%) were supplemented to the basal diet to create diets 2-7 in both studies. In experiment 1, both sources of methionine linearly reduced N excreted in the urine and linearly increased N retention (% absorbed) (P ≤ 0.03). The estimated relative bioavailability for L-Met compared to DL-Met was 106% (95% CI - confidence interval: 39 to 173%) for N retention (% absorbed) on an equi-molar basis. In experiment 2, supplementation with both Met sources linearly decreased urinary N excretion and linearly increased total N retention, N retention (% ingested and% absorbed) (P ≤ 0.04). The estimated bioavailability of L-Met compared to DL-Met was 95% (95% CI: 13 to 17... (Complete abstract click electronic access below) / Mestre

Title: Study of cerium oxide thin films for biosensing applications Author: Yuliia Kosto Department: Department of Surface and Plasma Science Supervisor: Prof. RNDr. Vladimír Matolín, DrSc. Abstract: The presented scientific work was conducted in two main directions. The first one is an investigation of the simple biomolecules (glycine and sarcosine) bonding to cerium oxide model films by surface science techniques: photoelectron and near-edge X-ray absorption spectroscopies. Adsorption chemistry and thermal stability of the molecules on the oxides were studied in relation to the oxidation state of ceria cations, film morphology, and molecular deposition method. The oxygen vacancies in the oxide were shown to affect the adsorption geometry of glycine and stimulate molecular decomposition. The polycrystalline oxide morphology provided stabilizing effect on the glycine adlayer. Sarcosine deposited in vacuum formed densely packed adlayer with the molecules directed outwards. Interestingly, the results revealed that molecular film deposited from the aqueous solution, in contrast to deposition in vacuum, induces continuous reduction of the cerium oxide during thermal annealing. The second part is a study of polycrystalline cerium oxide thin films as an electrode for electrochemical and electrochemiluminescent...

This bachelor thesis covers the initial development of a synthesis of fullerene dimers using two different types of linking reactions. Different setups for [3+2] cycloadditions to fullerenes (Prato reaction) were tested, and for that purpose, an N-alkylated amino acid was synthesised. Hydroarylation of fullerene using Rh-catalysis was also studied, using both MIDA protected and unprotected boronic acids, as well as by using cycloaddition products. A range of model compounds in form of fulleropyrrolidenes were synthesised. Products were puried with HPLC and analysed with MALDI-MS and 1H NMR. A range of new compounds were synthesised and characterisation of them was begun. With MALDI-MS, indications that the fullerene dimer had formed were found. Using synthesised model compounds, by-products of the hydroarylation reaction were identied. / Denna kandidatuppsats behandlar påborjandet av syntesutvecklingen för bildandet av fullerendimerer genom användandet av två olika sorters länkningskemi. Olika förhållanden och reagens for [3+2]-cykloaddition till fullerener (Pratoreaktionen) studerades, och i samband med det syntetiserades en N-alkylerad aminosyra. Hydroarylering av fullerener med hjälp utav rodiumkatalys studerades även, genom reaktioner med både skyddade och oskyddade borsyror, inklusive fulleropyrrolidiner. Produkter har renats upp med HPLC och analyserats med MALDI-MS och 1H NMR. En uppsättning nya substanser har syntetiserts, men karaktäriseringen av dessa har inte slutförts. Genom användning av MALDI-MS har indikationer att fullerendimer bildats framkommit. Genom att använda syntetiserade modellsubstanser har biprodukter från hydroaryleringsreaktionen identierats.

The field of chemical graph theory utilizes simple graphs as models of molecules. These models are called molecular graphs, and quantifiers of molecular graphs are known as molecular descriptors or topological indices. Today's chemists use molecular descriptors to develop algorithms for computer aided drug designs, and computer based searching algorithms of chemical databases and the field is now more commonly known as combinatorial or computational chemistry. With the completion of the human genome project, related fields are emerging such as chemical genomics and pharmacogenomics. Recent advances in molecular biology are driving new methodologies and reshaping existing techniques, which in turn produce novel approaches to nucleic acid modeling and protein structure prediction. The origins of chemical graph theory are revisited and new directions in combinatorial chemistry with a special emphasis on biochemistry are explored. Of particular importance is the extension of the set of molecular descriptors to include graphical invariants. We also describe the use of artificial neural networks (ANNs) in predicting biological functional relationships based on molecular descriptor values. Specifically, a brief discussion of the fundamentals of ANNs together with an example of a graph theoretic model of RNA to illustrate the potential for ANN coupled with graphical invariants to predict function and structure of biomolecules is included.

The most common structural platform in biology, the βα-repeat classes of proteins, are represented by the (βα)8TIM barrel topology and the α/β/α sandwich, CheY-like topology. Previous studies on the folding mechanisms of several members of these proteins have suggested that the initial event during refolding involves the formation of a kinetically trapped species that at least partially unfolds before the native conformation can be accessed. The simple topologies of these proteins are thought to permit access to locally folded regions that may coalesce in non-native ways to form stable interactions leading to misfolded intermediates. In a pair of TIM barrel proteins, αTS and sIGPS, it has been shown that the core of the off-pathway folding intermediates is comprised of locally connected clusters of isoleucine, leucine and valine (ILV) residues. These clusters of Branched Aliphatic Side Chains (BASiC) have the unique ability to very effectively prevent the penetration of water to the underlying hydrogen bond networks. This property retards hydrogen exchange with solvent, strengthening main chain hydrogen bonds and linking tertiary and secondary structure in a cooperative network of interactions. This property would also promote the rapid formation of collapsed species during refolding. From this viewpoint, the locally connected topology and the appropriate distribution of ILV residues in the sequence can modulate the energy landscapes of TIM barrel proteins. Another sequence determinant of protein stability that can significantly alter the structure and stability of TIM barrels is the long-range main chain-side chain hydrogen bond. Three of these interactions have been shown to form the molecular underpinnings for the cooperative access to the native state in αTS. Global analysis results presented in Chapter II and Chapter III, suggest that the off-pathway mechanism is common to three proteins of the CheY-like topology, namely CheY, NT-NtrC and Spo0F. These results are corroborated by Gō-simulations that are able to identify the minimal structure of kinetically trapped species during the refolding of CheY and Spo0F. The extent of transient, premature structure appears to correlate with the number of ILV side chains involved in a large sequence-local cluster that is formed between the central β-sheet and helices α2, α3 and α4. The failure of Gō-simulations to detect off-pathway species during the refolding of NT-NtrC may reflect the smaller number of ILV side chains in its corresponding hydrophobic cluster. In Chapter IV, comparison of the location of large ILV clusters with the hydrogen exchange protected regions in 19 proteins, suggest that clusters of BASiC residues are the primarily determinants of the stability cores of globular proteins. Although the location of the ILV clusters is sufficient to determine a majority of the protected amides in a protein structure, the extent of protection is over predicted by the ILV cluster method. The survey of 71 TIM barrel proteins presented in Chapter V, suggests that a specific type of long-range main chain-side chain hydrogen bond, termed “βα hairpin clamp” is a common feature in the βα-repeat proteins. The location and sequence patterns observed demonstrate an evolutionary signature of the βαβ modules that are the building blocks of several βα-repeat protein families. In summary, the work presented in this thesis recognizes the role of sequence in modulating the folding free energy landscapes of proteins. The formation of off-pathway folding intermediates in three CheY-like proteins and the differences in the proposed extent of structure formed in off-pathway intermediates of these three proteins, suggest that both topology and sequence play important and concerted roles in the folding of proteins. Locally connected ILV can clusters lead to off-pathway traps, whereas the formation of the productive folding path requires the development of long-range nativelike topological features to form the native state. The ability of ILV clusters to link secondary and tertiary structure formation enables them to be at the core of this cooperative folding process. Very good correlations between the locations of ILV clusters and both strong protection against exchange and the positions of folding nuclei for a variety of proteins reported in the literature support the generality of the BASiC hypothesis. Finally, the discovery of a novel pattern of H-bond interactions in the TIM barrel architecture, between the amide hydrogen of a core ILV residue with a polar side chain, bracketing βαβ modules, suggests a means for establishing cooperativity between different types of side chain interactions towards formation of the native structure. See Additional Files for copies of the source code for the global analysis program and the cluster analysis program.