Cyclophilin A (CypA) is the well-studied member of a group of ubiquitous and evolutionarily conserved families of enzymes called peptidyl–prolyl isomerases (PPIases). These enzymes catalyze the cis-trans isomerization of peptidyl-prolyl bond in many proteins. The distinctive functional path triggered by each isomeric state of peptidyl-prolyl bond renders PPIase-catalyzed isomerization a molecular switching mechanism to be used on physiological demand. PPIase activity has been implicated in protein folding, signal transduction, and ion channel gating as well as pathological condition such as cancer, Alzheimer’s, and microbial infections. The more than five order of magnitude speed-up in the rate of peptidyl–prolyl cis–trans isomerization by CypA has been the target of intense research. Normal and accelerated molecular dynamic simulations were carried out to understand the catalytic mechanism of CypA in atomistic details. The results reaffirm transition state stabilization as the main factor in the astonishing enhancement in isomerization rate by enzyme. The ensuing intramolecular polarization, as a result of the loss of pseudo double bond character of the peptide bond at the transition state, was shown to contribute only about −1.0 kcal/mol to stabilizing the transition state. This relatively small contribution demonstrates that routinely used fixed charge classical force fields can reasonably describe these types of biological systems. The computational studies also revealed that the undemanding exchange of the free substrate between β- and α-helical regions is lost in the active site of the enzyme, where it is mainly in the β-region. The resultant relative change in conformational entropy favorably contributes to the free energy of stabilizing the transition state by CypA. The isomerization kinetics is strongly coupled to the enzyme motions while the chemical step and enzyme–substrate dynamics are in turn buckled to solvent fluctuations. The chemical step in the active site of the enzyme is therefore not separated from the fluctuations in the solvent. Of special interest is the nature of catalysis in a more realistic crowded environment, for example, the cell. Enzyme motions in such complicated medium are subjected to different viscosities and hydrodynamic properties, which could have implications for allosteric regulation and function.

Studies toward the total synthesis of (+)-providencin (1), a highly oxygenated cembranoid dipterpene with a unique bicyclo[12.2.0]hexadecane skeleton and pronounced biological activity, are described. These studies resulted in the synthesis of advanced intermediates 320 and 332 which contain all of the carbon atoms of 1. In a first generation approach toward 1, a zirconium-mediated deoxygenative ring contraction of furanose 177 was used to furnish enantiopure cyclobutanol 176. Olefination of furan aldehyde 197 with phosphonate 214 completed cyclobutylfuran segment 215. A second generation approach toward cyclobutylfuryl subunit 221 via ring-closing metathesis of diene 237 was unproductive, but the iodolactone subunit 228 needed for 1 was prepared successfully using carbometallation-iodination of alkyne 231. Nucleophilic substitution of tosylate 230 with the dianion of phenylselenyl acetic acid (252) followed by acid-catalyzed lactone formation was employed for construction of the γ-lactone moiety of 228. A third generation route to the cyclobutylfuryl subunit of 1 involved a tin(II) chloride-mediated stereoselective allenol synthesis by reaction of aldehyde 302 with propargyllic bromide 264. A silver-catalyzed allenone-to-furan isomerization of 309 completed the synthesis of cyclobutylfuran subunit 288. Attempts to couple the two major fragments, 228 and 288, using palladium-catalyzed C-H activation of the furan component were unsuccessful, but linkage of two major subunits was achieved at the C12-C13 bond via an intermolecular aldol reaction to give 332 and at the C6-C7 bond using intermolecular palladium-catalyzed cross-coupling to afford 320. / Graduation date: 2012

Thesis (Ph. D.)--University of Alabama at Birmingham, 2008. / Additional advisors: Houston Byrd, Chris Lawson, Sadanandan Velu, Charles Watkins. Description based on contents viewed Feb. 9, 2009; title from PDF t.p. Includes bibliographical references.

Uncaria tomentosa (Willd.) DC. (Rubiaceae), popularmente conhecida como cat’s claw ou “unha-de-gato”, é uma liana encontrada principalmente na região Amazônica assim como Uncaria guianensis (Aubl.) Gmel. (Rubiaceae), que é utilizada como substituinte ou adulterante em relação a U. tomentosa devido à sua maior abundância e menor valor comercial. A diferenciação de ambas pode ser realizada com base em aspectos morfoanatômicos, mas limita-se à composição química em derivados, como extratos fluidos e secos. As cascas do caule de U. tomentosa são compostas majoritariamente por derivados triterpênicos, polifenóis e alcaloides oxindólicos, aos quais são atribuídas as principais atividades biológicas da espécie. Contudo, o perfil de alcaloides oxindólicos é variável devido à ocorrência de quimiotipos e a elevada susceptibilidade dos mesmos à isomerização. Assim, a presente tese teve como objetivo avaliar a relevância dos alcaloides oxindólicos em U. tomentosa no que tange ao reconhecimento de adulteração na espécie, ocorrência de quimiotipos e isomerização desses compostos. Para isso, foram construídos modelos de classificação e regressão multivariada a partir das análises de CLAE-PDA, IV e UV destinados a diferenciação entre U. tomentosa e U. guianensis e ao reconhecimento de adulteração e determinação do percentual de adulterante em amostras de U. tomentosa. Os resultados obtidos demonstraram que os critérios farmacopéicos atualmente utilizados no controle de qualidade da matéria-prima vegetal e derivados de U. tomentosa baseados nos alcaloides oxindólicos são inefetivos em relação ao reconhecimento de adulteração. (Continuação A avaliação da atividade citotóxica dos diferentes quimiotipos baseados no perfil de alcaloides oxindólicos em U. tomentosa frente a leucócitos humanos e as células tumorias de bexiga (T24) e glioblastoma (U-251-MG) humanos, demonstrou que a seletividade frente às células tumorais é depentente do quimiotipo. Adicionalmente, a complexação dos alcaloides oxindólicos com sulfobutil-éter-β-ciclodextrina (SBE-βCD) minimizou a velocidade de isomerização sob condições de incubação (pH = 7,4; 37 ºC), sem contudo inibir o processo de isomerização. / Uncaria tomentosa (Willd.) DC. (Rubiaceae), popularly known as cat’s claw, is a liana found mainly in the Amazon rainforest as well as Uncaria guianensis (Aubl.) Gmel. (Rubiaceae) used as substituent or adulterant due to their higher wild population and lower market value. The differentiation among the raw material of both species can be performed from morphological and microscopic characteristics, but is limited in derivatives such as fluid and freeze-dried extracts. The stem bark from U. tomentosa is composed mainly by quinovic acid glycosides, polyphenols and oxindole alkaloids, to which have been assigned the major biological activities of the specie. However, the oxindole alkaloids profile in the U. tomentosa is variable due to chemotype occurrence and their susceptibility to isomerization. Thus, this study aimed to evaluate the relevance of oxindole alkaloids at U. tomentosa in relation to adulteration recognition, chemotype occurrence and oxindole alkaloids isomerization. Classification and multivariate regression models were built from HPLC-PDA, FT-IR and UV data to differentation between U. tomentosa e U. guianensis, as well as for adulteration recognition and determination of the adulterant level in the U. tomentosa. The current U.S. pharmacopeia monographs specifications for quality control of stem bark raw material from U. tomentosa, as well as for their derivatives, such as powdered dried extract, based on the oxindole alkaloids were ineffective for adulteration recognition. The cytotoxic activity evaluation of the different chemotypes, based on the oxindole alkaloid profile, against the human leukocytes and against human bladder cancer cell line (T24) and human glioblastoma cell line (U-251-MG) demonstrated that selectivity against the tumoral cells is dependent of the chemotype. In addition, the complexation of the oxindole alkaloids with Sulfobutyl ether β-cyclodextrin (SBE-βCD) minimize the isomerization rate under incubation conditions (pH = 7.4; 37 ºC) but without, however, inhibit the isomerization process.

Made available in DSpace on 2014-06-11T19:31:34Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-05-08Bitstream added on 2014-06-13T21:02:51Z : No. of bitstreams: 1 cerqueira_vc_dr_botfca.pdf: 1017835 bytes, checksum: f5e403927b163c750f9e0cca2acae31a (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Universidade Estadual Paulista (UNESP) / Os produtos das hidrólises de amido são glicose, maltose e uma série de oligossacarídeos e polissacarídeos que encontram utilização principalmente na indústria de alimentos. Neste grupo enquadram-se os adoçantes que aditam sabores a produtos que são demandados por consumidores específicos. Atualmente o açúcar mais utilizado no Brasil é a sacarose, produto extraído da cana-de-açúcar, e o mais utilizado mundialmente é a frutose obtida a partir da hidrólise do milho e posterior isomerização da glicose para frutose. A frutose apresenta capacidade edulcorante 30% maior que a sacarose, 2,5 vezes maior que a glicose e 2 vezes mais solúvel que a glicose, com isso, pode ser utilizada em menor quantidade, diminuindo o poder calórico do alimento e viabilizando sua utilização no tratamento da obesidade. Levando em consideração a importância dos adoçantes para o mercado de alimentos, o presente trabalho teve como objetivo realizar estudos sobre o processo de obtenção da frutose a partir de amido de mandioca. Para a execução dos ensaios utilizou-se fontes comerciais de α– amilase e amiloglucosidase, Liquozyme Supra 2.2X e Saczyme 750 AGUg-1, respectivamente, aplicadas em substrato de amido de mandioca em reator agitado com temperatura controlada. Após o processo de hidrólise enzimática, o hidrolisado passou por um processo de purificação utilizando terra diatomácea e carvão ativado em quatro temperaturas (30, 40, 50 e 60°C), com a finalidade de remoção de contaminantes originários da matéria prima, que levam a odor, cor e sabores indesejáveis. Após o tratamento com carvão ativo e terra diatomácea foram realizados ensaios para estabelecer os melhores parâmetros para a realização do processo de isomerização, buscando a conversão de parte da glicose à frutose, utilizando a enzima... / The products of starch hydrolyses are glucose, maltose and a series of oligosaccharides and polysaccharides which have their main utilization in food industry. This group comprises sweeteners that add flavor to products demanded by specific consumers. Currently the most used sugar in Brazil is sucrose, a product extracted from sugarcane, while the most used sugar worldwide is fructose obtained from maize hydrolysis and subsequent glucose isomerization to fructose. The sweetening capacity of fructose is 30% higher than that of sucrose and 2.5-fold higher than that of glucose; in addition, fructose is 2-fold more soluble than glucose and thus can be used in smaller quantities, decreasing the food’s caloric potential and making its use viable in obesity treatment. Considering the importance of sweeteners for the food market, the present study aimed to investigate the process of fructose production from cassava starch. The assays were performed by using commercial sources of α–amylase and amyloglucosidase, Liquozyme Supra 2.2X and Saczyme 750 AGUg-1, respectively, applied to cassava starch substrate in an agitated reactor at controlled temperature. Following the process of enzymatic hydrolysis, the hydrolysate underwent a purification process using diatomaceous earth and activated charcoal at four temperatures (30, 40, 50 and 60°C), in order to remove contaminants originated from the raw material, which lead to undesirable smell, color and flavor. After the treatment with activated charcoal and diatomaceous earth, assays were carried out to establish the best parameters for the isomerization process, aiming at the conversion of part of glucose into fructose, using the enzyme isomerase. The process selected for the studies was in a continuous system where the glucose syrup, previously purified, was continuously pumped... (Complete abstract click electronic access below)

Uncaria tomentosa (Willd.) DC. (Rubiaceae), popularmente conhecida como cat’s claw ou “unha-de-gato”, é uma liana encontrada principalmente na região Amazônica assim como Uncaria guianensis (Aubl.) Gmel. (Rubiaceae), que é utilizada como substituinte ou adulterante em relação a U. tomentosa devido à sua maior abundância e menor valor comercial. A diferenciação de ambas pode ser realizada com base em aspectos morfoanatômicos, mas limita-se à composição química em derivados, como extratos fluidos e secos. As cascas do caule de U. tomentosa são compostas majoritariamente por derivados triterpênicos, polifenóis e alcaloides oxindólicos, aos quais são atribuídas as principais atividades biológicas da espécie. Contudo, o perfil de alcaloides oxindólicos é variável devido à ocorrência de quimiotipos e a elevada susceptibilidade dos mesmos à isomerização. Assim, a presente tese teve como objetivo avaliar a relevância dos alcaloides oxindólicos em U. tomentosa no que tange ao reconhecimento de adulteração na espécie, ocorrência de quimiotipos e isomerização desses compostos. Para isso, foram construídos modelos de classificação e regressão multivariada a partir das análises de CLAE-PDA, IV e UV destinados a diferenciação entre U. tomentosa e U. guianensis e ao reconhecimento de adulteração e determinação do percentual de adulterante em amostras de U. tomentosa. Os resultados obtidos demonstraram que os critérios farmacopéicos atualmente utilizados no controle de qualidade da matéria-prima vegetal e derivados de U. tomentosa baseados nos alcaloides oxindólicos são inefetivos em relação ao reconhecimento de adulteração. (Continuação A avaliação da atividade citotóxica dos diferentes quimiotipos baseados no perfil de alcaloides oxindólicos em U. tomentosa frente a leucócitos humanos e as células tumorias de bexiga (T24) e glioblastoma (U-251-MG) humanos, demonstrou que a seletividade frente às células tumorais é depentente do quimiotipo. Adicionalmente, a complexação dos alcaloides oxindólicos com sulfobutil-éter-β-ciclodextrina (SBE-βCD) minimizou a velocidade de isomerização sob condições de incubação (pH = 7,4; 37 ºC), sem contudo inibir o processo de isomerização. / Uncaria tomentosa (Willd.) DC. (Rubiaceae), popularly known as cat’s claw, is a liana found mainly in the Amazon rainforest as well as Uncaria guianensis (Aubl.) Gmel. (Rubiaceae) used as substituent or adulterant due to their higher wild population and lower market value. The differentiation among the raw material of both species can be performed from morphological and microscopic characteristics, but is limited in derivatives such as fluid and freeze-dried extracts. The stem bark from U. tomentosa is composed mainly by quinovic acid glycosides, polyphenols and oxindole alkaloids, to which have been assigned the major biological activities of the specie. However, the oxindole alkaloids profile in the U. tomentosa is variable due to chemotype occurrence and their susceptibility to isomerization. Thus, this study aimed to evaluate the relevance of oxindole alkaloids at U. tomentosa in relation to adulteration recognition, chemotype occurrence and oxindole alkaloids isomerization. Classification and multivariate regression models were built from HPLC-PDA, FT-IR and UV data to differentation between U. tomentosa e U. guianensis, as well as for adulteration recognition and determination of the adulterant level in the U. tomentosa. The current U.S. pharmacopeia monographs specifications for quality control of stem bark raw material from U. tomentosa, as well as for their derivatives, such as powdered dried extract, based on the oxindole alkaloids were ineffective for adulteration recognition. The cytotoxic activity evaluation of the different chemotypes, based on the oxindole alkaloid profile, against the human leukocytes and against human bladder cancer cell line (T24) and human glioblastoma cell line (U-251-MG) demonstrated that selectivity against the tumoral cells is dependent of the chemotype. In addition, the complexation of the oxindole alkaloids with Sulfobutyl ether β-cyclodextrin (SBE-βCD) minimize the isomerization rate under incubation conditions (pH = 7.4; 37 ºC) but without, however, inhibit the isomerization process.

A Dissulfeto Isomerase Proteína (PDI) é uma chaperona redox essencial responsável pela inserção correta das ligações dissulfeto em proteínas nascentes no retículo endoplasmático. Nesta localização celular, bem como em outras regiões, como na superfície celular, a PDI atua na manutenção da homeostase redox e sinalização. Houve substanciosa evolução no conhecimento sobre a estrutura e funções da PDI, graças a estudos in vitro que utilizam a PDI purificada, quimeras ou seus domínios isolados. Nestas abordagens experimentais, as medidas das atividades redutase e chaperona da PDI são realizadas de forma relativamente simples. Entretanto, medir a atividade isomerase, que é a atividade autêntica da família das PDIs, é tecnicamente bastante complexo. Em células e tecidos, o papel da PDI tem sido descrito com base principalmente em estratégias experimentais de ganho e perda de função. Todavia, ainda há pouca informação na correlação entre os resultados funcionais com a medida das atividades da PDI. Este trabalho compila os principais métodos descritos para medir as quatro atividades da PDI: tiol redutase, tiol oxidase, tiol isomerase e chaperona, com ênfase na descrição de controles e interferentes críticos, como os tampões que contém surfactantes. Ainda, discutir-se-á criticamente os resultados obtidos quando da transposição destes métodos para amostras de homogenatos (celular ou tecidual) / Protein disulfide isomerase is an essential redox chaperone from endoplasmic reticulum, responsible for correct disulfide bond insertion in nascent proteins. At the endoplasmic reticulum and other locations including the cell surface, PDI accounts for redox homeostasis and signaling. Knowledge about PDI structure and function evolved substantially from in vitro studies using purified PDI and chimeras. In these experimental scenarios, PDI reductase and chaperone are readily approachable. However, isomerase activity, the hallmark of PDI family, is significantly complex. Assessment of PDI roles in cells and tissues mainly relies on gain- or loss-of-function experiments. However, there is limited information regarding correlation of these results with PDI activities. In this manuscript, we put together the main methods described for measuring the four PDI activities: thiol reductase, thiol oxidase, thiol isomerase and chaperone, with emphasis on controls and critical interferents, such as detergent-containing buffers. We also discuss the transposition of these methods from purified PDI to cellular or in vivo samples, with critical thoughts about the interpretation of results

Orientador: Adriana Zerlotti Mercadante / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimento / Made available in DSpace on 2018-08-19T05:24:49Z (GMT). No. of bitstreams: 1 Gurak_PolianaDeyse_D.pdf: 2576170 bytes, checksum: 75f41dadc16bd530f6cea22fa2213682 (MD5) Previous issue date: 2011 / Resumo: Muitos processos utilizados na indústria de alimentos empregam altas temperaturas e proporcionam o contato dos alimentos com substâncias pró-oxidantes. Tais condições tornam a sequência de ligações duplas conjugadas presente nos carotenoides susceptível à isomerização geométrica, oxidação e degradação. Portanto, o objetivo principal deste trabalho foi estudar a degradação térmica e química do b-caroteno, através da identificação dos compostos primários de degradação e sua relação com a capacidade antioxidante e as propriedades de cor. Os experimentos realizados foram: a) aquecimento a 120 °C na presença de ar; b) aquecimento a 120 °C sob fluxo de oxigênio, c) aquecimento a 120 °C na presença de ar e adição de galato de propila; d) aquecimento a 150 °C na presença de ar; e) aquecimento a 150 °C sob fluxo de oxigênio; f) aquecimento a 150 °C sob fluxo de nitrogênio; g) clivagem oxidativa com permanganato de potássio (KMnO4) e h) reação de epoxidação com ácido meta-cloro-perbenzóico (MCPBA). A degradação do b-caroteno foi monitorada através da análise de carotenóides totais por espectrofotometria, a avaliação da cor por colorimetria (parâmetros CIELAB) e análise do perfil de carotenóides por cromatografia líquida de alta eficiência com detectores de arranjo de fotodiodos e espectrometria de massas (HPLC-DAD-MS/MS). As alterações na capacidade antioxidante foram avaliadas por meio da capacidade de desativação do radical ABTS¿+ (2,2¿-azinobis-(3-etilbenzotiazolina-6-sulfonato)) e da proteção contra o oxigênio singlete (1O2) utilizando o 9,10-dimetil-antraceno como actinômetro e azul de metileno como sensibilizador. Foram identificados 16 carotenóides gerados pela degradação térmica e química do b-caroteno. O aquecimento resultou na diminuição da concentração de all-trans-b-caroteno com a formação de isômeros (13-cis, 9-cis, 15-cis, 9,13-di-cis, 9,15-di-cis, 9,13¿-di-cis, 13,15-di-cis-ß-caroteno), epóxidos (5,6 e 5,8-epóxi-ß-caroteno) e, em menor quantidade, apocarotenóides (ß-apo-8¿-carotenal, ß-apo-10¿-carotenal, ß-apo-12¿-carotenal). Na oxidação química com KMnO4, o all-trans-b-caroteno foi totalmente degradado após 30 min de reação com formação de b-apo-8¿-carotenal, b-apo-10¿-carotenal, b-apo-12¿-carotenal, b-apo-15-carotenal e semi-b-carotenona. Já na reação com MCPBA, o all-trans-b-caroteno não foi completamente degradado e os produtos de degradação formados em maior proporção foram 5,6-epóxi-b-caroteno, 5,6:5¿,6¿-diepóxi-b-caroteno, 5,6:5¿,8¿-diepóxi-b-caroteno e 5,8-epóxi-b-caroteno, além de pequena quantidade de 13-cis-b-caroteno e 9-cis-b-caroteno. Em todos os experimentos foi observada a existência de correlação superiores a 0,91 entre alguns parâmetros físicos de cor (b* e C*ab) e o parâmetro químico (teor de carotenóides totais), indicando que estes parâmetros de cor podem ser utilizados para monitorar a degradação de carotenóides. O mecanismo proposto para os dois tipos de degradação (térmica e química) envolveu reações reversíveis e irreversíveis, para formação de compostos de isomerização e de oxidação, respectivamente. A análise da capacidade antioxidante mostrou que a presença isolada de b-caroteno ou a mistura de b-caroteno com produtos de degradação térmica apresentaram valores similares de TEAC (capacidade antioxidante equivalente a trolox) e de porcentagem de proteção contra 1O2. Por outro lado, os produtos de oxidação gerados na reação química com KMnO4 resultaram em um aumento nos valores de TEAC e maior eficiência da desativação do 1O2 com o aumento do tempo de reação / Abstract: Many processes in the food industry aplly high temperatures and allow the contact with pro-oxidant substances, such conditions in which the sequence of conjugated double bonds, present in carotenoids, is susceptible to geometric isomerization, oxidation and degradation. Therefore, the main aim of this work was to study the thermal and chemical degradation of b-carotene, identifying the primary degradation compounds and its relation with the antioxidant capacity and colour properties. The experiments were: a) heating at 120 °C with air exposure; b) heating at 120 °C under flow of pure oxygen; c) heating at 120 °C with air exposure and addition of propyl gallate; d) heating at 150 °C with air exposure; e) heating at 150 °C under flow of pure oxygen; f) heating at 150 °C under a flow of pure nitrogen; g) oxidative cleavage with potassium permanganate (KMnO4); and h) epoxidation with meta-chloroperbenzoic acid (MCPBA). In all experiments, the degradation and formation of isomerization and oxidation products were monitored by analysis of total carotenoids by spectrophotometer, colour evaluation by colorimetry and carotenoid profile analysis by high-performance liquid chromatography with photodiode array detector and mass spectrometry (HPLC-DAD-MS). Changes in the antioxidant capacity were monitored by the scavenging capacity against the ABTS¿+ (2,2-azinobis(3-ethylbenzthiazoline-6-sulphonic acid)), and protection against singlet oxygen (1O2) using 9,10-dimethyl-anthracene as actinometer and methylene blue as sensitizer. A total of sixteen carotenoids were identified in both the chemical and thermal degradation of b-carotene. Heating caused a decrease in the all-trans-b-carotene content with the formation of cis isomers (13-cis, 9-cis, 15-cis, 9,13-di-cis, 9,15-di-cis, 9,13¿-di-cis, 13,15-di-cis-b-carotene), epoxides (5,6 and 5,8-epoxy-b-carotene) and apocarotenoids (b-apo-8'-carotenal, b-apo-10'-carotenal, b-apo-12'-carotenal). The chemical degradation with KMnO4 completely degraded the all-trans-b-carotene in 30 minutes of reaction, with the formation of b-apo-8'-carotenal, b-apo-10'-carotenal, b-apo-12'-carotenal, b-apo-15-carotenal and semi-b-carotenone. In the reaction with MCPBA, all-trans-b-carotene was not completely degraded and the major products were 5,6-epoxy-b-carotene, 5,6:5¿,6¿-diepoxy-b-carotene, 5,6:5¿,8¿-diepoxy-b-carotene and 5,8-epoxy-b-carotene, with small amounts of 13-cis-b-carotene and 9-cis-b-carotene. All experiments showed correlations above 0.91 between some physical colour parameters (b* and C*ab) and chemical parameters (content of total carotenoids), indicating that some colour parameters can be used to monitor carotenoid degradation. The proposed mechanism in both types of degradation (thermal and chemical) involved reversible and irreversible reactions, to the formation of isomerization and oxidation compounds, respectively. The analysis of the antioxidant capacity showed that both pure b-carotene and the mixture of b-carotene with thermal degradation products had similar values of TEAC (trolox equivalent antioxidant capacity), as well as similar protection percentage against 1O2. On the other hand, the products formed in the chemical reaction with KMnO4 resulted in increase in both the TEAC values and protection against 1O2 with the increase in reaction time / Doutorado / Ciência de Alimentos / Doutor em Ciência de Alimentos

Abstract Protein folding of outer membrane and secreted proteins, including receptors, cytokines and antibodies is often linked to disulphide bond formation. Native disulphide bond formation is complex and is usually the rate limiting step in the folding of such proteins. The enzymes which catalyse the slow steps in disulphide bond formation belong to the protein disulphide isomerase (PDI) family. PDI catalyses formation, reduction and isomerization of newly synthesized disulphide bonds. The mechanisms of action of the PDIs are currently poorly understood and this not only inhibits our understanding of the biogenesis of a range of medically important proteins, and hence associated disease states, but also prevents the effective manipulation of the cellular environment by the biotechnology industry for the production of high value therapeutic proteins. Hence, understanding the mechanism of action of these enzymes is vital for a wide range of medically important processes and therapies. In this study the role of a conserved arginine residue in the catalytic activity of PDI was shown. The movement of this residue into and out of the active site locale of PDI was shown to modulate the pKa of the C-terminal active site cysteine of PDI and by that way to allow the enzyme to act efficiently as catalyst both of oxidation and isomerization reactions. The possible role of hydrogen peroxide produced by sulphydryl oxidases during disulphide bond formation was studied in an oxidative protein refolding assay. Analysis showed that hydrogen peroxide can be used productively to make native disulphide bonds in folding proteins with minimal side reactions. In addition, the kinetics of oxidation and reduction of the <b>a</b> domains of PDI and Pdi1p by glutathione was studied in this thesis. The kinetics obtained with stopped-flow and quenched-flow experiments showed the reactions to be more rapid and complex than previously thought. Significant differences exist between the kinetics of PDI and Pdi1p. This implies that the use of yeast systems to predict physiological roles for mammalian PDI family members should be treated cautiously.

Ring closing metathesis (RCM) is a chemical transformation that converts a bisalkene compound into a cycloalkene. It is catalyzed by transition metal complexes containing carbene ligands (that feature metal-carbon double bonds). The mechanism is well-understood, however, there are numerous details of the reaction that are less well understood, especially concerning catalyst activation and decomposition and formation of byproducts. This thesis takes a new approach to the study of RCM: analysis of the reaction using real-time mass spectrometric techniques. Electrospray ionization (ESI) mass spectrometry was employed in this study, and the real-time aspect was enabled by using pressurized sample infusion (PSI). Observation of the reactants and products was enabled using charge-tagged bis-alkenes of the general formula [Bu2N{(CH2)nCH=CH2}2]+ [PF6]–. These were synthesized in two steps using a generally applicable methodology to generate a wide range of ring sizes of the product, from 5- to 15-membered rings. Examination of their behavior under carefully optimized RCM conditions using Grubbs’ second-generation catalyst showed a wide variation in reaction rates and amount of byproducts, largely due to ring-strain effects (especially high for 5- and 9-membered rings). Byproducts always exhibited a 14 Da mass unit difference from starting materials or products, and Orbitrap MS analysis confirmed it was CH2. Isomerization was suspected to lead to byproducts. A pathway for byproducts via isomerization and cross metathesis was proposed. The source of actual isomerization catalyst was believed to be from the precatalyst itself as the evidence of precatalyst decomposition was observed. Finally, to prove our isomerization hypothesis, an authentic isomerization catalyst was deliberately added into a fast and clean reaction along with Grubbs’ second-generation catalyst, and it produced the expected byproducts. Only small amounts of oligomeric intermediates were observed, probably because of the low concentrations used. [ClPCy3]+ was a new short-lived decomposition product stemming from catalyst breakdown, along with already-known imidazolium and protonated phosphine decomposition products. Overall, the thesis provides deep new insights into the nature of RCM reactions, in particular revealing the importance of isomerization in RCM reactions that are slow due to ring strain effects and in uncovering a new decomposition pathway for important RCM catalysts. / Graduate