The next generation of toxic chemicals and hazardous wastes from sophisticated chemical industries will demand the environmental agencies to employ biological methods over the conventional physical and chemical remediation methods. Over the past decade, natural metallo-enzymes have been identified to degrade some of the major chemical contaminants through electron transfer pathways. However, these natural enzymes are less stable in organic solvents and they are not effective for the degradation of toxic compounds such as polychlorinated biphenyls or dioxins. This thesis explores the use of protein design approaches to produce chemically and molecularly modified enzymes, which are highly stable, possess little substrate specificity, and have higher activity than the natural enzymes. The experiments presented in this thesis make use of solid phase synthesis and site-directed mutagenesis for the synthesis and production of these enzymes and popular chromatographic techniques for their purification. The partial characterization of these proteins revealed the essential structural features of these proteins, and their catalytic activity was demonstrated by the use of peroxidase assays. / Master of Science

A esclerose lateral amiotrófica (ELA) é uma doença neurodegenerativa que afeta os neurônios motores levando a atrofia muscular e morte por insuficiência respiratória. Esta patologia se manifesta de forma esporádica ou familiar, que são indistinguíveis clinicamente. Mutações na enzima antioxidante superóxido dismutase 1 (hSod1) respondem por aproximadamente 20% dos casos familiares de ELA. Além disso, o caráter autossômico dominante destas mutações revela que a hSod1 adquire propriedades tóxicas aos neurônios motores. Atualmente, duas hipóteses não mutuamente excludentes existem para explicar o caráter tóxico das mutantes da hSod1 relacionadas à ELA. A primeira refere-se à produção de oxidantes pela atividade peroxidásica exacerbada das mutantes contribuindo para o estresse oxidativo observado em ELA. A segunda refere-se à agregação de proteínas como ocorre em outras doenças neurodegenerativas. Digno de nota, o radical carbonato produzido na atividade peroxidásica da hSod1 causa a formação de um dímero covalente da proteína análogo a uma espécie de hSod1 frequentemente detectada em modelos experimentais e pacientes da doença e associada à propriedade tóxica das mutantes. Desta forma, o presente trabalho buscou esclarecer o mecanismo de produção do radical carbonato pela hSod1, bem como caracterizar o dímero covalente da proteína para posterior estudo de sua formação em um modelo de ELA em ratos que superexpressam a mutante G93A da hSod1. Os estudos cinéticos da variação do pH sobre os efeitos de bicarbonato/CO2, nitrito e formato na atividade peroxidásica da hSod1, medidos pelo consumo de peróxido de hidrogênio e produção de radical, permitiram excluir o mecanismo de Fenton para explicar o ciclo peroxidativo da enzima em tampão bicarbonato em favor de outros intermediários reativos. Já, os experimentos de 13C RMN, modelagem molecular e cinética de fluxo interrompido com mistura assimétrica demonstraram que o ânion peroxomonocarbonato constitui o precursor do radical carbonato produzido pela hSod1. A caracterização do dímero covalente da hSod1 por proteólise com tripsina seguida de análise por HPLC/UV-vis e HPLC/ESI-MS identificou um peptídeo característico do dímero covalente da hSod1. A digestão enzimática em H2 18O demonstrou de forma inequívoca a natureza dímerica deste peptídeo pela marcação da extremidade C-terminal. Ainda, o sequenciamento do peptídeo dimérico por MS/MS revelou a estrutura primária ESNGPVKVW(ESNGPVKVWGSIK)GSIK, na qual as cadeias polipeptídicas estão ligadas através de um aduto de ditriptofano composto por resíduos Trp32 da proteína. Por fim, este peptídeo dimérico pode ser empregado como marcador bioquímico específico para o estudo do dímero covalente da hSod1 in vivo. A análise do extrato de proteínas das medulas dos ratos modelo de ELA identificou quinze candidatos a dímero covalente da hSod1 por Western-blot, sendo que dois deles foram excluídos por espectrometria de massa, pois tiveram o resíduo Trp32 identificado. O peptídeo ESNGPVKVW(ESNGPVKVWGSIK)GSIK não foi observado, porém as treze espécies restantes permanecem candidatas e deverão ser reexaminadas em trabalhos que darão sequência a esta tese de doutorado. Em suma, o peroxomonocarbonato constitui o intermediário na produção do radical carbonato pela hSod1 e o peptídeo ESNGPVKVW(ESNGPVKVWGSIK)GSIK uma ferramenta importante no estudo da agregação covalente da hSod1 em ELA. / Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motors neurons that causes muscle atrophy, weakness, and death by respiratory failure. This pathology occurs in both sporadic and familiar forms that are clinically indistinguishable. Mutations in the antioxidant enzyme superoxide dismutase 1 (hSod1) respond to about 20% of the familiar cases of ALS. Besides, the autosomal dominant nature of these hSod1-associated ALS suggests that the mutants gain toxic properties to motor neurons. Currently, two hypotheses exist to explain the toxicity of hSod1 mutants but they do not exclude each other. The first one is related to the production of oxidants by the increased peroxidase activity of the ALS-linked mutants that could contribute to the oxidative stress reported in ALS. The second refers to protein aggregation as proposed in other neurodegenerative diseases. Noteworthy, the carbonate radical produced during hSod1 peroxidase activity leads to the formation of a covalent dimer of the protein similar to a hSod1 species often detected in experimental models and patients of the disease and implicated in the toxic properties of hSod1 mutants. Thus, the present work aimed to determine the mechanism of carbonate radical production by hSod1 and to characterize the covalent dimer of the protein in vitro followed by the study of covalent aggregates of hSod1 in a rat model of ALS that overexpresses the G93A mutant of the protein. The kinetic studies of the effect of bicarbonate/CO2, nitrite and formate in the peroxidase activity of hSod1 at various pH, measured by hydrogen peroxide consumption and radical production, permitted to exclude the Fenton mechanism to explain the enzyme peroxidative cycle in bicarbonate buffer in favor of other reactive intermediates. Furthermore, 13C NMR, molecular docking and stopped-flow experiments with asymmetric mixing demonstrated that the anion peroxomonocarbonate is the precursor of the carbonate radical produced by hSod1. The characterization of hSod1 covalent dimer by proteolysis with trypsin followed by HPLC/UV-vis and HPLC/ESI-MS analysis identified a peptide characteristic of the covalent dimer of the protein. The enzymatic digestion in H2 18 O irrefutably demonstrated the dimeric nature of this peptide because of the C-terminal labeling with oxygen-18 isotopes. In addition, sequencing of the dimeric peptide by MS/MS determined the primary structure ESNGPVKVW(ESNGPVKVWGSIK)GSIK, in which the polipeptide chains are crosslinked through a ditryptophan adduct formed by a covalent bond between the Trp32 residues of each subunit. So, this dimeric peptide can be employed as a biochemical marker for studying the hSod1 covalent dimer in vivo. The analysis of protein extracts from the spinal cord of the rat model of ALS by Western-blot identified fifteen candidates to hSod1 covalent dimer, but two of them were excluded by mass spectrometry analysis that identified unmodified Trp32 residues. Moreover, neither the dimeric peptide nor the Trp32 residue were observed in the remaining species. Therefore, these thirteen candidates must be reexamined in subsequent studies. In conclusion, the anion peroxomonocarbonate is the key intermediate in the production of the carbonate radical by hSod1 and the dimeric peptide constitutes a specific tool to study hSod1 covalent aggregation in ALS

Although considered as a poison for long time, the importance of selenium as an essential trace element is now well recognized. In proteins, the redox active selenium moiety is incorportated as selenocysteine (Sec), the 21st amino acid. In mammals, selenium exerts its redox activities through several selenocysteine-containing enzymes, which include glutathione peroxidase (GPx), iodothyronine deiodinase (ID) and thioredoxin reductase (TrxR). Although these enzymes have Sec in their active sites, they catalyze completely different reactions and their substrate specificity and cofactor or co-substrate systems are significantly different. The most widely studied selenoenzyme GPx protects various organisms from oxidative stresses by catalyzing the reduction of hydroperoxides by using glutathione (GSH) as cofactor. The chemical aspects of the reduction of hydroperoxide by GPx have been extensively studied with the help of synthetic selenium and tellurium compounds. For example, 2-phenyl, 1, 2-benzoisoselenazol-3(2H)-one, commonly known as ebselen exhibits significant GPx activity by using GSH as cofactor. The anti-inflammatory, antiatherosclerotic and cytoprotective properties of ebselen have led to the design and synthesis of nex GPx mimics for potential therapeutic applications. In the first chapter, the importance of selenium in biochemistry in general and the function of selenoenzyme GPx and its synthetic mimics in particular are discussed. In the second chapter, the importance of ebselen as a GPx mimic and how thiol exchange reaction in the selenenyl sulfide intermediate deactivates its catalytic cycle and the possible ways to overcome thiol exchange reaction are described. The third chapter deals with the first synthetic chemical model that effectively mimics the unusual cyclization of sulfenic acid to a sulfenyl amide in protein Tyrosien Phosphatase 1B(PTP1B). PTP1B is a cysteine containing enzyme where the sulfenic acid (PTP1B-SOH) intermediate produced in response to its oxidation by H2O2 is rapidly converted into a sulfenyl amide species, in which sulfur atom of the catalytic cysteine is covalently bonded to the main chain nitrogen of an adjacent serine residue. This unusual protein modification in PTP1B has been proposed to protect the sulfur centre from irreversible oxidation to sulfinic acid and and sulfonic acids. In the fourth chapter, it is shown that not only the catalytic efficiency of ebselen but also its phosphatase like behavior is important for its antioxidant activity. Ebselen is regenerated from selenenic acid (R-SeOH) under a verity of conditions, which protects its selenium centre from irreversible oxidation and thus reduces its toxicity. The fifth chapter deals with spirodizaselenurane and Spirodiazatellurane. Although the chemistry of spirodioxyselenuranes and spirodiazasulfuranes has been studied extensively due to their interesting structural and stereochemical properties, there is no example of stable spirodiazaselenurane and its tellurium analogues. In the fifth chapter, the synthesis, structure and GPx-like activity of the spirodizzaselenurane and spirodiazatellurane are discussed. In summary, the synthetic sulfenic acids and seleneric acids undergo cyclization to their corresponding sulfenyl amides and selenenyl amides and thus protect their sulfur and selenium centers from irreversible inactivation. We have also observed that selenoxides and telluroxides with nearby amide moieties undergo cyclization to their corresponding cyclic spiro compounds. This unusual transformation of sulfenic acids has been recently discovered in PTP1B. As the redox regulation cycle of PTP1B and the catalytic cycle of GPx are similar we believe that GPx may involve a selenenyl amide intermediate in its catalytic cycle.

A esclerose lateral amiotrófica (ELA) é uma doença neurodegenerativa que afeta os neurônios motores levando a atrofia muscular e morte por insuficiência respiratória. Esta patologia se manifesta de forma esporádica ou familiar, que são indistinguíveis clinicamente. Mutações na enzima antioxidante superóxido dismutase 1 (hSod1) respondem por aproximadamente 20% dos casos familiares de ELA. Além disso, o caráter autossômico dominante destas mutações revela que a hSod1 adquire propriedades tóxicas aos neurônios motores. Atualmente, duas hipóteses não mutuamente excludentes existem para explicar o caráter tóxico das mutantes da hSod1 relacionadas à ELA. A primeira refere-se à produção de oxidantes pela atividade peroxidásica exacerbada das mutantes contribuindo para o estresse oxidativo observado em ELA. A segunda refere-se à agregação de proteínas como ocorre em outras doenças neurodegenerativas. Digno de nota, o radical carbonato produzido na atividade peroxidásica da hSod1 causa a formação de um dímero covalente da proteína análogo a uma espécie de hSod1 frequentemente detectada em modelos experimentais e pacientes da doença e associada à propriedade tóxica das mutantes. Desta forma, o presente trabalho buscou esclarecer o mecanismo de produção do radical carbonato pela hSod1, bem como caracterizar o dímero covalente da proteína para posterior estudo de sua formação em um modelo de ELA em ratos que superexpressam a mutante G93A da hSod1. Os estudos cinéticos da variação do pH sobre os efeitos de bicarbonato/CO2, nitrito e formato na atividade peroxidásica da hSod1, medidos pelo consumo de peróxido de hidrogênio e produção de radical, permitiram excluir o mecanismo de Fenton para explicar o ciclo peroxidativo da enzima em tampão bicarbonato em favor de outros intermediários reativos. Já, os experimentos de 13C RMN, modelagem molecular e cinética de fluxo interrompido com mistura assimétrica demonstraram que o ânion peroxomonocarbonato constitui o precursor do radical carbonato produzido pela hSod1. A caracterização do dímero covalente da hSod1 por proteólise com tripsina seguida de análise por HPLC/UV-vis e HPLC/ESI-MS identificou um peptídeo característico do dímero covalente da hSod1. A digestão enzimática em H2 18O demonstrou de forma inequívoca a natureza dímerica deste peptídeo pela marcação da extremidade C-terminal. Ainda, o sequenciamento do peptídeo dimérico por MS/MS revelou a estrutura primária ESNGPVKVW(ESNGPVKVWGSIK)GSIK, na qual as cadeias polipeptídicas estão ligadas através de um aduto de ditriptofano composto por resíduos Trp32 da proteína. Por fim, este peptídeo dimérico pode ser empregado como marcador bioquímico específico para o estudo do dímero covalente da hSod1 in vivo. A análise do extrato de proteínas das medulas dos ratos modelo de ELA identificou quinze candidatos a dímero covalente da hSod1 por Western-blot, sendo que dois deles foram excluídos por espectrometria de massa, pois tiveram o resíduo Trp32 identificado. O peptídeo ESNGPVKVW(ESNGPVKVWGSIK)GSIK não foi observado, porém as treze espécies restantes permanecem candidatas e deverão ser reexaminadas em trabalhos que darão sequência a esta tese de doutorado. Em suma, o peroxomonocarbonato constitui o intermediário na produção do radical carbonato pela hSod1 e o peptídeo ESNGPVKVW(ESNGPVKVWGSIK)GSIK uma ferramenta importante no estudo da agregação covalente da hSod1 em ELA. / Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motors neurons that causes muscle atrophy, weakness, and death by respiratory failure. This pathology occurs in both sporadic and familiar forms that are clinically indistinguishable. Mutations in the antioxidant enzyme superoxide dismutase 1 (hSod1) respond to about 20% of the familiar cases of ALS. Besides, the autosomal dominant nature of these hSod1-associated ALS suggests that the mutants gain toxic properties to motor neurons. Currently, two hypotheses exist to explain the toxicity of hSod1 mutants but they do not exclude each other. The first one is related to the production of oxidants by the increased peroxidase activity of the ALS-linked mutants that could contribute to the oxidative stress reported in ALS. The second refers to protein aggregation as proposed in other neurodegenerative diseases. Noteworthy, the carbonate radical produced during hSod1 peroxidase activity leads to the formation of a covalent dimer of the protein similar to a hSod1 species often detected in experimental models and patients of the disease and implicated in the toxic properties of hSod1 mutants. Thus, the present work aimed to determine the mechanism of carbonate radical production by hSod1 and to characterize the covalent dimer of the protein in vitro followed by the study of covalent aggregates of hSod1 in a rat model of ALS that overexpresses the G93A mutant of the protein. The kinetic studies of the effect of bicarbonate/CO2, nitrite and formate in the peroxidase activity of hSod1 at various pH, measured by hydrogen peroxide consumption and radical production, permitted to exclude the Fenton mechanism to explain the enzyme peroxidative cycle in bicarbonate buffer in favor of other reactive intermediates. Furthermore, 13C NMR, molecular docking and stopped-flow experiments with asymmetric mixing demonstrated that the anion peroxomonocarbonate is the precursor of the carbonate radical produced by hSod1. The characterization of hSod1 covalent dimer by proteolysis with trypsin followed by HPLC/UV-vis and HPLC/ESI-MS analysis identified a peptide characteristic of the covalent dimer of the protein. The enzymatic digestion in H2 18 O irrefutably demonstrated the dimeric nature of this peptide because of the C-terminal labeling with oxygen-18 isotopes. In addition, sequencing of the dimeric peptide by MS/MS determined the primary structure ESNGPVKVW(ESNGPVKVWGSIK)GSIK, in which the polipeptide chains are crosslinked through a ditryptophan adduct formed by a covalent bond between the Trp32 residues of each subunit. So, this dimeric peptide can be employed as a biochemical marker for studying the hSod1 covalent dimer in vivo. The analysis of protein extracts from the spinal cord of the rat model of ALS by Western-blot identified fifteen candidates to hSod1 covalent dimer, but two of them were excluded by mass spectrometry analysis that identified unmodified Trp32 residues. Moreover, neither the dimeric peptide nor the Trp32 residue were observed in the remaining species. Therefore, these thirteen candidates must be reexamined in subsequent studies. In conclusion, the anion peroxomonocarbonate is the key intermediate in the production of the carbonate radical by hSod1 and the dimeric peptide constitutes a specific tool to study hSod1 covalent aggregation in ALS