Made available in DSpace on 2014-06-11T19:32:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-08-07Bitstream added on 2014-06-13T19:22:45Z : No. of bitstreams: 1 knob_a_dr_rcla.pdf: 1207813 bytes, checksum: 318e70abc84de2d440d3a9b60c7b7088 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Enzimas degradadoras de xilana, principal componente da hemicelulose, têm sido utilizadas em várias aplicações biotecnológicas, sendo que em alguns processos é necessário o uso de enzimas purificadas. Aplicações comerciais para as enzimas xilanolíticas envolvem a hidrólise enzimática da xilana, que está presente nos resíduos agrícolas e agroindustriais, sendo convertido a xilose e outros açúcares, que podem ser utilizados como substratos em processos fermentativos para a obtenção de proteínas celulares, combustíveis líquidos e outras substâncias químicas. A utilização destas enzimas também diminui a liberação de agentes poluentes em determinados efluentes, como da indústria de polpa de celulose. Xilanases e β- xilosidases são produzidas principalmente por bactérias e fungos, sendo que em geral, os fungos as produzem em níveis mais elevados. O gênero Penicillium apresenta espécies já caracterizadas como boas produtoras destas enzimas. Uma linhagem deste gênero, isolada de solo brasileiro, na região da Mata Atlântica e identificada como Penicillium sclerotiorum destacou-se por produzir xilanase em níveis elevados. O objetivo deste trabalho consistiu na avaliação da influência das condições de cultivo sobre a produção do complexo xilanolítico produzido por P. sclerotiorum, na caracterização físico-química desse sistema, bem como purificação e caracterização bioquímica de seus principais componentes. Por meio da determinação das condições ótimas de produção e da caracterização deste complexo enzimático foi possível estabelecer metodologias eficientes de purificação de xilanases e uma β-xilosidase. Através da caracterização físico-química das enzimas purificadas, foi possível avaliar seu potencial biotecnológico, visando futuras aplicações em processos industriais. / Xylan degrading enzymes, the main component of hemicellulose, have been used in various biotechnological applications, and in some cases the use of purified enzymes is necessary. Commercial applications of xylanolytic enzymes involve the enzymatic hydrolysis of xylan, which is present in agricultural and agro-industrial wastes, and can be converted to xylose and other sugars, which can be further used as substrates in fermentation processes to obtaining cellular protein, liquid fuels and other chemicals. The utilization of these enzymes also decreases the release of certain pollutants in wastewater, as in the pulp and paper industry. Xylanases and β-xilosidases are mainly produced by bacteria and fungi, and in general, the fungi produce them at higher levels. The genus Penicillium presents species already characterized as good producers of these enzymes. One strain of this genus isolated from Brazilian soil in the Mata Atlântica region and identified as Penicillium sclerotiorum attracted attention by producing xylanase in high levels. The objective of this study was to evaluate the influence of culture conditions on the production of the xylanolytic complex produced by P. sclerotiorum to characterize physical and chemical properties of this system as well to purify and biochemical characterize its main components. By determining optimal conditions for production and by characterizing this enzymatic complex it was possible to establish efficient methodologies for purification of xylanases and one β-xylosidase. Through their physical and chemical characterization, it was possible to evaluate their biotechnological potential for future applications in industrial processes.

Maintenance of membrane performance requires inevitable cleaning or defouling of fouled membranes. Membrane cleaning using enzymes such as proteases, lipases, α-glucosidases from a sulphidogenic bioreactor was investigated. At first, dilute and concentrated enzyme extract were prepared form the sulphidogenic pellet. Enzyme assays on 0.5 % azocaisen, 1 % triacetin and 1 mg/ml ρ-nitrophenyl-α-D-glucopyranoside were performed using the concentrated enzyme extract (0 – 200 mg/ml). For membrane fouling, an abattoir effluent was obtained from Ostritech Pty (Ltd), Grahamstown, South Africa. The effluent was characterised for presence of potential foulants such as lipids, proteins, amino acids and carbohydrates. Static fouling of polysulphone membranes (0.22 μm, 47 mm) was then performed using the abattoir effluent. Cleaning of the fouled membranes was also performed using at first the dilute and then the concentrated form (200 mg/ml) of enzyme extracts. Qualitative and quantitative biochemical analysis for proteins, lipids and carbohydrates was performed to ascertain the presence of foulants on polysulphone membranes and their removal by dilute or concentrated enzyme extracts. The ability of dilute enzyme extracts to remove proteins lipids, and carbohydrates fouling capillary UF membrane module; their ability to restore permeate fluxes and transmembrane pressure after cleaning/defouling was also investigated. Permeate volumes from this UF membrane module were analysed for protein, amino acids, lipids, and carbohydrates concentrations after fouling and defouling. Fouling was further characterized by standard blocking, cake filtration and pore blocking models using stirred UF cell and polyethersulphone membranes with MWCO of 30 000, 100 000 and 300 000. After characterization of fouling, polyethersulphone membranes with MWCO of 30 000 and 300 000 were defouled using the concentrated enzyme extract (100 mg ml). Enzyme activities at 200 mg/ml of enzyme concentration were 8.071 IU, 86.71 IU and 789.02 IU for proteases, lipases and α-glucosidases. The abattoir effluent contained 553 μg/ml of lipid, 301 μg/ml of protein, 141 μg/ml of total carbohydrate, and 0.63 μg/ml of total reducing sugars. Proteins, lipids and carbohydrates fouling polysulphone membranes after a day were removed by 23.4 %, when a dilute enzyme was used. A concentrated enzyme extract of 200 mg/ml was able to remove proteins, lipids and carbohydrates up to 5 days of fouling by 100 %, 82 %, 71 %, 68 % and 76 % respectively. Defouling of dynamically fouled capillary ultrafiltration membranes using sulphidogenic proteases was successful at pH 10, 37°C, within 1 hour. Sulphidogenic proteases activity was 2.1 U/ml and flux Recovery (FR %) was 64. Characterization of fouling revealed that proteins and lipids were major foulants while low concentration of carbohydrates fouled polyethersulphone membranes. Fouling followed standard blocking for 10 minutes in all the membranes; afterwards fouling adopted cake filtration model for membranes with 30 000 MWCO and pore blocking model for membranes with 300 000 MWCO. A concentration of 100 mg/ml of enzyme extract was able to remove fouling from membranes with MWCO of 30 000. Defouling membranes that followed pore blocking model i.e. 300 000 MWCO was not successful due to a mass transfer problem. From the results of defouling of 30 000 and 300 000 MWCO it was concluded that defouling of cake layer fouling (30 000 MWCO) was successful while defouling of pore blocking fouling was unsuccessful due to a mass transfer problem. The ratio of enzymes present in the enzyme extract when calculated based on enzymatic activity for proteases, lipases and α-glucosidases was 1.1 %, 11 % and 87.9 %. It was hypothesized that apart from proteases, lipases, α and β-glucosidases; phosphatases, sulphatases, amonipeptidases etc. from a sulphidogenic bioreactor clean or defoul cake layer fouling by organic foulants and pore blocking fouling provided the mass transfer problem is solved. However, concentration of enzymes from a sulphidogenic bioreactor has not been optimized yet. Other methods of concentrating the enzyme extract can be investigated for example use of organic solvents.

A maca (Lepidium meyenii Walpers) é uma planta herbácea bienal da família Brassicae, cultivada principalmente na região dos Andes da América do Sul. A parte subterrânea vem sendo consumida por muito tempo devido a seu valor nutricional e energético, mas é mais conhecida no mercado peruano e internacional por alegadas propriedades terapêuticas. Esta raiz apresenta até 76% de carboidratos, dos quais 30% é amido. Este trabalho teve como objetivos estudar: as propriedades físico-químicas e funcionais do amido isolado; os parâmetros enzimáticos durante o armazenamento e a purificação parcial de enzimas amilolíticas. Em relação às propriedades do amido, este apresentou um teor de amilose de 20% valor semelhante aos encontrados em raízes e tubérculos similares. A turbidez das suspensões de amido apresentou estabilidade durante o armazenamento. A temperatura de gelatinização e a viscosidade da pasta foram a 45,7° e 46°C, respectivamente. Com base nos dados obtidos, o amido de maca seria indicado para alimentos que requeiram temperaturas moderadas no processamento, não sendo apropriado para o emprego em alimentos congelados. Os parâmetros enzimáticos medidos tais como teor de amido total, teor de açúcares solúveis, atividade amilolítica total, atividade de α e β amilases, não mostraram diferenças significativas entre as medidas durante um período de armazenamento de 16 dias. As microscopias eletrônicas de varredura (MEV) dos grânulos de amido mostraram grãos íntegros com superfícies lisas, com algumas depressões ao redor dos grânulos os quais poderiam indicar o inicio de ataque enzimático, ou fraturas na purificação. Em relação à purificação de enzimas amilolíticas, foi possível separar uma fração ativa com a carboximetilcelulose (CMC) seguida de cromatografia liquida de alta resolução (CLAE) que permitiu a separação de duas frações protéicas, analisadas por eletroforese SDS-PAGE e eletroforese bidimensional (2D). Os polipeptídeos identificados no gel 2D apresentaram massa molecular semelhante entre 22 a 27 kDa, e os pontos isoelétricos entre 4,8 e 7,3. / Maca (Lepidium meyenii Walpers) is a biennial herbaceous plant from Brassicae family, grown mainly in the Andes of South America. The underground part has been consumed for a long time due to its nutritional value and energy, but is best known in the Peruvian and international market for alleged therapeutic properties. This root has up to 76% carbohydrates, of which 30% is starch. This work aimed to study: the physico-chemical properties of isolated starch, the enzymatic parameters during storage and partial purification of amylases. In relation to the properties of starch, the amylose content showed a 20% value similar to those found in roots and tubers alike. The turbidity of starch suspensions was stable during storage. The gelatinization temperature and viscosity of the paste were 45.7 ° and 46 ° C, respectively. Based on data obtained from the starch of litter would be given to foods that require moderate temperatures in processing and is not suitable for use in frozen foods. The enzymatic parameters measured such as total starch content, soluble sugars, total amylolytic activity, activity of α and β amylases, showed no significant differences between the measures over a storage period of 16 days. Electronic microscopy (SEM) of starch granules showed grains with smooth surfaces, with some depressions around the granules which could indicate the beginning of enzymatic attack, or fractures in the purification. Regarding the purification of amylases was possible to separate an active fraction with carboxymethylcellulose (CMC) followed by high-resolution liquid chromatography (HPLC) which allowed the separation of two protein fractions, analyzed by SDS-PAGE and two-dimensional electrophoresis (2D ). The polypeptides had a molecular mass between 22 and 27 kDa and isoelectric points ranging from 4.8 to 7.3.

This thesis describes studies directed towards understanding structure-function relationships of triosephosphate isomerase (TIM), from a protozoan parasite Plasmodium falciparum and a thermophilic archaea Methanocaldococcus jannaschii. Triosephosphate isomerase, a ubiquitous glycolytic enzyme, has been the subject of biochemical, enzymatic and structural studies for the last five decades. Studies on TIM have been central to the development of mechanistic enzymology. The present study investigates the role of specific residues in the structure and function of Plasmodium falciparum triosephosphate isomerase (PfTIM). The structure and stability of a tetrameric triosephosphate isomerase from Methanocaldococcus jannaschii (MjTIM) is also presented. Chapter 1 provides a general introduction to the glycolytic enzyme triosephosphate isomerase, conservation of TIM sequences, its fold and three dimensional organization. The isomerisation reaction interconverting dihydroxyacetone phosphate and glyceraldehyde 3phosphate catalyzed by triosephosphate isomerase is an example of a highly stereospecific proton transfer process (Hall & Knowles, 1975; Rieder & Rose, 1959). This chapter briefly reviews mechanistic features and discusses the role of active site residues and the functional flexible loop 6. Triosephosphate isomerase adopts the widely occurring ( β/ α)8 barrel fold and mostly occurs as a dimer (Banner et al., 1975). Protein engineering studies, related to folding, stability and design of monomeric TIM are also addressed. A brief introduction to thermophilic TIMs and higher oligomeric TIMs is given. The role of this enzyme in disease states like hemolytic anemia and neuromuscular dysfunction is surveyed. The production of methylglyoxal, a toxic metabolite, as a byproduct of the TIM reaction is also considered. Many proteins utilize segmental motions to catalyze a specific reaction. The omega loop (loop 6) of triosephosphate isomerase is important for preventing the ene-diol intermediate from forming the cytotoxic byproduct, methylglyoxal. The active site loop-6 of triosephosphate isomerase moves about 7Ǻ on ligand binding. It exhibits a hinged lid motion alternating between two well defined, “open” and “closed”, conformations (Joseph et al., 1990). Though the movement of loop 6 is not ligand gated, in crystals the ligand bound forms invariably reveal a closed loop conformation. Plasmodium falciparum TIM is an exception which predominantly exhibits “open” loop conformations, even in the ligand bound state (Parthasarathy et al., 2002). Phe 96 is a key residue that is involved in contacts between the flexible loop-6 and the protein body in PfTIM. Notably, in all TIM sequences determined thus far, with the exception of plasmodial sequences, this residue is Ser 96. In Chapter 2 the mutants F96S, F96H and F96W are reported. The crystal structures of the mutant enzymes with or without bound ligand are described. In all the ligand free cases, loop-6 adopts an “open” conformation. Kinetic parameters for all the mutants establish that residue 96 does not play an essential role in modulating the loop conformation but may be important for ligand binding. Structural analysis of the mutants along with WT enzyme reveals the presence of a water network which can modulate ligand binding. Subunit interfaces of oligomeric proteins provide an opportunity to understand protein- protein interactions. Chapter 3 describes biochemical and biophysical studies on two separate dimer-interface destabilizing mutants C13E and W11F/W168F/Y74W of PfTIM. The intention was to generate a stable monomer by disrupting the interaction hubs. C13 is a part of a large hydrophobic patch (Maithal et al., 2002a) at the dimer interface. Introduction of a negative charge at position 13 destabilizes the interface and reduces activity. Y74 is a part of an aromatic cluster of the interface (Maithal et al., 2002b). The Y74W triple mutant was designed to disrupt the aromatic cluster by introducing additional atoms. Tryptophan is also a fluorophore, allowing studies of the dimer disruption by fluorescence, after mutating the two inherent tryptophan residues, W11 and W168 to phenylalanine. The mutants showed reduced activity and were more sensitive than the wild type enzyme to chemical denaturants as well as thermal denaturation. Evidenced for monomer formation is presented. These studies together with previous work reveal that the interface is important for both activity and stability. In order to develop a model for understanding the relationship between protein stabilization and oligomeric status, characterization of the TIM from Methanocaldococcus jannaschii (MjTIM) has been undertaken. Chapter 4 describes the purification and characterization of MjTIM. The MjTIM gene was cloned and expressed in pTrc99A and protein was isolated from AA200 E. coli cells. Hyperexpressed protein was purified to homogeneity and relevant kinetic parameters have been determined. The tetrameric nature of MjTIM is established by gel filtration studies. Circular dichroism (CD) studies establish the stability of the overall fold, even at temperatures as high as 95ºC. A surprising loss of enzyme activity upon prolonged incubation at high temperature was observed. ESI-MS studies establish that oxidation of thiol groups of the protein may be responsible for the thermal inactivation. Chapter 5 describes the molecular structure of MjTIM, determined in collaboration with Prof. MRN Murthy’s group at the Indian Institute of Science (Gayathri et al., 2007). The crystal structure of the recombinant triosephosphate isomerase (TIM) from the archaeabacteria Methanocaldococcus jannaschii has been determined at a resolution of 2.3 Å. MjTIM is tetrameric, as suggested by solution studies and from the crystal structure, as in the case of two other structurally characterised archaeal TIMs. The archaeabacterial TIMs are shorter compared to the dimeric TIMs, with the insertions in the dimeric TIMs occurring in the vicinity of the putative tetramer interface, resulting in a hindrance to tetramerization in the dimeric TIMs. The charge distribution on the surface of archaeal TIMs also facilitates tetramerization. Analysis of the barrel interactions in TIMs suggests that these interactions are unlikely to account for the thermal stability of archaeal TIMs. A feature of the unliganded structure of MjTIM is the complete absence of electron density for the loop 6 residues. The disorder of the loop may be ascribed to a missing salt bridge between residues at the N- and C- terminal ends of the loop in MjTIM. Chapter 6 is a follow up of an interesting observation made by Vogel and Chmielewski (1994), who noticed that subtilisin cleaved rabbit muscle triosephosphate isomerase religated spontaneously upon addition of organic solvents. Further extension of this nicking and religation process with PfTIM emphasizes the importance of tertiary interactions in contributing to the stability of the (β/α)8 barrel folds (Ray et al., 1999). This chapter establishes that subtilisin nicking and religation is also facile in thermophilic MjTIM. Fragments generated by subtilisin nicking were identified using MALDI mass spectrometry at early and late stages of the cleavage for both the dimeric PfTIM and tetrameric MjTIM. This chapter also describes the comparative thermal and denaturant stability of both the enzymes. The accessibility of the Cys residues of MjTIM has been probed by examining the rates of labeling of thiol groups by iodoacetamide. The differential labeling of Cys residues has been demonstrated by mass spectrometry. Chapter 7 summarizes the main results and conclusions of the studies described in this thesis.

A maca (Lepidium meyenii Walpers) é uma planta herbácea bienal da família Brassicae, cultivada principalmente na região dos Andes da América do Sul. A parte subterrânea vem sendo consumida por muito tempo devido a seu valor nutricional e energético, mas é mais conhecida no mercado peruano e internacional por alegadas propriedades terapêuticas. Esta raiz apresenta até 76% de carboidratos, dos quais 30% é amido. Este trabalho teve como objetivos estudar: as propriedades físico-químicas e funcionais do amido isolado; os parâmetros enzimáticos durante o armazenamento e a purificação parcial de enzimas amilolíticas. Em relação às propriedades do amido, este apresentou um teor de amilose de 20% valor semelhante aos encontrados em raízes e tubérculos similares. A turbidez das suspensões de amido apresentou estabilidade durante o armazenamento. A temperatura de gelatinização e a viscosidade da pasta foram a 45,7° e 46°C, respectivamente. Com base nos dados obtidos, o amido de maca seria indicado para alimentos que requeiram temperaturas moderadas no processamento, não sendo apropriado para o emprego em alimentos congelados. Os parâmetros enzimáticos medidos tais como teor de amido total, teor de açúcares solúveis, atividade amilolítica total, atividade de α e β amilases, não mostraram diferenças significativas entre as medidas durante um período de armazenamento de 16 dias. As microscopias eletrônicas de varredura (MEV) dos grânulos de amido mostraram grãos íntegros com superfícies lisas, com algumas depressões ao redor dos grânulos os quais poderiam indicar o inicio de ataque enzimático, ou fraturas na purificação. Em relação à purificação de enzimas amilolíticas, foi possível separar uma fração ativa com a carboximetilcelulose (CMC) seguida de cromatografia liquida de alta resolução (CLAE) que permitiu a separação de duas frações protéicas, analisadas por eletroforese SDS-PAGE e eletroforese bidimensional (2D). Os polipeptídeos identificados no gel 2D apresentaram massa molecular semelhante entre 22 a 27 kDa, e os pontos isoelétricos entre 4,8 e 7,3. / Maca (Lepidium meyenii Walpers) is a biennial herbaceous plant from Brassicae family, grown mainly in the Andes of South America. The underground part has been consumed for a long time due to its nutritional value and energy, but is best known in the Peruvian and international market for alleged therapeutic properties. This root has up to 76% carbohydrates, of which 30% is starch. This work aimed to study: the physico-chemical properties of isolated starch, the enzymatic parameters during storage and partial purification of amylases. In relation to the properties of starch, the amylose content showed a 20% value similar to those found in roots and tubers alike. The turbidity of starch suspensions was stable during storage. The gelatinization temperature and viscosity of the paste were 45.7 ° and 46 ° C, respectively. Based on data obtained from the starch of litter would be given to foods that require moderate temperatures in processing and is not suitable for use in frozen foods. The enzymatic parameters measured such as total starch content, soluble sugars, total amylolytic activity, activity of α and β amylases, showed no significant differences between the measures over a storage period of 16 days. Electronic microscopy (SEM) of starch granules showed grains with smooth surfaces, with some depressions around the granules which could indicate the beginning of enzymatic attack, or fractures in the purification. Regarding the purification of amylases was possible to separate an active fraction with carboxymethylcellulose (CMC) followed by high-resolution liquid chromatography (HPLC) which allowed the separation of two protein fractions, analyzed by SDS-PAGE and two-dimensional electrophoresis (2D ). The polypeptides had a molecular mass between 22 and 27 kDa and isoelectric points ranging from 4.8 to 7.3.