Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (leaves 155-168).

Orientador: Paulo Roberto Bueno / Coorientador: Gustavo Troiano Feliciano / Banca: Herida Regina Nunes Salgado / Banca: Ariela Veloso de Paula / Banca: Frank Nelson Crespilho / Banca: Paula Homem de Mello / Resumo: Esta tese de doutoramento apresentou o entendimento de processos redox enzimáticos, detalhando o mecanismo envolvido na troca eletrônica, a qual resulta na formação de um produto, por catálise enzimática. Observou-se a influência de um eletrodo sob a ação de um potencial estacionário aplicado (E) na reação enzima/substrato. Realizou-se eletroanálises, como: Voltametria Cíclica (VC) e Espectroscopia de Impedância Eletroquímica (EIE), para a penicilinase. Os resultados obtidos dão indícios de que a reação enzimática se beneficia de determinados potenciais, pois o parâmetro utilizado, Rct, resistência à transferência de cargas, sugere que ocorre maior troca eletrônica em alguns potenciais ótimos (faixa de -0,3 a -0,5 V). A Simulação Molecular serviu para estudar o comportamento atomístico por métodos clássicos (Dinâmica Molecular - DM) para as condições impostas experimentalmente, esclarecendo o mecanismo de reação enzimática por métodos quânticos (DFT - Teoria do Funcional de Densidade) e híbridos (QM/MM), cabendo salientar que a penicilinase não pertence à classe das enzimas oxirredutivas. / Abstract: This doctoral thesis presented the understanding of enzymatic redox processes, detailing the mechanism involved in the electronic exchange, which results in the formation of a product by enzymatic catalysis. The influence of an electrode under the action of an applied stationary potential (E) on the enzyme/substrate reaction was observed. Electroanalysis was performed, such as: Cyclic Voltammetry (VC) and Electrochemical Impedance Spectroscopy (EIS), for the penicilinase. The results obtained indicate that the enzymatic reaction benefits from certain potentials, since the parameter used, Rct, resistance to the transfer of charges, suggests that there is greater electronic exchange in some optimal potentials (range the -0.3 to -0.5 V). The Molecular Simulation was used to study the atomistic behavior by classical methods (Molecular Dynamics - DM) for experimentally imposed conditions, clarifying the mechanism of enzymatic reaction by quantum methods (DFT) and hybrids (QM/MM). That penicillinase does not belong to the class of oxidoreductive enzymes. / Doutor

The cell extract protein content of acetate- and methanol-grown Methanosarcina thermophila was examined by two-dimensional polyacrylamide gel electrophoresis to determine the extent of regulation by the growth substrate. More than 100 mutually-exclusive spots were present in acetate- and methanol-grown cells suggesting a high degree of regulation. Spots corresponding to acetate kinase, phosphotransacetylase, and the five subunits of the nickel-containing carbon monoxide dehydrogenase (CODH) complex were identified in acetate-grown cells. The nickel-containing methyl coenzyme M methylreductase from acetate-grown M. thermophila was purified 16-fold from a cell extract to apparent homogeneity. The enzyme had a native molecular weight of between 132,000 and 141,000 and contained three subunits with a configuration of a1B1y1-. The as-isolated enzyme was inactive, but could be reductively reactivated by either titanium (III) citrate or reduced ferredoxin. Reactivation with ferredoxin was a simplification over previously reported reactivation systems. ATP stimulated, but was not required for reactivation. The CO dehydrogenase enzyme complex from M. thermophila was purified and separated into its respective components: the CO-oxidizing nickel/iron-sulfur (Ni/Fe-S) component and the cobalt-containing corrinoid/iron sulfur (Co/Fe-S) component. EPR spectroscopy and spectroelectrochemical titration of the Fe-S centers of the Ni/Fe-S component indicated the presence of two low-potential [4Fe-4S]2+/1+ centers and third high-potential center whose Fe-S configuration is unknown. When reduced with CO, the NilFe-S component exhibited a previously unobserved Ni-Fe-C EPR signal. The Co/Fe-S component contained one [4Fe-4S]2+/1+ cluster, and the as-isolated corrinoid in the component was in the base-off conformation suggesting that modulation of the electron density of the cobalt ion may result in a modified reactivity of the active site of the corrin. The CODH enzyme complex and isolated Co/Fe-S component reductively dechlorinated trichloroethylene to cis-dichloroethylene, trans-dichloroethylene, 1,1-dichloroethylene, vinyl chloride, and ethylene. Factor III also catalyzed the dechlorination of trichloroethylene when in the presence of titanium (III) citrate. Reconstitution of the Co/Fe-S component with the CO-reduced NilFe-S component also allowed dechlorination demonstrating an electron transfer from the reduced Ni/Fe-S component to the Co/Fe-S component. / Ph. D.

Thesis (MSc (Biochemistry))--University of Stellenbosch, 2009. / This study: 1. Describes the preparation of unfermented and fermented rooibos methanol and aqueous extracts. 2. Investigates the influence of unfermented and fermented rooibos methanol and aqueous extracts on the binding of natural steroid substrates to ovine adrenal microsomal cytochrome P450 enzymes, demonstrating that the binding of natural steroids is inhibited in the presence of rooibos extracts. 3. Describes an assay demonstrating the inhibitory effect of rooibos extracts on the catalytic activity of cytochrome 17α-hydroxylase (CYP17) and cytochrome 21-hydroxylase (CYP21) in ovine adrenal microsomes. 4. Investigates the influence of unfermented and fermented rooibos methanol extracts on the catalytic activity of individual cytochrome P450 enzymes – CYP17 and baboon CYP21, that are expressed in COS1 cells. 5. Demonstrates that fractions of the unfermented rooibos methanol extract inhibits the binding of natural steroid substrate to microsomal cytochrome P450 enzymes as well as the catalytic activity of baboon CYP21 expressed in COS1 cells. 6. Investigates the inhibitory influence of individual rooibos flavonoids on the catalytic activity of baboon CYP21 expressed in COS1 cells.

"July 2001" / Includes bibliographical references (leaves 144-183) / xv, 193 leaves : ill., plates (col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Applied and Molecular Ecology, 2002

Thesis (Ph. D.)--University of Canterbury, 2006. / Typescript (photocopy). "20-July-2006." Includes bibliographical references. Also available via the World Wide Web.

Meprins are oligomeric cell-surface metalloproteinases that are expressed at high concentrations in the renal brush border membranes of mice. Meprins consist of two types of subunits, α and β, which are the products of two different genes. The β subunit cDNA was cloned and sequenced from mouse kidneys, and the membrane association and the in vivo proteolytic processing of mouse meprin subunits were investigated. The primary translation product of the meprin β subunit is composed of 704 amino acids, and contains several domains, including a signal sequence at the NH₂-terminus, a prosequence, a protease domain, an adhesion domain (MAM domain), an epidermal growth factor-like domain, a potential transmembrane-spanning domain, and a short cytoplasmic tail. The B subunit is evolutionarily related to the α subunit. The α and β subunit share about 42% overall sequence identity, and have a similar arrangement of functional domains; however, a 56 amino acid segment near the COOH-terminus of a is missing in β, and the signal sequences, transmembrane and cytoplasmic domains share no significant sequence similarity. The protease domains of o and B are 55% identical. NH₂-terminal protein sequencing of detergent-solubilized meprin subunits from mouse kidneys showed that the prosequence in a is removed in the mature subunit. By contrast, only the signal sequence is removed from the mature β subunit NH₂-terminus, and the β subunit retains the prosequence. Further, the mature α subunit, but not the β subunit, is proteolytically processed at the COOH-terminus and does not contain the transmembrane and the EGF-like domains encoded by the meprin α cDNA. The β subunit is a type I integral membrane protein. By contrast, α does not transverse the membrane, and its membrane association depends on disulfide bonds. The oligomeric organization of membrane-bound meprins was analyzed by SDSPAGE under non-reducing conditions, and by isoelectric focusing. ICR mouse kidneys express αβ heterodimers and α₂ homodimers; C3H/He mice contain β₂ dimers. Transfection of COS-1 cells with the full-length meprin α subunit cDNA resulted in the secretion of meprin dimers into the culture medium, indicating that the COOH-terminal transmembrane domain of meprin α subunits is posttranslationally removed from the protein in COS-1 cells, as it is in mouse kidney cells. Replacement of the COOH-terminal 137 amino acids of a with the COOH-terminus of B, or deletion of the 56 amino acid inserted domain in α, resulted in mutant proteins that were not secreted into the medium, but rather were membrane-bound, indicating that the inserted domain of α is essential for proteolytic cleavage and secretion. Deletion of the COOH-terminal 133 residues of a did not affect meprin α dimerization or intracellular transport. The meprin a subunits secreted from transfected COS-1 cells were catalytically inactive, but could be activated by limited proteolysis with trypsin. Thus, processing at the NH,-terminus differed in COS-1 cells and in mouse kidney. COS-1 cells did not remove the prosequence from the α subunit protein, and removal of the prosequence was essential for catalytic activity of the a subunit. These results have implications for the biosynthesis and regulation of a cell surface proteinase, and thus relate to the elucidation of the mechanisms by which biological events at the cell surface are regulated. / Ph. D.

Amyotrophic lateral sclerosis (ALS) is a devastating disease characterized by the progressive degeneration of motor neurons. Dominantly-inherited mutations to the antioxidant enzyme Cu,Zn superoxide dismutase (SOD1) cause 3-6% of all ALS cases. The complete mechanism behind the toxicity of mutant SOD1 remains unclear, although significant evidence points to aberrant or incomplete metal-binding having a role in a toxic gain-of-function. However, the relevance of the metal-binding of SOD1 to mutant-SOD1-linked ALS remains controversial. Direct assessments of protein metal-binding from transgenic, SOD1-overexpressing rodent models of the disease are difficult to acquire due to the non-covalent nature of the interaction. The relatively small amount of disease-afflicted spinal cord tissue in which the motor neurons reside compounds the difficulty of measuring the protein metal binding of SOD1 from transgenic mice. This dissertation addresses the metals bound to SOD1 throughout the disease course in transgenic mice using a novel mass spectrometry assay. The methodology developed here offers the first detailed examination of partially unfolded intermediates of SOD1 present in the spinal cord of pre-symptomatic, symptomatic, and end-stage transgenic mice overexpressing the ALS-associated SOD1 mutation G93A (glycine mutated to alanine at position 93). These results were compared to age-matched transgenic mice expressing wild-type SOD1 that do not develop ALS symptoms. To extract SOD1 from relevant spinal cord tissue, a 300 ��m necropsy punch was used to remove a small piece of tissue from the ventral or dorsal gray matter of a 1 mm-thick slice of spinal cord. Physiological salts that interfere with electrospray mass spectrometry were removed by binding the proteins to a C4 Ziptip��, a pipette tip containing hydrophobic, reversed-phase packing material. Washing the Ziptip-bound proteins with water eliminated interfering salts. Bound proteins could then be eluted into a mass spectrometer with low concentrations of acetonitrile plus formic acid. Electrospray ionization conditions were determined that could keep both copper and zinc bound to SOD1. Using a high-resolution Fourier transform-ion cyclotron resonance mass spectrometer, we used the assay to collect isotopically-resolved protein mass data. Theoretical protein isotope distributions were calculated from the empirical formulas of SOD1 and matched to the experimental data with a least squares fitting algorithm to determine the multiple intermediates of SOD1 present. Spinal cord tissue, wild-type in particular, was notable for containing significantly more one-metal SOD1 than any other tissue, despite having 3-fold less SOD1 than liver. We quantitatively compared the levels of soluble, partially unfolded intermediates of SOD1 from wild-type and G93A SOD1 spinal cords. Wild-type mouse spinal cord contained significantly more of all of the partially unfolded intermediates copper-deficient SOD1, disulfide reduced SOD1, and apo SOD1. The amount of zinc-containing SOD1 was exceptionally high in wild-type mice, comprising 60% of the total SOD1 in wild-type spinal cord. The larger amounts of these SOD1 intermediates in wild-type transgenic mice indicate that they are not directly responsible for toxicity in vivo. However, copper-containing, zinc-deficient SOD1 was the one species found in higher concentrations in G93A SOD1 spinal cord. The concentration was on average 0.6-0.8 ��M in G93A spinal cord, compared to 0.1-0.3 ��M zinc-deficient SOD1 found in the wild-type mouse spinal cord. A concentration above 0.5 ��M zinc-deficient SOD1 was sufficient to induce motor neuron death in vitro. These results suggest that copper-containing, zinc-deficient SOD1 could be the toxic species responsible for motor neuron death in ALS. / Graduation date: 2013

Histone deacetylases (HDACs) are a class of enzymes that play a crucial role in DNA expression by removing an acetyl group from the ɛ-N-acetyl lysine residue on histone proteins. Out of 18 isoforms of HDAC enzymes which are classified into 4 classes, only 11 of them are metalloenzymes that require zinc for its catalytic activity. HDACs are considered promising target for drug development in cancer and other parasitic diseases due to their role in gene expression. Histone deacetylase inhibitors (HDACi) can cause cell cycle arrest, and induce differentiation or apotosis. While HDACi shows promising antitumor effects, their mechanism of action and selectivity against cancer cells have not been adequately defined yet. In addition, low oral bioavailability, short half-life time, bone marrow toxicity, and cardiotoxicity limit their use in clinic. Therefore, there is considerable interest in developing compounds with selectivity and specificity towards individual family members of HDACs. The prototypical pharmacophore for HDAC inhibitors consist of a metal-binding moiety that coordinates to the catalytic metal ion within the HDAC active site, a capping group that interacts with the residues at the entrance of the active site and a linker that appropriately positions the metal-binding moiety and capping group for interactions in the active site. It has been shown that modification of cap, cap linking moiety, linker or zinc binding group (ZBG) shows promises of superior potency and isoform selectivity. My thesis research involves manipulating different aspects of the pharmacophoric model to yield not only more potent, selective, and effective drugs but also to help understand the biology of HDAC isoforms. In addition, I was successful in extending studies on HDAC isoforms to other zinc metalloenzymes such as leishmanolysin (gp63) and spliceosome associated zinc-metalloenzymes to understand biology of these zinc metalloenzymes by developing potent and selective small molecule inhibitors. This will aid in improvement of existing therapeutics for treatment of cancer, leishmania, malaria and other genetic disorders.

Depuis la révolution industrielle, la chimie ne cesse de prospérer en développant des procédés de plus en plus performants souvent aux dépens de l’environnement. Dans le cadre du développement d’une chimie durable, des procédés catalytiques dans le domaine de la chimie d’oxydation sont mis en place en utilisant des métaux physiologiques et des oxydants doux. En combinant les avantages de la catalyse homogène et de la biocatalyse, de nouveaux catalyseurs bio-inspirés ont émergé, les métalloenzymes artificielles. Elles sont constituées d’un complexe inorganique, choisi en fonction de la réaction visée, qui est ancré au sein d’une protéine, qui apporte la sélectivité de la réaction. Au cours des travaux de cette thèse, de nouvelles métalloenzymes artificielles ont été créées par ancrage de divers complexes de Fe ou de Ru au sein de la protéine NikA. Dans un premier temps, l’hybride NikA/Ru-bpza a été synthétisé pour réaliser l’hydroxychloration d’alcènes en présence d’un iode hypervalent. Bien que d’excellentes propriétés catalytiques aient été obtenues, l’amélioration de la stabilité de ce type de catalyseurs, en particulier pour des réactions d’oxydation, reste un challenge important à relever pour leur utilisation au niveau industriel. Une des solutions originale est basée sur le développement de la catalyse hétérogène, en utilisant de cristaux de métalloenzymes artificielles grâce à la technologie CLEC (Cross-Linked Enzyme Crystals). Cette technologie permet, d’une part, d’améliorer la stabilité et la recyclabilité des catalyseurs, et d’autre part, d’élargir les conditions réactionnelles utilisées (solvants, pH, températures). Trois réactivités ont été développées à base de CLEC NikA/FeL : (i) la sulfoxydation de thioéthers, (ii) l’hydroxychloration d’alcènes en présence d’Oxone® et de chlore et (iii) la coupure oxydante d’alcènes par activation d’O2. Ces résultats ont permis d’explorer de nouvelles réactivités en chimie cascade soit en combinant les CLEC mis au point, soit en combinant différents catalyseurs homogènes. / Since the industrial revolution, chemistry has continually thriven by developing new efficient processes at the expense of the environment. As an example, oxidation reactions are performed under harsh conditions with the use of toxic oxidants. With the emergence of green chemistry, catalytic processes using physiological metals and soft oxidants are privileged. Combining the advantages of biocatalysis and homogeneous catalysis, the design of novel bioinspired catalysts, consisting on the synthesis of artificial enzymes has recently emerged. These hybrids are composed of an inorganic complex, driving the reactivity of the enzyme, inserted into a protein, which drives the reaction selectivity. The thesis described new developments in original artificial metalloenzymes, based on the use of the NikA protein and Fe or Ru catalysts. First, a new hybrid has been developed by anchoring the Ru-bpza complex to NikA to catalyze alkene hydroxychloration with hypervalent iodine. Although excellent catalytic efficiencies were obtained, the stability improvement remains a major challenge for the industrial use of these catalytic processes, especially when oxidation chemistry is concerned. One possible strategy is based on the development of heterogeneous catalysis, by using a crystal/solution version of the artificial metalloenzymes thank to the cross-linked enzyme crystals (CLEC) technology. On the one hand, this technology allows to increase the stability and the recyclability of the catalysts. On the other hand, catalysis can be performed under a various reactions conditions (organic solvent, temperature, pH). Three reactivities have been developed with NikA/FeL-CLEC catalysts: (i) thioether sulfoxidation with NaOCl, (ii) alkene hydroxychloration with Oxone® and chloride source and (iii) oxidative cleavage of alkenes by O2 activation. To go further, new reactivities in cascade reactions have been explored combining either NikA-based CLEC developed, or different homogenous catalysts.