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Phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) is a conserved eukaryotic mechanism to limit protein synthesis under stress conditions. Baculovirus PK2, which resembles the C-terminal half of a protein kinase domain, inhibits eIF2α family kinases in vivo, thereby increasing viral fitness in the face of host immunological and stress responses. The mechanism by which PK2 modulates eIF2α stress response signaling remains unknown. To address this issue, a combination of biochemical, biophysical and in vivo approaches were employed to probe the mechanism of PK2 inhibition on a prototypical human eIF2α kinase, the RNA-dependent protein kinase (PKR). We discovered that PK2 inhibits PKR catalytic activity by directly binding its kinase domain. This direct interaction requires both the kinase-like C-lobe fold of PK2 and a critical 22 residue N-terminal extension that precedes it. We further show that the PK2 N-terminal extension is required but not sufficient for the ability of PK2 function.

Phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) is a conserved eukaryotic mechanism to limit protein synthesis under stress conditions. Baculovirus PK2, which resembles the C-terminal half of a protein kinase domain, inhibits eIF2α family kinases in vivo, thereby increasing viral fitness in the face of host immunological and stress responses. The mechanism by which PK2 modulates eIF2α stress response signaling remains unknown. To address this issue, a combination of biochemical, biophysical and in vivo approaches were employed to probe the mechanism of PK2 inhibition on a prototypical human eIF2α kinase, the RNA-dependent protein kinase (PKR). We discovered that PK2 inhibits PKR catalytic activity by directly binding its kinase domain. This direct interaction requires both the kinase-like C-lobe fold of PK2 and a critical 22 residue N-terminal extension that precedes it. We further show that the PK2 N-terminal extension is required but not sufficient for the ability of PK2 function.

Domino catalysis is an ideal strategy in the synthesis of heterocyclic scaffolds, as multiple bonds can be formed under a single set of reaction conditions. In this work, we present the development of two novel domino processes which afford access to aza-analogues of the dihydrodibenzoxepine motif. Careful optimisation revealed that the Rh catalysed hydroarylation proceeds under mild conditions as compared to the C-O coupling. Furthermore, Pd was not required for the C-O bond formation when using alkenyl pyrazines as substrates. Variation of the substituents on both the heterocycle and on the boronic ester provided insight into the structural features required for successful domino reaction, and a stepwise protocol was developed for incompatible substrates. We have also developed the first multi-metal, multi-ligand domino reaction featuring both a chiral and achiral ligand in the same pot, still leading to an enantioenriched product.

Zero-valent metals such as bulk iron and zinc are known to dechlorinate toxicorganic compounds. Enhancement in reaction rates has been achieved through bimetallicnanosized particles such as nickel/iron (Ni/Fe) and palladium/iron (Pd/Fe). Batchdegradation of model compounds, trichlroethylene (TCE) and 2,2'-dichlorobiphenyls(DCB), were conducted using bimetallic Ni/Fe and Pd/Fe nanoparticles. Completedegradation of TCE and DCB is achieved at room temperature. Zero-valent iron, as themajor element, undergoes corrosion to provide hydrogen and electrons for the reductivecatalytic hydrodechlorination reaction. The second dopant metals of nickel and palladium(in nanoscale) act as catalyst for hydrogenation through metal hydride formation thatproduces completely dechlorinated final product. Different compositions of bimetallicNi/Fe and Pd/Fe nanoparticles were synthesized and their reactivity was characterized interms of reaction rate constants, hydrogen generation through iron corrosion, andproducts formation. The observed TCE degradation rate constant was two orders ofmagnitude higher than the bulk iron and nanoiron, indicating that the bimetallicnanoparticles are better materials compared to the monometallic iron systems. Longevitystudy through repeated cycle experiments showed minimum loss of activity. The surfacearea-normalized rate constant was found to have a strong correlation with the hydrogengeneration by iron corrosion reaction. A mathematical model was derived thatincorporates the reaction and Langmuirian-type sorption terms to estimate the intrinsicreaction rate constant and rate-limiting step in the degradation process. Bimetallicnanoparticles were also immobilized into the chitosan matrix for the synthesis of ananocomposite membrane reactor to achieve membrane-phase destruction of chlorinatedorganics under convective flow condition. Formation of uniformly distributed nanosizedparticles is confirmed by high resolution transmission electron microscopy. Themembrane-phase degradation results demonstrated similar trends with the previoussolution phase analysis with the observed enhanced reaction rates. The advantage of themembrane system is its ability to prevent the agglomeration of the nanoparticles in themembrane matrix, to minimize the loss of precious metals into the bulk solution phase,and to prevent the formation of precipitated Fe(III) hydroxide. These are due to thechelating effect of the amine and hydroxyl functional groups in the chitosan backbones.

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is a functionally diverse large group of proteins sharing a jelly roll β-barrel fold. An enzymatic member 3-hydroxyanthranilate-3,4-dioxygenase (HAO) and a non-enzymatic member pirin, which is a human nuclear metalloprotein of unknown function present in all human tissues, were selected for structural and functional studies in this dissertation work. HAO is an important enzyme for tryptophan catabolism and for 2-nitrobenzoic acid biodegradation. In this work, seven catalytic intermediate were captured in HAO single crystals, enabling for the first time a nearly complete structural snapshot viewing of the entire molecular oxygen activation and insertion mechanism in an iron- and O2-depedent enzyme. The rapid catalytic turnover rate was found achieved in large part by protein dynamics that facilitates O2 binding to the catalytic iron, which is bound to the enzyme by a facile 2-His-1-carboxylate ligand motif. An iron storage and chaperon mechanism was also discovered in the bacterial source of this enzyme, which led to a proposed novel biological function of a mononuclear iron-sulfur center. Although human pirin protein shares the same structural fold with HAO, its iron ion is coordinated by a 3-His-1-carboxylate ligand motif. Pirin belongs to a subset of proteins whose members are playing regulatory functions in the superfamily. In this work, pirin is shown to act as a redox sensor for the NF-κB transcription factor, a critical mediator of intracellular signaling that has been linked to cellular responses to pro-inflammatory signals which controls the expression of a vast array of genes involved in immune and stress responses.

The central dogma of molecular biology outlines the process of information transfer from a DNA sequence, to a protein chain. Beyond the step of protein synthesis, there are a variety of post-translational modifications that can take place, one of which is addition of carbohydrate chains to nascent proteins, known as glycosylation. The N-linked glycosylation pathway is responsible for the covalent attachment of multifunctional carbohydrate chains on asparagine residues of nascent proteins at Asn-X-Ser/Thr consensus sequences. These carbohydrate chains are thought to aid in cell signaling, immune recognition, and other processes. Golgi alpha-mannosidase II (GMII) is the enzyme in the N-glycosylation pathway that is responsible for cleaving two mannose linkages in the oligosaccharide GnMan5Gn2 (where Gn is N-acetylglucosamine and Man is mannose), thereby producing GnMan3Gn2 , which is the committed step in complex N-glycan synthesis. It has been speculated that GMII is an excellent therapeutic target for cancer treatment, as the unusual distribution of carbohydrates on the surface of tumour cells has been characterized in many cancers. In addition, swainsonine-—a strong, yet nonspecific inhibitor of GMII—-has been shown to block metastasis and improve the clinical outcome of patients with certain cancers, including those of the colon, breast and skin. This thesis examines Golgi alpha-mannosidase II from Drosophila melanogaster (dGMII) as a model for all GMII enzymes. First, a 1.80 Angstrom resolution crystal structure of a weak inhibitor, kifunensine, binding to dGMII provides mechanistic insights into the substrate distortion in the GMII reaction. It is hypothesized that the GMII reaction proceeds via a 1 Sinterintermedi-ate. Second, a 1.40 Angstrom resolution structure of a mutant dGMII bound to its natural substrate, GnMan5Gn, identifies key substrate binding and catalytic residues, as well as expanding the definition of the GMII active site to include two distant sugar−binding subsites. Finally, the results are taken together, with knowledge of other related enzymes to synthesize a plausible itinerary for the GMII reaction.

The human protein kinase superfamily consists of over 500 members that individually control specific aspects of cell behavior and collectively control the complete range of cellular processes. That such a large group of proteins is able to uniquely diversify and establish individual identities while retaining common enzymatic function and significant sequence/structural conservation is remarkable. The means by which this is achieved is poorly understood, and we have begun to examine the issue by performing a comparative analysis of the catalytic domain of protein kinases. A novel approach for protein structural alignment has revealed a high degree of similarity found across the kinase superfamily, with variability confined largely to a single region thought to be involved in substrate binding. The similarity detected is not limited to amino acids, but includes a group of conserved water molecules that play important structural roles in stabilizing critical residues and the fold of the kinase domain. The development of a novel technique for identifying kinase substrates on a large scale directly from cell lysate has revealed that substrate specificity is not what discriminates the closely related p38α and β mitogen-activated protein kinases. Instead cellular localization appears to be their distinguishing characteristic, at least during myoblast differentiation. Together these results highlight the extent of conservation, as well as the minimal variability, that is found in the catalytic domain of all protein kinase superfamily members, and that while distantly related kinases may be distinguished by substrate specificity, closely related kinases are likely to be distinguished by other factors. Although these results focus on representative members of the kinase superfamily, they give insight as to how all protein kinases likely diversified and established unique non-redundant identities. In addition, the novel techniques developed and presented here for structural alignment and substrate discovery offer new tools for studying molecular biology and cell signaling.

The diesel engine is growing in popularity due to its energy efficiency and solving the emissions issues associated with diesel engine exhaust would clear the way for further growth. The key pollutants are NOx, particulate matter and unburned hydrocarbons. Selective catalytic reduction (SCR) catalysis is likely the best choice for NOx control. In SCR, NH3 selectively reacts with NOx to form N2 – the selectivity refers to NH3 reacting with NOx instead of the abundant O2. Urea is used as the NH3 source, being injected into the exhaust as an aqueous solution where the urea decomposes and NH3 is generated. Spatial resolution characterization techniques have been gaining attention in the catalysis field because of the higher level of information provided. In this thesis, a new spatial resolution technique, called SpaciFTIR (spatially-resolved, capillary-inlet Fourier transform infra-red spectroscopy), was developed, which overcomes the interference of water in the detection of NH3 in an earlier developed technique, SpaciMS (spatially-resolved, capillary-inlet mass spectrometry). With the new test method, three SCR topics were addressed. First, the three key SCR reactions were spatially resolved. These are the standard SCR reaction (2NO + 2NH3 + 1/2O2 = 2N2 + 3H2O), the fast SCR reaction (NO + NO2 + 2NH3 = 2N2 + 3H2O), and NO2-SCR, (6NO2 + 8NH3 = 7N2 + 12H2O). Results show that in the presence of NO2, but at a NO2/NOx ratio < 0.5, the fast SCR reaction proceeds followed by the standard SCR reaction, i.e. in series. If the NO2/NOx ratio exceeds 0.5, the NO2-SCR and fast SCR reactions occur in parallel. Compared to the standard integral test method, this spatial resolution technique clearly showed such trends. Secondly, the spatial resolution technique was used to characterize the effects of thermal aging on catalyst performance. It was found that for a highly aged catalyst, there was a radial activity profile due to an inhomogeneous temperature distribution in the process of aging. Aging effects on various key SCR reactions, i.e. NO oxidation, NH3 oxidation, and the reduction reactions, were studied. Last but not least, for the purpose of passive SCR system development, transient NH3 storage profiles along the monolith channel were measured with SpaciFTIR. Passive SCR is a system where the NH3 is generated on an upstream catalyst, such as a three-way catalyst or lean-NOx trap, instead of via urea injection. In such a system, NH3 is therefore not constantly being fed to the SCR catalyst, but “arrives” in pulses. Factors such temperature, NH3 concentration, pulsing time, flow rate and thermal aging were investigated. For the first time, NH3 migration was observed and its effect on SCR reactions along the length of catalyst was studied.