Superoxide dismutases (SODs) catalyze the dismutation of superoxide radicals to oxygen and hydrogen peroxide. Mn SOD is localized in mitochondria, Cu-Zn SOD is in the cytosol and chloroplast, and Fe SOD is in chloroplasts. The effects of a chloroplast-localized oxidative stress, caused by methyl viologen or 3-(3, 4-dichlorphenyl)-1-1′ dimethylurea (DCMU) on SOD populations were investigated. A cloned Arabidopsis thaliana Fe SOD gene was expressed in Escherichia coli and was purified from transformed cells. This protein was used to raise antibodies against A. thaliana Fe SOD which in turn were used to quantify the effects of oxidative stress on Fe SOD protein. Effects of oxidative stress on enzyme activity were measured in native gels. Fe SOD responded to oxidative stress with an increase in activity, but not in antibody reactive protein. Two novel forms of Fe SOD activity, with faster migration rates in activity gels, were detected. Mn SOD, a mitochondrial enzyme, responded to the stress with an increase in activity. In contrast, the activity or amount of Cu-Zn SOD protein did not respond to this oxidative stress. In light of these results, we propose that SODs respond to oxidative stress at the enzyme and gene levels. Mitochondrial Mn SOD responded to a chloroplast-localized stress with an increase in activity, suggesting either that the site of action for methyl viologen is not exclusively in the chloroplast or that there are other signals among the compartments of the cell. Fe SOD, but not Cu-Zn SOD responded to stress, suggesting that Fe SOD may be the stress responsive enzyme in this organelle. Evolutionary relationships among different isoforms were investigated based on the known primary, secondary, and tertiary structures of these isoforms. The three dimensional structure of A. thaliana Fe SOD was modeled by using structures of crystallized E. coli and Pseudomonas ovalis Fe SODs as templates. Comparison of prokaryotic Fe SOD with eukaryotic isoforms showed that Fe and Mn SODs are structurally homologous, whereas Cu Zn SOD is not. / Ph. D.

Tn7 and Tn7-like transposons are complex elements found in disparate environments and are responsible for mobilizing a wide variety of genes and forming pathogenicity/fitness islands. They are novel in their ability to recognize both a single site in the chromosome and specifically target transposition into mobile plasmids via dedicated TnsD and TnsE targeting proteins. TnsE recognizes mobile plasmids through an association with the processivity clamp and a 3′ recessed DNA end during conjugal replication. However, the mechanism for the specific recognition of 3′ recessed DNA ends remains unclear. Structural analyses of the C-terminal domain of TnsE identified a novel protein fold including a central V-shaped loop that toggles between two distinct conformations. The structure of a robust TnsE gain-of-function variant has this loop locked in a single conformation, suggesting that conformational flexibility regulates TnsE activity. Structure-based analysis of a series of TnsE variants relates transposition to DNA binding stability. Follow up studies of full length TnsE bound to DNA are in progress. / Thesis / Master of Science (MSc)

Serum amyloid A (SAA) is a small, evolutionarily well-conserved, acute-phase protein best known as the protein precursor for amyloid A amyloidosis. During acute injury, infection, or inflammation, SAA plasma concentration rapidly rises 1000-fold, but the benefit of this dramatic increase is unclear. SAA functions in the innate immune response, cell signaling, and lipid homeostasis. Most SAA circulates on plasma high-density lipoproteins (HDL), where it reroutes HDL for lipid recycling. The aim of this dissertation is to provide a structural basis for understanding SAA-lipid interactions and to elucidate the structure-function relationship in this ancient protein. SAA is an intrinsically disordered protein that acquires ~50% helical structure when bound to lipids, and is ~80% helical in three available atomic-resolution x-ray crystal structures. We took advantage of these crystal structures of lipid-free SAA to propose the binding site for various lipids, including lipids in HDL. We postulated that SAA, as a monomer, binds lipids via two amphipathic helices, h1 and h3, that form a concave hydrophobic surface, and that the curvature of this surface defines the binding preference of SAA for HDL versus larger lipoproteins. Next, we used murine SAA1.1 and a membrane-mimicking model phospholipid, palmitoyl-oleoyl phosphocholine (POPC), to reconstitute SAA-lipid complexes and characterize their overall structure, stability and stoichiometry using an array of spectroscopic, electron microscopic, and biochemical methods. We observed preferential formation of ~10 nm particles that mimic HDL size, accompanied by the α-helical folding. To probe the local protein conformation and dynamics in these SAA-POPC particles, we used hydrogen-deuterium exchange mass spectrometry. Analysis of the amount and the kinetics of deuterium uptake clearly established h1 and h3 as the lipid-binding site. Moreover, we determined that SAA binding to lipid follows a mixed model that combines induced fit, promoting α-folding in h3, with conformational selection, stabilizing pre-existing conformations in h1 and around the h2-h3 linker. Taken together, our results provided the structural basis necessary for understanding SAA-lipid interactions, which are central to beneficial functions of SAA as a housekeeping molecule, and to its misfolding in amyloid. This research sets the stage for understanding SAA interactions with its numerous other functional ligands.

Rous Sarcoma Virus (RSV) is an avian retrovirus with an enclosing capsid protein (CA) shell. RSV CA is studied due to its similar molecular structure to other retrovirus capsid proteins such as Human Immunodeficiency Virus (HIV). In this project, turbidity assay is used to track the assembly process of RSV CA, while solid state nuclear magnetic resonance (ssNMR) is used to probe the CA structure at a site specific level and investigate the morphology of the spherical structure of the I190V mutated strain of RSV CA. The I190V mutant is a naturally occurring mutation and is able to form into roughly uniform spheres, where the wild type RSV CA cannot form as pure spheres as possible. Turbidity assay results of the mutated RSV CA revealed a lack of a noticeable lag time before assembly began, as well as, a prolonged time period to reach saturation when compared to the wild-type RSV CA. Using ssNMR, and the TALOS-N program the torsion angles of the protein backbone were found. Using Ramachandran plots, it was found that the mutation of the 190th residue from Isoleucine to Valine caused a changed in the secondary structure of residues, from α-helix to β-sheet and vice versa. These changes were concentrated at the loops between select interfaces of helices that make up the structure of RSV CA. In particular, between helices 4 (residues 65-85), 8 (residues 165-177), and 11 (residues 215-225). The differing secondary structure in the mutant RSV CA was supported by the overlaying of the NMR spectra of the wild-type RSV CA on to the spherically assembled mutant RSV CA. It can be concluded that the spherical assembly of the mutated RSV CA displays noticeable differences in assembly and overall structure when compared to the wild-type RSV CA.

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Kinases are involved in a multitude of signaling pathways, such as cellular growth, proliferation, and apoptosis, and have been discovered to be important in numerous diseases including cancer, Alzheimer's disease, cardiovascular health, rheumatoid arthritis, and fibrosis. Due to the involvement in a wide variety of disease types, kinases have been studied for exploitation and use as targets for therapeutics. There are many limitations with developing kinase target therapeutics due to the high similarity of kinase active site composition, making the utilization of new techniques to determine kinase exploitability for therapeutic design with high specificity essential for the advancement of novel drug strategies. In silico approaches have become increasingly prevalent for providing useful insight into protein structure-function relationships, offering new information to researchers about drug discovery strategies. This work utilizes streamlined computational techniques on an atomistic level to aid in the identification of orthologue and isoform exploitability, identifying new features to be utilized for future inhibitor design. By exploring two separate kinases and kinase targeting domains, we found that orthologues and isoforms contain distinct features, likely responsible for their biological roles, which can be utilized and exploited for selective drug development. In this work, we identified new exploitable features between kinase orthologues for treatment in Human African Trypanosomiasis and structural morphology differences between two kinase isoforms that can potentially be exploited for cancer therapeutic design. / Master of Science in Life Sciences / Numerous diseases such as cancer, Alzheimer's disease, cardiovascular disease, rheumatoid arthritis, and fibrosis have been attributed to different cell growth and survival pathways. Many of these pathways are controlled by a class of enzymes called kinases. Kinases are involved in almost every metabolic pathway in human cells and can act as molecular switches to turn on and off disease progression. Due to the involvement of these kinases' in a wide variety of disease types, kinases have been continually studied for the development of new drugs. Developing effective drugs for kinases requires an extensive understanding of the structural characteristics due to the high structural similarity across all kinases. In silico, or computational, techniques are useful strategies for drug development practices, offering new information into protein structure-function relationships, which in turn can be utilized in drug discovery advancements. Utilizing computational methods to explore structural features can help identify specific protein structural features, thus providing new strategies for protein specific inhibitor design. In this work, we identified new exploitable features between kinase orthologues for treatment in Human African Trypanosomiasis and structural morphology differences between two kinase isoforms that can potentially be exploited for cancer therapeutic design.

Yes / In Escherichia coli, the biogenesis of both cytochrome bd-type quinol oxidases and periplasmic cytochromes requires the ATP-binding cassette-type cysteine/GSH transporter, CydDC. Recombinant CydDC was purified as a heterodimer and found to be an active ATPase both in soluble form with detergent and when reconstituted into a lipid environment. Two-dimensional crystals of CydDC were analyzed by electron cryomicroscopy, and the protein was shown to be made up of two non-identical domains corresponding to the putative CydD and CydC subunits, with dimensions characteristic of other ATP-binding cassette transporters. CydDC binds heme b. Detergent-solubilized CydDC appears to adopt at least two structural states, each associated with a characteristic level of bound heme. The purified protein in detergent showed a weak basal ATPase activity (approximately 100 nmol Pi/min/mg) that was stimulated ∼3-fold by various thiol compounds, suggesting that CydDC could act as a thiol transporter. The presence of heme (either intrinsic or added in the form of hemin) led to a further enhancement of thiol-stimulated ATPase activity, although a large excess of heme inhibited activity. Similar responses of the ATPase activity were observed with CydDC reconstituted into E. coli lipids. These results suggest that heme may have a regulatory role in CydDC-mediated transmembrane thiol transport. / This work was supported by Biotechnology and Biological Sciences Research Council grant BBS/B/14418 (Membrane Protein Structure Initiative).

Pattern discovery in protein structures is a fundamental task in computational biology, with important applications in protein structure prediction, profiling and alignment. We propose a novel approach for pattern discovery in protein structures using Particle Swarm-based flying windows over potentially promising regions of the search space. Using a heuristic search, based on Particle Swarm Optimization (PSO) is, however, easily trapped in local optima due to the sparse nature of the problem search space. Thus, we introduce a novel fitness-based stagnation detection technique that effectively and efficiently restarts the search process to escape potential local optima. The proposed fitness-based method significantly outperforms the commonly-used distance-based method when tested on eight classical and advanced (shifted/rotated) benchmark functions, as well as on two other applications for proteomic pattern matching and discovery. The main idea is to make use of the already-calculated fitness values of swarm particles, instead of their pairwise distance values, to predict an imminent stagnation situation. That is, the proposed fitness-based method does not require any computational overhead of repeatedly calculating pairwise distances between all particles at each iteration. Moreover, the fitness-based method is less dependent on the problem search space, compared with the distance-based method. The proposed pattern discovery algorithms are first applied to protein contact maps, which are the 2D compact representation of protein structures. Then, they are extended to work on actual protein 3D structures and interaction networks, offering a novel and low-cost approach to protein structure classification and interaction prediction. Concerning protein structure classification, the proposed PSO-based approach correctly distinguishes between the positive and negative examples in two protein datasets over 50 trials. As for protein interaction prediction, the proposed approach works effectively on complex, mostly sparse protein interaction networks, and predicts high-confidence protein-protein interactions — validated by more than one computational and experimental source — through knowledge transfer between topologically-similar interaction patterns of close proximity. Such encouraging results demonstrate that pattern discovery in protein structures and interaction networks are promising new applications of the fast-growing and far-reaching PSO algorithms, which is the main argument of this thesis. / Thesis (Ph.D, Computing) -- Queen's University, 2014-04-21 12:54:03.37