published_or_final_version / Medicine / Doctoral / Doctor of Philosophy

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

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The formation of large, complex structures from small building blocks through self-assembly is widely seen in proteins and provides a tool for the creation of functional nanoscale devices. However, the factors controlling protein self-assembly are complex and often poorly understood. Peroxiredoxins are a large family of proteins, many of which are able to form a variety of large structures from a small, basic unit. This assembly has been shown to be strongly influenced by the redox state of the enzyme, which functions as a switch, controlling self-assembly. This thesis uses a protein from this family, human peroxiredoxin 3 (hPrx3) as a model system to investigate whether the self-assembly properties of hPrx3 can be influenced by rational protein engineering. Three forms of hPrx3 were purified and examined. These were the wild type and two variants: a mutant (S78A) and a His-tagged form. Size exclusion chromatography showed that each form showed a different ratio of dimers and larger species. Both variants showed preference for larger species, especially in the His-tagged form. This was shown to be partially dependent on metal binding in the His-tagged form. Larger species formed from multiple rings were also identified. SAXS measurement indicated that in the wild type enzyme, higher order species were dodecameric rings. For the His-tagged variant, SAXS measurement showed that the species observed had a different structure than that of the wild type. Electron microscopy showed that higher order structures seen in both wild type hPrx3 and His-tagged hPrx3 were ring shaped, with dimensions consistent with dodecamers. A competitive assay showed that the wild type, with kcat/km values near 2 x 10⁷, consistent with published results. Both variant forms showed evidence of slightly higher activity than the wild type, indicating a link between activity and assembly. A peroxiredoxin from the thermophilic bacteria Thermus aquaticus, TaqPrx was also examined, in an attempt to investigate a peroxiredoxin capable of self-assembly at high temperatures, which would be very useful for a nanoscale device. TaqPrx was cloned, purified and examined, however, no evidence of self-assembly was observed. Protein modelling and dynamic light scattering measurement indicated that the protein purified was monomeric and had a structure. Sparse matrix crystal screening identified conditions that allowed crystal formation, although strongly diffracting crystals were not produced. A novel assay for peroxiredoxin activity was developed, and suggested that TaqPrx shows peroxiredoxin activity. This thesis shows that peroxiredoxins are a useful model system for the investigation of how protein self-assembly is controlled, and how it can be influenced by protein engineering.

Oskar (Osk) is a posterior body patterning determinant in Drosophila melanogaster oocytes. oskar (osk) mRNA is translationally repressed until it reaches the posterior of the oocyte where Osk protein accumulates. Translational repression of osk prior to posterior localization is mediated by the RNA binding protein, Bruno (Bru). To better define Bru binding sites, I performed in vitro selections using full length Bru and the fragments containing either the first two RRMs (RRM1+2) or the third RRM (RRM3+). The aptamers from the final round from each of the selections produced a multitude of overrepresented primary sequence motifs. Examples of each of these motifs were found in the 3’UTRs of the mRNAs that Bru is known to regulate during oogenesis. GFP reporter transgenes under the control of the UAS-Gal4 expression system were constructed with each class of the binding sites within the reporter transgenes’ 3’UTRs to test the motifs’ ability to repress the reporters in vivo. In a wildtype background, the GFP reporters containing the binding sites were translationally repressed. In the aret mutant background, the GFP levels of the repressed GFP reporters increased with reduced Bru activity, suggesting the transgenes’ repression is mediated by Bru. Three of the motifs isolated in the in vitro selections reside in the AB and C regions of the osk 3’UTR, and the three classes of sites were mutated in the AB and C regions. The mutated AB and C regions were used to assay for a reduction of Bru binding affinity for the mutant RNAs. Additionally, the mutations were incorporated into an osk genomic transgene that was introduced into an osk RNA null as well as an Osk protein null background. The mutations reduced Bru binding to the AB and C regions. The transgenes containing the mutated Bru binding sites could not fully rescue the osk RNA null phenotype but can fully rescue the Osk protein null phenotype, suggesting an osk transcript can regulate other osk mRNAs in trans. / text

No description available.

Regional and global trends in aquaculture production, value and price are assessed for the last 30 years relative to trends in wild caught species. Based on data from the Fisheries and Aquaculture Department of the Food and Agriculture Organization of the United Nations for aquaculture production, data is extracted for the first time to address regional (Europe, North America, South America, Africa, Oceania and Asia) trends in production focused on the top five aquaculture produced species. Previous uses of the database have largely focused on global production. Of the top five species (whiteleg shrimp Penaeus vannamei, Atlantic salmon Salmo salar, silver carp Hypophthalmichthys molitrix, common carp Cyprinus carpio, and giant tiger prawn Penaeus monodon), Asia accounts for most of the global production (with the exception of Atlantic salmon Salmo salar). The central issue considered in this thesis concerns the likelihood and capacity of aquaculture production of fish and shellfish protein for human consumption relative to that of exploited wild stocks. Over the last 30 years or so, aquaculture production has risen exponentially and captures of wild caught fish have now plateaued. The relative status, rearing practices, production and basic economic perspectives of the principle aquaculture produced species globally are compared with wild caught production. The principle finding is that total global aquaculture production will exceed that of commercial wild caught species by about 2015. The significance of this is discussed in terms of current views of environmental (e.g. pollution, disease and habitat degradation) and economic (e.g. production level, farm price, marketing economics, fixed costs (facility and equipment depreciation, loan interest, land lease, fixed wages), variable costs (cost of seed stock, feed, energy)) impacts of aquaculture. Similarly, these issues are considered for the fishing industry (e.g. fishing down the food web, likelihood of expansion of bottom fisheries into deeper waters, reduction of biodiversity, declining global catches). It is concluded that aquaculture is a necessity and that if current trends continue aquaculture production can more than supplement human fish protein needs even in the given context of the rapid growing population, but that in the long term aquaculture production will itself be substantially supplemented by “rebounding” wild fishery production.

No description available.

Canola protein isolate (CPI) has tremendous potential as a protein alternative to soy within the global protein ingredient market. The overall goal of this thesis was to compare and contrast the gelling mechanism of CPI with a commercial soy protein isolate (SPI) ingredient. Specifically, the gelation properties of CPI and SPI were evaluated as a function of protein concentration (5.0–9.0%), destabilizing agent [0.1 – 5.0 M urea; 0.1 and 1.0% 2-mercaptoethanol], ionic strength (0.1, 0.5 M NaCl) and pH (3.0, 5.0, 7.0, 9.0). The fractal properties of CPI were evaluated as a function of protein concentration (5.0 – 9.0%) and pH (3.0, 5.0, 7.0, 9.0). In the first study, the gelling properties of CPI and SPI as a function of concentration were evaluated, along with the nature of the interactions within their respective gel networks. Overall, the magnitude of the storage modulus (G') of the gel was found to increase with increasing concentration at pH 7.0, whereas the gelling temperature (Tgel) remained constant at ~88ºC. As the NaCl level was increased from 0.1 to 0.5 M, the zeta potential was found to be reduced from ~-20 to -4 mV, but with little effect on Tgel or network strength. In the presence of 2-mercaptoethanol, networks became weaker, indicating the importance of disulfide bridging within the CPI network. Disulfide bridging, electrostatics and hydrogen bonding are all thought to have a role in CPI gelation. In the case of SPI, the magnitude of the storage modulus (G') and Tgel were found to increase and decrease (~80ºC to 73ºC), respectively, with increasing urea concentration at pH 7.0. Increases in NaCl from 0.1 to 0.5 M reduced the zeta potential from ~-44 to -13 mV and caused a shift in Tgel from ~84ºC to 67ºC, and increased G'. No gels were formed in the presence of 2-mercaptoethanol. In the second study, the effect of pH on the gelling properties of CPI and SPI was evaluated. Surface charge (i.e., zeta potential) measurements as a function of pH found CPI to be positively (+18.6 mV), neutral and negatively (-32 mV) charged at pH 3.0, ~5.6 and 9.0, respectively. On the other hand, SPI was observed to be positively (+35.4 mV), neutral and negatively (-51 mV) charged at pH 3.0, 5.0 and 9.0, respectively. An increases in NaCl concentration from 0 M to 0.1 M resulted in a reduction in surface charge at all pHs for both CPI and SPI. Differential scanning calorimetry was performed to determine the thermal properties of CPI. The gelation temperature was found to be above the onset temperature for denaturation. For CPI, the onset of denaturation was found to occur at ~68ºC and then increased to ~78-79ºC at pH 7.0-9.0. With respect to rheological properties, SPI did not gel at pH 9.0, and G' declined as pH increased from 3.0 to 7.0. CPI did not gel at pH 3.0, however the network formed at pH 5.0 became stronger (higher G') as pH increased. The SPI gelling temperature at pH 3.0, 5.0 and 7.0 was observed to be ~85.6, ~46 and ~81ºC, respectively. SPI gels formed at pH 5.0 earlier due to increased protein aggregation near its isoelectric point (pI). The gelation temperature for CPI at pH 5.0 and 7.0 were similar (~88ºC), then declined at pH 9.0 (~82ºC). Network structure of CPI as a function of pH also was investigated using confocal scanning light microscopy (CSLM). As the pH became more alkaline from pH 7.0 to pH 9.0, there was a decrease in lacunarity (~0.41->~0.25). However, the fractal dimension was found to increase (from ~1.54 to ~1.82) showing that increasing the pH resulted in a more compacted CPI network. In summary, protein-protein aggregation induced either by increasing concentration or changing the pH resulted in network formation for both CPI and SPI, where both networks were thought to be stabilized by disulfide bridging and hydrogen bonding. SPI underwent protein aggregation earlier than CPI near its pI value, whereas CPI gels formed the strongest networks away from its pI under alkaline conditions. In all cases, CPI grew in diffusion-limited cluster-cluster aggregation to from the gel network.

The basic unit of life is the cell, from single-cell bacteria to the largest creatures on the planet. All cells have DNA, which contains the blueprint for proteins. This information is transported in the form of messenger RNA from the genome to ribosomes where proteins are produced. Proteins are the main functional constituents of the cell, they usually have one or several functions and are the main actors in almost all essential biological processes. Proteins are what make the cell alive. Proteins are found as solitary units or as part of large complexes. Proteins can be found in all parts of the cell, the most common place being the cytoplasm, a central space in all cells. They are also commonly found integrated into or attached to various membranes. Membranes define the cell architecture. Proteins integrated into the membrane have a wide number of responsibilities: they are the gatekeepers of the cell, they secrete cellular waste products, and many of them are receptors and enzymes. The main focus of this thesis is the study of protein interactions, from the molecular level up to the protein domain level. In paper I use reoccurring local protein structures to try and predict what sections of a protein interacts with another part using only sequence information. In papers II and III we use a randomization approach on a membrane protein motif that we know interacts with a sphingomyelin lipid to find other candidate proteins that interact with sphingolipids. These are then experimentally verified as sphingolipid-binding. In the last paper, paper IV, we look at how protein domain interaction networks overlap and can be evaluated. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.</p>