Ice-binding proteins adsorb to their ligand via anchored clathrate waters

The main success of my thesis has been to establish the mechanism by which antifreeze proteins (AFPs) bind irreversibly to ice crystals, and hence prevent their growth. AFPs organize ice-like water on their ice-binding site, which then merges and freezes with the quasi-liquid layer of ice. This was revealed from studying the exceptionally large (ca. 1.5-MDa) Ca 2+-dependent AFP from the Antarctic bacterium Marinomonas primoryensis (MpAFP). The 34-kDa antifreeze- active region of MpAFP was predicted to fold as a novel Ca 2+-binding β-helix. Site-directed mutagenesis confirmed the model and demonstrated that its ice-binding site (IBS) consisted of solvent-exposed Thr and Asx parallel arrays on the Ca 2+-binding turns. The X-ray crystal structure of the antifreeze region was solved to a resolution of 1.7 Å. Two of the four molecules within the unit cell of the crystal had portions of their IBSs freely exposed to solvent. Identical clathrate-like cages of water molecules were present on each IBS. These waters were organized by the hydrophobic effect and anchored to the protein via hydrogen bonds. They matched the spacing of water molecules in an ice lattice, demonstrating that anchored clathrate waters bind AFPs to ice. This mechanism was extended to other AFPs including the globular type III AFP from fishes. Site-directed mutagenesis and a modified ice-etching technique demonstrated this protein uses a compound ice-binding site, comprised of two flat and relatively hydrophobic surfaces, to bind at least two planes of ice. Reinvestigation of several crystal structures of type III AFP identified anchored clathrate waters on the solvent-exposed portion of its compound IBS that matched the spacing of waters on the primary prism plane of ice. Ice nucleation proteins (INPs), which can raise the temperature at which ice forms in solution to just slightly below 0oC, have the opposite effect to AFPs. A novel dimeric β-helical model was proposed for the INP produced by the bacterium Pseudomonas borealis. Molecular dynamics simulations showed that INPs are also capable of ordering water molecules into an ice- like lattice. However, their multimerization brings together sufficient ordered waters to form an ice nucleus and initiate freezing.

Optical Characterization of Indium Gallium Nitride for Application in High-Efficiency Solar Photovoltaic Cells

The semiconductor alloy indium gallium nitride (InxGa1-xN) offers substantial potential in the development of high-efficiency multi-junction photovoltaic devices due to its wide range of direct band gaps, strong absorption and other optoelectronic properties. This work uses a variety of characterization techniques to examine the properties of InxGa1-xN thin films deposited in a range of compositions by a novel plasma-enhanced evaporation deposition system. Due to the high vapour pressure and low dissociation temperature of indium, the indium incorporation and, ultimately, control of the InxGa1-xN composition was found to be influenced to a greater degree by deposition temperature than variations in the In:Ga source rates in the investigated region of deposition condition space. Under specific deposition conditions, crystalline films were grown in an advantageous nano-columnar microstructure with deposition temperature influencing column size and density. The InxGa1-xN films were determined to have very strong absorption coefficients with band gaps indirectly related to indium content. However, the films also suffer from compositional inhomogeneity and In-related defect complexes with strong phonon coupling that dominates the emission mechanism. This, in addition to the presence of metal impurities, harms the alloy’s electronic properties as no significant photoresponse was observed. This research has demonstrated the material properties that make the InxGa1-xN alloy attractive for multi-junction solar cells and the benefits/drawbacks of the plasma-enhanced evaporation deposition system. Future work is needed to overcome significant challenges relating to crystalline quality, compositional homogeneity and the optoelectronic properties of In-rich InxGa1-xN films in order to develop high-performance photovoltaic devices.

Terrain Controls and Landscape-Scale Susceptibility Modelling of Active-Layer Detachments, Sabine Peninsula, Melville Island, Nunavut

Modelling the susceptibility of permafrost slopes to disturbance can identify areas at risk to future disturbance and result in safer infrastructure and resource development in the Arctic. In this study, we use terrain attributes derived from a digital elevation model, an inventory of permafrost slope disturbances known as active-layer detachments (ALDs) and generalised additive modelling to produce a map of permafrost slope disturbance susceptibility for an area on northern Melville Island, in the Canadian High Arctic. By examining terrain variables and their relative importance, we identified factors important for initiating slope disturbance. The model was calibrated and validated using 70 and 30 per cent of a data-set of 760 mapped ALDs, including disturbed and randomised undisturbed samples. The generalised additive model calibrated and validated very well, with areas under the receiver operating characteristic curve of 0.89 and 0.81, respectively, demonstrating its effectiveness at predicting disturbed and undisturbed samples. ALDs were most likely to occur below the marine limit on slope angles between 3 and 10° and in areas with low values of potential incoming solar radiation (north-facing slopes).