Antifreeze proteins (AFPs) protect organisms from freezing damage at subzero temperatures. They do this by adsorbing to the surface of nascent ice crystals to block further ice growth. The key property of AFPs is to be soluble in liquid water but bind irreversibly to water in the solid state. Hypotheses for the mechanism by which AFPs recognize and bind ice have gone through several radical revisions without a consensus emerging. The remarkable diversity of independently evolved AFP structures, the multiple ice planes bound by AFPs, and uncertainty about the location of the ice-binding site(s) have all added to the difficulty of deducing a unified mechanism of AFP action. The central thesis of my research is that the characterization of additional AFPs will elucidate rather than obfuscate the mechanism of action. To this end I have advanced knowledge about three hyperactive AFPs. A reliable protocol to express and purify a sufficient quantity of type I hyperactive AFP was developed for further characterization studies. Initial crystallization trials using the recombinant material have produced consistent crystals for diffraction and resolution. A model of the recently discovered snow flea AFP was generated via de novo methods. The folding scheme is polyproline type II helices stacked into anti-parallel sheets, which was to our knowledge previously unobserved in monomeric proteins. The model was subsequently confirmed to be within 1 Å accuracy by X-ray crystallography performed by another group. I have also screened several insects for antifreeze activity. By using mass-spectrometry sequencing and a cDNA library, novel AFPs (3 kDa and 8kDa) were discovered from overwintering inchworms. The translated proteins were subsequently de novo modelled. After a thorough analysis of the literature, I reason that conflicting results from various AFP studies can be resolved. The hydrogen-bond ice-binding hypothesis was re-introduced to work coherently with elements of the hydrophobic ice-binding theory. We have proposed a unifying mechanism termed “anchored clathrate water,” which is supported by the water bonding on ice-binding surfaces reported both in in silico and in NMR studies. The new data I have obtained have further reinforced and expanded the hypothesis. / Thesis (Ph.D, Biochemistry) -- Queen's University, 2011-04-15 14:54:55.315

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Antifreeze proteins (AFPs) help cold-adapted organisms survive below 0 ◦C by binding to and inhibiting the growth of ice crystals. In this way, AFPs depress the freezing point of aqueous fluids below the melting point of ice (thermal hysteresis; TH). They also have the ability to inhibit ice recrystallization in the frozen state (ice recrystallization inhibition; IRI). Some AFPs show an order of magnitude higher TH activity than others, and are termed ‘hyperactive’. One of the objectives of this thesis was to see if IRI activities of the hyperactive AFPs are also an order of magnitude higher than the moderately active AFPs. Using a capillary-based assay for IRI, the activities of three hyperactive and three moderately active AFPs were determined. There was no apparent correlation between hyperactivity in TH and high IRI activity. However, mutations of residues on the ice-binding face (IBF) of both types of AFP reduced IRI and TH activities to a similar extent. In this way, the use of IBF mutant AFPs showed that the IBF responsible for an AFP’s TH activity is also responsible for its IRI activity. Analysis of the diverse AFP structures solved to date indicate that their IBFs are relatively flat, occupy a significant proportion of the protein’s surface area and are more hydrophobic than other surfaces of the protein. The IBFs also often have repeating sequence motifs and tend to be rich in alanine and/or, threonine. The de novo design of an ice-binding protein was undertaken using these features to verify the underlying physicochemical requirements necessary for a protein’s interaction with ice. Using site-directed mutagenesis, a total of sixteen threonine substitutions were made on one of the four faces of a cyanobacterial protein with no endogenous TH activity. The inclusion of eight paired threonines on one face of this quadrilateral helix gave the engineered protein low levels of TH activity, but at the cost of destabilizing the structure to some extent. The results of this study have validated some of the properties needed for the ice-binding activity of AFPs. / Thesis (Master, Biochemistry) -- Queen's University, 2010-01-29 17:37:24.322

Ice-associating proteins (IAPs) are proteins that interact directly with ice crystals, either by offering a site for nucleation, i.e. ice nucleating proteins (INPs), or by binding to nascent crystals to prevent addition of more water molecules, i.e. antifreeze proteins (AFPs). AFPs have been found to inhibit the formation of clathrate-hydrates, ice-like crystalline solids composed of water-encaged guest molecules. Study of AFP-hydrate interaction is leading to a greater understanding of AFP adsorption and of the mechanism behind the “memory effect” in hydrates, wherein previously frozen crystals reform more quickly after a brief melt. AFP is currently the only known memory inhibitor. Such a low-dosage hydrate inhibitor (LDHI) is of great interest to the oil and gas industry, as hydrate formation and reformation in the field is a huge problem. Bacterial AFPs, though largely uncharacterized, may be the best candidates for large-scale production of hydrate inhibitors, given the difficulties in obtaining AFP from other sources. The popular kinetic inhibitors (KIs) polyvinylpyrrolidone (PVP) and polyvinylcaprolactam (PVCap) were used for points of comparison in experiments exploring the hydrate-inhibition activity of several ice-associating bacteria and proteins. The addition of the soil microbe, Chryseobacterium, increased the average lag-time to tetrahydrofuran (THF) hydrate formation by 14-fold, comparable to PVP or PVCap. Samples containing Pseudomonas putida, a bacterium having both ice-nucleation protein (INP) and AFP activity, had lag-times double that of the control. Solutions with P. putida and Chryseobacterium sometimes formed hydrate slurries of stunted crystal nuclei instead of solid crystals. No inhibition of memory or nucleation was noted in bacterial assays, however bacteria with INP activity was linked to unusually rapid memory reformation. Quartz crystal microbalance experiments with dissipation (QCM-D) showed that a tight adsorption to SiO2 and resistance to rinsing are correlated with a molecule’s inhibition of hydrate formation and reformation. These results support a heterogeneous nucleation model of the memory effect, and point to the affinity of AFP for heterogeneous nucleating particles as an important component of memory inhibition. / Thesis (Master, Biology) -- Queen's University, 2008-05-30 15:20:38.749

Antifreeze proteins (AFPs) protect marine teleosts from freezing in icy seawater by binding to nascent ice crystals and preventing their growth. It has been suggested that the gene dosage for AFPs in fish reflects the degree of exposure to harsh winter climates. The starry flounder, _Platichthys stellatus_, has been chosen to examine this relationship because it inhabits a range of the Pacific coast from California to the Arctic. This flatfish is presumed to produce type I AFP, which is an alanine-rich, amphipathic alpha-helix. Genomic DNA from four starry flounder was Southern blotted and probed with a cDNA of a winter flounder liver AFP. The hybridization signal was consistent with a gene family of approximately 40 copies. Blots of DNA from other starry flounder indicate that California fish have far fewer gene copies whereas Alaska fish have far more. This analysis is complicated by the fact that there are three different type I AFP isoforms. The first is expressed in the liver and secreted into circulation, the second is a larger hyperactive dimer also thought to be expressed in the liver, and the third is expressed in peripheral tissues. To evaluate the contribution of these latter two isoforms to the overall gene signal on Southern blots, hybridization probes for the three isoforms were isolated from starry flounder DNA by genomic cloning. Two clones revealed linkage of genes for different isoforms, and this was confirmed by genomic Southern blotting, where hybridization patterns indicated that the majority of genes were present in tandem repeats. The sequence and diversity of all three isoforms was sampled in the starry flounder genome by PCR. All coding sequences derived for the skin and liver isoforms were consistent with the proposed structure-function relationships for this AFP, where the flat hydrophobic side of the helix is conserved for ice binding. There was greater sequence diversity in the skin and hyperactive isoforms than in the liver isoform, suggesting that the latter evolved recently from one of the other two. The genomic PCR primers are currently being used to sample isoform diversity in related right-eyed flounders to test this hypothesis. / Thesis (Master, Biochemistry) -- Queen's University, 2009-01-30 13:38:08.346

The study of marine antifreeze proteins has provided new findings. The blue mussel (Mytilus edulis) was known to have antifreeze activity; however, the antifreeze protein or other molecule responsible has never been characterized. Activity was evident in mussels from each of the Maritime provinces, Canada. The antifreeze molecule was shown to alter ice crystal morphology. It functioned over a wide range of pH values and it showed protease resistance. Nonetheless, its purification was not achieved. A winter flounder (Pseudopleuronectes americanus) ?-helical antifreeze protein, wflAFP6, has been shown to form amyloid-like fibrils during freezing. Separation of different aspects of the freezing process demonstrated that equilibrium freezing with an ice template is necessary for conversion of the wflAFP6 to the amyloid-like conformation. Amyloid-like conformation was determined by dye binding and electron microscopy. The effects of wflAFP6 concentration and solution properties were determined in order to better understand the process of conversion.

<p> Four stucturally distinct types of macromolecular antifreezes have been previously isolated from the sera of polar marine fish. When the water temperature surrounding these organisms drops below -0.7°C, the freezing point of their bodily fluids, any contact with surrounding ice will nucleate internal ice crystal growth. The antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) synthesized by the fish act to inhibit the growth of existing ice crystals in their sera through direct adsorption to the ice lattice. The α-helical structure of type I AFP from winter flounder has been solved to atomic resolution and its mechanism of ice binding has been proposed. The NMR solution structure of a type III AFP from ocean pout has identified proteins in this class to exist in a β-sandwich conformation, however their mechanism of action remains uncertain.</p> <p> To facilitate the pursuit of an x-ray crystal structure solution, we subcloned the gene for a type III AFP (HPLC6) into pET15b and expressed recombinant His-rHPLC6 AFP in E. coli. Purified rmHPLC6 product has been successfully crystallized, and heavy atom soaks were performed in order to attempt a structure solution by multiple isomorphous replacement. The lone tyrosine in this recombinant AFP has been successfully derivatized in solution with iodine, and the modified protein was crystallized. In order to optimize the measurement of anomalous scattering information, modifications to our data collection system were required. Cryocrystallography techniques were employed to improve the quality of collected data.</p> <p> The expression, purification, crystallization and optimized data collection on an iodine-derivatized type III AFP from ocean pout will be presented here. This work has been instrumental in providing the high quality x-ray data required to solve the crystal structure to atomic resolution. Future examination of the solved structure will promote an increased understanding of the ice-binding mechanism exhibited by this class of proteins.</p> / Thesis / Master of Science (MSc)

Certain organisms, including some bugs (both insects and microbes) are able to survive low temperatures by the production of either ice nucleating proteins (INPs) or antifreeze proteins (AFPs). INPs direct crystal growth by inducing rapid ice formation whereas AFPs adsorb to ice embryos and decrease the temperature at which the ice grows. We have also shown that certain AFPs can inhibit the crystallization of clathrate hydrates and eliminate more rapid recrystallization or “memory effect”. Here we examine several bacterial species with iceassociating properties for their effect on tetrahydrofuran (THF) hydrate crystallization. The bacteria Chryseobacterium sp. C14, which shares the ice recrystallization inhibition ability of AFPs, increased induction time to THF hydrate crystallization in isothermal experiments. In an effort to understand the association between AFPs and THF hydrate we have produced bacterially-expressed AFPs as probes for hydrate binding. Although the structure of hydrates is clearly distinct from ice, the apparent potential for these products to perturb clathrate hydrate growth compels us to explore new techniques to uncover “green inhibitors” for hydrate binding.

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