The bacterium Burkholderia strain 2.2 N is a soil isolate and a member of a group of non-obligative predator bacteria that can prey on other microorganisms or grow saprophytically. The bacterium has anti-bacterial, anti-fungal, anti-yeast and anti-protozoan activities. Burkholderia strain 2.2 N culture shows hydrolysis on Milk Casein Agar, indicating the bacterium also produces a protease. Azocoll hydrolysis was used to detect and measure protease activity. Protease activity was two-fold higher at pH of 7.5 than pH 9.0 and 25-fold at pH 4.0. Cultures grown in media containing 1.0 % yeast extract (YE), tryptic soy, tryptone or beef extract had protease activity, whereas activity was absent in cultures grown in media containing peptone, soytone, casitone, or tryptone as sole protein source. Addition of 1.0 % sucrose or glucose to 1.0 % YE medium increased protease activity 1.8-fold and 1.4-fold, respectively. Protease activity was 2-fold higher in cultures grown in media containing 1.0 % YE and 10 mM MgCl₂ or FeCl₂, than in 1.0 % YE medium lacking metals or containing 10 mM MnCl2 or CaCl2. The 1.0 % YE medium containing either ZnCl₂ or CuCl₂ lacked protease activity (< 5.0 %). In cultures grown in 1.0 % YE at 30°C with rotation at 120 rpm, protease activity was higher in stationary phase (0.38 units /mg protein) than in exponential phase (0.04 units/mg protein). The Burkholderia strain 2.2 N protease is evidently exported from cells because 86 % of the total proteolytic activity of cells was found in the cell-free culture medium. The cell free filtered culture supernatant medium assayed at 4°C had protease activity, however at a three-fold lower specific activity compared to the same supernatant assayed at 3°C. Protease activity was lower in filtered culture supernatants stored at 4°C, room temperature, and 30°C. Protease activity in samples stored at 4°C was only 40 % (24 hours) and 15 % (48 hours) of activity at time zero. Protease activity in samples stored at room temperature was only 45 % (24 hours) and 35 % (48 hours) of activity at time zero. Protease activity in samples stored at 30°C was only 78 % (24 hours) and 9 % (48 hours) of activity at time zero. Purification of the protease from filtered culture supernatant medium by ammonium sulfate precipitation, increased the protease activity 20-fold. An eluted protein fraction from DEAE-Sepharose column chromatography had 50-fold higher protease activity. Protease activity was inhibited by 10 mM 1-10-phenathroline, EDTA and EGTA, all metalloprotease inhibitors. Purified protease activity inactivated with 10 mM 1-10-phenanthroline or 10 mM EGTA was regained through the addition of Ca2+ or Mg2+. Protease activity was reduced by exposure to dithiothreitol (29 % with 1 mM and 84 % with 10 mM), a disulfide bond inhibitor. Protease activity was not inhibited by leupeptin or phenylmethylsulphonyl flouride. Casein polyacrylamide zymography revealed a band of hydrolysis at approximately 60,000 Da. SDS-PAGE resolved a doublet band present at 60,000 Da present in both the filtered culture supernatant sample and the ammonium sulfate / DEAE-Shepharose column chromatography purified protease sample. Burkholderia strain 2.2 N protease is a metalloprotease with a broad temperature range of activity. It has a molecular weight of approximately 60,000 Da. / Master of Science

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Apolipoprotein A-I (apoA-I) and ATP-Binding Cassette A1 (ABCA1) transporter play important roles in nascent high density lipoprotein (nHDL) biogenesis – the first step in the reverse cholesterol transport pathway. Based on the crystal structure of a C-terminally truncated form of apoA-I (apoA-I(1-184)) determined in the laboratory, structurally designed and naturally occurring mutants of apoA-I were conformationally characterized in solution. The function of these mutants in nHDL formation was assessed in ABCA1-transfected HEK293 cells. An apoA-I mutant designed to destabilize the N-terminal helical bundle at the first hinge region, 38/40G, exhibited a locally reduced α-helical content, destabilized overall structure, and increased lipid binding ability in solution, indicating a destabilized N-terminal helical bundle. In the cellular system, 38/40G showed significantly enhanced nHDL forming ability, suggesting that a destabilized N-terminal bundle will facilitate nHDL formation. Other designed N-terminal mutants (Q41A, P66G, G65A, V67P, T68P, 65/67/68P) and the naturally occurring mutants (R153P, L178P, and insertion mutant apoA-INashua) all showed either unchanged or destabilized overall structure, unchanged lipid binding abilities in solution and unchanged nHDL formation and cholesterol efflux promotion from the cells. Mutants designed to progressively extend the C-terminus (1-184, 1-198, 1-209, 1-220, 1-231) yielded progressively increased nHDL formation and cholesterol efflux, suggesting that the C-terminus of apoA-I is critical for these two activities. Central Helix 5 triple glycine mutation (H5 3xG) designed to lock the monomer conformation of apoA-I resulted in reduced nHDL formation but unaffected cholesterol efflux, suggesting that hindering apoA-I monomer to dimer conversion could retard nHDL formation. Remarkably, studies of cholesterol efflux and nHDL particle formation indicated that the two processes might be two uncoupled events. Analysis of the nHDL particles revealed the presence of ganglioside (GM1) in the complexes. Cross-linking data demonstrated binding of apoA-I to ABCA1-expressing cells. The binding level of apoA-I mutants to ABCA1-expressing cells was positively correlated with nHDL forming ability of these mutants. ABCA1 was isolated from FreeStyle™ HEK293-F cells in suspension by detergent solubilization and was shown to have ATPase activity. A direct interaction between apoA-I and amphipol solubilized- ABCA1 in solution was detected for the first time. Furthermore, the successful purification of ABCA1 has laid the foundation of structure determination of this protein in the future.

Four and a half LIM domains protein 1 (FHL1), consisting of 4.5 protein interaction mediating LIM domains, is a predominantly skeletal muscle protein that has consistently been upregulated in a variety of cardiovascular diseases. Since proteins mediate their functions in conjunction with other proteins, it was considered that delineation of interactions would provide insight into FHL1’s regulation and regulatory functions. We performed tandem affinity purification (TAP) from human embryonic kidney 293 (HEK-293) cells to purify tagged FHL1 and interacting proteins. Samples were analyzed using gel-free liquid chromatography mass spectrometry (LC-MS). 61 high confidence potential interactors were identified from multiple experiments. Validation of interactions was then performed by co-immunoprecipitation (co-IP) or streptavidin bead pull down, and supported by immunofluorescent colocalization studies. FHL1 interactions could thus be supported for four novel candidates: non-muscle α-actinin 1 (ACTN1), PDZ and LIM domain protein 1 (PDLIM1), cytoplasmic gelsolin (GSN), and ryanodine receptor 1 (RYR1).

Four and a half LIM domains protein 1 (FHL1), consisting of 4.5 protein interaction mediating LIM domains, is a predominantly skeletal muscle protein that has consistently been upregulated in a variety of cardiovascular diseases. Since proteins mediate their functions in conjunction with other proteins, it was considered that delineation of interactions would provide insight into FHL1’s regulation and regulatory functions. We performed tandem affinity purification (TAP) from human embryonic kidney 293 (HEK-293) cells to purify tagged FHL1 and interacting proteins. Samples were analyzed using gel-free liquid chromatography mass spectrometry (LC-MS). 61 high confidence potential interactors were identified from multiple experiments. Validation of interactions was then performed by co-immunoprecipitation (co-IP) or streptavidin bead pull down, and supported by immunofluorescent colocalization studies. FHL1 interactions could thus be supported for four novel candidates: non-muscle α-actinin 1 (ACTN1), PDZ and LIM domain protein 1 (PDLIM1), cytoplasmic gelsolin (GSN), and ryanodine receptor 1 (RYR1).

Glutathione transferases (GSTs) catalyse the conjugation of the electrophilic herbicides atrazine, metolachlor, alachlor and fluorodifen with the tripeptide glutathione (GSH). Maize (Zea mays L), contains multiple GSTs with differing substrate specificities which confer tolerance to a variety of herbicides. In contrast far less is known regarding the GSTs in competing weed species. In vivo metabolism studies using seedlings of maize and the weeds Panicum miliaceum. Digitaria sanguinalis, Sorghum bicolor. Setaria faberi. Abutilon theophrasti and Echinochloa crus-galli demonstrated that all species were capable of metabolising radiolabelled atrazine to GSH conjugates and the relative rates of metabolism related well to GST activities. Similarly, GST activities toward atrazine, metolachlor and alachlor correlated well with herbicide tolerance, with GSH availability being less important. GST activities towards metolachlor, alachlor and atrazine were highest in young maize plants and decreased with age, whilst GST activities in S.faberi remained unchanged. At 35 days GST activities were similar in the two species and the atrazine selectivity was lost. GSH content decreased with age in both species. Protein purification studies showed that S.faberi contains 4 GST isoenzymes with differing substrate specificities. The major GST was estimated to account for 0.1 % of die total soluble protein in S.faberi. PCR-amplification of a cDNA prepared from mRNA showed that S.faberi contains a GST with 88% identity to GST I from maize at the nucleotide level and 82% identity at the amino acid level. Similarly antibodies raised to maize and wheat GSTs recognised GSTs in S.faberi. It is concluded that GSTs determine the relative tolerance to chloroacetanilides and atrazine in weed seedlings but may be less important in older plants. The GSTs in S.faberi are similar in complexity to those determined in maize but are expressed at lower levels.

Lysyl oxidase (LOX) and the four lysyl oxidase like proteins, LOXL, LOXL2, LOXL3 and LOXL4, are copper-containing amine oxidases constitute a heterogeneous family of enzymes that oxidize primary amine substrates to reactive aldehydes, catalyzing the cross-linking of extracellular matrix (ECM) proteins. LOXL2 induces epithelial-to-mesenchymal transition (EMT), which is associated with hypoxia, enhanced invasion, cancer metastasis and poorer cancer prognosis. Furthermore, upregulation of LOXL2 mRNA and/ or protein levels has been detected in undifferentiated breast, colon, esophagus and larynx carcinomas. The aim here is to create and optimize a method to produce large yields of enzymatically active recombinant LOXL2 protein from mammalian cells. Two viral transductions systems were used to transfect CHO-K1 cells to overexpress LOXL2 protein. Comparing lentivirus transduction with adenovirus transduction, it was found that adenovirus transduction expressed 2.18 fold the amount of enzymatically active LOXL2 compared to lentivirus transduction (P<0.05). The average LOXL2 yield of lentivirus and adenovirus transduction systems as calculated by BCA assay was 184.5 µg and 403 µg, respectively. The average specific LOXL2 enzymatic activity were calculated using an Amplex red assay and found to be 0.443 and 0.444 nmol/μg of LOXL2 in 30 minutes in lentivirus and adenovirus methods, respectively, with no statistically significant difference (P>0.05). Expression and purification of LOXL2 were confirmed by SDS-PAGE and Western blot. Optimizing this method to purify large yields of LOXL2 is a practical aid in revealing the exact structure and function of the LOX family of proteins.

The cystic fibrosis transmembrane conductance regulator (CFTR) is an ABC transporter family protein that acts as an ion channel. Mutations in CFTR cause the most common genetic disease in Caucasian populations, cystic fibrosis (CF). The high-resolution X-ray crystal structure of CFTR is now needed to aid the design of CFTR-targeted drugs for CF treatment and also to elucidate the molecular mechanisms behind its unique function as an ATP-ligand gated ion channel. However, until now, such structural studies have been severely limited by the lack of sufficient quantities of purified full-length CFTR protein. This thesis reports the novel over-expression and purification of milligram quantities of the chicken orthologue of CFTR protein from a Saccharomyces cerevisiae (yeast) expression system. A green fluorescent protein (GFP) tag fused to the CFTR C-terminus allowed rapid detection of the protein throughout the purification procedure. CFTR was expressed under an inducible promoter and appeared localised at, or near to, the plasma membrane, where it represented around 1 % of total protein after isolation in yeast microsomes. CFTR was solubilised from microsomes and purified using the detergents dodecylmaltoside (DDM) and lyso-phosphatidyl glycerol (LPG), by nickel affinity and size exclusion chromatography (SEC) to yield 1-2 mg of CFTR protein per 18 L fermentation culture. CFTR thermal stability was probed using fluorescent measurements to reveal a two-state cooperative unfolding transition around 40 °C for the DDM-purified protein, but no such transition was observed for the LPG-purified material. Light scattering and electron microscopy techniques revealed that, in LPG, CFTR was a homogenous population of monomeric particles around 60-Å in length that were soluble up to 8 mg/ml protein concentration. In DDM, CFTR was only soluble below 0.4 mg/ml protein concentration where is existed as a very heterogenous population of different sized amorphous particles, including dimeric particles around 180-Å in length. The DDM-purified CFTR protein could be crystallised as monomers in two-dimensional (2D) crystals with similar lattice parameters to 2D crystals of CFTR purified from mammalian cells. The ATPase activity of DDM-purified and reconstituted CFTR was similar to already published rates, at around 13 nmol Pi/min/mg integrated over a reaction time of 60 min, with an apparent affinity Km for ATP of 0.14 mM. Such a low ATPase rate compared to other ABC transporters may be due to the observed rapid run-down of activity with time and correlation with published CFTR channel gating kinetics. CFTR showed reduced ATPase activity after purification in LPG, suggesting a structural destabilisation in this detergent. The protocols presented here can now be used to provide sufficient quantities of purified CFTR protein for novel biochemical and biophysical studies. The tendency of CFTR to aggregate in a mild detergent remains a major obstacle towards 3D crystallisation trials and a high-resolution structure.