Single particle electron cryomicroscopy (cryo-EM) is a rapidly developing structural biology technique for the study of macromolecular protein complexes. Presently, cryo-EM fills an important niche by facilitating acquisition of 3-D structures of protein complexes not amenable to structure determination by other techniques. Expansion of cryo-EM beyond this niche requires continued improvement in the types of specimens that can be studied as well as the final resolutions achieved. Two studies were undertaken to address these issues. The first examined resolution limitations by quantifying the effect of beam-induced motion in images of beam-sensitive paraffin crystals. The second explored the possibility of using cryo-EM to study the interaction of small effector proteins with a large multi-protein complex, V-ATPase. The results of these studies exposed the fact that fundamental aspects of the imaging and specimen preparation processes remain poorly understood and must be addressed to facilitate future improvements in cryo-EM structure determination.

Ferrochelatase (FeCH) is an ubiquitous enzyme producing heme, an essential pigment for all forms of organisms. In photosynthetic organism, heme is synthesized together with the chlorophyll in one branched pathway and the FeCH enzyme appears to be important for regulation of both the chlorophyll and the heme biosynthesis. To understand regulatory role of this protein, an active recombinant FeCH from photosynthetic organism would be invaluable. The aim of this project is to express FeCH from cyanobacterium Synechocystis 6803 in Escherichia coli and to prepare a protocol for the purification of this protein as a highly active enzyme.

The corn grain biofactory was used to produce Cel7A, an exo-cellulase (cellobiohydrolase I) from Hypocrea jecorina. The enzymatic activity on small molecule substrates was equivalent to its fungal counterpart. The corn grain-derived enzyme is glycosylated and 6 kDa smaller than the native fungal protein, likely due to more sugars added in the glycosylation of the fungal enzyme. Our data suggest that corn seed-derived cellobiohydrolase (CBH) I performs as well as or better than its fungal counterpart in releasing sugars from complex substrates such as pre-treated corn stover or wood. This recombinant protein product can enter and expand current reagent enzyme markets as well as create new markets in textile or pulp processing. The purified protein is now available commercially.

Tobacco has long been considered as a host to produce large quantities of high-valued recombinant proteins. However, dealing with large quantities of biomass with a dilute concentration of product is a challenge for down-stream processing. Aqueous two-phase extraction (ATPE) has been used in purifying proteins from various sources. It is a protein-friendly process and can be scaled up easily. ATPE was studied for its applicability to recombinant protein purification from tobacco using egg white lysozyme as the model protein. Separate experiments with polyethyleneglycol(PEG)/salt/tobacco extract, and PEG/salt/lysozyme were carried out to determine the partition behavior of tobacco protein and lysozyme, respectively. Two level fractional factorial designs were used to study the effects of factors such as PEG molecular weight, PEG concentration, the concentration of phase forming salt, sodium chloride concentration, and pH on protein partitioning. The results showed that PEG/sodium sulfate system was most suitable for lysozyme purification. Detailed experiments were conducted by spiking lysozyme into the tobacco extract. The conditions with highest selectivity of lysozyme over native tobacco protein were determined using a response surface design. The purification factor was further improved by decreasing the phase ratio along the tie line corresponding to the phase compositions with the highest selectivity. Under selected conditions the lysozyme yield was predicted to be 87% with a purification factor of 4 and concentration factor of 14. The binodial curve and tie line corresponding to the optimal condition for lysozyme recovery for the PEG 3400/sodium sulfate system were developed. The selectivity at the optimal condition was experimentally determined to be 47 with a lysozyme yield of 79.6 % with a purification factor of 10 and a concentration factor of 20. From this study, ATPE was shown to be suitable for initial protein recovery and partial purification from transgenic tobacco. / Master of Science

Tobacco has been studied as a host for producing recombinant therapeutic proteins on a large-scale, commercial basis. However, the proteins expressed in tobacco usually need to be purified to high yield and purity from large amounts of biomass in order for their production to be commercially viable. The methods needed to purify proteins from tobacco are very challenging and not well studied. The objective of this research was to develop a process for the purification of the acidic model protein, recombinant β-glucuronidase (rGUS), from transgenic tobacco leaf tissue to high yield and purity. Polyelectrolyte precipitation with polyethyleneimine (PEI) was identified as an initial purification step for purifying acidic recombinant proteins from tobacco. Polyethyleneimine precipitation allowed for high recovery and concentration of the target protein while removing large amounts of impurities from the initial extract. At dosages of 700-800 mg PEI/g total protein, nearly 100% of the rGUS activity was precipitated with generally more than 90% recovered from the pellet. In addition, more than 60% of the native tobacco proteins were removed in the process, resulting in a purification factor near 4. Recombinant GUS was further purified by a step of hydrophobic interaction chromatography (HIC) followed by a step of hydroxyapatite chromatography (HAC). The HIC step served to remove PEI and other contaminants such as nucleic acids that were accumulated during the precipitation step, while the HAC step served to separate rGUS from the remaining native tobacco proteins, most notably ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco). Nearly 40% of the initial rGUS activity was recovered as a near homogeneous fraction based on SDS-PAGE analysis after the three step process. The main steps used in this process are anticipated to be scalable and do not rely on affinity separations, making the process potentially applicable to a wide variety of acidic recombinant proteins expressed in tobacco as well as other leafy crops. / Master of Science

Porcine reproductive and respiratory syndrome virus (PRRSV) is the cause of a pandemic that has been devastating the U.S. and global swine industry for more than twenty years. PRRSV vaccine development is challenging due to virus heterogeneity. Evidence indicates that the major envelope protein, GP5, is the primary target for a subunit vaccine. In native virions GP5 primarily exists as a disulfide linked complex with the membrane protein, M, which also possesses immunogenic properties. Recent studies report that the GP5/M complex is a more significant vaccine candidate. Currently, no bulk purification methods have been reported for PRRSV proteins. The objective of this research was to develop a purification process for GP5 or GP5/M from native virions. PRRS virions were isolated and concentrated through sucrose cushion ultracentrifugation and target envelope proteins were solubilized with Triton X-100 detergent for further processing. GP5/M was not consistently identified in samples and was therefore abandoned. GP5 was identified by Western blot throughout processing with a αORF5 antibody. Cation exchange chromatography (CEX) was utilized for partial fractionation of GP5, although the viral nucleocapsid protein, N, was a major impurity in CEX elution fractions. As a second chromatographic step, hydrophobic interaction chromatography (HIC) further purified GP5 by means of a two-stage elution scheme. Pure GP5 was eluted from the HIC resin in the second HIC elution stage by Triton X-100 displacement; however the protein is present as a homodimeric/tetrameric aggregate. This process will be useful in PRRSV vaccine development and the purified GP5 product could be used as much needed positive controls in animal studies. / Master of Science

Triglycerides are the majority lipid component of most biochemical mixtures and are virtually water insoluble. Lipid removal is desired prior to protein purification processing to decrease nonspecific fouling of downstream chromatographic matrices. Transgenic pig milk was used as a model system to study delipidation from therapeutic protein sources. The majority of triglycerides was extracted from stable lipid micelles and removed with a method that can be incorporated in downstream protein purification processing without denaturing the target protein. An efficient delipidation treatment used TNBP, a non-polar solvent, to extract lipid micelles and then phase transfer milk lipids into a TNBP-swelled dextran particulate. A batch incubation of a whey/TNBP mixture with pre-swollen Sephadex LH-20 or hydroxyalkoxypropyl dextran (HAPD) beads at 4 C for 24 hours removed 67 + 2 % (0.645 mg triglycerides/ml Sephadex LH-20) and 71 o + 1 % (0.628 mg triglycerides/ml HAPD) of the triglycerides present in the skimmed transgenic whey, respectively. Fully swollen beads removed 20% more triglycerides than beads which were wetted but not swollen in TNBP, indicating that a larger phase volume and internal adsorption of the lipids onto the Sephadex matrix dominates over surface adsorption. Polyclonal ELISAs indicated that 89 + 6% of the recombinant human Protein C was still present in the transgenic whey after this delipidation treatment, indicating this treatment did not denature or harm the target protein. / Master of Science

Food allergies are an increasing health problem throughout the developed world. Among these, peanut allergy is particularly significant, due to its exceptional severity and frequent lifelong duration. Much of its aetiology remains unclear. In particular, it remains unknown why, unlike other food allergies, peanut allergy incidence correlates poorly with average dietary peanut consumption. A popular explanation for this discrepancy is that peanut allergy is more common in regions where predominantly dry-roasted (DR) peanuts are consumed, leading to speculation that DR-induced chemical modifications may contribute to pathological T_h2 responses in humans. Yet to date, no research group has demonstrated an enhanced immunogenicity of DR peanuts relative to raw in a murine model of sensitisation. This thesis begins with the hypothesis that dry-roasting does indeed alter the chemical composition of peanut proteins in such a way as to increase immunogenicity and allergenicity. To test this hypothesis robustly, I have first addressed flaws in previous studies by developing a methodology to thoroughly characterise samples of raw and DR peanut protein, as well as purifying samples of individual peanut allergens. Using these samples, I have demonstrated an enhanced immunogenicity of DR peanut protein relative to raw, in intragastric, subcutaneous and epicutaneous models of mouse sensitisation, and furthermore, that such enhanced responses feature a pronounced T_h2 bias and functional IgE production. I will present evidence that this difference is not caused by either protein aggregation or the presence of other non-protein substances, but is due to an intrinsic property of the DR peanut proteins. I will go on to clarify candidate molecular mechanisms of this effect, examining several putative receptors and probing the effects of roasting on dendritic cell binding and interactions of peanut proteins. I conclude in light of these investigations that the dry-roasting hypothesis remains the most plausible explanation for the epidemiological distribution of peanut allergy, although many additional questions remain regarding the nature of the chemical modifications produced by roasting and the molecular basis of their recognition by the immune system.

<p>The obligate intracellular pathogen, Chlamydia trachomatis, is becoming an ever greater public health threat worldwide. Despite aggressive public health awareness campaigns and treatment with antibiotics, chlamydial infections continue to be the most frequently reported sexually transmitted infection in the United States and the cause of 3% of worldwide blindness. While research into understanding various mechanisms of chlamydial pathogenesis is ongoing, efforts to identify critical protein targets are hampered by the lack of facile genetic manipulation systems available for Chlamydia. Without the ability to perform genetic studies, researchers have employed chemical biology tools to close the gap in understanding how Chlamydia survives and thrives in the host cell.</p><p>Chlamydial protease-like activity factor (CPAF) has been identified as a central virulence factor in chlamydial pathogenesis. Several studies have indicated a role for CPAF-mediated degradation of host proteins in the late stages of infection. CPAF is hypothesized to interfere with myriad host cell processes, including inflammation, cell proliferation, cytoskeletal development, and immunity presentation. However, recent studies have called into question the methods used to previously identify bona fide in vivo CPAF targets, as CPAF has been shown to retain proteolytic activity even in the presence of broad spectrum protease inhibitors. As a result of these new finding, there is a renewed call to carefully identify CPAF substrates using methods that ensure total inhibition of post-lysis proteolysis.</p><p>This dissertation aims to clarify the role of CPAF in chlamydial pathogenesis and to identify mechanisms by which CPAF exhibits substrate specificity. Because enzymes can manifest specificity through kinetic mechanisms, sequence recognition, secondary site substrate binding, or protein structure level specificity, multiple methods of biochemical characterization were employed to distinguish between these modes of specificity. </p><p>Optimized HPLC-based and fluorescence quenching assays were developed and used to investigate the chemical and kinetic mechanism of CPAF proteolysis, as well as to characterize CPAF resistance to broad spectrum protease inhibitors. Peptide library proteomics were designed to probe active site sequence recognition of specific amino acids. Bioinformatic approaches were used to recognize and annotate a cryptic PDZ-like domain in CPAF, which bears strong structural similarity to human epithelial tight junction proteins. Using a new endocervical cellular model of infection, a recently developed C. trachomatis mutant lacking CPAF activity was investigated. Mass spectrometry proteomics analysis was employed to detect differential cleavage of host proteins in endocervical cells infected with CPAF+ and CPAF- strains of C. trachomatis. Lastly, methods for N-terminal labeling and enrichment were adapted for further identifying CPAF substrates in a cellular infection model. The subtiligase system for biotinylation of N-terminal amines was adapted for integration with C. trachomatis infection assays and downstream mass spectrometry proteomics. Ultimately, the dissertation offers clarification of the role of CPAF in chlamydial infection and provides chemical biology tools for further study of protease function in bacterial pathogenesis.</p> / Dissertation

Hepatitis C is a serious disease that affects about 200 million people worldwide. No anti-HCV vaccine or specific anti-viral drugs are available today. Non-structural protein 3 (NS3) of HCV is a bifunctional serine protease/helicase, and the protease has become a prime target in the search for anti-HCV drugs. In this work, the complete HCV NS3 gene has been cloned and expressed, and the protein has been purified using affinity chromatography. An assay for measuring the protease activity of full-length NS3 protease has been developed and used for inhibition studies. A series of peptide-based inhibitors of NS3 protease varying in length, the composition of the side-chain and the N- and C-terminal groups have been studied. Potent tetra-, penta- and hexapeptide inhibitors of the NS3 protease were discovered. Hexapeptides with an acyl sulfonamide C-terminal residue were the most potent inhibitors of the NS3 protease, having nanomolar Ki-values. The selectivity of the inhibitors was assessed using other serine and cysteine proteases. NS3 protease inhibitors with electrophilic C-terminal groups were non-selective while those comprising a C-terminal carboxylate or acyl sulfonamide group were selective. All inhibitors with a small hydrophobic P1 side-chain residue were non-selective for the NS3 protease, being good inhibitors of human leukocyte elastase. This result highlights the importance of the P1 residue for inhibitor selectivity, which stems from the major role of this residue in determining substrate specificity of serine proteases. Electrophilic inhibitors often cause slow-binding inhibition of serine and cysteine proteases. This was observed with other proteases used in our work but not with NS3 protease, which indicates that mechanism of inhibition of NS3 protease by electrophilic inhibitors may not involve formation of a covalent bond. The structure-activity relationships obtained in this work can be used for improvement of peptide-based inhibitors of HCV NS3 protease towards higher inhibitory potency and selectivity.