<p>Parkinson’s disease (PD) is a detrimental neurodegenerative disorder characterized by the presence of large protein aggregates in the brain called Lewy bodies, which are primarily composed of the protein α-synuclein (αSyn). Due to the dysregulation of αSyn levels in PD, controlling its levels through the manipulation of protein degradation pathways has been suggested as a therapeutic avenue for the treatment of PD and related diseases. Although αSyn is known to be degraded through the autophagy and proteasome pathways, it is one of only a few known substrates of the ubiquitin-independent proteasome pathway, which utilizes the 20S core particle of the proteasome (20S CP) to degrade proteins. We therefore hypothesize that small molecule stimulation of the 20S CP will enhance αSyn degradation and reduce αSyn pathology, providing a therapeutic benefit in PD models.</p><p>We began our studies by developing a fluorescence resonance energy transfer (FRET) reporter assay to monitor 20S CP activity and screen for small molecule stimulators. This assay provides a greater dynamic range to detect 20S CP stimulation compared to the most commonly used assay to monitor proteasome activity. Using the FRET assay, we were able to identify a number of novel 20S CP stimulators that differ in structure as well as potency and degree of stimulation. We next evaluated the ability of four small molecule stimulators to enhance protein degradation by the 20S CP in a biochemical assay using 15 different purified proteins. These 15 proteins include known substrates of the 20S CP and vary in size and degree of disorder. From this assay, we demonstrate that a 20S CP stimulator is likely to enhance the degradation of highly disordered proteins, such as αSyn, but the effect on other protein levels appears to be distinct for each stimulator. Two of our more potent stimulators, AM-404 and miconazole, were used with the proteasome inhibitor bortezomib for subsequent studies in HEK-293T cells in which we corroborated the results of our biochemical assay. While both AM-404 and miconazole were shown to impact highly disordered proteins, there was not much overlap between the proteins shown to be affected by each stimulator. Due to the distinct effect of each stimulator on protein regulation by the 20S CP, this study indicates the potential of tailoring a small molecule 20S CP stimulator to enhance the degradation of particular substrates.</p><p>Since AM-404 and miconazole were shown to impact 20S CP activity in different ways, we next evaluated whether either stimulator would be able to prevent the αSyn-induced inhibition of the 20S CP. High levels of αSyn have been shown to lead to proteasome impairment in biochemical and cell studies. We confirm 20S CP impairment in the presence of micromolar amounts of αSyn, and we demonstrate that miconazole, but not AM-404, is effective at maintaining 20S CP activity in the presence of increasing concentrations of αSyn. We also show that αSyn-overexpressing PC12 cells (PC12 C4 cells) display reduced proteasome activity compared to the parent cell line. Miconazole and AM-404 increased proteasome activity in PC12 C4 cells, which were more sensitive to 20S CP stimulation than non-transfected PC12 cells, but miconazole was shown to be more effective at modulating αSyn phosphorylated at Ser129 in PC12 C4 cells. </p><p>Our results reveal the dynamic nature of the 20S CP and the ways in which its activity can be modulated to affect protein levels. While AM-404 is effective at stimulating the 20S CP to enhance the degradation of some proteins, miconazole was shown to be more efficient at modulating αSyn levels and impacting αSyn pathology, as it relates to 20S CP impairment. While the results described here mark the beginning of an exciting area of study, we do demonstrate the therapeutic potential of 20S CP stimulation to combat PD. </p><div><br></div>

<div>Cyclic peptides are important sources of medicines. </div><div>They are advantageous compared to linear peptides because they possess lower flexibility, which allows for high-affinity target binding and enhanced proteolytic stability. Unfortunately, achieving head-to-tail cyclization of peptides is quite challenging, as it is hard to control efficiency and regiospecificity of peptide macrocyclization. Many have attempted to improve peptide cyclization, including the use of different synthetic reagents as well as synthetic techniques to allow amide-bond formation and promote cyclization. While these strategies have offered great potential solutions, the aim of this study is to explore an alternative strategy that utilizes biocatalysis as a method of achieving successful peptide cyclization. Biocatalysis is the use of enzymes as natural process catalysts under artificial in vitro conditions. Biocatalysis is often more environmentally friendly and safer compared to traditional organic synthesis methods. Non-ribosomal peptide synthetases (NRPSs) are one of the major sources of cyclic peptides in nature. These are systems of large multifunctional proteins are organized into functional domains that act as an assembly line to generate peptide natural products. Normally, the thioesterase domain is responsible for hydrolysis and cyclization of the peptide. Recently, a novel cyclase (SurE) that is physically discrete from the NRPS was discovered. Based on this unique quality, we hypothesized that SurE would be easier to express compared to thioesterase domains and, for this reason, SurE could be a fantastic biocatalyst for the cyclization of peptides. To test this, we designed and generated an expression vector for SurE. We then expressed and purified the SurE protein. We also synthesized three linear peptides of varying lengths. To test for SurE activity, we attempted to add N-acetylcysteamine (SNAC) to mimic its native substrate. Unfortunately, we were unable to successfully attach the SNAC to our linear peptide. To combat this issue, a new synthesis strategy is currently being developed. This work is currently ongoing in the Parkinson lab, with the aim being to test the SurE protein, as well as other PBP-like cyclases, on other modified linear peptides and demonstrate whether the protein has the ability to cyclase a wide scope of peptides.</div><div><br></div>

Biocompatibility is an important issue for the development of chromatographic stationary phases for the analysis of biomolecules (including proteins and peptides). A biocompatible stationary phase material is a material that resists nonspecific adsorption of biomolecules and does not interact with them in a way that would alter or destroy their structures or biochemical functions. The monolithic column format is a good alternative to typical spherical particle packed columns for capillary liquid chromatography of biomacromolecules. Several novel anion-exchange polymer monoliths for the analysis of proteins were synthesized for improved biocompatibility. Two novel polymeric monoliths were prepared in a single step by a simple photoinitiated copolymerization of 2-(diethylamino)ethyl methacrylate and polyethylene glycol diacrylate (PEGDA), or copolymerization of 2-(acryloyloxy)ethyl trimethylammonium chloride (AETAC) and PEGDA, in the presence of selected porogens. The resulting monoliths contained functionalities of diethylaminoethyl (DEAE) as a weak anion exchanger and quaternary amine as a strong anion exchanger, respectively. An alternative weak anion exchange monolith with DEAE functionalities was also synthesized by chemical modification after photoinitiated copolymerization of glycidyl methacrylate (GMA) and PEGDA. The dynamic binding capacities of the three monoliths were comparable or superior to values that have been reported for various other monoliths. Chromatographic performances were also similar to those provided by a modified poly(GMA-co-ethylene glycol dimethacrylate) monolith. Separations of standard proteins were achieved under gradient elution conditions using these monolithic columns. This work represents a successful attempt to prepare functionalized monoliths via direct copolymerization of monomers with desired functionalities. Compared to earlier publications, laborious surface modifications were avoided and the PEGDA crosslinker improved the biocompatibility of the monolithic backbone. Protein separations by capillary size exclusion chromatography (SEC) require a monolith that is biocompatible, has sufficient pore volume, has the appropriate pore size distribution, and is rigid. Most polymer monoliths have not possessed a biomodal pore-size distribution, i.e., especially with one distribution in the macropore region and the other in the mesopore region. Furthermore, non-specific adsorption of proteins in these stationary phases has persisted as a major unresolved problem. To overcome these difficulties, a porous poly[polyethylene glycol methyl ether acrylate (PEGMEA)-co-PEGDA] monolith which can resist adsorption of both acidic and basic proteins when using an aqueous buffer without any organic solvent additives was developed. Based on this biocompatible monolith, surfactants were introduced as porogens with the hope of significantly increasing the mesopore volume within the polymer. Two types of surfactants were studied, including poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) or PPO-PEO-PPO and Brij. Pore size distributions were examined using a well-defined molecular weight range series of proteins and peptides by inverse size exclusion chromatography, which indicated relatively large volume percentages of mesopores and micropores. The two new monoliths demonstrated different SEC behaviors, low nonspecific adsorption of proteins, and high mechanical rigidity. High density lipoprotein (HDL) is a heterogeneous class of lipoprotein particles with subspecies that differ in apolipoprotein and lipid composition, size, density, and charge. In this work, I developed a new capillary SEC method for size separation of native HDL particles from plasma using a capillary packed with BioSep-SEC-4000 particles, Three major sizes of HDL particles were separated. Additionally, capillary SEC and capillary strong anion-exchange chromatography of non-delipidated HDL were accomplished using poly(PEGMEA-co-PEGDA) and poly(AETAC-co-PEGDA) monoliths. These new LC methods using packed and monolithic stationary phases provided rapid separation of HDLs and excellent reproducibility.

<div>The use of computational approaches to understand kinase substrate preference has been a powerful tool in the search to develop artificial peptide probes to monitor kinase activity, however, most of these efforts focus on a small portion of the human kinome. The use of high throughput techniques to identify known kinase substrates plays an important role in development of sensitive protein kinase activity assays.</div><div>The KINATEST-ID pipeline is an example of a computational tool that uses known kinase substrate sequence information to identify kinase substrate preference. This approach was used to design three artificial substrates for ABL, JAK2 and SRC family kinases. These biosensors were used to design ELISA and lanthanide-based assays to monitor in vitro kinase activity. The KINATEST-ID pipeline relies on a high number of reported kinase substrates to predict artificial substrate sequences, however, not all kinases have the sufficient number of known substrates to make an accurate prediction. </div><div>The adaptation of kinase assay linked with phosphoproteomics technique was used to increase the number of known FLT3 kinase variant substrate sequences. Subsequently, a set of data formatting tools were developed to curate the mass spectrometry data to become compatible with a command line version of the KINATEST-ID pipeline modules. This approach was used to design seven pan-FLT3 artificial substrate (FAStides) sequences. The pair of FAStides that were deemed the most sensitive toward FLT3 kinase phosphorylation were assayed in increasing concentrations of clinically relevant tyrosine kinase inhibitors. </div><div>To improve the automation of the mass spectrometry data analysis and formatting for use with the KINATEST-ID pipeline, a streamlined process was developed within a bioinformatic platform, GalaxyP. The data formatting tools used to process the FLT3 mass spectrometry data were converted into compatible versions to execute within the GalaxyP framework. This process was used to design four BTK artificial substrates (BAStide) to monitor kinase activity. Additionally, one of the BAStide sequences was designed in the lanthanide chelating motif to develop an antibody-free activity assay for BTK. </div><div>Lastly, a multicolored time resolved lanthanide assay was designed by labeling SYK artificial substrate and a SRC family artificial substrate to measure the activity of both kinases in the same kinase reaction. This highlighted the functionality of lanthanide-based time resolved assays for potential multiplexing assay development. </div><div><br></div>

<p>Ends of linear chromosomes are maintained by specialized structures known as telomeres. These structures are protected by a number of essential protein complexes including the shelterin complex and CST (CTC1 – STN1 – TEN1) complex. CST is an RPA-like ssDNA binding protein that is vital for telomere length maintenance <i>via</i> inhibition of telomerase and stimulation of DNA polymerase α -primase during C-strand fill-in synthesis. CST is also known to possess additional genome-wide roles in regulating DNA replication and repair including helping facilitate replication re-start at stalled forks, activating checkpoint signaling at double-strand breaks, and promoting replication origin firing. Proper and efficient repair of DNA is critical in order to protect the integrity of the genome and prevent extreme mutagenesis. Telomeres have a strong predisposition to oxidative DNA damage in the form of 8-oxoguanine caused by exposure to reactive oxygen species and free radicals. These oxidative lesions are repaired by the base-excision repair (BER) pathway. Previous work has implicated telomeric proteins such as the shelterin complex in mediating BER. Here we show for the first time that the CST complex and individual subunits robustly stimulate a myriad of proteins involved in the BER pathway including Pol β, APE1, FEN1, and LIGI. CST’s ability to augment these BER-associated proteins could be instrumental in promoting efficient DNA repair. Additionally, we find that CTC1 and STN1 are able to significantly enhance the polymerase activity of Pol δ and Pol α on both random-sequence and telomeric-sequence DNA substrates <i>in vitro</i>. What is more, we establish the ability of CST to resolve G4 structure and promote Pol δ synthesis, which we predict is a key feature of CST’s involvement in DNA replication at telomeres, which are known to form replication-inhibiting G4’s. Our results define important mechanistic insight into CST’s role in DNA replication and repair, and provide a strong foundation for future studies relating defective telomere maintenance to aging disorders and cancers which impact human health.</p>

<p>Cardiovascular diseases (CVD) and their risk factors remain the leading cause of morbidity and mortality in North America. Food-derived bioactive peptides (BAP) have been shown to play a role in regulating physiological pathways of CVD risk factors including hypertension, diabetes, and chronic inflammation. Common sources of BAP include dairy and plant proteins. In addition to being an alternative protein source, it is now accepted that edible insect proteins can also confer health benefits beyond nutrition. However, as with any novel protein source, allergenicity remains a major concern surrounding edible insect consumption. </p> <p>This dissertation aimed to: 1) Evaluate the bioactive potential of peptides from an edible cricket species and; 2) determine the effects of BAP production methods on immunoreactivity. First, peptide-rich extracts were generated from farmed food-grade crickets via enzymatic hydrolysis techniques with the commercial protease Alcalase™. To measure the <i>in vitro</i> bioavailability, cricket peptides were also subject to simulated gastrointestinal digestion (SGD). Peptides and their digests were tested for relevant bioactivities and active groups were further fractionated by chromatographic methods to identify the major peptides responsible for the bioactivity. When tested for <i>in vitro</i> antihypertensive and anti-glycemic properties, cricket peptides were found to inhibit the activities of angiotensin converting enzyme, dipeptidyl peptidase-4, α-amylase, and α-glucosidase. The anti-inflammatory potential was expounded using RAW-264.7 macrophages and human umbilical vein endothelial cells (HUVEC). Cricket peptides (after SGD) effectively lowered NF-κB, MCP-1, and IL-6 production in cells without affecting their viability. Proteomic analyses identified 18 sequences from the enriched cationic peptide fraction that showed the highest activity. Three novel peptides were identified via molecular docking, as potent ACE-inhibitors and binding was similar to that of the commercial drug captopril. Key binding characteristics included interaction with hydrophobic amino acids (Phe, Pro, Leu) near the C-terminal position and coordination with Zn (II) ions near the ACE active site.</p> <p>Immunological reactivity was measured by IgE-binding from shrimp-allergenic patient sera to antigens present within cricket peptides. Our studies demonstrate that immunoreactivity was impacted by enzymatic hydrolysis, depending on the conditions and heating source used. Tropomyosin (a major shrimp allergen) was extracted from both untreated crickets and protein hydrolysates, and verified as the major reactive protein. Tropomyosin reactivity decreased (under both partial and extensive hydrolysis) or retained (under conditions which prevented epitope cleavage). However, using microwave-assisted enzymatic hydrolysis was effective at decreasing tropomyosin reactivity in all immunoassays tested (IgG and IgE). Proteomic and immunoinformatic analyses revealed prominent allergen binding regions of cricket tropomyosin available for cleavage during enzymatic hydrolysis. Conserved antigen regions showed greater homology with other crustacean species, but not with other well studied allergenic insect proteins (i.e., cockroach). Lastly, LC-MS/MS and FT-Raman spectrometry suggests that reactivity was affected due to distinct epitope cleavage within the protein instead of decreased antigen extractability/solubility. </p> <p>The findings of this dissertation support that edible cricket proteins are a potential source of bioactive peptides for functional food or nutraceutical development. Additionally, using protein extraction methods such as microwave-assisted hydrolysis seems a promising tool for minimizing the immunoreactivity of the allergen present in this edible cricket species.</p>

<p dir="ltr">Cyclic peptides are a growing drug class with over 40 FDA-approved drugs, with natural product cyclic peptides being the inspiration for many of these medicines (e.g., the antibiotic daptomycin, the immunosuppressant cyclosporine A, and the antifungal caspofungin). Two major types of cyclic peptide natural products exist: (1) the ribosomally synthesized and post-translationally modified peptides (RiPPs) and (2) those made by nonribosomal peptide synthetases (NRPSs). Even though many uncharacterized cyclic peptide biosynthetic gene clusters (BGCs) exist, the discovery of new cyclic peptide natural products remains a challenge because many BGCs are cryptic. Herein, we describe the development of a new approach to access the products of these cryptic NRPS BGCs and the discovery of many novel bioactive compounds from this approach. Specifically, we utilized bioinformatics programs to predict the amino acid sequences associated with the multimodular NRPS and the presence of a nearby penicillin-binding protein (PBP)-like thioesterase (TE, PBP-TE) to determine that the predicted peptides are head-to-tail cyclized. Following the bioinformatics-guided predictions, solid phase peptide synthesis (SPPS) followed by solution phase cyclization enabled access to a library of predicted cyclic peptides that we then screened for interesting bioactivities. From this screening, we have identified molecules that stimulate the proteasome, inhibit the growth of free-living amoebas, selectively lyse Gram-negative bacteria, and suppress the immune system. Structure activity relationships for these molecules have been determined, with more potent analogs being discovered. Future directions include mechanism of action studies, as well as expanding the peptide library to include more off-loading methods and tailoring enzymes that might modify the peptide after release from the NRPS.</p>

<p dir="ltr">Interest in proteins has expanded beyond biology. Proteins have found use in fields as varied as lanthanide separation, solar cell technology, medicine and fluorescent dyes. To develop proteins for each of these applications, it is necessary to understand each protein's structure. Through understanding the structure we are able to either improve that protein's function or design materials to target and inhibit its function. To this end, it is necessary to be able to screen a protein's structure and to study the protein's function in a quick and efficient manner. Spectroscopic techniques are able to fill this gap due to their low material requirements. To fully take advantage of the small sample size requirements of these techniques, this thesis reports on the development of a set of small-volume methods that need minimal material and are compatible with a wide range of instrumentation.</p>

<p>A significant development in mass spectrometry instrumentation and software in the past decade has led to its application in solving complex biological problems. One of the emerging areas is Chemical Proteomics that involves design and use of chemical reagents to probe protein functions in ‘a live cell’ environment. Another aspect of Chemical Proteomics is the identification of target proteins of a drug or small molecule. This is assisted by photoreactive groups, which on exposure to UV light, covalently link the target proteins that can be purified by affinity-based enrichment followed by mass-spectrometric identification. This phenomenon of Photoaffinity labeling (PAL) has been widely used in a broad range of applications. Herein, we have designed chemical tools to study Zika endocytosis and phosphoproteomics.</p> <p>Zika virus has attracted the interest of researchers globally, following its outbreak in 2016. While a significant development has been made in understanding the structure and pathogenesis, the actual mechanism of Zika entry into host cells is largely unknown. We designed a chemical probe to tag the live virus, leading to the identification of the virus receptors and other host factors involved in viral entry. We further validated neural cell adhesion molecule (NCAM1) as a host protein involved in early phase entry of Zika virus into Vero cells.</p> <p>The second aspect is the development of the DIGE (Difference Gel Electrophoresis) technology for phosphoproteomics. Phosphoproteins are known to be involved in various signaling pathways and implicated in multiple diseased states. We designed chemical reagents composed of titanium (IV) ion, diazirine and a fluorophore, to covalently label the phosphoproteins. Cyanine3 and cyanine5 fluorophores were employed to reveal the difference in phosphorylation between samples for the comparative proteomics. Thus far, we have successfully demonstrated the labeling of standard phosphoproteins in both simple and complex protein mixtures, and the future efforts are towards applying the technology to identify phosphoproteins in a cell lysate.</p>

<p>Parkinson’s disease is a neurodegenerative disorder characterized by a loss of dopaminergic neurons, where mitochondrial dysfunction and neuroinflammation are implicated in this process. However, the exact mechanisms of mitochondrial dysfunction, oxidative stress and neuroinflammation leading to the onset and development of Parkinson’s disease are not well understood. There is a lack of tools necessary to dissect these mechanisms, therefore we engineered genetically encoded fluorescent biosensors to monitor redox status and an inflammatory signal peptide with high spatiotemporal resolution. To measure intracellular redox dynamics, we developed red-shifted redox sensors and demonstrated their application in dual compartment imaging to study cross compartmental redox dynamics in live cells. To monitor extracellular inflammatory events, we developed a family of spectrally diverse genetically encoded fluorescent biosensors for the inflammatory mediator peptide, bradykinin. At the organismal level, we characterized the locomotor effects of mitochondrial toxicant-induced dopaminergic disruption in a zebrafish animal model and evaluated a behavioral assay as a method to screen for dopaminergic dysfunction. Pairing our intracellular redox sensors and our extracellular bradykinin sensors in a Parkinson’s disease animal model, such as a zebrafish toxicant-induced model will prove useful for dissecting the role of mitochondrial dysfunction and inflammation in Parkinson’s disease. </p>