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1
Smith, Gregory K. "Simulations of chemical catalysis." Thesis, The University of New Mexico, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3612623.
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<p> This dissertation contains simulations of chemical catalysis in both biological and heterogeneous contexts. A mixture of classical, quantum, and hybrid techniques are applied to explore the energy profiles and compare possible chemical mechanisms both within the context of human and bacterial enzymes, as well as exploring surface reactions on a metal catalyst. A brief summary of each project follows. </p><p> Project 1 - Bacterial Enzyme SpvC </p><p> The newly discovered SpvC effector protein from <i>Salmonella typhimurium </i> interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a β-elimination mechanism. The dynamics of the enzyme substrate complex of the SpvC effector is investigated with a 3.2 ns molecular dynamics simulation, which reveals that the phosphorylated peptide substrate is tightly held in the active site by a hydrogen bond network and the lysine general base is positioned for the abstraction of the alpha hydrogen. The catalysis is further modeled with density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31 G(d,p) level of theory. The truncated model suggested the reaction proceeds via a single transition state. After including the enzyme environment in <i>ab initio</i> QM/MM studies, it was found to proceed via an E1cB-like pathway, in which the carbanion intermediate is stabilized by an enzyme oxyanion hole provided by Lys104 and Tyr158 of SpvC. </p><p> Project 2 - Human Enzyme CDK2 </p><p> Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensable role in cellular signaling, and their malfunctioning is implicated in many diseases. Ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a dissociative, metaphosphate-like structure, stabilized by the Mg(II) ion and several hydrogen bonds. The calculated free-energy barrier is consistent with experimental values. </p><p> Project 3 - Bacterial Enzyme Anthrax Lethal Factor </p><p> In this dissertation, we report a hybrid quantum mechanical and molecular mechanical study of the catalysis of anthrax lethal factor, an important first step in designing inhibitors to help treat this powerful bacterial toxin. The calculations suggest that the zinc peptidase uses the same general base-general acid mechanism as in thermolysin and carboxypeptidase A, in which a zinc-bound water is activated by Glu687 to nucleophilically attack the scissile carbonyl carbon in the substrate. The catalysis is aided by an oxyanion hole formed by the zinc ion and the side chain of Tyr728, which provide stabilization for the fractionally charged carbonyl oxygen. </p><p> Project 4 - Methanol Steam Reforming on PdZn alloy </p><p> Recent experiments suggested that PdZn alloy on ZnO support is a very active and selective catalyst for methanol steam reforming (MSR). Plane-wave density functional theory calculations were carried out on the initial steps of MSR on both PdZn and ZnO surfaces. Our calculations indicate that the dissociation of both methanol and water is highly activated on flat surfaces of PdZn such as (111) and (100), while the dissociation barriers can be lowered significantly by surface defects, represented here by the (221), (110), and (321) faces of PdZn. The corresponding processes on the polar Zn-terminated ZnO(0001) surfaces are found to have low or null barriers. Implications of these results for both MSR and low temperature mechanisms are discussed.</p>
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Barriga, Jeffrey. "Characterization of the emulsifying mannoproteins of Saccharomyces cerevisiae." Thesis, McGill University, 1995. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=23364.
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Mannoproteins from Saccharomyces cerevisiae (Baker's yeast) were extracted in high yield. The crude extract was resolved into two components, $ alpha$ and $ beta$, using capillary electrophoresis. These were both shown to be fragments from the cell wall mannoproteins. The $ alpha$ component consisted mainly of the protein portion of the mannoproteins and the $ beta$ component consisted of the long highly phosphorylated mannan chains. Fragmentation occurred when the covalent bonds between the mannans and the asparagine residues were hydrolysed during the hot citrate extraction procedure.<br>The $ alpha$ component was identified as the active emulsifying agent. Although the $ beta$ component was not an emulsifier, it was an effective coemulsifier and improved the properties of the $ alpha$ component.<br>The emulsifying properties of these materials were related to the ability to bind the dye Coomassie blue. Removal of the long mannan chains both increases emulsifying ability and exposes the protein chain for binding to the dye.
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Garofalo, Flavio A. (Flavio Alberto). "Serum cholesterol depletion using immobilized pseudomonas pictorum." Thesis, McGill University, 1989. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=74354.
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Pseudomonas pictorum can deplete serum cholesterol. Cholesterol depleted includes free cholesterol, esterified cholesterol and cholesterol bound to different lipoproteins. Temporarily accumulated cholestenone was metabolized as reaction continued. The reaction kinetics controls the global cholesterol depletion rate during the initial part of the fermentation. Then, mass transfer takes control. In the latter, the global rate was first order with respect to the cholesterol concentration and zero order with respect to the bacterial concentration. The half time was 330 min. The activation energy was 83 kJ/mol. These results are consistent with the aqueous cholesterol diffusion model. P. pictorum was immobilized in alginate beads, polylysine microcapsules and open pore agar beads. The latter depleted serum cholesterol. The depletion rates were similar to those of free P. pictorum, suggesting a barrier free mass transfer. The matrix effect diffusivity for lipoproteins at 37$ sp circ$C was 6.7 $ times$ 10$ sp{-11}$ m$ sp2$/s. The beads effectively retained P. pictorum. No leakage was detected.
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Marin, Joseph R. "Production of sophorolipids from long-chain fatty acids by candida bombicola." Thesis, McGill University, 2003. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=79250.
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Tall oil, a mixture of long-chain oleic and linoleic acids, was found to be a suitable lipophilic substrate for the production of sophorolipid, an extracellular glycolipid surfactant, by Candida bombicola ATCC 22214. Oxygen limitation was found to decrease sophorolipid production in this system. Partitioning experiments with sophorolipid revealed that the surfactant increases the affinity of oleic acid for the aqueous phase of a two phase system. C. bombicola therefore has potential applications in the remediation of pulp and paper effluent containing recalcitrant long-chain fatty acids; both for its ability to degrade the acids and for the tendency of sophorolipid to make fatty acids more bioavailable to organisms involved in downstream activated sludge treatment. A novel capillary gas chromatography method was developed to rapidly and quantitatively analyze long-chain fatty acids.
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Gu, Lina. "Heterologous expression of manganese peroxidase from Phanerochaete chrysosporium in Pichia pastoris." Related Electronic Resource: Current Research at SU : database of SU dissertations, recent titles available full text, 2003. http://wwwlib.umi.com/cr/syr/main.
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Aguinaga-Diaz, de Leon Pablo 1965. "Polymers modification with metal chelates and their application to the recovery of metals and biocompounds from aqueous solutions." Thesis, The University of Arizona, 1992. http://hdl.handle.net/10150/278196.
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This work presents the results of studies for protein and metal separations from aqueous solutions by means of metal-chelating interactions using salt-polymer aqueous two-phase systems. Several polymer-chelates were synthesized and characterized. Polyethylene glycol (8000 M.W.) and sodium sulfate along with four different chelates (IDA, TED, Cm-TREN and L-ASP) coupled to monomethoxy polyethylene glycol (M-PEG), were used for the preparation of aqueous two-phase systems and the recovering of metals. The PEG-Chelators synthesized complexed with Cu⁺² Ni⁺² Co⁺² and Zn⁺² were used for the recovery of proteins from aqueous solutions. The influence of the pH, the chelated metal as well as the number of accessible histidine groups on proteins partitioning was investigated and found not to follow a linear relationship for all cases.
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Agarwal, Kitty. "Characterization of cell-secreted microvesicles: modulators of cell-cell communication." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1388511983.
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Menegatti, Stefano. "Design, Selection, and Development of Novel Peptide Ligands for Bioseparations and Diagnostics." Thesis, North Carolina State University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3575894.
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<p> The relevance of protein-based biopharmaceuticals has increased dramatically in the past decades and a variety of products are now available for human therapy. Antibodies in particular are currently the most heavily consumed protein therapeutics, with a current market volume expected to reach 1 trillion US$ in 2015 and a compound annual growth rate (CAGR) of 3-6%. Meeting the increasing demand for these therapeutics at lower prices while complying with increasingly stringent regulatory environments, calls for the development of new technologies and platform approaches for efficient downstream protein purification. Extended use of affinity chromatography holds great promise in meeting the urgent demand for affordable high-quality biological products. This technology, however, is still dependent on the use of biological ligands, such as Protein A, Protein G, and Protein L, that have significant issues associated with their high cost, harsh elution conditions, narrow specificity, low chemical stability, and immunogenicity in patients if they leach into the product stream. Small, robust, synthetic ligands may offer an effective alternative to protein ligands. Peptides in particular combine levels of affinity and specificity similar to those of biological ligands with high chemical and biochemical stability, broader specificity, low immunogenicity and ease of synthesis that can reduce costs.</p><p> The work in this thesis aims to discover and characterize novel peptide ligands to produce efficient, robust, and affordable affinity adsorbents for improved downstream purification of biologics. Two main areas have been investigated: (a) the development of linear hexapeptide – based adsorbents for the purification of human antibodies and (b) the design and screening of novel libraries of cyclic peptides for the discovery of novel ligands.</p><p> The research conducted on the characterization and development of competitive peptide-based affinity adsorbents comprises: (a.1) testing existing peptide ligands for the purification of antibodies from a variety of sources; (a.2) optimizing the protocol of ligand coupling on chromatographic resins to increase adsorbent binding capacity; (a.3) a method of modification of the resin’s surface chemistry to increase the adsorbent's chemical stability in harsh alkaline conditions; and (a.4.) a combined computational and chemical strategy for the design of protease-stable peptide ligands. The resulting peptide affinity adsorbents compete well with advanced Protein A – based adsorbents in terms of product yield and purity, dynamic binding capacity (~ 50 – 60 g/L), resistance to alkaline cleaning and sanitization, and biochemical stability in the presence of proteolytic enzymes.</p><p> In the second part of this work, two methods are presented for the design, synthesis, and screening of libraries of cyclic peptides for the identification of novel affinity ligands. The first method involves the generation and screening of (b.1) a biological mRNA-display library of cyclic peptides, and the second method (b.2) uses a synthetic solid-phase library of “reversible cyclic peptides”. Both libraries have been screened for the identification of ligands for human antibodies. The results of these studies indicate that these libraries are very promising tools for the discovery of robust, selective and affordable peptide ligands.</p><p> The methods presented herein offer a new set of tools, not only for affinity ligand discovery, but also for finding new drugs and diagnostic methods. Besides their technological value, these studies also offer insights into the mechanisms of non-covalent interaction that underlie the phenomena of biorecognition and protein activity.</p>
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Garcia-Barron, Javier Enrique. "Synthesis and study of chelating polymers and their application to protein and metal separation from aqueous solutions using novel metal affinity interaction techniques." Diss., The University of Arizona, 1999. http://hdl.handle.net/10150/283931.
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The main objective of this research work was the development, synthesis, and study of polymeric chelating derivatives. These derivatives were characterized in terms of their specific metal affinity interaction with biomolecules and metal ions. These engineered materials were used to test their feasibility as tools for separation of proteins and heavy metal ions from aqueous solutions using different affinity separation techniques. Linear and branched polymers were synthesized to create a variety of materials. Among the linear polymers synthesized was the chelated monomethoxy poly(ethylene) glycol (PEG-IDA). This derivative was used in metal affinity partitioning and metal affinity electrophoresis for fast protein-metal interaction analysis. Also a linear heterobifunctional poly(ethylene) glycol (Biotin - PEG - IDA) was synthesized and used as a tool to develop a modified enzyme-linked immuno sorbent assay (ELISA). A multi-armed high molecular weight chelating poly(ethylene) glycol (Star PEG-IDA) was prepared to enhance the separation of protein mixture in gel permeation chromatography. Iminodiacetic poly(ethyleneimine) (PEI-IDA) was prepared and used as a soluble chelating polymer in complexation-ultrafiltration studies for heavy metal ion removal from aqueous solutions. Similar PEIs were also used as casting polymers for the synthesis of affinity adsorbents useful in chromatographic applications. Either as a soluble macromolecule or as a casting polymer for the preparation of adsorbents, PEI chelated derivatives were used for ultratrace metal ion preconcentration and metal ion separations. All polymeric materials prepared were characterized using analytical techniques which include elementary analysis, atomic absorption, UV and IR spectroscopy, high performance liquid chromatography and several colorimetric assays for the determination of end groups and product purity. Metal affinity separation techniques studied with the aforementioned derivatives included: affinity partitioning, affinity electrophoresis and affinity size exclusion for protein purification; affinity complexation-ultrafiltration and metal ion affinity chromatography for removal of heavy metal. Efficient separation of protein mixtures were achieved based on selective affinity by some of the chelated polymers here described and extremely high metal adsorption capacities were found for some of the PEI-based adsorbents prepared. Even though, some of these techniques are still in developmental stages, the results are very promising and encouraging for biotechnical and environmental applications.
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Jouzi, Maryam. "Carbon nanotube nanoneedles and their electrical-mechanical-chemical interactions with biological systems." View abstract/electronic edition; access limited to Brown University users, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3318334.
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Cabana, Hubert. "Élimination des perturbateurs endocriniens nonylphénol, bisphénol A et triclosan par l'action oxydative de la laccase de Coriolopsis polyzona." [S.l. : s.n.], 2008.
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Lokko, Kaarina. "The Effect of Cysteine Modifications Kinetics of Paraoxonase-1 and Glycosylation of PON1." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1578070312150032.
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Wu, Haiyan. "Design and Development of New Chemistry for Biosensing." University of Akron / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=akron1502459975409826.
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Chalker, Justin M. "Reaction engineering for protein modification : tools for chemistry and biology." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:52d92917-5c7f-4223-b554-2e1b4fc0b2ea.
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Chemical modification of proteins is critical for many areas of biochemistry and medicine. Several methods for site-selective protein modification are reported in this Thesis that are useful in accessing both natural and artificial protein architectures. Multiple, complementary methods for the conversion of cysteine to dehydroalanine are described. Dehydroalanine is used as a general precursor to several post-translational modifications and glycosylation, polyprenylation, phosphorylation, and lysine methylation and acetylation are all accessible. These modifications and their mimics were explored on multiple proteins, including histone proteins. Unnatural modifications were also explored. The first examples of olefin metathesis and Suzuki-Miyaura cross-coupling on protein substrates are reported. Allyl sulfides were discovered to be remarkably reactive substrates in olefin metathesis, allowing use of this reaction in water and on proteins. For Suzuki-Miyaura cross-coupling, a new catalyst is described that is fully compatible with proteins. Both olefin metathesis and cross-coupling allow the formation of carbon-carbon bonds on proteins. The prospects of these transformations in chemical biology are discussed. Finally, a novel strategy is reported for the installation of natural, unnatural, and post-translationally modified amino acid residues on proteins. This technology relies on addition of carbon radicals to dehydroalanine. This method of "chemical mutagenesis" is anticipated to complement standard genetic manipulation of protein structure.
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Wijekoon, Asanka. "Preparation and Characterization of Multifunctional Stationary Phases for Multimode Separations." Kent State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=kent1263945054.
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Johnson, Eachan Oliver Daniel. "Protein-protein recognition in biological systems exhibiting highly-conserved tertiary structure : cytochrome P450." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:d19f5f52-d1ce-4ec2-be83-fd52f01124f8.
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Protein tertiary structure is more conserved than amino acid sequence, leading to a diverse range of functions observed in the same fold. Despite < 20 % overall sequence identity, cytochromes P450 all have the same fold. Bacterial Class I P450s receive electrons from a highly specific, often unidentified, ferredoxin, in which case the hemoprotein is termed “orphaned”. CYP199A2, a Class I P450, accepts electrons from ferredoxins Pux and HaPux. Five orientation-dependent and one orientation-independent DEER measurements on paramagnetic HaPux and spin-labelled CYP199A2 yielded vector restraints, which were applied to building a model of the CYP199A2:HaPux complex in silico. A different binding mode was observed compared to P450cam:Pdx and P450scc:Adx, both recently elucidated by X-ray crystallography. This protocol was also applied to the CYP101D1:Arx complex. The first three measurements indicate that this heterodimer does not have a similar orientation to CYP199A2:HaPux, P450cam:Pdx, or P450scc:Adx. P450cam was fused to putidatredoxin reductase (PdR) to explore the kinetic effects with a view to improving electron transfer to orphan P450s. Heme incorporation of this enzyme depends on linker length. In whole cells, the fusion was more active after longer incubations. In vitro kinetics of the fusion exhibited some co-operativity and enhanced kinetics over the unfused system under steady-state conditions. The putative iron-sulfur biosynthesis ferredoxin PuxB had been engineered by rational mutagenesis to support catalysis by CYP199A2. It was confirmed this arose from improved protein-protein recognition. Engineering of E. coli ferredoxin based on these findings was carried out, resulting in electron-transfer to CYP199A4 from a novel engineered alien ferredoxin.
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GUPTA, ROCKENDRA. "Pressure Assisted Thermal Processing: Tomato Carotenoid Stability during Processing and Storage and Feasibility of Using Chemical Markers for Evaluating Process Uniformity." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1293632615.
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Dhameri, Sulaiman Ali A. "Rheological Properties and Decomposition Rates of Gellan Gum." University of Toledo / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1562780919692096.
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Ghimire, Chiran. "FUSION OF LIPID DROPLETS AND SUBMOLECULAR DISSECTION OF DNA G-QUADRUPLEX USING OPTICAL TWEEZERS." Kent State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=kent1501231695038118.
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Thompson, Kayla Dawn. "Structural Characterization of β-Lactoglobulin in Sodium Dodecyl Sulfate and Lauryldimethylamine Oxide". Miami University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=miami1604698714328977.
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Roberts, Alexander Colin. "Production and Harvest of Microalgae in Wastewater Raceways with Resource Recycling." DigitalCommons@CalPoly, 2015. https://digitalcommons.calpoly.edu/theses/1537.
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Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research.
A pilot facility was operated with nine CO2-supplemented raceway ponds, each with a 33-m2 surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously fed primary-clarified municipal wastewater at either a 2-day or 3-day hydraulic residence time (HRT), and one set fed the clarified effluent of the 3-day pond set. This second pond-in-series was operated with a 3-day HRT.
Areal biomass productivity is reported as gross and net, the former based only on biomass in the pond effluents and the latter subtracting the volatile suspended solids in the influent from those in the effluent. An estimate was also made of autotrophic biomass productivity, as differentiated from heterotrophic growth.
Over a year, net productivity averaged 83 metric tons per hectare per year (MT/ha-yr) for the 2-day HRT ponds, 52 MT/ha-yr for the 3-day HRT ponds, and 44 MT/ha-yr for the 3-day HRT ponds receiving clarified effluent of the first set of 3-day HRT ponds (i.e., recycled water). The lower net productivity of the pond receiving water recycling was attributed to two factors. First, the relatively high influent suspended solids concentrations were subtracted from the effluent suspended solids concentrations before net productivity was calculated. Second, the recycled water contained less soluble organic matter than the primary-clarified wastewater leading to less heterotrophic biomass production. The accumulation of inhibitory allelochemicals is a possible third cause of lower productivity
, but no specific information was collected on allelopathy.
Algae were harvested from pond effluent by sedimentation, with harvest efficiency most affected by the extent of natural bioflocculation occurring in the ponds. Some forms of bioflocculation are thought to be mediated by bacteria, which often make-up a substantial fraction of the settled flocs. Pond samples settled in 1-L Imhoff cones averaged/L total suspended solids after 24 hours of settling; but all ponds fell short of meeting an averaged/L total suspended solids after a 2 hour interval which would be ideally achieved for wastewater effluent. No relationship was seen between settling performance and the bacterial content of flocs.
Soluble carbonaceous biochemical oxygen demand (scBOD5) removal by the raceway ponds was sufficient to meet wastewater treatment requirements year around. Influent scBOD5 concentrations averaged 83 mg/L, and the effluent averaged 5.1 mg/L and 4.2 mg/L for the 2-day and 3-day HRT pond sets, respectively.
The variable with the greatest influence on productivity in all pond sets, and settling performance in the recycled water pond set, was season (i.e., co-correlated variables of solar insolation and pond temperature). Neither productivity nor settling appeared to be related to prominent algae genera or prevalence of grazers.
The high net productivity achieved with a growth medium of primary clarifier effluent and the generally high settleability of algal-bacterial flocs indicate a good potential for algae wastewater treatment and biofuel production. However, the settling of algae grown on recycled water needs improvement to achieve the full potential of wastewater-grown algae biofuel production.
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Chooi, Kok Phin. "Synthetic phosphorylation of kinases for functional studies in vitro." Thesis, University of Oxford, 2014. https://ora.ox.ac.uk/objects/uuid:2adc517a-2876-4a0b-8ead-e9bf164ebc6f.
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The activity of protein kinases is heavily dependent on the phosphorylation state of the protein. Kinase phosphorylation states have been prepared through biological or enzymatic means for biochemical evaluation, but the use of protein chemical modification as an investigative tool has not been addressed. By chemically reacting a genetically encoded cysteine, phosphocysteine was installed via dehydroalanine as a reactive intermediate. The installed phosphocysteine was intended as a surrogate to the naturally occurring phosphothreonine or phosphoserine of a phosphorylated protein kinase. Two model protein kinases were investigated on: MEK1 and p38α. The development of suitable protein variants and suitable reaction conditions on these two proteins is discussed in turn and in detail, resulting in p38α-pCys180 and MEK1-pCys222. Designed to be mimics of the naturally occurring p38α-pThr180 and MEK1-pSer222, these two chemically modified proteins were studied for their biological function. The core biological studies entailed the determination of enzymatic activity of both modified proteins, and included the necessary controls against their active counterparts. In addition, the studies on p38α-pCys180 also included a more detailed quantification of enzymatic activity, and the behaviour of this modified protein against known inhibitors of p38α was also investigated. Both modified proteins were shown to be enzymatically active and behave similarly to corresponding active species. The adaptation of mass spectrometry methods to handle the majority of project's analytical requirements, from monitoring chemical transformations to following enzyme kinetics was instrumental in making these studies feasible. The details of these technical developments are interwoven into the scientific discussion. Also included in this thesis is an introduction to the mechanism and function of protein kinases, and on the protein chemistry methods employed. The work is concluded with a projection of implications that this protein chemical modification technique has on kinase biomedical research.
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Bludin, Alexey O. "Peptide-Porphyrin Self-Assembled Materials." Bowling Green State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1308097842.
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Pryor, Donald Edward. "Synthesis and Bioactivity Studies of Nanoparticles Based on Simple Inorganic and Coordination Gallium Compounds as Cellular Delivering Vehicles of Ga(III) Ions for Potential Therapeutic Applications." Kent State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=kent1543554532063877.
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Olszewski, Amy L. "Synthesis, Biological Functionalization, and Integration ofCarbon Nanotubes for Bio-Sensing Textiles." Youngstown State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1369854838.
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Ricq, Emily. "Chemical Neurobiology of the Histone Lysine Demethylase KDM1A." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493305.
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Epigenetic mechanisms regulate gene expression and mediate interactions between genetic factors and environmental exposures. The enzymes responsible for epigenetic regulation may thus be important therapeutic targets for multifactorial neurological syndromes. KDM1A, the first histone lysine demethylase to be discovered, regulates the maturation of neurons and is inactivated by non-selective monoamine oxidase inhibitors such as the antidepressant tranylcypromine. This thesis entails the development of small-molecule tools to study KDM1A in a neurobiological context, with application towards the development of new therapeutic agents.
We leveraged the chemical scaffold of tranylcypromine to generate novel KDM1A inhibitors. In chapter 2, we profile these analogs using biochemical, cellular, and in vivo assays. We show that RN1 potently inhibits KDM1A, exhibits high brain uptake, and affects the behavior of mice in a novel object recognition assay. Thermal shift assays reveal engagement of KDM1A by tranylcypromine in the brains of systemically-treated rats, suggesting that inhibition of KDM1A by non-selective antidepressants in a clinical setting warrants further examination.
We sought to discover new mechanisms of KDM1A inhibition in order to gain further selectivity versus the monoamine oxidases. In chapter 3, we present outcomes of a high-throughput screen and secondary assays which reveal a predominant mode of KDM1A inhibition based on thiol-reactivity, and widespread contamination of test compounds by elemental sulfur. We show that KDM1A is inhibited by the FDA-approved drug disulfiram, and disclose two novel scaffolds for medicinal chemistry development.
In chapter 4, we further profile the thiol-reactivity of KDM1A and show that catalytically-generated hydrogen peroxide negatively regulates demethylase activity. MALDI-TOF mass spectrometry indicates that hydrogen peroxide blocks labeling of cysteine 600, which we propose forms an intramolecular disulfide bond with cysteine 618. This activity-dependent regulation is unique among histone-modifying enzymes but consistent with redox sensitivity of epigenetic regulators. KDM1A may use this thiol/disulfide switch as a mechanism to sense other cellular oxidants, such as the monoamine neurotransmitter dopamine.<br>Chemistry and Chemical Biology
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Ojha, Yagya Raj. "Selection and Characterization of ssDNA Aptamers for Salivary Peptide Histatin 3 and Their Application Towards Assay and Point-of-Care Biosensing." University of Toledo / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1575992671104993.
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Hwang, William. "Droplet interface bilayers for the study of membrane proteins." Thesis, University of Oxford, 2008. http://ora.ox.ac.uk/objects/uuid:0ba680ba-75f1-4cd9-9600-3e251b948a3d.
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Aqueous droplets submerged in an oil-lipid mixture become enclosed by a lipid monolayer. The droplets can be connected to form robust networks of droplet interface bilayers (DIBs) with functions such as a biobattery and a light sensor. The discovery and characterization of an engineered nanopore with diode-like properties is enabling the construction of DIB networks capable of biochemical computing. Moreover, DIB networks might be used as model systems for the study of membrane-based biological phenomena. We develop and experimentally validate an electrical modeling approach for DIB networks. Electrical circuit simulations will be important in guiding the development of increasingly complex DIB networks. In cell membranes, the lipid compositions of the inner and outer leaflets differ. Therefore, a robust model system that enables single-channel electrical recording with asymmetric bilayers would be very useful. Towards this end, we incorporate lipid vesicles of different compositions into aqueous droplets and immerse them in an oil bath to form asymmetric DIBs (a-DIBs). Both α-helical and β-barrel membrane proteins insert readily into a-DIBs, and their activity can be measured by single-channel electrical recording. We show that the gating behavior of outer membrane protein G (OmpG) from Escherichia coli differs depending on the side of insertion in an asymmetric DIB with a positively charged leaflet opposing a negatively charged leaflet. The a-DIB system provides a general platform for studying the effects of bilayer leaflet composition on the behavior of ion channels and pores. Even with the small volumes (~100 nL) that can be used to form DIBs, the separation between two adjacent bilayers in a DIB network is typically still hundreds of microns. In contrast, dual-membrane spanning proteins require the bilayer separation to be much smaller; for example, the bilayer separation for gap junctions must be less than 5 nm. We designed a double bilayer system that consists of two monolayer-coated aqueous spheres brought into contact with each side of a water film submerged in an oil-lipid solution. The spheres could be brought close enough together such that they physically deflected without rupturing the double bilayer. Future work on quantifying the bilayer separation and studying dual-membrane spanning proteins with the double bilayer platform is planned.
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Ferguson, Ronald Dale 1966. "Design, synthesis and biological screening of combinatorial chemical libraries." Thesis, The University of Arizona, 1996. http://hdl.handle.net/10150/278584.
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Although combinatorial libraries owe their inception to applications in peptide and bacteriophage libraries, the breadth of current applications include solution phase chemical reaction optimization, material science investigation, natural products modifications, and agricultural research. As a conceptual application, combinatorial library techniques can enhance a researcher's ability to transcend beyond the examination of one or several compounds to that of thousands or millions of these species simultaneously. The work described here, limited to scaffolded combinatorial chemical libraries, focuses primarily on the design and synthesis of these systems and how they have been analyzed against biological targets. Of the three scaffolded libraries, two were developed from aromatic templates (3,5-diaminobenzoic acid and 1,2,4-benzenetricarboxylic acid) while the last was built upon the cyclohexyl, Kemp's triacid platform. Although these libraries did not provide compounds with high affinity for the receptors investigated, they served to improve the understanding of combinatorial chemistry as a practice.
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Ducay, Rey Nann Mark Abaque. "Direct Detection of Aggregates in Turbid Colloidal Suspensions." Miami University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=miami1439434385.
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Shokouhimehr, Mohammadreza. "Prussian Blue Nanoparticles and its Analogues as New-Generation T1-Weighted MRI Contrast Agents for Cellular Imaging." Kent State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=kent1275612500.
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Taralp, Alpay. "Aqueous and nonaqueous chemical approaches to elucidating structure and function in proteins." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0012/NQ28377.pdf.
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Spiciarich, David. "Chemical Glycoproteomics for Identification and Discovery of Glycoprotein Alterations in Human Cancer." Thesis, University of California, Berkeley, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10688096.
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<p> Changes in glycosylation have long been appreciated to be part of the cancer phenotype; sialylated glycans are found at elevated levels on many types of cancer and have been implicated in disease progression. However, the specific glycoproteins that contribute to cell surface sialylation are not well characterized, specifically in <i>bona fide</i> human cancer. Metabolic and bioorthogonal labeling methods have previously enabled enrichment and identification of sialoglycoproteins from cultured cells and model organisms. The goal of this work was to develop technologies that can be used for detecting changes in glycoproteins in clinical models of human cancer. </p><p> In Chapter 1 of this dissertation, I present an overview of the structures and functions of glycans and their relationship to cancer progression. I also discuss applications of <i>in vivo</i> bioorthogonal labeling in model organisms and how in humans, the significant regulatory and ethical barriers associated with introducing chemically altered sugars into people have hindered it. Finally, I review mass spectrometry-based proteomics and how it can be applied to clinical glycoproteomics. </p><p> In Chapter 2, I demonstrate the first application of this bioorthogonal labeling in a glycoproteomics platform applied to human tissues cultured <i> ex vivo</i>. Both normal and cancerous prostate tissues were sliced and cultured in the presence of functionalized derivatives of N-acetyl mannosamine, the sialic acid biosynthetic precursor. Chemical biotinylation followed by enrichment and mass spectrometry led to the identification of glycoproteins that were found at elevated levels or uniquely in cancerous prostate tissue. This work therefore extends the use of bioorthogonal labeling strategies to problems of human clinical relevance. </p><p> Secretome proteins play important roles in regulation of many physiological processes and show utility as potential biomarkers and for noninvasive diagnostics and treatment monitoring. In Chapter 3, I discuss a platform for identifying sialoglycoproteins that were secreted in the conditioned media from bioorthogonally labeled human prostate tissue slice cultures. This platform could be used to identify disease biomarkers in a faithful clinical model of human disease. </p><p> Mutations in granulocyte colony-stimulating factor 3 receptor (CSF3R), also known as G-CSFR, occur in the majority of patients with chronic neutrophilic leukemia (CNL) and are more rarely present in other kinds of leukemia. In Chapter 4, I discuss novel variants in CSF3R at asparagine residue N610, one of which was germline. Interestingly, these N610 substitutions are potently oncogenic and result in ligand-independent receptor activation. They confer activation of the JAK-STAT signaling pathway and concurrent sensitivity to JAK kinase inhibitors. The N610 residue is part of a consensus N-linked glycosylation motif in the receptor. Detailed mass spectrometry analysis demonstrates that this site is occupied by both complex and complex bisecting glycans. Further analysis demonstrates that N610 is the primary site of sialylation of the receptor. This study demonstrates that membrane-proximal N-linked glycosylation is critical for maintaining the ligand dependence of the receptor. Furthermore, it expands the repertoire of potently oncogenic mutations in CSF3R that are therapeutically targetable.</p><p>
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Stewart, Nicolas Andre Stirling. "In vacuo chemical modifications of proteins and peptides." Thesis, University of Ottawa (Canada), 2004. http://hdl.handle.net/10393/29170.
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A novel approach for the chemical modification of proteins and peptides was developed, namely the chemical modification under vacuum (in vacuo) of lyophilized proteins and peptides. This method was used with iodomethane to produce peptides with a permanent positive charge by converting their amino groups to trimethylammonium derivatives for analysis by matrix assisted laser desorption ionization mass spectrometry (MALDI MS). Peptides with such a permanent charge have a higher ionization yield under MALDI MS resulting in a dramatic increase in detection. The signal intensity of the trimethylammonium derivative in MALDI MS is much greater compared to the unmodified peptide. The trimethylammonium derivative of alpha-amino groups of peptides derived from test lyophilized peptides and a lyophilized protein, and an epsilon-amino group of a peptide derived from the solitary lysine residue of the oxidized B-chain of insulin were shown to have a large increase in signal intensity compared to the unmodified peptides. The in vacuo methylation procedure is readily amenable to the use of a combination of isotopes, e.g. 12CH3I and 13CH3I or CH3I and CD3I, yielding a doublet signal to discriminate between peptide and non-peptide signals in the mass spectrum providing an even greater increase in sensitivity. This strategy was employed to isolate an N-terminal peptide derived from an enzymatic digest of human hemoglobin and to facilitate the analysis of spectra. Proteins and peptides lyophilized from slightly alkaline solutions yielded the greatest amount of derivatization. However, a peptide lyophilized under acidic conditions could also be methylated to give an increased MALDI signal. In light of these results a mechanism is proposed where the vacuum facilitates the removal of gaseous counter-ions to drive the reaction to the trimethylammonium derivative.
In order to selectively isolate the C-terminal peptides from enzymatic digests of proteins, lyophilized proteins were reacted with iodomethane under conditions where reaction occurred mainly with carboxylate groups. A proof of concept has been demonstrated for a method of general applicability for the determination of the C-terminal sequences of proteins. Separation and isolation of the C-terminal peptides generated from enzymatic digests for further sequencing either by chemical means (N-terminal Edman degradation chemistry) or by tandem mass spectrometry (MS/MS) was accomplished by the use of two dimensional (2D) high voltage paper electrophoresis (HVPE). (Abstract shortened by UMI.)
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Wu, Taifeng. "Studies on the chemical synthesis of natural and novel oligoribonucleotides using alkylsilyl protecting groups." Thesis, McGill University, 1989. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=74341.
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The phenoxyacetyl group was investigated as a base protecting group in oligoribonucleotide synthesis using the phosphoramidite coupling procedure. The N-phenoxyacetyl protected ribonucleoside methylphosphoramidites were prepared and they were evaluated in the synthesis of a number of oligoribonucleotides, including a 75-unit-long molecule whose base sequence is related to the yeast formylmethionine initiator tRNA.<br>A side reaction leading to some cleavage of the assembled oligoribonucleotide chain was observed in oligoribonucleotide synthesis, following the standard procedure. The nature of this side reaction was identified and a procedure to eliminate it was developed.<br>An extensive study has been carried out to prove the fidelity of alkylsilyl groups as the 2$ sp prime$-hydroxyl protecting group in oligoribonucleotide synthesis. A series of natural dinucleotides were prepared. The corresponding dinucleotides with the unnatural 2$ sp prime$-5$ sp prime$ phosphate linkage were also synthesized. The products from the synthesis as well as the intermediates during the synthesis were characterized by $ sp1$H and $ sp{31}$P NMR and HPLC. Unambiguous chemical evidence of the stability of the phosphate linkages in synthetic oligoribonucleotides was provided.<br>Several ribozymes and their substrates were chemically synthesized. A general procedure to prepare novel mixed DNA-RNA polymers was developed. The usefulness of this type of molecule in molecular biology has been demonstrated in the study of the mechanism of ribozyme catalysis.
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Singh, Kulveer. "Structure-function studies of the oxidoreductase bilirubin oxidase from Myrothecium verrucaria using an electrochemical quartz crystal microbalance with dissipation." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:0376cc7e-f572-4e0c-96f0-43b0b4b91d99.
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This thesis presents the development and redesign of a commercial electrochemical quartz crystal microbalance with dissipation (E–QCM–D). This was used to study factors affecting the efficiency of the four electron reduction catalysed by the fuel cell enzyme bilirubin oxidase from Myrothecium verrucaria immobilised on thiol modified gold surfaces. Within this thesis, the E–QCM–D was used to show that application of a constant potential to bilirubin oxidase adsorbed to thiol-modified gold surfaces causes activity loss that can be attributed to a change in structural arrangement. Varying the load by potential cycling distorts the enzyme by inducing rapid mass loss and denaturation. Attaching the enzyme covalently reduces the mass loss caused by potential cycling but does not mitigate activity loss. Covalent attachment also changes the orientation of the surface bound enzyme as verified by the position of the catalytic wave (related to the overpotential for catalysis) and reactive labelling followed by mass spectrometry analysis. The E–QCM–D was used to show how electrostatic interactions affect enzyme conformation where high pH causes a reduction in both mass loading at the electrode and a reduction in activity. At pH lower than the enzyme isoelectric point, there is a build up of multilayers in a clustered adsorption. When enzyme adsorbs to hydrophobic surfaces there is a rapid denaturation which completely inactivates the enzyme. Changing the surface chemistry from carboxyl groups to hydroxyl and acetamido groups shows that catalysis is shifted to more negative potentials as a result of an enzyme misorientation. Further to this, increasing the chain length of the thiol modifier indicates that an increased distance between surface and enzyme reduces activity, enzyme loading and results in a conformational rearrangement that permits electron transfer over longer distances.
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Vakos, Helen T. "Applications of the in vacuo chemical modification technique to the study of protein structure and function." Thesis, University of Ottawa (Canada), 2001. http://hdl.handle.net/10393/6179.
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Sensitive NMR methods have been developed for analyzing N- and C-termini in protein structure for investigating protein purity, identity, and homogeneity. The in vacuo chemical modification procedure allows for the incorporation of isotopically labeled reagents (13C, 14C, 2H, 3H) into protein with a high degree of reaction specificity in a cost-effective manner, since there is no competing reaction with water and only microlitre quantities are required to derivatize milligram quantities of lyophilized protein. Reaction in vacuo at 75°C with 13C-iodomethane results in the preferential 13C-trimethylation of alpha-amino groups in proteins lyophilized from aqueous solutions at pH (LpH) 6 to 7. In vacuo trimethylation of alpha-amino groups and analysis by 13C-NMR spectroscopy provides a new approach for determining the number and types of N-terminal amino acid residues and for verifying the presence of a free or blocked amino-terminus in a protein preparation. Reaction of lyophilized proteins in vacuo at 75°C with 13C-iodomethane at LpH values between 3 and 4 effects the preferential esterification of carboxyl groups, and is in accord with the pH memory effect. The extent of reaction increases with an increase in amount of deprotonated carboxyl groups at higher LpH values, but trimethylation of amino groups is the predominant reaction at LpH values greater than 4 or 5. In contrast, the novel in vacuo esterification reaction (75°C) of lyophilized proteins (LpH 3) with gaseous 13C-methanol/HCl or 13C-ethanol/HCl results in the exclusive, rapid, and extensive formation of alpha-, gamma- and delta-carboxyl 13C-methyl or 13C-ethyl ester derivatives with no protein degradation, which could be distinguished by the distinct chemical shifts of their resonances. Reaction in vacuo with 14C- or 3H-enriched iodomethane results in a higher incorporation of specific radioactivity into lyophilized proteins than can be achieved in aqueous environments. The chemical tag can serve as a probe of structure and function in tracer studies for proteins that are not enzymes. Trace-radiolabeled proteins (e.g., 14C-methylated Bacillus thuringiensis (Bt) insecticidal toxin, 14C-methylated insulin) show a high specific activity, and retain bioactivity (e.g., 14C-methylated Bt toxin). In a separate study, pure bovine and porcine cholesterol esterase (CE) and human milk bile salt-activated lipase are obtained using a cholate-derivatized affinity column and a taurocholate concentration gradient in the eluent, which is critical to the success of the method. Taurocholate induces dimerization of bovine CE in SIDS as observed by SDS-PAGE. Studies of the bile salt-modulated stereoselectivity of CE-catalyzed hydrolysis of alpha-tocopheryl acetates show that, in competitive experiments, the diastereoselectivity of CE depends on the bile salt used, which is relevant if the bile salt-modulated effect on CE-catalyzed reactions is to be exploited in organic syntheses. (Abstract shortened by UMI.)
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Arendall, William Bryan. "X-ray structures of novel intermediates in the thymidylate synthase models for chemical mechanism and conformational change." Diss., The University of Arizona, 2001. http://hdl.handle.net/10150/279920.
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The catalytic mechanism of thymidylate synthase (TS) was investigated using X-ray crystallography: four structures that yield new information about the early stages of TS action are reported. TS catalyzes the production of thymidylate (TMP), one of the four nucleotide bases of DNA, from the substrate, deoxyuridylate and cofactor, methylenetetrahydrofolate (MTF). Knowledge about the TS mechanism is important for both the medical and basic sciences. TS is the sole de novo source of TMP and it is thus a target for anti-proliferative drugs aimed at addressing cancer and other diseases marked by rapidly dividing cells. To aid this effort, past research on TS has developed two models to explain how TS works. A detailed, sequential chemical mechanism explains the methylene and hydride transfers from one cofactor to the substrate. And, a two state, dynamical model explains the conformational change that TS undergoes during its catalytic cycle. Combining these two models will lead to a fuller understanding of protein structure, function, and dynamics interrelationships. Two of the new structures contain cofactor in a heretofore unseen state, bound in the active site with its imidazolidine ring intact. Finding that this is an allowed enzyme-cofactor state indicates that ring opening and formation of the highly reactive iminium cation may occur relatively late in the methylene transfer, after preparation of the substrate; and, the reaction may perhaps be concerted. Further, details of these two structures show that protonation of the correct imidazolidine ring nitrogen (N10) may be selected by the geometry and environment imposed on the bent cofactor by TS. N5, the "wrong" ring nitrogen, is blocked and in a hydrophobic environment, while N10 is rehybridized to sp3 and its lone pair (nascent hydrogen) is pointed into an aqueous cavity trapped within the enzyme. A proposal coming from this dissertation is for a combination of the two models describing TS catalysis. The chemical mechanism model and the conformational change model both describe the same phenomena and these models should be connected and combined into one larger model to further increase our knowledge of the connections between structure, dynamics and function. The four structures reported here begin that connection process.
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Michaelides, Alecos. "Chemical and enzymatic fragmentation of tetanus toxin and immunological studies on anti-tetanus toxin and toxoid sera." Thesis, University of Ottawa (Canada), 1996. http://hdl.handle.net/10393/9661.
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This thesis describes the immunization protocols for the production of antibodies against tetanus toxin and toxoid in guinea pigs and mice. Antibodies were successfully raised against the toxin without mortalities in either species. The murine sera obtained, were isotyped by ELISA and the toxin was proven to be a superior antigen in eliciting production of IgG$\rm\sb{2a}$ and IgG$\sb3$. The two isotypes which have demonstrated antitumor activity. The anti-toxoid sera exhibited a lower reactivity towards the toxin and toxoid when compared with anti-toxin sera. The reactivity of recombinant tetanus toxin fragment C was studied and the results indicated that in the murine serum, 72% of anti-toxin or anti-toxoid antibodies were directed against epitopes on fragment C. The study of the guinea pig sera suggested that similar to mouse serum, it can develop in response to toxin as an antigen, antibodies against toxin which are mostly directed against the fragment C portion. On the other hand. guinea pigs seem to respond to the toxoid as an antigen by producing antibodies to more than fragment C. (Abstract shortened by UMI.)
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Pulido-Cejudo, Gabriel. "Chemical and biological properties of iron-pyruvate-transferrin complexes." Thesis, McGill University, 1990. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=74529.
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The preparation of a novel complex, ferric bromopyruvate, is described. In solutions from which most of the carbonate has been removed, ferric bromopyruvate can be used both as an iron and pyruvate source for the full iron saturation of apotransferrin. Using ferric bromopyruvate as an iron donor, iron incorporation into human apotransferrin is biphasic; the N-terminal domain is saturated three times faster than its homologous C-terminal iron binding site. Following the reaction of apotransferrin with ferric bromopyruvate, 4 moles of pyruvate per mole of transferrin are covalently bound. Based on the effect of acetylation on pyruvate and iron binding, it is suggested that lysyl residues could be the target of pyruvate bonding. However, the reaction of pyruvate with other positively charged amino acid residues cannot be excluded. The possible sites of pyruvate binding within the N-terminal domain of human serum transferrin are discussed. Covalent attachment of pyruvate to cationic amino acid residues decreased both in vitro and in vivo iron release, preferentially from the N-terminal domain of transferrin. The decreased rate of iron incorporation from iron-pyruvate-transferrin complexes by rabbit reticulocytes caused a lower iron incorporation into heme. It is suggested that an impairment of iron release from transferrin may decrease the rate of heme synthesis in reticulocytes. In vitro studies on the iron removal from iron-pyruvate-transferrin complexes showed that pyrophosphate can remove iron from this complex at an acid pH to a similar extent to the cellular mediated iron release from this complex. Based on this data, a model for the intravesicular iron release from transferrin is proposed.
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Federation, Alexander Joel. "The Development of Chemical and Computational Tools to Study Transcriptional Regulation in Cancer." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17463980.
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Eukaryotic gene regulation is a complex process requiring the action of many multicomponent complexes in the cell. Specific inhibitors of chromatin-associated factors allow the functional study of protein domains without genetic removal of the entire protein. Here, two small molecule probes were used to study the role of DOT1L and BET proteins in cancer biology.
DOT1L is a histone methyltransferase with activity correlating with positive regulation of transcription. In MLL-rearranged leukemia, DOT1L is recruited aberrantly to early developmental transcription factors, leading to their inappropriate expression and leukemia maintenance. The development of an assay platform for DOT1L allowed the investigation of many small molecule DOT1L inhibitors, leading to compounds with improved potency and pharmacokinetics.
Studying the action of BET bromodomain inhibitors led to the identification of super enhancers, large tissue-specific regulatory elements driving the expression of genes critical for the function of the cell. Super enhancers are often found in oncogenic translocation events, especially in B cell malignancies. This study identified a subset of super enhancers that promote off-target DNA damage from the B cell antibody diversity enzyme AID, leading to double strand break events and translocations.
Super enhancers also regulate the expression of master transcription factors (TFs) in a given cell type. Using the topology of the super enhancer, the sites of master TF binding can be predicted, allowing the construction of network models for transcriptional regulation. These models were built in a large number of healthy and diseased cell types, including the pediatric malignancy medulloblastoma. In medulloblastoma, a network motif was identified that matches an expression pattern seen in a transient cell population in the developing cerebellum, providing evidence for the previously unknown cell of origin for Group 4 medulloblastoma.<br>Chemical Biology
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West, Anthony A. "Structural studies in tellurium chemistry." Thesis, Aston University, 1989. http://publications.aston.ac.uk/9705/.
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The primary theme of this research was the characterisation of new and novel organo-tellurium complexes, using the technique of single crystal X-ray analysis to establish more firmly the various coordination modes of tellurium. In each study the unit cell dimensions and intensity data were collected using an Enraf-Nonius CAD-4, four circle diffractometer. The raw data collected in turn was transferred to the Birmingham University Honeywell Multics System and processed using the appropriate computer packages for the determination of crystal structures. The molecular and crystal structures of: bis[2-(2-pyridyl)phenyl]tritelluride, bis[2-(N-hydroxy)iminophenyl] ditelluride, 2-(2-pyridyl)phenyltellurium(IV) tribromide, (2-N,N-dimethylbenzylamine-C,N')tellurium(IV)tribromide, 2-dichloro(butyl)tellurobenzaldehyde, 2-dichlorobutotelluro-N-dimethylbenzyl ammonium chloride, dimethyldithiocarbamato[2-(2-pyridyl)phenyl]tellurium(II), dimethyldithiocarbamato[2-(2-quinolinyl)phenyl]tellurium(II) and para-ethoxypheny[2-(2-pyridyl)phenyl]telluride are described. In each structure, the Lewis acidity of tellurium appears to be satisfied by autocomplex formation, through short-range intramolecular secondary bonds between tellurium and an electron denoting species, (generally nitrogen in these structures) with long range weak inter molecular contacts forming in the majority of the tellurium(IV) structures. The order of Lewis acidity in each structure can be considered to be reflected by the length of the short range intramolecular secondary bond, identified, that is, when tellurium has a low Lewis acidity this interaction is long. Interestingly, no primary bonds are found trans to a Te-C covalent bond in any of the above structures, highlighting the strong trans effect of aromatic and aryl groups in tellurium complexes.
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York, Andrew P. E. "Methane conversion chemistry." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.334954.
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Cooper, Roland Arthur 1963. "Pyrrolizidine alkaloids: Chemical basis of toxicity." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/290581.
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In humans, livestock and experimental animals, pyrrolizidine alkaloids (PAs) are toxic as a consequence of their hepatic metabolism to reactive pyrrolic esters, or dehydroalkaloids (DHAs). Despite their similarity in structures, PAs often vary markedly in their lethality (LD₅₀s) and in the organs in which toxicity is expressed. We have examined whether there are differences in the physicochemical properties of certain DHAs which are associated with differences in patterns of metabolism and toxicity produced by the parent PA. Using a potentiometric method to measure hydrolysis, it was determined that the half-lives of the corresponding DHAs of retrorsine, seneciphylline, monocrotaline and trichodesmine were 1.06, 1.60, 3.39 and 5.36 sec, respectively. These values were supported by similar results from experiments measuring reactivity of DHAs toward 4-(p-nitrobenzyl)pyridine. Studies from the isolated rat liver perfused with PAs show that DHA stability is related to patterns of metabolism and toxicity. Perfusion of the primarily hepatotoxic retrorsine and seneciphylline is associated with a greater proportion of metabolite released as non-toxic 7-glutathionyl-6,7-dihydro-1-hydroxymethyl-5H-pyrrolizine (7-GSDHP), a greater proportion alkylating liver macromolecules, and a lower proportion released as DHA into the circulation. Perfusion with monocrotaline and trichodesmine, PAs producing extrahepatic toxicity, produced lower proportions of 7-GSDHP release and liver alkylation, and higher proportions of DHA released into the circulation. Other studies characterizing DHAs included the use of an in vitro enzyme assay in which DHAs were shown to inhibit the phosphotransferase activity of yeast and rat brain hexokinase. Parent PAs, and the hydrolysis product of DHAs, (±)-6,7dihydro-1-hydroxymethyl-5H-pyrrolizine (DHP) did not affect enzyme activity. In vivo studies in rats have established that glutathione and cysteine-conjugated pyrrolic metabolites of PAs likely represent detoxication pathways, providing further support for DHAs as the primary toxic metabolite. We have examined the chemical form of sulfur-bound pyrroles to establish the importance of the 7-ester position in PA toxicity. Additionally, we have developed an efficient technique for the rapid separation and purification of large quantities of PAs using high-speed counter-current chromatography.
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Yin, Hang. "Supramolecular encapsulation of bioactive molecules by a synthetic receptor :modulation of chemical and biological properties." Thesis, University of Macau, 2018. http://umaclib3.umac.mo/record=b3952180.
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Class, Caleb Andrew. "Predicting organosulfur chemistry in fuel sources." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/98155.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2015.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>Desulfurization of fossil fuels with supercritical water (SCW) has been the topic of many studies over the past few decades. This process does not require the use of any catalyst, eliminates the need for a hydrogen feed, and minimizes coke formation. Previous research has shown that it has the potential to be a viable commercial process, and recent experimental studies have proven that water acts as one hydrogen source for sulfur removal in this process. However, the exact desulfurization mechanism is largely unknown, as are many other reaction mechanisms involving sulfur compounds. Recent work has greatly expanded our ability to build comprehensive reaction mechanisms automatically for the decomposition of organic sulfur compounds using the automated Reaction Mechanism Generator (RMG). This thesis presents the implementation of this and other tools to investigate chemical processes relevant to our use of fuel sources containing sulfur compounds, and it shows some steps that have been taken to improve our predictions for these mechanisms and those that will be generated in the future. Previous investigations had focused on the pyrolysis of small sulfur compounds containing less than six heavy atoms, so RMG is first used to study the pyrolysis of t-butyl sulfide. A detailed reaction mechanism is then presented for the SCW desulfurization of hexyl sulfide. Comprehensive kinetic mechanisms for these larger molecules are likely to include thousands of reactions, so RMG builds this model in a systematic and unbiased way using a database of ab initio data. This database is expanded with potentially relevant thermochemical and kinetic parameters using transition state theory and quantum chemical calculations at the CBS-QB3 and CCSD(T)-F12 levels of theory. With these data, as well as previously calculated rates for hydrocarbon and sulfur kinetics, RMG is used to build a reaction mechanism for the conversion of hexyl sulfide to hydrogen sulfide, pentane, and carbon monoxide in the presence of SCW. This mechanism is validated with results from batch and flow reactor experiments, and predictions are accurate within a factor of two for reactant and major product concentrations. Analysis of the proposed mechanism shows that the molecular addition of water to the carbonsulfur double-bond in hexanethial is a key step in the SCW process, as this not only leads to the desulfurization of the compound, but also prevents the thioaldehyde from undergoing addition reactions with other hydrocarbons in a process that could eventually form coke. Thus, this work not only has implications in the SCW desulfurization process, but in the overall crude oil upgrading process as well. The calculated kinetic and thermochemical parameters are used to generate predictive reaction mechanisms for other processes relevant in fuel chemistry, such as the geological formation of oil and gas from kerogen. This not only allows us to model experimental work investigating the effect sulfur compounds have on the oil-to-gas process, but we also explore how these effects differ at geological conditions and timescales. And as the possible applications of RMG grow, the need for accurate parameters in mechanism generation become even more critical. A thermochemical database is generated for a wide variety of sulfur compounds using the highaccuracy CCSD(T)-F12/cc-pVTZ-F12 method, and this provides a basis for the investigation of organosulfur chemistry with tighter uncertainty.<br>by Caleb Andrew Class.<br>Ph. D.
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Houghton, Stephen Richard. "Improving access to biologically and pharmaceutically relevant molecules by understanding mechanisms of biosynthesis and improving chemical synthesis." Related electronic resource: Current Research at SU : database of SU dissertations, recent titles available full text, 2008. http://wwwlib.umi.com/cr/syr/main.
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Wipulaguna, M. A. Anushika Shiromi. "Use of metabolomic studies to understand the chemical role of ETHE1 in Arabidopsis thaliana." Miami University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=miami1417604333.
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Park, Seongsoon. "Enhancing hydrolase activity and selectivity by medium, substrate, and protein engineering." Thesis, McGill University, 2003. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=83088.
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Researchers use enzymes for enantio- and regioselective reactions because of their high selectivity and activity toward natural substrates. However, researchers sometimes need to modify the reaction system or the enzyme itself to get reliable selectivity and activity when they deal with unnatural substrates. To obtain researcher's need, one can change the solvent, modify the substrates, or alter the enzyme itself. These processes are called medium, substrate, and protein engineering, respectively.<br>This thesis deals with hydrolases, which are classified by EC 3. We applied the proper approach to improve their activity and selectivity depending on the reactions. For the first approach, highly polar ionic liquids were applied to lipase-catalyzed acylation. Ionic liquids worked reliably in enantio- and regioselective lipase-catalyzed reactions. In particular, ionic liquids dissolved polar substrates such as glucose and L-ascorbic acid, thereby facilitating their acylations. In the second approach to improving enantioselectivity of CAL-B (Candida antarctica lipase B) in beta-lactam ring opening reactions, we changed the nucleophile from water to a range of alcohols. Longer, secondary alcohols increased the reaction rate as well as the enantioselectivity. Molecular modeling revealed that the high enantioselectivity of CAL-B and the critical role of alcohols. For the last approach, structure-guided random mutagenesis was applied to increase the enantioselectivity of PFE ( Pseudomonas fluorescens esterase) toward MBMP (methyl 3-bromo-2-methylpropionate). The homology model was used to select amino acid residues for mutagenesis near the stereocenter of the docked tetrahedral intermediate of the substrate. Randomization of these residues yielded a Val122Ser mutant with E increased to 61 (from 12 of wild type enzyme), as well as a Val122Met mutant to 36.
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Wang, Zhongqiang. "Process Development and Metabolic Engineering for Enhanced Propionic Acid Production by Propionibacterium freudenreichii subsp. shermanii." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1374189444.
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