Matching Items (34)

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Synthesis of Hybrid DNA-Protein Nanostructures

Description

While DNA and protein nanotechnologies are promising avenues for nanotechnology on their own, merging the two could create more diverse and functional structures. In order to create hybrid structures, the

While DNA and protein nanotechnologies are promising avenues for nanotechnology on their own, merging the two could create more diverse and functional structures. In order to create hybrid structures, the protein will have to undergo site-specific modification, such as the incorporation of an unnatural amino, p-azidophenylalanine (AzF), via Shultz amber codon suppression method, which can then participate in click chemistry with modified DNA. These newly synthesized structures will then be able to self-assemble into higher order structures. Thus far, a surface exposed residue on the aldolase protein has been mutated into an amber stop codon. The next steps are to express the protein with the unnatural amino acid, allow it to participate in click chemistry, and visualize the hybrid structure. If the structure is correct, it will be able to self-assemble.

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  • 2017-05

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Determining Magnesium Metal Affinity of Alpha L- Id in pH 5

Description

Integrin is a protein in cells that manage cell adhesion. They are crucial to the biochemical functions of cells. L 2 is one type of integrin. Its I domain is

Integrin is a protein in cells that manage cell adhesion. They are crucial to the biochemical functions of cells. L 2 is one type of integrin. Its I domain is responsible for ligand binding. Scientists understand how Alpha L I domain binds Mg2+ at a pH of 7 but not in acidic environments. Knowing the specificity of integrin at a lower pH is important because when tissues become inflamed, they release acidic compounds. We have cloned, expressed, and purified L I-domain and using NMR analysis, we determined that wild type Alpha L I domain does not bind to Mg2+ at a pH of 5.

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  • 2017-05

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Incorporation, Expression, and Retained Enzymatic Activity of Six Tryptophan Analogues in Dihydrofolate Reductase at Positions 30 and 47

Description

Due to a continued interest in the fundamental properties of dihydrofolate reductase (DHFR) and its enzymatic activities, this study employed the use of six fluorescent tryptophan derivatives, for single site

Due to a continued interest in the fundamental properties of dihydrofolate reductase (DHFR) and its enzymatic activities, this study employed the use of six fluorescent tryptophan derivatives, for single site amino acid replacements. The two positions 30 and 47 within DHFR were studied to discover the rate at which these larger tryptophan analogues may be incorporated. Additionally, it was to be determined how much activity the mutated DHFR’s could retain when compared to their wild type counterpart. Through a review of literature, it was shown that previous studies have illustrated successful incorporation and toleration of unnatural amino acids.
Each of the six analogues A through F were relatively efficiently incorporated into the enzyme and well tolerated. Each maintained at least a third of their catalytic activity, measured through the consumption of β-nicotinamide adenine dinucleotide phosphate. Primarily, derivatives B, C, and D were able to retain the highest amount of activity in each position; B and D were the most tolerated in positions 30 and 47 with respective values of 68 ± 6.1 and 80 ± 12. The findings in this study illustrate that single tryptophan derivatives are able to be incorporated into Escherichia coli DHFR while still allowing the maintenance of a significant portion of its enzymatic activity.

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  • 2015-05

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Nucleoporin Gle1: Crystallographic Analysis and the Future of Neuron Disease Pathology

Description

Gle1 is an mRNP export mediator with major activity localized to the nuclear pore complex in eukaryotic cells. The protein's high preservation across vast phylogenetic distances allows us to approximate

Gle1 is an mRNP export mediator with major activity localized to the nuclear pore complex in eukaryotic cells. The protein's high preservation across vast phylogenetic distances allows us to approximate research on the properties of yeast Gle1 (yGle1) with those of human Gle1 (hGle1). Research at Vanderbilt University in 2016, which provides the research basis of this thesis, suggests that the coiled-coil domain of yGle1 is best crystallized in dicationic aqueous conditions of pH ~8.0 and 10\u201420% PEG 8000. Further exploration of crystallizable microconditions revealed a favorability toward lower pH and lower PEG concentration. Following the discovery of the protein's native crystallography conditions, a comprehensive meta-analysis of scientific literature on Gle1 was conducted on the association of Gle1 mutations with neuron disease.

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  • 2016-12

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Quantifying Solvent Kinetics in Molecular Dynamics Simulations of Biomolecules

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The relation between water and protein physics is a topic of much interest. Molecular dynamics (MD) simulations of biomolecules are a common computational technique to obtain atomistic insight into the

The relation between water and protein physics is a topic of much interest. Molecular dynamics (MD) simulations of biomolecules are a common computational technique to obtain atomistic insight into the physical behavior of biomolecules, including the nature of the interaction between water and the protein. In order to model biomolecules at the highest level of accuracy, an explicit, atomistic representation of the water is typically necessary. The number of water molecules that need to be simulated is normally on the order of thousands. The high dimensional MD dataset is then expanded with considerably more dimensions. We describe here a set of tools which can be used to extract general features of the water behavior, which can then be utilized to build simplified models of the water kinetics which make quantitative predictions, such as the flux rate through a pore.

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  • 2015-12

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Protein-mediated Synthesis of Gold Nanoparticles

Description

Gold nanoparticles are valuable for their distinct properties and nanotechnology applications. Because their properties are controlled in part by nanoparticle size, manipulation of synthesis method is vital, since the chosen

Gold nanoparticles are valuable for their distinct properties and nanotechnology applications. Because their properties are controlled in part by nanoparticle size, manipulation of synthesis method is vital, since the chosen synthesis method has a significant effect on nanoparticle size. By aiding mediating synthesis with proteins, unique nanoparticle structures can form, which open new possibilities for potential applications. Furthermore, protein-mediated synthesis favors conditions that are more environmentally and biologically friendly than traditional synthesis methods. Thus far, gold particles have been synthesized through mediation with jack bean urease (JBU) and para mercaptobenzoic acid (p-MBA). Nanoparticles synthesized with JBU were 80-90nm diameter in size, while those mediated by p-MBA were revealed by TEM to have a size between 1-3 nm, which was consistent with the expectation based on the black-red color of solution. Future trials will feature replacement of p-MBA by amino acids of similar structure, followed by peptides containing similarly structured amino acids.

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  • 2018-05

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An evaluation of the ecological and human health factors in protein source decisions

Description

Protein is an essential macronutrient in the human diet, but the source of this protein has both human health and environmental impacts. Health complications can result from protein deficiency, but

Protein is an essential macronutrient in the human diet, but the source of this protein has both human health and environmental impacts. Health complications can result from protein deficiency, but the practices by which protein sources are raised, grown, or harvested have environmental consequences, potentially reducing biodiversity, essential habitat, and crucial stocks of natural resources. Terrestrial cultivation encroaches on natural habitats and consumes resources inefficiently, while overfishing has greatly depleted wild fishery stocks. These environmental factors, along with concerns about nutrients, contaminants and the ethics of animal protein has led to confusion about weighing the risks and benefits associated with alternative sources of protein. Providing consumers \u2014 and policy makers \u2014 with a comprehensive account of major protein sources and their impacts in an understandable form is crucial to reducing environmental degradation and improving human health. Here I provide a general framework to compare the health and environmental impacts of livestock, seafood, and plant protein, and illustrate the application of this framework with case studies for each of these categories.

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  • 2014-05

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Nutritional Factors Influencing Canine Food Preferences

Description

Dogs' health and wellbeing is of great importance to their owners. The most common nutritional problem for pet dogs is obesity, with 22-40% of pet dogs being classified as overweight

Dogs' health and wellbeing is of great importance to their owners. The most common nutritional problem for pet dogs is obesity, with 22-40% of pet dogs being classified as overweight or obese. With many adverse health effects associated with obesity, this is a major concern for owners and veterinarians. The degree to which dogs enjoy consuming certain foods can have substantial implications for their body weight, so it is important to understand which aspects of foods make them appealing to dogs. This study aimed to determine whether nutritional aspects of commercial dog foods predict dogs' preferences for those foods. It was found that consumption preference is positively correlated with protein content (p < .001), therefore implying that the protein content of commercial dry dog foods may predict dogs' consumption preferences. Consumption preferences were not predicted by other available measures of food content or caloric value. Dogs' preference for foods high in protein content may be due to the satiating effect of protein. Since foods high in protein both reduce the amount of energy consumed and are found to be palatable to dogs, high-protein dog foods may offer a way for dog food manufacturers, veterinarians, and pet owners to combat obesity in pet dogs.

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  • 2016-05

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Characterization of Designed Ankyrin Repeat Proteins for Neurodegenerative Disease Diagnostics

Description

The following paper discusses the potential for Designed Ankyrin Repeat Proteins (DARPin) use as a diagnostic tool for neurodegenerative diseases in particular Alzheimer's disease (AD) and Parkinson's disease (PD). The

The following paper discusses the potential for Designed Ankyrin Repeat Proteins (DARPin) use as a diagnostic tool for neurodegenerative diseases in particular Alzheimer's disease (AD) and Parkinson's disease (PD). The two structures investigated for AD and PD were ADC7 and PDC1. Plasmid transformation was performed in order to grow the DARPin in E. coli for simple expression. Following growth and purification the proteins were validated using SDS-PAGE, Western Blot, BCA and indirect sandwich ELISA using transgenic mouse brain tissue. Targeted functionality of the DARPin structure was utilized during characterization methods to ensure the efficacy of the protein as a diagnostic for the respective disease targets. Both the ADC7 and PDC1 demonstrated improved binding with transgenic mice compared to wild type with a maximum 1.8 and 1.7 relative ratio, respectively. Additionally, both of the proteins demonstrated exclusive binding to their disease target and did not provide false positive results.

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  • 2016-12

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CO2 Reduction via Functionalized Protein/Organometallic Complexes

Description

As prices for fuel along with the demand for renewable resources grow, it becomes of paramount importance to develop new ways of obtaining the energy needed to carry out the

As prices for fuel along with the demand for renewable resources grow, it becomes of paramount importance to develop new ways of obtaining the energy needed to carry out the tasks we face daily. Costs of production due to energy and time constraints impose severe limitations on what is viable. Biological systems, on the other hand, are innately efficient both in terms of time and energy by handling tasks at the molecular level. Utilizing this efficiency is at the core of this research. Proper manipulation of even common proteins can render complexes functionalized for specific tasks. In this case, the coupling of a rhenium-based organometallic ligand to a modified myoglobin containing a zinc porphyrin, allow for efficient reduction of carbon dioxide, resulting in energy that can be harnessed and byproducts which can be used for further processing. Additionally, a rhenium based ligand functionalized via biotin is tested in conjunction with streptavidin and ruthenium-bipyridine.

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  • 2014-12