Biochemistry Commons^™

Investigations Of The Structure-Function Relationship In Kainate Receptors Using FöRster Resonance Energy Transfer, Douglas Litwin

Dissertations and Theses (Open Access)

Kainate receptors belong to the family of ion channels known as the ionotropic glutamate receptors. Ionotropic glutamate receptors mediate the majority of excitatory synaptic transmission, modulate the release of presynaptic glutamate, and facilitate dendrite formation. Kainate receptors are unique among the ionotropic glutamate receptors in being modulated by sodium ions. They have also been implicated in the development of higher learning and epilepsy. In recent years a wealth of structural data has become available for the AMPA and NMDA classes; however, the structural characterization of kainate receptors has been limited. The work in this dissertation utilizes luminescence resonance energy transfer …

Investigation Of The Molecular Determinants And Extrinsic Factors That Regulate Prmt Product Specificity, Tamar B. Cáceres

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein arginine methylation is an important modification of proteins, involved in many cellular processes. Some examples are transcription, RNA editing, cellular communication, DNA repair, viral replication and chromatin remodeling. In recent years, the significance of protein arginine methyltransferases (PRMTs) in human diseases has been increasingly studied, especially in cardiovascular disease and cancer. Although the importance of these enzymes is recognized, the understanding of how exactly PRMTs function is still limited. Very little information is available to explain how or why any of the different PRMTs interact with other proteins or, what determines where in that protein to place their methyl …

A Universal Mechanism For N2 Binding To And Differing Reactivity Of The E4(4h) State Of Mo-, V-, And Fe-Nitrogenases, Derek Franklin Harris

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As a basic building block in many biological molecules, the element nitrogen (N) is essential for life. Dinitrogen (N₂) is abundant in Earth’s atmosphere, but this form is biologically unavailable. To be biologically available, N₂ must undergo a reduction reaction to the fixed form, ammonia (NH₃). The industrial Haber-Bosch process, which accounts for approximately 50% of the worlds fixed nitrogen, uses energy from fossil fuels to achieve high pressures and temperatures to catalyze the reaction. The energy used by Haber-Bosch accounts for approximately 2% of the world’s annual supply. The remainder of fixed nitrogen is …

Investigation Of Protein Dynamics And Communication In Adomet-Dependent Methyltransferases: Non-Ribosomal Peptide Synthetase And Protein Arginine Methyltransferase, Kyle M. May

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

For many enzymes to function correctly they must have the freedom to display a level of dynamics or communication during their catalytic cycle. The effects that protein dynamics and communication can have are wide ranging, from changes in substrate specificity or product profiles, to speed of reaction or switching activity on or off. This project investigates the protein dynamics and communication in two separate systems, a non-ribosomal peptide synthetase (NRPS), and a protein arginine methyltransferase (PRMT).

PRMT1, the enzyme responsible for 80% of arginine methylation in humans, has been implicated in a variety of disease states when functioning incorrectly. For …

Biophysical And Structural Characterization Of Shigella Atpase Spa47 Oligomerization Provides Insight Into Type Three Secretion System Activation And Virulence, Jamie L. Burgess

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Several bacterial pathogens including Shigella (shigellosis), Escherichia coli (urinary tract infections), Pseudomonas (lung infections), Salmonella (food poisoning), and Yersinia (plague) critically rely on a complex type three secretion system (T3SS) for infection. With the rise in multi-antibiotic resistant strains of several of these pathogens, we turn to the T3SS as a promising target for the development of novel therapeutics. The Dickenson lab at Utah State University has been the first to identify and characterize the ATPase Spa47, the energy source of the Shigella infection system. We show that Spa47 is necessary for proper T3SS formation and function, being ultimately responsible …

Hybrid Fusion Protein For Inhibition Of Multiple Proteases For Chronic Wound Healing, Graham L. Strauss

USF Tampa Graduate Theses and Dissertations

Many diseases display a multitude of relevant factors that contribute to the persistence of the disease and difficulty treating it. The multifactorial characteristics of some diseases lead to the requirement of combination of treatments in order to restore health. The latter may necessitate the mixing of treatments, medications, and therapeutics to first halt the disease, then assist the human body in returning itself to a state of normality. For example, chronic wounds exhibit this multifactor characteristic in which there exist many factors that lead to the body’s inability to properly heal in a timely manner. This presents a further threat …

Reduced Alphabet Of Prebiotic Amino Acids Optimally Encodes The Conformational Space Of Diverse Extant Protein Folds, Armando D. Solis

Publications and Research

Background

There is wide agreement that only a subset of the twenty standard amino acids existed prebiotically in sufficient concentrations to form functional polypeptides. We ask how this subset, postulated as {A,D,E,G,I,L,P,S,T,V}, could have formed structures stable enough to found metabolic pathways. Inspired by alphabet reduction experiments, we undertook a computational analysis to measure the structural coding behavior of sequences simplified by reduced alphabets. We sought to discern characteristics of the prebiotic set that would endow it with unique properties relevant to structure, stability, and folding.

Results

Drawing on a large dataset of single-domain proteins, we employed an information-theoretic measure …

Substituted Anthraquinones Represent A Potential Scaffold For Dna Methyltransferase 1-Specific Inhibitors, Rebecca L. Switzer, Jessica Medrano, David A. Reedel, Jill Weiss

Faculty Journal Articles

In humans, the most common epigenetic DNA modification is methylation of the 5-carbon of cytosines, predominantly in CpG dinucleotides. DNA methylation is an important epigenetic mark associated with gene repression. Disruption of the normal DNA methylation pattern is known to play a role in the initiation and progression of many cancers. DNA methyltransferase 1 (DNMT1), the most abundant DNA methyltransferase in humans, is primarily responsible for maintenance of the DNA methylation pattern and is considered an important cancer drug target. Recently, laccaic acid A (LCA), a highly substituted anthraquinone natural product, was identified as a direct, DNA-competitive inhibitor of DNMT1. …

Lignin Biopolymers In The Age Of Controlled Polymerization, Mitra S. Ganewatta, Hasala N. Lokupitiya, Chuanbing Tang

Faculty Publications

Polymers made from natural biomass are gaining interest due to the rising environmental concerns and depletion of petrochemical resources. Lignin isolated from lignocellulosic biomass is the second most abundant natural polymer next to cellulose. The paper pulp process produces industrial lignin as a byproduct that is mostly used for energy and has less significant utility in materials applications. High abundance, rich chemical functionalities, CO2 neutrality, reinforcing properties, antioxidant and UV blocking abilities, as well as environmental friendliness, make lignin an interesting substrate for materials and chemical development. However, poor processability, low reactivity, and intrinsic structural heterogeneity limit lignins′ polymeric applications …

Translational Control Of Antibiotic Resistance, Anne Witzky, Rodney Tollerson Ii, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Many antibiotics available in the clinic today directly inhibit bacterial translation. Despite the past success of such drugs, their efficacy is diminishing with the spread of antibiotic resistance. Through the use of ribosomal modifications, ribosomal protection proteins, translation elongation factors and mistranslation, many pathogens are able to establish resistance to common therapeutics. However, current efforts in drug discovery are focused on overcoming these obstacles through the modification or discovery of new treatment options. Here, we provide an overview for common mechanisms of resistance to translation-targeting drugs and summarize several important breakthroughs in recent drug development.

Electron Transfer Activity Of Mitochondria Neet-Proteins, Yiming Wang

LSU Doctoral Dissertations

Mitochondrial NEET proteins are recently discovered iron-sulfur proteins that are localized within mitochondria. There are three NEET proteins: mitoNEET, a type II diabetes drug pioglitazone binding target, a mitoNEET related protein 1 (Miner1 or NAF-1), and a mitoNEET-related protein 2 (Miner2). While both mitoNEET and Miner1 are mitochondrial outer membrane proteins, Miner2 is a mitochondrial matrix protein. All three NEET proteins bind at least one [2Fe-2S] cluster via CDGSH (Cys-Asp-Gly-Ser-His) motif. In this work, we have investigated the electron transfer activity of mitoNEET, and found that the CDGSH-type [2Fe-2S] clusters of mitoNEET can be reduced by the reduced flavin mononucleotide …

A Small Rna And Dna Binding Protein Contribute To Biofilm Development In Bartonella Henselae, Udoka Okaro

USF Tampa Graduate Theses and Dissertations

A biofilm, which is associated with 80% of chronic infections in humans, is formed when bacteria aggregate, attach to a substrate and secrete a matrix protecting the bacteria from host cell defenses and antibiotics. Bartonella henselae (B. henselae) is the causative agent of cat scratch disease, persistent bacteremia, and one of the most frequently reported causes of blood-culture negative endocarditis (BCNE) in patients. The ability of B. henselae to adhere to the heart valve, form a biofilm and vegetation to cause endocarditis increases the morbidity and mortality rate in infected patients. The presence of a trimeric autotransporter adhesin (TAA) called …

Organic Chemistry With A Biological Emphasis Volume Ii, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for …

Organic Chemistry With A Biological Emphasis Volume I, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for …

3d Printed Microfluidic Devices For Bioanalysis, Michael J. Beauchamp

Theses and Dissertations

This work presents the development of 3D printed microfluidic devices and their application to microchip analysis. Initial work was focused on the development of the printer resin as well as the development of the general rules for resolution that can be achieved with stereolithographic 3D printing. The next stage of this work involved the characterization of the printer with a variety of interior and exterior resolution features. I found that the minimum positive and negative feature sizes were about 20 μm in either case. Additionally, micropillar arrays were printed with pillar diameters as small as 16 μm. To demonstrate one …

Dna Capture Via Magnetic Beads In A Microfluidic Platformfor Rapid Detection Of Antibiotic Resistance Genes, David Hyrum Harris

Theses and Dissertations

Antibiotic resistant infections are a growing health care concern, with many cases reported annually. Infections can cause irreversible bodily damage or death if they are not diagnosed in a timely matter. To rapidly diagnose antibiotic resistance in infections, it is important to be able to capture and isolate the DNA coding for the resistance genes. This is challenging because bacteria are present in blood in minute concentrations. To enrich the DNA to detectable levels, I modified magnetic microbeads with ssDNA sequences complementary to the target DNA to capture the DNA via hybridization. I compared DNA capture efficiency in three different …

Tracing Nutrient Sources To Lipid Production In Insects Using Stable Isotope (Δ13c, Δ2h) Tracers: Implications For Nutritional Physiology Of Migratory Species., Libesha Anparasan, Keith A. Hobson

Western Research Forum

Using stable isotope measurements of insect tissues to determine origin and migratory patterns is well established. However, isotopically determining nutritional origins of lipids, the primary fuel of migration, has not been as thoroughly researched. We explored isotopic links between diet and stored lipids in laboratory raised True armyworm moths (Mythimna unipuncta) using δ¹³C and δ²H measurements. Pupae were randomly separated into four groups (n=20) and fed isotopically distinct nectar, each consisting of a combination of high δ¹³C (C4 sugar), or low δ¹³C (C3 sugar) carbohydrate, with high δ²H (deuterium spiked), …

The Wet Bridge Transfer System: An Novel In Vitro Tool For Assessing Exogenous Surfactant As A Pulmonary Drug Delivery Vehicle, Brandon J. Baer

Western Research Forum

Background:

Due to its complex branching structure, direct drug delivery to the remote areas of the lung is a major challenge. Consequently, most therapies, such as those treating pulmonary infection and inflammation, must utilize large systemic dosing, with the potential for adverse side effects. A novel alternative strategy is to use exogenous surfactant, a material capable of distributing throughout the lung, as a pulmonary drug delivery vehicle.

Objective:

Utilize an in vitro transferring system to assess exogenous surfactant (BLES) as a pulmonary delivery vehicle for different therapeutics.

Methods:

An in vitro technique was developed to simultaneously study surfactant delivery and …

Iron-Sulfur Cluster Biosynthesis In Methanogens, Cuiping Zhao

LSU Doctoral Dissertations

Methanogens live in a syntrophic consortium with bacteria, taking advantage of the metabolic abilities of their syntrophic partners to overcome energetic barriers and break down compounds that they cannot digest by themselves. Interspecies electron transfer, which is a major type of microbial communication in syntrophic processes, improves methanogenesis and anaerobic oxidization of methane (AOM) processes involved in syntrophic consortia. These processes have a significant impact on the global carbon cycle. Most of the essential enzymes involved in methanogenesis are iron-sulfur proteins. Iron-sulfur clusters are one of the oldest and most versatile cofactors present in all domains of life. To date, …

Nepal Ambient Monitoring And Source Testing Experiment (Namaste): Emissions Of Particulate Matter And Sulfur Dioxide From Vehicles And Brick Kilns And Their Impacts On Air Quality In The Kathmandu Valley, Nepal, Min Zhong, Eri Saikawa, Alexander Avramov, Chen Chen, Boya Sun, Wenlu Ye, William C. Keene, Robert J. Yokelson, Thilina Jayarathne, Elizabeth A. Stone, Maheswar Rupakheti, Arnico K. Panday

Chemistry and Biochemistry Faculty Publications

Air pollution is one of the most pressing environmental issues in the Kathmandu Valley, where the capital city of Nepal is located. We estimated emissions from two of the major source types in the valley (vehicles and brick kilns) and analyzed the corresponding impacts on regional air quality. First, we estimated the on-road vehicle emissions in the valley using the International Vehicle Emissions (IVE) model with local emissions factors and the latest available data for vehicle registration. We also identified the locations of the brick kilns in the Kathmandu Valley and developed an emissions inventory for these kilns using emissions …