Biochemistry, Biophysics, and Structural Biology Commons^™

Prep-Hplc Method Development To Isolate Potentially-Carcinogenic, Arginine-Based Heterocyclic Amines, Victoria S. Kim

Honors Theses

Heterocyclic amines (HCAs) are carcinogenic molecules generated from the reaction of creatin(in)e and amino acids at high cooking temperatures in meat. Previous research has shown that replacing creatine with arginine leads to new, uncharacterized HCA molecules. This research entails implementing and optimizing the preparative HPLC analysis of extracts from multiple burnings of arginine with phenylalanine. Isolated fractions from the prep-HPLC analysis were further analyzed using the Ames test to identify mutagenic compounds. Prep-HPLC provides quality control to the burning process along with isolation of larger quantities of materials for further characterization and molecular structure identification.

Design And Synthesis Of Analogs Of Myo-Inositol, Serine, And Cysteine To Enable Chemical Biology Studies, Tanei J. Ricks

Doctoral Dissertations

Phosphorylated myo-inositol compounds including inositol phosphates (InsPs) as well as the phosphatidylinositol polyphosphate lipids (PIP_ns) are critical biomolecules that regulate many of the most important biological processes and pathways. They are aberrant in many disease states due to their regulatory function. The same is true of the phospholipid phosphatidylserine (PS) which can serve as a marker to begin apoptosis. However, the full scope of activities of these structures is not clear, particularly since techniques that enable global detection and analysis of the production of these compounds spatially and temporally are lacking. With all of these obstacles in …

Water Chemistry Dynamics In Four Vernal Pools In Maine, Usa, Lydia H. Kifner

Electronic Theses and Dissertations

Vernal pools are small seasonal wetlands that are a common landscape feature that contribute to biodiversity in northeastern North American forests. However, even basic information about their biogeochemical functions, such as carbon cycling, is limited. Dissolved gas concentrations (CH₄, CO₂) and other water chemistry parameters were monitored weekly at the bottom and surface of four vernal pools in central and eastern Maine, USA, from April to August 2016. The vernal pools were supersaturated with respect to CH₄ and CO₂ at all sampling dates and locations. Concentrations of dissolved CH₄ and CO₂ ranged …

Capacity Of Human Immunodeficiency Virus Targeting Chimeric Antigen Receptor T Cells To Eliminate Follicular Dendritic Cells Bearing Human Immunodeficiency Virus Immune Complexes, Matthew T. Ollerton

Theses and Dissertations

An important obstacle to a functional cure for HIV/AIDS is the persistence of viral reservoirs found throughout the body in various cells and tissues. Reservoirs can be latently infected cells, or in the case of follicular dendritic cells (FDC), non-infected cells that trap infectious virus on their surface through immune complexes (HIV-IC). Although several strategies have been employed to target and eliminate viral reservoirs, they are short-lived and ineffective. In an attempt to provide a long-term approach, chimeric antigen receptor T (CAR-T) cells were designed to eliminate native HIV on FDCs. Although effective at eliminating HIV-infected cells, and halting spreading …

Detection Of Survival And Proliferation Of Sulfate Reducers Under Simulated Martian Atmospheric And Soil Conditions, Sergio Mosquera Mora

Graduate Theses and Dissertations

Numerous studies have tried to determine the survivability and proliferation of microorganisms under simulated Martian conditions. Furthermore, most of them have been focused on the ability of these microbes to cope with high brines’ salt (NaCl) concentrations inherent of the Martian surface. However, there are not studies related to the ability of bacteria to survive on subsurface environments that have increasing concentrations of sulfate compounds. For this research, a group of microorganisms known as sulfate-reducing bacteria or simply sulfate reducers were chosen due to their ability to use sulfate compounds as terminal electron acceptors to produce metabolic energy, their tolerance …

Nbpmf: Novel Network-Based Inference Methods For Peptide Mass Fingerprinting, Zhewei Liang

Electronic Thesis and Dissertation Repository

Proteins are large, complex molecules that perform a vast array of functions in every living cell. A proteome is a set of proteins produced in an organism, and proteomics is the large-scale study of proteomes. Several high-throughput technologies have been developed in proteomics, where the most commonly applied are mass spectrometry (MS) based approaches. MS is an analytical technique for determining the composition of a sample. Recently it has become a primary tool for protein identification, quantification, and post translational modification (PTM) characterization in proteomics research. There are usually two different ways to identify proteins: top-down and bottom-up. Top-down approaches …

Design And Synthesis Of Cpg-Lytic Peptide Conjugate, Brachytherapy Beads And A Combinatorial Library Of Primary Amines Used As Potential Therapeutics In The Treatment Of Cancers, Josanne-Dee Woodroffe

USF Tampa Graduate Theses and Dissertations

Cancer remains one of the most feared diseases affecting the modern world. Second to heart disease, it is the largest cause of deaths, affecting one in three persons. Cancer cells are formed when normal, healthy cells become damage, losing their normal regulatory mechanism that control cell growth. There are many different types and progression of these cancer cells that determine the type of treatment a patient receives. The primary focus of this dissertation is to propose three studies of anticancer agents. In Chapter one, a CpG-lytic peptide conjugate was designed to target receptors on the cell membrane to concentrate the …

Thermodynamic And Kinetic Aspects Of Hen Egg White Lysozyme Amyloid Assembly, Tatiana Miti

USF Tampa Graduate Theses and Dissertations

Deposition of protein fibers with a characteristic cross-β sheet structure is the molecular marker associated with human disorders ranging from Alzheimer's disease to type II diabetes and spongiform encephalopathy. Given the large number of non-disease related proteins and peptides that have been shown to form amyloid fibrils in vitro, it has been suggested that amyloid fibril formation represents a generic protein phase transition. In the last two decades it has become clear that the same protein/peptide can assemble into distinct morphologically and structurally amyloid aggregates depending on the solution conditions. Moreover, recent studies have shown that the early stage, oligomeric …

Kinetic Characterization Of Listeria Monocytogenes 2-C- Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase ( Cms ) Enzymes Using High Performance Liquid Chromatography ( Hplc ), Mark Oblazny

Theses and Dissertations

Infectious diseases, with increasing prevalence of antibiotic resistant bacteria, coupled with the declining rate in discovery of antimicrobial agents, impose one of the most significant threats to human health. Here we identify 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (CMS) as a valid target for antibiotic development which is an enzyme in pathogenic organisms that leads to the biosynthesis of isoprene precursor molecules. Isoprene molecules are one of nature’s most common building blocks that are vital to many biological metabolic processes and are synthesized via the mevalonic acid dependent (MVA), or methylerythritol phosphate (MEP) pathway. Vertebrates utilize the MVA pathway, while many pathogenic bacteria …

The Biochemical Assessment Of Two Secreted Acid Phosphatases From Leishmania Tarentolae, Their Response To Electric Fields, Glycosidase Incubation, And / Or Vanadium, Benjamin M. Dorsey

Theses and Dissertations

Leishmaniasis, as defined by the Center for Disease Control and Prevention, is a neglected tropical disease with 1.6 million new cases reported each year. However, there is yet to be safe, effective, and affordable treatments provided to those affected by this disease1. Still underappreciated as a potential pharmaceutical targets, especially for cutaneous leishmaniasis infections, are the two isozymes of secreted acid phosphatase (SAP); secreted acid phosphatase 1 (SAP1) and secreted acid phosphatase 2 (SAP2). These enzymes are involved in the survival of the parasite in the sand fly vector, and the prevention of host macrophages from forming parasitophorous vacuole and …

2-D Electrophoresis Modeling Of Multienzyme Cutting Of Polypeptides, Howard Mayes

Theses

2-Dimensional Electrophoresis is one of the tools in the identification of proteins by molecular weight and pH. The display of molecular weight allows the researcher to quickly identify whether a specific protein or peptide string is in the sample. The pH measurement allows even better resolution between different species in the sample. The MultiEnzyme ElectroPhoresis (MEEP) program tries to model that by providing a graph that displays separated protein strings by both molecular weight and pH. The ability to cleave the protein with 43 different enzyme variations allows the researcher to analyze appropriate enzymes to isolate a protein subsequence before …

Marine Reserves Promote Coral Reef Resilience By Mitigating Human Impacts Through The Restoration Of Parrotfish Populations, Increasing Their Reproductive Output And Seeding Neighboring Overfished Reefs, Brian L. Stockwell

Biological Sciences Theses & Dissertations

Coral reefs are some of the most productive ecosystems on the planet, providing fisheries resources for over a billion people with billions of dollars in revenue from tourism for developing nations. Coral reefs are under threat from overfishing and water pollution, resulting in less productive algae dominated reefs. Marine reserves are widely expected to promote the resilience of reefs by protecting and increasing the abundance of herbivorous fishes that can graze on algae, therefore directly or indirectly preventing coral to algal phase shifts. However, the ability of marine reserves to mitigate human impacts, restore herbivorous fish populations and seed nearby …

Computational Investigation Of The Pore Formation Mechanism Of Beta-Hairpin Antimicrobial Peptides, Richard Lipkin

Dissertations, Theses, and Capstone Projects

β-hairpin antimicrobial peptides (AMPs) are small, usually cationic peptides that provide innate biological defenses against multiple agents. They have been proposed as the basis for novel antibiotics, but their pore formation has not been directly observed on a molecular level. We review previous computational studies of peptide-induced membrane pore formation and report several new molecular dynamics simulations of β-hairpin AMPs to elucidate their pore formation mechanism. We simulated β-barrels of various AMPs in anionic implicit membranes, finding that most of the AMPs’ β-barrels were not as stable as those of protegrin. We also performed an optimization study of protegrin β-barrels …

Sequence Determinants Of The Individual And Collective Behaviour Of Intrinsically Disordered Proteins, Alexander S. Holehouse

Arts & Sciences Electronic Theses and Dissertations

Intrinsically disordered proteins and protein regions (IDPs) represent around thirty percent of the eukaryotic proteome. IDPs do not fold into a set three dimensional structure, but instead exist in an ensemble of inter-converting states. Despite being disordered, IDPs are decidedly not random; well-defined - albeit transient - local and long-range interactions give rise to an ensemble with distinct statistical biases over many length-scales. Among a variety of cellular roles, IDPs drive and modulate the formation of phase separated intracellular condensates, non-stoichiometric assemblies of protein and nucleic acid that serve many functions. In this work, we have explored how the amino …

Effects Of Nucleosome Structure On Dna Photoproduct Formation And Deamination, Kesai Wang

Arts & Sciences Electronic Theses and Dissertations

Cyclobutane pyrimidine dimers (CPDs) are DNA photoproducts linked to skin cancer, whose mutagenicity depends in part on their frequency of formation and deamination. Nucleosomes modulate CPD formation, favoring outside facing sites, and disfavoring inward facing sites. A similar pattern of CPD formation in protein-free DNA loops suggest that DNA bending causes the modulation of photoproduct formation in nucleosomes. To systematically study the cause and effect of nucleosome structure on CPD formation and deamination, we had developed a circular permutation synthesis strategy for positioning a target sequence at different superhelix locations (SHLs) across a nucleosome in which the DNA has been …

Determining The Molecular Mechanisms Of Huntington’S Disease Through Multi-Scale Modeling, Kiersten Ruff

Arts & Sciences Electronic Theses and Dissertations

Huntington’s disease (HD) is associated with a mutational CAG repeat expansion within exon 1 of the huntingtin (Htt) gene. Post-transcriptional processing leads to the generation of N-terminal Htt protein fragments (Htt-NTFs), including those that encompass exon 1 (Httex1). Within Httex1, the CAG-repeat encoded polyglutamine (polyQ) tract is flanked N-terminally by a 17-residue amphipathic stretch (N17) and C-terminally by a 50-residue proline rich (PR) domain. Htt-NTFs, including Httex1, are among the smallest fragments that recapitulate HD pathology in mouse models. However, the direct link between Htt-NTFs with polyQ expansions and neurodegeneration that leads to HD remains unresolved. Despite being a monogenic …

Mass Spectrometry-Based Structural Proteomics: Methodology And Application Of Fast Photochemical Oxidation Of Proteins (Fpop), Ben Niu

Arts & Sciences Electronic Theses and Dissertations

The dissertation will be solely focused on using mass spectrometry to characterize protein high order structures (HOS), it emphasizes the use of hydroxyl radical footprinting (FPOP) coupled to bottom-up MS approach. A detailed background information about FPOP, and the corresponding method developments as well as applications will be covered.

The first chapter will be a comprehensive review regarding the FPOP. Following this, chapter 2, 3, and 4 will be focused on the method developments. Chapter 2 describes an isotope dilution GC-MS method to quantitate OH radicals in FPOP; chapter 3 describes the incorporation of Leu-enkephalin as reporter peptide for a …

Machine Learning Based Protein Sequence To (Un)Structure Mapping And Interaction Prediction, Sumaiya Iqbal

University of New Orleans Theses and Dissertations

Proteins are the fundamental macromolecules within a cell that carry out most of the biological functions. The computational study of protein structure and its functions, using machine learning and data analytics, is elemental in advancing the life-science research due to the fast-growing biological data and the extensive complexities involved in their analyses towards discovering meaningful insights. Mapping of protein’s primary sequence is not only limited to its structure, we extend that to its disordered component known as Intrinsically Disordered Proteins or Regions in proteins (IDPs/IDRs), and hence the involved dynamics, which help us explain complex interaction within a cell that …

A Novel Method For Synthesis Of Hydroxytyrosol, Emmanuel Onobun

Electronic Theses and Dissertations

Hydroxytyrosol, 3,4-dihydroxyphenolethanol, a naturally occurring polyphenol most common in olive tree (Olea europaea), is one of the most effective member of the polyphenols family, because of its remarkable antioxidant activity, its ability to inhibit oxidation of low density lipids (LDL), and its protection against DNA oxidative damage. Hydroxytyrosol, which is widely used in cosmetics and food supplements industries, can be purchased as an olive oil extract that contains low concentration of hydroxytyrosol besides other polyphenols. The price and low natural abundance of hydroxytyrosol make alternative synthetic sources very attractive. In this research, a novel method for the synthesis of pure …

Interaction With Nitric Oxide Of The Nitrosomonas Europaea Tetraheme Protein Cytochrome C554, And Two Of Its Variants, In Increasingly Reducing Environments, Jennifer M. Mcgarry

Theses and Dissertations

A re-investigation of the interaction with NO of the small tetraheme protein cytochrome c554 (C554) from Nitrosomonas europaea has shown that the 5-coordinate heme II of the 2-electron or 4-electron reduced protein will nitrosylate reversibly. The nitrosylation process was found to be first order in C554, first-order in NO, and second-order overall. The rate constant for NO binding to the heme was determined to be 3000 ± 140 M-1s-1, while the rate constant for dissociation was 0.034 ± 0.009 s-1; the degree of protein reduction does not appear to significantly influence the nitrosylation rate. In contrast to a previous report, …

Part – I: Development Of A Two-Step Regiospecific Synthetic Route For Multigram Scale Synthesis Of Β-Carboline Analogs For Studies In Primates As Anti-Alcohol Agents,Part – Ii: Design And Synthesis Of Novel Antimicrobials For The Treatment Of Drug Resistant Bacterial Infections Part – Iii: A Novel Synthetic Method For The Synthesis Of The Key Quinine Metabolite (3s)-3-Hydroxyquinine, Veera Venkata Naga Phani Babu Tiruveedhula

Theses and Dissertations

PART – I

Development of a Two-Step Regiospecifc Synthetic Route for Multigram-Scale Synthesis of β-Carboline Analogs for Studies in Primates as Anti-Alcohol Agents

β-Carboline and their derivatives are important structural motifs in synthetic organic and medicinal chemistry because of their novel biological activity, especially in regard to the reduction of alcohol self-administration [binge drinking (BD)], a major problem increasing day by day in modern society. This anti-alcohol effect is proposed to be due to the activity of ligands at the benzodiazepine site of the GABAA receptor in the central nervous system acting as antagonists at the α1 subunit. The past …

Biomedical Applications Of Mid-Infrared Spectroscopic Imaging And Multivariate Data Analysis: Contribution To The Understanding Of Diabetes Pathogenesis, Ebrahim Aboualizadeh

Theses and Dissertations

Diabetic retinopathy (DR) is a microvascular complication of diabetes and a leading cause of adult vision loss. Although a great deal of progress has been made in ophthalmological examinations and clinical approaches to detect the signs of retinopathy in patients with diabetes, there still remain outstanding questions regarding the molecular and biochemical changes involved. To discover the biochemical mechanisms underlying the development and progression of changes in the retina as a result of diabetes, a more comprehensive understanding of the bio-molecular processes, in individual retinal cells subjected to hyperglycemia, is required. Animal models provide a suitable resource for temporal detection …

Crispr/Cas9 In Leishmania Genome Editing : Towards A Proof Of Concept, Zein Kasbo

Theses, Dissertations and Culminating Projects

Leishmaniasis is a parasitic Neglected Tropical Disease (NTD) that affects mostly poor countries of the third word due to their limited access to clean water and health care. The disease is transmitted through the bite of a sand fly of the genus Phlebotomus in the Old World, and of the genus Lutzomyia in the New World. Historically, NTDs have not been given adequate attention or research funding and finding curative treatments has been slow. However, the fact that the insect vector and the parasite can live and thrive in any ecological system in the world, and under the current circumstances …

A Numerical Study Of The Interaction Between One Dimensional Carbyne Chain And Single Stranded Dna, Zeina Salman

Graduate Theses and Dissertations

resolution at the single nucleotide level when developing DNA sequencers. The purpose of this research was to numerically study the electrical properties associated with the interaction between 1D carbon chain, known as carbyne, and ssDNA. First, the electrical properties of the carbyne chain were calculated. Second, the electrical properties of the carbyne chain were calculated in the presence of different ssDNA bases. Analyzing the differences between the two cases led to determining the effects of these different bases on the electrical properties. The numerical simulation approach conducted in this research was based on the first-principle simulation. The first-principle simulation was …

Functionalization Of Indium-Based Quantum Dots For Use As A Non-Viral Gene Therapy Vector, Nicholas A. Mundt

MSU Graduate Theses

This work aims to develop functionalized, water-soluble indium-based quantum dots (QDs) as a non-viral gene therapy vector. The QDs were solubilized in water by exchanging native hydrophobic surface ligands with 11-mercaptoundecanioc acid (MUA); an amphiphilic ligand providing terminal carboxylate groups that impart water solubility to the QDs. The aqueous QDs were then functionalized with a terminal tertiary amine to impart a positive surface charge, allowing negatively-charged DNA to complex with the nanoparticles. The QDs were characterized via electrophoresis to determine their ability to bind DNA. Results show that further work is needed to optimize DNA binding. In addition, this work …

Mechanistic Studies Of Peptide-Mediated Protein Transport Across Droplet-Interface Bilayers, Jing Huang

Doctoral Dissertations

Pep-1 is a promising peptide tool that delivers proteins and peptides into cells with conserved bioactivity. Pep-1 has great potential because of the high efficiency and lack of toxicity. The mechanism of Pep-1-mediated transport is not fully understood. In my thesis, droplet-interface bilayer (DIB) has been used for the mechanistic studies of Pep-1. Here, DIB is developed for different functions such as quantitation of protein translocation, solution exchange to a formed bilayer and simultaneous observation of multiple membranes. Research work on Pep-1 with DIB reveals that the negative charge of the inner membrane leaflet plays a significant role in promoting …

Relationship Between Structure And Function In Nickel Proteins And Enzymes, Carolyn Carr

Doctoral Dissertations

Nickel is a rarely used but biologically important metal that is utilized in all three domains of life. In nickel utilizing organisms there is a corresponding trafficking system specifically designed to capture nickel, deliver, and export excess nickel to prevent toxic effects. It is critical to understand the mechanisms by which organisms achieve metal selectivity to duplicate or disrupt this process for the benefit of human health and to further understanding of regulation mechanisms in biology. RcnR is a Ni(II) and Co(II) responsive transcriptional regulator in E. coli. The research reported in this dissertation focuses on the relationship between …

Vitreous Gel Physics, Svetlana Morozova

Doctoral Dissertations

The transparent vitreous, which fills the posterior cavity of the eye, is incredibly engineered. The charged polyelectrolyte hyaluronic acid (HA) network swells to maintain the pressure in the eye, while stiff collagen type II bundles help absorb any external mechanical shock. Our investigations have contributed to a few key developments related to the physical properties of the vitreous: (1) The stiff collagen network that supports the soft gel network is self-assembled from single triple-helix collagen proteins. Electrostatic interactions drive this assembly, such that the size and concentration are optimized at physiological salt concentrations. The width of the assemblies remarkably changes …

Mechanistic Studies Of Proton Gradient-Driven Protein Translocation By Droplet-Interface Bilayer Techniques, En-Hsin Lee

Doctoral Dissertations

Transmembrane proton gradient plays a fundamental role in protein translocation across cellular membranes, including the transport of secreted enzymes from bacterial pathogens into host cells. Much attention has been devoted to understanding the machinery of such delivery and how it functions. Over the past decade, translocation of anthrax toxin has been widely studied not only because of its central role in the deadly pathogenesis of Bacillus anthracis, but also because that it is one of the most tractable toxins and thus serves as an attractive model for studying the translocation machinery that is dependent on proton gradient across membrane. …

Rational Drug Design Directed At Blocking The Initial Signaling Events In Lipopolysaccharide-Induced Sepsis., Christopher A. Tipton

Theses

Systemic Inflammatory Response Syndrome (SIRS) is classified as an immune system response to an infectious state. If left untreated, SIRS leads to sepsis, septic shock, end-organ dysfunction, and death. As a patient progresses through these stages, associations of acute respiratory distress, disseminated intravascular coagulation, and acute renal failure persist, resulting in millions of deaths annually. Lipopolysaccharide (LPS), a bacterial endotoxin, is released into the blood stream, triggering SIRS. LPS is found in the outer cell-wall of Gram-negative bacteria and is responsible for initiation of a devastating cytokine storm. One of the regions of LPS, lipid A, is a polyacylated glucosamine …