Biochemistry, Biophysics, and Structural Biology Commons^™

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 …

An Unexpected Rhenium(Iv)–Rhenium(Vii) Salt: [Co(Nh3)6]3[Reviio4][Reivf6]46h2o, James Louis_Jean, Samudee Mariappan Balasekaran, Adelheid Hagenbach, Frederic Poineau

Chemistry and Biochemistry Faculty Research

The title hydrated salt, tris[hexaamminecobalt(III)] tetraoxidorhenate(VII) tetrakis[hexafluoridorhenate(IV)] hexahydrate, arose unexpectedly due to possible contamination of the K2ReF6 starting material with KReO4. It consists of octahedral [Co(NH3)6] 3+ cation (Co1 site symmetry 1), tetrahedral [ReVIIO4] anions (Re site symmetry 1) and octahedral [ReIVF6] 2 anions (Re site symmetries 1and 3). The [ReF6] 2 octahedral anions (mean Re—F = 1.834 A˚ ), [Co(NH3)6] 3+ octahedral cations (mean Co—N = 1.962 A˚ ), and the [ReO4] tetrahedral anion (mean Re—O = 1.719 A˚ ) are slightly distorted. A network of N—HF hydrogen bonds consolidates the structure. The crystal studied was refined as a …

Identification And Characterization Of Preferred Dna-Binding Sites For The Thermus Thermophilus Hb8 Transcriptional Regulator Ttha0973, James Shell Cox, Kristi Moncja, Mykala Mckinnes, Michael W. Van Dyke

Faculty Articles

Advances in genomic sequencing have allowed the identification of a multitude of genes encoding putative transcriptional regulatory proteins. Lacking, often, is a fuller understanding of the biological roles played by these proteins, the genes they regulate or regulon. Conventionally this is achieved through a genetic approach involving putative transcription factor gene manipulation and observations of changes in an organism’s transcriptome. However, such an approach is not always feasible or can yield misleading findings. Here, we describe a biochemistry-centric approach, involving identification of preferred DNA-binding sequences for the Thermus thermophilus HB8 transcriptional repressor TTHA0973 using the selection method Restriction Endonuclease Protection, …

An Insight Into The Biological Functions, The Molecular Mechanism And The Nature Of Interactions Of A Set Of Biologically Important Proteins., Adam A. Aboalroub

USF Tampa Graduate Theses and Dissertations

Characterization of protein structural properties is crucial to determine its role in normal and pathological conditions. In this dissertation, we have employed NMR spectroscopy in a combination of other biochemical and biophysical techniques to investigate the catalytic function, the molecular mechanism, and nature of the interactions of bmAANAT3, Cdc37, and TIMP2, respectively.

In the first project, we have employed an arylalkylamine N-acetyltransferases (AANATs) from Bombyx mori (bmAANAT3) to determine the role of the acetyl-group in coordinating the catalytic cycle in this family of enzymes. We have found that the occupancy of the acetyl-moiety in the catalytic funnel of these enzymes …

Intrinsically Disorder Proteins And Liquid-Liquid Phase Transitions In Neurodegenerative Diseases, April Lynn Darling

USF Tampa Graduate Theses and Dissertations

Neurodegenerative diseases have a negative impact on health and economics, effecting more than 20 million people in the United States and costing around $800 billion in 2018. Additionally, most neurodegenerative diseases such as Alzheimer’s Disease (AD), Amyotrophic Lateral Sclerosis (ALS), Frontotemporal Dementia (FTD), and several others are fatal and have no cure or effective treatment. Many of these diseases have a common theme of protein aggregates being present in disease tissue. These aggregates are thought to be toxic to the cell and prevention of pathological aggregation and elimination of these cellular aggregates may serve as a potential therapeutic approach to …

Novel Strategies On Characterizing Biologically Specific Protein-Protein Interaction Networks, Bi Zhao

USF Tampa Graduate Theses and Dissertations

The function, behavior, and environmental response of biological systems are essentially determined by the complex interaction and regulation of biomolecules inside the systems. Therefore, it is critical to characterize the inter-molecular interaction and regulation of biomolecules inside these systems. In this direction, many experimental techniques have been developed and these techniques have been used in many different model systems under various conditions. Consequently, a massive amount of data has been generated. These data cover multiple aspects of molecular interaction and regulation, such as protein-protein interaction, microRNA-RNA interaction, gene expression profiles, etc. While carrying rich information, these data may also contain …

Targeting Pten For Therapy In Cancer And Ptenopathies, Emily Palumbo

USF Tampa Graduate Theses and Dissertations

PTEN, a dual protein and lipid phosphatase, regulates a myriad of cellular functions including PI3K pathway signaling, cell migration, proliferation, invasion and apoptosis. PTEN mutations often lead to multiple malignancies, including prostate, breast, endometrial, skin and brain cancers, associated with hyperactive PI3K signaling. PTEN mutations have also been associated with a variety of other diseases, classified as PTEN Hamartoma Tumor Syndromes (PHTS). In addition, compromised function or reduced expression of PTEN due to non-genomic mechanisms are associated with many types of hyperproliferative diseases, such as restenosis and neoplastic diseases, including melanoma, lung, breast, prostate and colon cancers. Although PI3K pathway …

Modulations Of Lipid Membranes Caused By Antimicrobial Agents And Helix 0 Of Endophilin, Nawal Kishore Khadka

USF Tampa Graduate Theses and Dissertations

Understanding the cellular membrane interaction with membrane active biomolecules and antimicrobial agents provides an insight in their working mechanism. Here, we studied the effect of antimicrobial agents; a recently developed peptidomimetics E107-3 and colistin as well as the N-terminal helix H0, of Endophilin A1 on the lipid bilayer.

It is important to discern the interaction mechanism of antimicrobial peptides with lipid membranes in battling multidrug resistant bacterial pathogens. We study the modification of structural and mechanical properties with a recently reported peptidomimetic on lipid bilayer. The compound referred to as E107-3 is synthesized based on the acylated reduced amide scaffold …

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 …

Roux-En-Y Gastric Bypass Attenuates Obesity-Related Liver Injury, Drew Alan Rideout

USF Tampa Graduate Theses and Dissertations

Obesity is a growing epidemic in the United States with significant co-morbidities. Non-Alcoholic Fatty Liver Disease (NAFLD) is a prevalent manifestation of obesity that can lead to cirrhosis. Roux-en-Y gastric bypass (RYGB) results in substantial long-term weight loss and resolution of obesity-related metabolic diseases. There appears to be a weight-independent molecular mechanism for the improvement of diabetes mellitus and NAFLD after RYGB, which is poorly understood. Obesity is associated with chronic inflammation that accompanies the hepatic steatosis. Through unknown mechanisms, RYGB in humans increases serum levels of the fat-derived adipocytokine, adiponectin. Adiponectin (an anti-inflammatory cytokine) is known to have a …

5,7,3’,4’-Hydroxy Substituted Flavonoids Reduce The Heme Of Cytochrome C With A Range Of Rate Constants, Veronica Moorman, Montserrat Rabago-Smith, Evan D. Kindl, Imani R. Williams

Natural Sciences Publications

Flavonoids are antioxidants known to be abundant in edible plants. Seven 5,7,3′,4′-tetrahydroxy substituted flavonoids representing each major flavonoid class were used as cytochrome c reductants to systematically investigate the redox role of their C-rings. Additional examples of flavonoids and benzenediols were investigated to better understand the role of the B-ring. Pseudo-first order rate constants (kobs) and apparent bimolecular rate constants (kapp) values were calculated from spectroscopic measurements. Of the seven flavonoids tested, five yielded measurable observed reduction rate constants. Butein (a chalcone) had the highest apparent bimolecular rate constant (kapp), followed by taxifolin (a flavanonol), catechin (a flavanol), eriodictyol …

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 …

A High Throughput Assay For The Detection Of Stimulator Of Interferon Genes (Sting) Agonists, Michael J. Ingling

Graduate School of Biomedical Sciences Theses and Dissertations

The innate immune system includes a menagerie of different cell types, each with a different role in the process of monitoring the body for invaders and presenting gathered debris (antigen) to the adaptive immune system. Somatic cells have intracellular receptors for the same purpose. Cancer cells, however, have avoided these methods of detection despite, in many cases, the tumor’s immunogenic traits. Immuno-oncology is a field dedicated to the immunological traits of tumors, more recently finding ways of instigating an immune response against tumors. In this regard, STING, a receptor of cyclic dinucleotides (CDN), has come to the forefront of immuno-oncology. …

Characterization Of Human Dutpase, Shawna Marie Rotoli

Graduate School of Biomedical Sciences Theses and Dissertations

Deoxyuridine nucleotidyl transferase (dUTPase) is an enzyme found in all organisms that have thymine as a component of DNA. It catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate thus precluding the buildup of dUTP pools as well as providing the substrate, dUMP, for the de novo synthesis of thymidylate. In Homo sapiens, there are four isoforms: mitochondrial (mDut), nuclear (nDut), variant 3 and variant 4. This work is largely focused on nDut. Using structural and MS analyses of recombinant dUTPase constructs, an intermolecular disulfide bridge between cysteine-3 of each nDut monomer was discovered. It was found that these two …

Characterizing Novel Pathways For Regulation And Function Of Ataxin-2, Elise Spencer Melhado

Theses and Dissertations

Ataxin-2 is an RNA-binding protein that is involved in many crucial cellular processes such as R-loop regulation, mRNA stability, TOR signaling regulation, and stress granule formation. Ataxin-2 is highly conserved, found in organisms ranging from Saccharomyces cerevisiae to Caenorhabditis elegans and Homo sapiens. Recently, ataxin-2 has been linked to the neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS). ALS is a fatal disease that causes loss of motor neurons. In addition to ataxin-2 interacting with known ALS risk factor proteins, research into the relationship between ataxin-2 and ALS shows that polyglutamine expansions in ataxin-2 are gain-of-function mutations that lead to overactivity of …

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 …

Snfing Glucose To Pass Mitochondrial Dysfunction: The Role Of Two Sensory Protein Kinases In Metabolic Diseases, Kai Li Ong

Theses and Dissertations

Mitochondria is no longer viewed as merely a powerhouse of the cell. It is now apparentthat mitochondria play a central role in signaling, maintaining cellular homeostasis and cell fate.Mitochondrial dysfunction has been linked to many human diseases caused by cellular metabolicderegulation, such as obesity, diabetes, neurodegenerative disease, cardiovascular disease andcancer. Eukaryotic organisms have evolved an efficient way in sensing, communicating andresponding to cellular stress and regulating mitochondrial activity correspondingly through acomplex network of intercommunicating protein kinases and their downstream effectors. Thisdissertation focuses on the interplay of two of the master metabolic regulators in the cell: AMPKand PASK, and characterization of …

The Expression Of Connexin-43 By Cd11c+ Dendritic Cells Is Required To Maintain Cd4+ Foxp3+ Regulatory T Cell Population In Peripheral Lymphoid Organs, Caroline Titus Miller

Biological Sciences Theses & Dissertations

Foxp3⁺ regulatory T cells (T_R) are an immunosuppressive subset of CD4⁺ T cells that maintain homeostasis of the immune system. They are sustained by the interaction between the Major Histocompatibility Complex (MHC) molecules present on antigen presenting dendritic cells and the T Cell Receptor (TCR) expressed on T_R cells that is specific for the MHC loaded with an antigenic peptide. Here, we show that in addition to MHC/TCR interaction, Connexin-43 (Cx43) expression by dendritic cells is required to maintain the TR cell population. CD11c⁺ dendritic cells represent a major subset of antigen presenting cells. …