Biochemistry, Biophysics, and Structural Biology Commons^™

Metatranscriptomic Insights Into The Interaction Between Microcystis Blooms And Hydrogen Peroxide, Taylor L. Hancock

USF Tampa Graduate Theses and Dissertations

For this dissertation I studied the interactions of hydrogen peroxide and cyanobacterial harmful algal blooms (cHABs) dominated by Microcystis in the Caloosahatchee River, FL. Specifically, I examined how taxonomic and functional succession relates to both natural hydrogen peroxide dynamics and hydrogen peroxide added to the environment as a cHAB treatment. Chapter 2 investigated how taxonomic succession and gene expression patterns relate to blooms and associated elevated hydrogen peroxide concentrations. The results showed that gene expressions related to cyanobacterial growth were positively correlated with hydrogen peroxide. The genes identified included enzymes capable of hydrogen peroxide generation which were expressed by blooming …

Integration Of Algae And Biomass Processes To Synthesize Renewable Bioproducts For The Circular Economy, Jessica Martin

USF Tampa Graduate Theses and Dissertations

Rapid population growth and global industrialization have substantially heightened the demand for fossil-based fuels and products in various sectors of the global economy, including energy production, transportation fuels, and as raw materials for petrochemicals. The intense consumption of fossil fuels has caused immense environmental impacts, especially pertaining to carbon dioxide emissions. Shifting to renewable feedstocks (raw materials) is expected to reduce these emissions by lowering the carbon footprint of fuels and products compared to traditional fossil-derived alternatives. This transition aligns with the goal of creating a sustainable and circular economy, emphasizing efficient resource use, and reducing waste generation through recycling …

Development Of Antiviral Peptidomimetics, Songyi Xue

USF Tampa Graduate Theses and Dissertations

Protein-protein interactions (PPIs) are essential for biological processes and are associated with a number of diseases, including cancer, infectious diseases, and neurodegenerative diseases. As a result, modulation of PPIs has been recognized as one of the most promising strategies to develop the novel drugs. Peptide modulators always exhibit higher specificity and affinities with targets than small compounds or monoclonal antibodies, but their broad medicinal effectiveness is constrained by their poor bioavailability and biostability. Peptidomimetics, which have been developed to mimic the structure as well as function of bioactive peptides and proteins, have shown excellent potential in protein surface mimicry and …

Apkcs Role In Neuroblastoma Cell Signaling Cascades And Implications Of Apkcs Inhibitors As Potential Therapeutics, Sloan Breedy

USF Tampa Graduate Theses and Dissertations

Neuroblastoma (NB) is a cancer that develops in the neuroblasts. It is the most common cancer in children under the age of 1 year, accounting for approximately 6% of all cancers. The prognosis of NB is linked to both age and degree of cell differentiation. This results in a range of survival rates for patients, with outcomes ranging from recurrence and mortality to high survival rates and tumor regression. Our previous work indicated that PKC-ι promotes cell proliferation in NB cells through the PKC-ι/Cdk7/Cdk2 cascade. We report on two atypical protein kinase inhibitors as potential therapeutic candidates against BE(2)-C and …

A Protein-Based Therapeutic Combination For The Treatment Of Hard-To-Heal Wounds, Graham L. Strauss

USF Tampa Graduate Theses and Dissertations

Chronic wounds present many clinical challenges in relation to the successful treatment and closure of the damaged tissue. Most current treatment methods focused on one or two aspects to drive wound closure, while most chronic wounds are multifactorial environments with many of those dependencies relying on the termination of one another to effectively gain tissue construction, closure, and full skin thickness and composition. Natural wound healing processes allude to potential biologics that can impede the chronic breakdown of tissue, while restoring deposition of new tissue, and effectively leading to a healed wound. Proteases secreted by the body’s immune system lay …

Development Of Enhanced Algae Strains And Sustainable Cultivation Processes For Production Of Algal Lipids For Biofuels And Bioproducts, Enlin Lo

USF Tampa Graduate Theses and Dissertations

The establishment of an algae industry is crucial for addressing global biofuel and bioproduct demand that meets the Sustainable Development Goals (SDG) worldwide. Photosynthetic microalgae are excellent sources for food, fiber, fuel, feed, and fertilizer, which are the 5Fs of the SDG. However, at present, algae-based materials are not cost-competitive or sufficiently sustainable. Improved productivity, lower cultivation cost, and reduced use of resources are required to transition from lab to industry, necessitating the development of superior strains that have high productivity and can tolerate environmental stress, such as temperature and salinity, so they can be cultivated at large scale outdoors …

Investigation Of Immobilized Enzymes In Confined Environment Of Mesoporous Host Matrices, Xiaoliang Wang

USF Tampa Graduate Theses and Dissertations

Enzyme immobilization in metal-organic frameworks (MOFs) as a promising strategy, is attracting the interest of scientists from different disciplines with the expansion of MOF’s development. Different from other traditional host materials, their unique strengths of high surface areas, large yet adjustable pore sizes, functionalizable pore walls, and diverse architectures make MOFs an ideal platform to investigate hosted enzymes, which is critical to the industrial and commercial process. In addition to the protective function of MOFs, the extensive roles of MOFs in the enzyme immobilization are being well-explored by making full use of their remarkable properties like well-defined structure, high porosity, …

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 …

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 …

Interrogation Of Protein Function With Peptidomimetics, Olapeju Bolarinwa

USF Tampa Graduate Theses and Dissertations

Proteins can be described as the “machineries” responsible for almost all tasks in the levels of organizational complexity in multi-cellular organisms namely: the cells, tissues, organs and systems. Any disorder in the function of a protein at any of these levels could result in disease, and a study of protein function is critical to understanding the pathological features of the disease at the molecular level. A quick glance at these abundantly present proteins reveals two striking features: large diversity of biological function, and the variations in structural complexity, which varies from simple random coils, to turns and helices, and on …

Elastin-Like Polypeptide Fusion Tag As A Protein-Dependent Solubility Enhancer Of Cysteine-Knot Growth Factors, Tamina L. Johnson

USF Tampa Graduate Theses and Dissertations

Elastin-like peptide (ELP) fusions promote therapeutic delivery and efficacy. Recombinant proteins, like neurotrophins, lack bioavailability, have short in vivo half-lives, and require high manufacturing costs. Fusing recombinant proteins with genetically encodable ELPs will increase bioavailability, enhance in vivo solubilization, as well as provide a cost-effective method for purification without the need for chromatography. During expression of neurotrophin-ELP (N-ELP) fusions, dense water-insoluble aggregates known as inclusion bodies (IBs) are formed. Inclusion bodies are partially and misfolded proteins that usually require denaturants like Urea for solubilization. Strong denaturants arrest ELPs stimuli-responsive property and increase unwanted aggregation, making purification difficult, yet possible. The …

Design, Synthesis, Application Of Biodegradable Polymers, Mussie Gide

USF Tampa Graduate Theses and Dissertations

Bacterial infections have posed a serious threat to the public health due to the significant rise of the infections caused by antibiotic-resistant bacteria. There has been considerable interest in the development of antimicrobial agents which mimic the natural HDPs, and among them biodegradable polymers are newly discovered drug candidates with ease of synthesis and low manufacture cost compared to synthetic host defense peptides. Herein, we present the synthesis of biocompatible and biodegradable polymers including polycarbonate polymers, unimolecular micelle hyperbranched polymers and dendrimers that mimic the antibacterial mechanism of HDPs by compromising bacterial cell membranes. The developed amphiphilic polycarbonates are highly …

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 …

Structure And Activity Of Metallo-Peptides, Christian C. Tang

USF Tampa Graduate Theses and Dissertations

Metal ions are ubiquitously found in all living systems and play vital roles in supporting life forms by performing an array of biological activities. Such biological activities include binding and transforming organic molecules, and also acting as active centers and cofactors for catalysis of various acid-base and redox reactions in biological system. The main focus in bioinorganic chemistry is to elucidate the structural and functional roles of metals in biological systems. Among all transition metal ions, Cu²⁺ and Fe³⁺ are especially versatile and important due to their abilities to go through redox efficiently.

This dissertation can be divided …

Inquiry Of Lipid Membranes Interacting With Functional Peptides And Polyphenol Drug Molecules, Chian Sing Ho

USF Tampa Graduate Theses and Dissertations

Cellular membranes are important targets for many membrane-active peptides and drug compounds. Here we are interested in deciphering how lipid membranes are perturbed by several membrane-active molecules, including the transmembrane domain of the influenza M2 protein (M2TM), aggregates formed by a synthetic polyglutamine peptide, and three polyphenol compounds (i.e., tamoxifen, genistein, and verapamil). We employ phase-separated ternary lipid model membranes in the form of giant unilamellar vesicles (GUVs) to simulate raft-like structures that have been proposed to govern many important processes in plasma membranes (e.g., intracellular singling and trafficking). Specifically, we use fluorescent microscopy to interrogate how those membrane additives …

Biophysical Investigation Of Amyloid Formation And Their Prion-Like Self-Replication, Mentor Mulaj

USF Tampa Graduate Theses and Dissertations

Growth and deposition of amyloid fibrils, polymers of proteins with a cross beta-sheet structure, are associated with a significant number of human pathologies including Alzheimer’s disease, Parkinson’s disease, prion diseases, type II diabetes, and senile systematic or dialysis-related amyloidoses. The broader objective of my research is to identify the basic mechanisms regulating nucleation and growth of amyloid fibrils. There is increasing evidence that amyloid formation may proceed along at least two distinct assembly pathways for the formation of rigid fibrils. One pathway involves the nucleated polymerization of the characteristic rigid fibrils from partially denatured monomers and the other proceeds via …

Novel Techniques In Chemical Ecology To Examine Life Histories In Fishes, Orian Tzadik

USF Tampa Graduate Theses and Dissertations

Diet and movements in fishes are often logistically challenging to study. Trace element and stable isotope analyses have advanced these fields considerably, but are still constrained by methodological impediments, such as the tendency towards lethal sampling. Studying endangered fishes is particularly challenging as representative samples are difficult to obtain. However, the information gained from such studies is often critical to the recovery of endangered fishes as knowledge of life history attributes has the potential to greatly influence the success of management strategies.

I tested the viability of using fin rays in fishes as a non-lethal approach to study diet and …

Novel Enzyme Perspectives: Arylalkylamine N-Acyltransferases From Bombyx Mori & 1-Deoxy- D-Xylulose-5-Phosphate Synthase From Plasmodium Falciparum And Plasmodium Vivax, Matthew R. Battistini

USF Tampa Graduate Theses and Dissertations

This dissertation is dedicated to the research and investigation of novel enzymes and the methods used to study them, with physiological roles ranging from isoprenoid biosynthesis to neurotransmitter production. Using a combination of bioinformatics, recombinant cloning, enzymology, and proteomics, we have contributed to the understanding and exploration of several human illnesses, including malaria, cancer, and endocrine dysfunction.

Our first project involved studying the enzymes responsible for N-acylarylalkylamide biosynthesis in Bombyx mori. Very little is known how these potent signaling molecules are produced in vivo, however, one possible pathway is the direct conjugation of an acyl-CoA to a corresponding …

Photoacoustic Calorimetry Studies Of The Earliest Events In Horse Heart Cytochrome-C Folding, Tarah A. Word

USF Tampa Graduate Theses and Dissertations

The protein folding problem involves understanding how the tertiary structure of a protein is related to its primary structure. Hence, understanding the thermodynamics associated with the rate-limiting steps for the formation of the earliest events in folding is most crucial to understanding how proteins adopt native secondary and tertiary structures. In order to elucidate the mechanism and pattern of protein folding, an extensively studied protein, Cytochrome-c (Cc), was chosen as a folding system to obtain detailed time-resolved thermodynamic profiles for the earliest events in the protein folding process. Cytochrome-c is an ideal system for understanding the folding process for several …

Gamma-Aapeptides As A New Class Of Peptidomimetics: Synthesis, Structures, And Functions, Haifan Wu

USF Tampa Graduate Theses and Dissertations

Peptidomimetics are synthetic oligomers that resemble the activities of peptides. Their advantages over peptides include high stability towards proteolysis and enormous chemical diversity. Over the past two decades, there have been extensive efforts to develop peptide mimics, such as beta-peptides, peptoids, D-peptides, etc. The research on peptidomimetics have led to many important applications in both medicinal and material science. In order to explore new functions, the discovery of peptidomimetics with novel frameworks is essential. We reported the synthesis and evaluation of a new class of peptidomimetics, termed as gamma-AApeptides. Previous studies of gamma-AApeptides have revealed that gamma-AApeptides are highly resistant …

Identification And Characterization Of N-Acyltransferase Enzymes That Are Involved In The Biosynthesis Of Fatty Acid Amides, Daniel Robert Dempsey

USF Tampa Graduate Theses and Dissertations

Fatty acid amides are an emerging family of bioactive lipids that consists of N-acylethanolamines, N-acylarylalkylamides, N-acylglycines, N-acyl amino acids, N-monoacylpolyamides, and primary fatty acid amides. Short chain fatty acid amides are products of inactivated biogenic amines such as dopamine, histamine, octopamine, and serotonin, whereas long chain fatty acid amides have been implicated in a number of physiological process such as the perception and inhibition of chronic pain through binding to their specific receptors. The most famous; therefore, the most studied long chain fatty acid amide is anandamide or also known as N-arachidonylethanolamine. The biosynthesis …

Biosynthesis Of Long-Chain Fatty Acid Amides, Kristen A. Jeffries

USF Tampa Graduate Theses and Dissertations

The vast variety of long-chain fatty acid amides identified in biological systems is intriguing. The general structure of a fatty acid amide is R-CO-NH-X, where R is an alkyl group and X is derived from an immense variety of biogenic amines. Although structurally simple, the bioactivities of these molecules as signaling lipids are very diverse and have just recently begun to emerge in the literature. Interest in the long-chain fatty acid amides dramatically increased following the identification and characterization of one specific N-acylethanolamine, N-arachidonoylethanolamine (anandamide), as the endogenous ligand for the cannabinoid receptors in the mammalian brain. Since …

Synthesis, Characterization And Mechanistic Studies Of Biomolecules@Mesomofs, Yao Chen

USF Tampa Graduate Theses and Dissertations

Encapsulation of biomolecules is of great interest to research advances related to biology, physiology, immunology, and biochemistry, as well as industrial and biomedical applications such as drug delivery, biocatalysis, biofuel, food and cosmetics. Encapsulation provides functional characteristics that are not fulfilled by free biomolecules and stabilizes the fragile biomolecules. In terms of biocatalysis, solid support can often enhance the stability of enzymes, as well as facilitate separation and recovery for reuse while maintaining activity and selectivity. Various kinds of materials have been used for encapsulation of biomolecules, among which, porous materials are an important group. Metal-organic frameworks (MOFs) have attracted …

Study Of The Motility Of Biological Cells By Digital Holographic Microscopy, Xiao Yu

USF Tampa Graduate Theses and Dissertations

In this dissertation, I utilize digital holographic microscopy (DHM) to study the motility of biological cells. As an important feature of DHM, quantitative phase microscopy by digital holography (DH-QPM) is applied to study the cell-substrate interactions and migratory behavior of adhesive cells. The traction force exerted by biological cells is visualized as distortions in flexible substrata. Motile fibroblasts produce wrinkles when attached to a silicone rubber film. For the non-wrinkling elastic substrate polyacrylamide (PAA), surface deformation due to fibroblast adhesion and motility is visualized as tangential and vertical displacement. This surface deformation and the associated cellular traction forces are measured …

Combination Of The Computational Methods: Molecular Dynamics, Homology Modeling And Docking To Design Novel Inhibitors And Study Structural Changes In Target Proteins For Current Diseases, Katherine Cristina Parra

USF Tampa Graduate Theses and Dissertations

In this thesis, molecular dynamics simulations, molecular docking, and homology modeling methods have been used in combination to design possible inhibitors as well as to study the structural changes and function of target proteins related to diseases that today are in the spotlight of drug discovery. The inwardly rectifying potassium (Kir) channels constitute the first target in this study; they are involved in cardiac problems. On the other hand, tensin, a promising target in cancer research, is the second target studied here.

The first chapter includes a brief update on computational methods and the current proposal of the combination of …

Reaction Enthalpy And Volume Profiles For Excited State Reactions Involving Electron Transfer And Proton-Coupled Electron Transfer, William Antonio Maza

USF Tampa Graduate Theses and Dissertations

Electron transfer, ET, and proton-coupled electron transfer, PCET, reactions are central to biological reactions involving catalysis, energy conversion and energy storage. The movement of electrons and protons in either a sequential or concerted manner are coupled in a series of elementary reaction steps in respiration and photosynthesis to harvest and convert energy consumed in foodstuffs or by absorption of light into high energy chemi-cal bonds in the form of ATP. These electron transfer processes may be modulated by conformational dynamics within the protein matrix or at the protein-protein interface, the energetics of which are still not well understood. Photoacoustic calorimetry …

Biochemical Aspects Of The Thermal Sensitivity And Energy Balance Of Polar, Tropical And Subtropical Teleosts, Eloy Martinez

USF Tampa Graduate Theses and Dissertations

The maintenance of a functional energy balance in ectothermic fauna could be challenging in a thermally disparate environment. Biochemical adaptations at the enzyme and membrane levels allows for a set compensatory mechanism that allow the individual to maintain an energetic surplus, thus allocating energy for growth and reproduction. The present work describes how the energetic machinery in the cell, particularly the mitochondrion, could be affected by temperature changes. More specifically, this work aimed to determine how environmental temperature affects the mitochondria energetic performance of fishes from disparate thermal regimes.

Mitochondrial ATP production efficiency was evaluated in fishes from polar, tropical …

The Role Of Hsp70 In Cancer: A Study Of The Hsp70 / Akt Relationship, John Koren

USF Tampa Graduate Theses and Dissertations

The Hsp70 family of molecular chaperones is essential for

protein folding, re-folding misfolded client proteins, clearance

of aberrant client proteins, and can also inhibit programmed

cell death. There are two major cytosolic members of this

family: the constitutive Hsc70, and the inducible Hsp72. Under

stress conditions the Hsp70 family protects the cell from

protein related damage by the induction of Hsp72. Hsc70 and

Hsp72 are highly homologous with minor differences in

substrate binding. In cancers, Hsp72 is commonly induced and

this induction is thought to aid in cancer cell survival. In these

studies we demonstrate the differential regulation of the …

Protein Profiling Of Adenine Nucleoside And Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-Azidoadenosine Analogs As Affinity Based Protein Profiling Probes, Shikha Mahajan

USF Tampa Graduate Theses and Dissertations

Identification of differential expressions of proteins in proteomic profiles of biological samples shows great potential as a valuable technique for the early diagnosis of various diseases. An important challenge in modern protein profiling approaches is to reduce the complexity of the samples by limiting the number of proteins that need to be evaluated for distinction in the expression between normal and deceased cells. In this research, an affinity based approach for the enrichment of nucleotide and nucleoside binding proteins from a complex cell proteome has been developed. To achieve this goal, new N6-biotinylated-8-azido-adenosine probes (AdoRs) have been designed and synthesized …