Biochemistry, Biophysics, and Structural Biology Commons^™

Habitability, And Evolution Of Microorganisms Under Extreme Conditions, Azarin Yazdani

Graduate Theses and Dissertations

The choice of a solvent determines the possible biochemistry of life. Life on Earth is based on carbon biochemistry and has evolved in an environment with water as a solvent. As a polar solvent abundant on Earth, water has unique physical properties, including a large range of liquidity and low viscosity, making it a very good solvent for terrestrial life. Liquids other than water are abundant in the universe, and the chemical nature of these liquids might lead to different chemistries of life. In the first chapter, we review the main characteristics of a good solvent, and then we use …

Cellular Mechanisms Underlying State-Dependent Neural Inhibition With Magnetic Stimulation, Hui Ye, Vincent Chiun-Fan Chen, Jenna Hendee

Engineering Science Faculty Publications

Novel stimulation protocols for neuromodulation with magnetic fields are explored in clinical and laboratory settings. Recent evidence suggests that the activation state of the nervous system plays a significant role in the outcome of magnetic stimulation, but the underlying cellular and molecular mechanisms of state-dependency have not been completely investigated. We recently reported that high frequency magnetic stimulation could inhibit neural activity when the neuron was in a low active state. In this paper, we investigate state-dependent neural modulation by applying a magnetic field to single neurons, using the novel micro-coil technology. High frequency magnetic stimulation suppressed single neuron activity …

Wdr5 Network Analysis Using Ensemble Approaches, Ali Imran

Dissertations - ALL

Understanding the properties of protein-protein interactions (PPIs) is necessary to deconvolute the processes inside living organisms. As such, research in this regard has significant implications for gaining insight into cancers and other diseases. Once understood, drugs can be designed to target these diseases. In these chapters we focus on the network of interactions of WD40 repeat protein 5 (WDR5), a known hub protein. Several of its interactions are significant for regulation of histone methylation and consequently epigenetic regulation. These interacting partners include the SET1 family of proteins and retinoblastoma binding protein-5 (RbBP5). In this work we used multiple ensemble measurement …

Nanophotonics And Nanomaterials For Microbial Inactivation, Sharad Ambardar

USF Tampa Graduate Theses and Dissertations

The study of light-matter interaction at nanoscale, also termed as nanophotonics, has gained vast attention due to its multidisciplinary application in the field of chemical engineering for the synthesis of nanomaterials, in the field of physics to study non-linear optical processes and optical phenomena in nanocavities and in the field of biology, biomedicine to study and develop novel optical nanoprobes for diagnostics, nanobiosensing and near-field imaging.

We studied UV-irradiation-based inactivation of SARS-CoV-2 and other respiratory viruses. In this work, we fabricated a device comprising a pulsed nanosecond 266 nm UV laser coupled to an integrating cavity (LIC), composed of a …

Autofluorescence Microscopy: Identifying Bacterial Signals On Rock Samples, Noel Case

University Honors Theses

One common method for identifying microbes present in fluid and non-fluid samples is fluorescent dye staining, in which samples are stained with a fluorophore - a molecule excited by an external light source that re-emits energy as higher-wavelength light. The excitation wavelength used greatly impacts the observability of microbes in the resulting fluorescence images, and deep ultraviolet excitation (200-280 nm) seems to provide the highest signal-to-noise ratio of any excitation range. By inoculating rock samples (gypsum and marble) with B. subtilis, staining with SYTO 9, Acridine Orange and FM 1-43 dyes, and imaging with deep UV (275 nm), near …

Utilizing Computational Methods To Study The Biomolecules, Wenhan Guo

Open Access Theses & Dissertations

COVID-19 is increasingly affecting human health and global economy. Understanding the fundamental mechanisms of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is highly demanded to develop treatments for COVID-19. SARS-CoV and SARS-CoV-2 share 92.06% identity in their N protein RBDs' sequences, which results in very similar structures. However, the SARS-CoV-2 is more easily to spread. Utilizing multi-scale computational approaches, this work studied the fundamental mechanisms of the nucleocapsid (N) proteins of SARS-CoV and SARS-CoV-2, including their stabilities and binding strengths with RNAs at different pH values. Electrostatic potential on the surfaces of N proteins show that both the N proteins …

Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer

Dissertations, Theses, and Capstone Projects

The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …

Modelling Juxtacrine Mediated Tumor-Fibroblast Interactions In Three-Dimensional Co-Cultures Of Pancreatic Ductal Adenocarcinoma, Eric Struth

Graduate Masters Theses

The tumor-microenvironment is a rich and complex milieu of mutated cancer cells and otherwise healthy cells engaged in dynamic interactions. Fibroblasts, the most abundant cellular component of human connective tissues, are implicated in a tumor promoting process known as stromal crosstalk. This stromal crosstalk is driven by numerous signaling pathways including contact mediated juxtacrine signaling and directed long distance paracrine signaling. Recent research suggests these signaling pathways are particularly important for two distinct types of fibroblasts. Mayofibroblastic cancer associated fibroblasts (MyCAFs) are associated with tumor suppression and shown to rely primarily on juxtacrine signaling, while inflammatory cancer associated fibroblasts (iCAFs) …

Mechanisms Of Voltage-Gated Sodium Channel (Nav1.5) Regulation By Intracellular Fgfs, Paweorn Angsutararux

McKelvey School of Engineering Graduate Student Theses & Dissertations

Voltage-gated sodium channels (NaV) conduct the inward current responsible for the initiation and propagation of the electrical signals in myocytes and neurons, known as action potentials (AP). Precise regulation of cardiac NaV1.5 opening and closing is essential for maintaining a normal heart beat. A disruption of NaV1.5 function, especially of its inactivation after opening, results in inherited cardiac arrhythmias such as Long QT Type 3 (LQT3) syndrome. This pathology is caused by an increase in the late INa that enters myocytes later in the AP and prolongs its duration. Late INa is also enhanced in acquired diseases such as heart …

Self-Organization Of Microtubule And Associated Protein Map65, Sumon Sahu

Dissertations - ALL

One of the most fascinating micron-scale structures in the biological world is the cell cytoskele- ton, with numerous components of different sizes, shapes, and geometries working together. How the local interactions of these macromolecules and polymers in nano-scale help self- organize into this higher-order micron-scale structure remains an open question in the field of biophysics. In this thesis, via a minimal two-protein in vitro system containing cytoskeletal fiber microtubule and associated protein MAP65, I try to address self-organization through passive entropic force mechanisms. I use techniques like protein purification, light microscopy, and image analysis to quantify my results. First, I …

Extracellular Mechanotransduction In Marfan Syndrome: An Equivalence Principle, Stephen Haller

Theses & Dissertations

Biological tissues continuously experience mechanical stress and have evolved sophisticated mechanisms to sense mechanical stimuli. While traditional viewpoints regard cells as the ultimate sensors and processors of mechanical information, compounding evidence demonstrates that extracellular matrix, the structural component of tissues, also exhibits evolved molecular responses to force. This led us to propose a new paradigm termed extracellular mechanotransduction, in which matrix orchestrates a complementary form of force integration distinct from traditional cellular and extracellular viewpoints. We thus propose that force-sensitive signaling mechanisms evolved within the extracellular space to help cells maintain mechanical homeostasis in tissues. In this dissertation, we apply …

Ongoing Calculus In The Cerebral Cortex, Luke Long

Physics Undergraduate Honors Theses

Various modes of neuronal computations have long been theorized to be possible based on the structure and geometry of the brain. These computations also seem necessary for many of the integral functions of the brain, like information processing and regulatory processes in the body. However, experimental data directly supporting these claims have been rare.

In this study, data collected in mice from a large number of neurons over a long period of time provided the opportunity to search for some of these computations, specifically change detection and squaring calculations. Using Matlab, the goal of this analysis was to find statistically …

Investigation Of The Binding Domain Interfaces Of The C-Terminus Of The Albino3 Insertase And The 43kda Chloroplast Signal Recognition Particle Subunit Via Single Molecule Förster Resonance Energy Transfer, Amanda Tomanek

Chemistry & Biochemistry Undergraduate Honors Theses

Fluorescent labeling is a technique used for visualizing functional groups contained in biomolecules by fluorescence imaging. This technique was used in this project to analyze post-translational targeting of light-harvesting chlorophyll-binding proteins (LHCP), which are the core complexes that harvest sunlight to drive photosynthetic electron transfer. This protein is synthesized in the cytosol and post-translationally targeted to the stroma of chloroplasts. CpSRP43 is a signal recognition particle (SRP) subunit unique to chloroplasts, which has been shown to interact with the stroma-soluble C-terminus of the thylakoid-bound Albino3 insertase (Alb3-Cterm). In the chloroplast stroma, targeting to thylakoids is performed via the cpSRP pathway …

Biophysical Insights Into The Transport Properties Of Lysenin Channels, Andrew Merlin Bogard

Boise State University Theses and Dissertations

The defense work focused on deciphering novel functionalities of lysenin channels with respect to adjustment of their regulation and transport properties in response to environmental changes. Lysenin is a pore-forming toxin extracted from the earthworm E. fetida, which self-assembles into large pores in artificial and natural lipid membranes containing sphingomyelin. Prior investigations on their functionality identified strong regulation by voltage and ligands as fundamental traits of lysenin, similar to ion channels. In addition, stochastic sensing, controlled switching, and hysteretic conductance have been added to the list of intricate biophysical properties of lysenin channels as potential enablers of biotechnological and biomedical …

The Electrostatic Features Of Dengue Virus Capsid Assembly, Alan Eduardo Lopez Hernandez

Open Access Theses & Dissertations

Dengue virus causes serious diseases and considerable deaths each year all around the globe. Dengue virus undergoes assembly in a capsid, matures and becomes viral. Revealing mechanisms of the viral capsid protein may lead to the discovery of novel drugs that prevent this assembly to happen and stop the virus from spreading. Here I present a computational work which is focused on the stability and assembly of the dengue viral capsid. The E and M proteins conform a heterotetramer, which consists of two copies of E and M proteins. The heterotetramers form a highly ordered capsid. In the electrostatic analysis …

Developing And Applying Computational Algorithms To Reveal Health-Related Biomolecular Interactions, Yixin Xie

Open Access Theses & Dissertations

Computational biology is an interdisciplinary area that applies computational approaches in biological big data, including protein amino acid sequences, genetic sequences, etc., which is widely used to analyze protein-protein interactions, make predictions in drug discovery, develop vaccines, etc. Popular methods include mathematical modeling, molecular dynamics simulations, data science mythology, etc. With the help of computational algorithms and applications, drug development is much faster than traditional processes, as it reduces risks early on in a drug discovery process and helps researchers select target candidates that have the highest potential for success. In my doctoral research, I applied multi-scale computational approaches to …

Modulation Of Kras Structure And Dynamics By Kras Ubiquitination And Membrane Depolarization, Vinay Nair

Dissertations and Theses (Open Access)

KRAS, a 21 kDa small GTPase protein, functions as a molecular switch playing a key role in regulating cell proliferation. Dysregulation of KRAS signaling by oncogenic mutations leads to uncontrolled cell proliferation, a hallmark of cancer cells. Attempts to therapeutically target oncogenic KRAS have led to limited success resulting in a need to identify new mechanisms to targeting KRAS. The interaction of KRAS with its regulators, effectors, and the membrane present one such avenue. In this study, we investigated how post-translational covalent and environmental modifications could modulate these interactions of KRAS. Using computational molecular dynamics simulations, nuclear magnetic resonance spectroscopy …

Optimization Of Modular, Long-Range, Ultra-Fast Optical Tweezers With Fluorescence Capabilities For Single-Molecule And Single-Cell Based Biophysical Measurements, Subash C. Godar

All Dissertations

An Optical tweezer is a tightly focused laser beam that applies and senses precise and localized optical force to a dielectric microsphere and offers a unique and effective tool for manipulating the single cell or cell components, including nucleotides and dynein motor proteins. Here, I used highly stabilized optomechanical components and ultra-sensitive detection modules to significantly improve the measurement capabilities over a wide range of temporal and spatial scales. I combined the optical tweezer-based force spectroscopy technique with fluorescence microscopy to develop an integrated high-resolution force-fluorescence system capable of measuring displacements at sub-nanometer, forces at sub-piconewton over a temporal range …

Supertertiary Structural Dynamics Modulate Function In Postsynaptic Density Protein 95, George L. Hamilton Iii

All Dissertations

Proteins, RNA, and DNA serve as the primary sub-cellular machinery that give rise to the necessary functions of life. The long-standing paradigm has been that the structures of biomolecules, or the arrangement of the subunits that make up a biomolecule, determine biological function. However, biomolecules are not static objects. Instead, they often undergo structural rearrangements that are crucial to enabling and regulating their functions. In my thesis I present several studies of the interplay between the structures, dynamics, and functions of biomolecules that combine experimental fluorescence spectroscopy and computational methods to probe these systems at the single-molecule level. In particular, …

Diffusive Dynamics Of Biological Macromolecules In The Cytoplasm Of Live Bacteria, Asmaa Ali Sadoon

Graduate Theses and Dissertations

Bacteria are small organisms that play important roles in our bodies and in maintaining our surrounding environment. However, bacterial infections are considered as one of the health diseases that threatens the lives of humans. Resistance of bacteria to antibiotics has made treating bacterial infections more challenging. With the emergence of many developed optical techniques, it has become possible to study various biological mechanisms of molecules inside these small organisms with high resolution and precise localization. In this research, single particle tracking photoactivation localization microscopy (sptPALM) technique was used to investigate the dynamics of fluorescent histonelike nucleoid-structuring proteins (H-NS) in live …

Computational Investigations Into Binding Dynamics Of Tau Protein Antibodies: Using Machine Learning And Biophysical Models To Build A Better Reality, Katherine Lee

University Scholar Projects

Misregulation of post-translational modifications of microtubule-associated protein tau is implicated in several neurodegenerative diseases including Alzheimer’s disease. Hyperphosphorylation of tau promotes aggregation of tau monomers into filaments which are common in tau-associated pathologies. Therefore, tau is a promising target for therapeutics and diagnostics. Recently, high-affinity, high-specificity single-chain variable fragment (scFv) antibodies against pThr-231 tau were generated and the most promising variant (scFv 3.24) displayed 20-fold increased binding affinity to pThr-231 tau compared to the wild-type. The scFv 3.24 variant contained five point mutations, and intriguingly none were in the tau binding site. The increased affinity was hypothesized to occur due …

Foldamers Reveal And Validate Therapeutic Targets Associated With Toxic Α-Synuclein Self-Assembly, Jemil Ahmed, Tessa C. Fitch, Courtney M. Donnelly, Johnson A. Joseph, Tyler D. Ball, Mikaela M. Bassil, Ahyun Son, Chen Zhang, Aurélie Ledreux, Scott Horowitz, Yan Qin, Daniel Paredes, Sunil Kumar

Chemistry and Biochemistry: Faculty Scholarship

Parkinson’s disease (PD) is a progressive neurodegenerative disorder for which there is no successful prevention or intervention. The pathological hallmark for PD involves the self-assembly of functional Alpha-Synuclein (αS) into non-functional amyloid structures. One of the potential therapeutic interventions against PD is the effective inhibition of αS aggregation. However, the bottleneck towards achieving this goal is the identification of αS domains/sequences that are essential for aggregation. Using a protein mimetic approach, we have identified αS sequences-based targets that are essential for aggregation and will have significant therapeutic implications. An extensive array of in vitro, ex vivo, and in vivo assays …

Eukaryotic Initiation Factor 4e (Eif4e) In Complex With Eif4e Binding Protein 1 (4e-Bp1) Binds With Higher Affinity To M7gpppn Cap Of A Subset Of Human Mrnas, Izza F. Nawaz

Theses and Dissertations

Fluorescence anisotropy binding assays were used to analyze the binding of eIF4E in complex with 4E-BP1 onto the 5’ m7G cap of a subset of mRNA that are known to carry cap-independent translation. These studies suggest that 4E-BP1 increases eIF4E binding affinity to 5’cap of both FGF-9 and HIF-1𝝰.

Fast Photochemical Oxidation And Footprinting Of Proteins Via Trifluoromethyl Radical Chemistry, Elaine Morrow

Honors Theses

Fast photochemical oxidation of proteins (FPOP) is a useful tool in proteomics because of the ability for modifications to occur on the scale of microseconds which reduces the modifications to tertiary and quaternary structure allowing for more accurate labeling of the protein. Labels for FPOP are generated from various radicals in our experiments which include hydroxyl radicals and trifluoromethyl radicals. Hydroxyl radicals are easily generated by using an excimer laser (KrF laser, 248 nm) or a UV flash lamp (as a part of the Fox™ System) by the photolysis of hydrogen peroxide. Trifluoromethyl radicals, however, need hydroxyl radicals to be …

A Pathway To Solving The Structure Of Cl-Par-4 Tumor Suppressor Protein: Challenges & Findings, Krishna Raut, Samjhana Pandey, Andrea M. Clark, Komala Ponniah, Steven M. Pascal

College of Sciences Posters

Prostate apoptosis response-4 (Par-4) is a pro-apoptotic tumor suppressor protein. Down-regulation of this protein has been reported in a myriad of cancers. Conversely, up-regulation of Par-4 is found to be associated with several neurodegenerative disorders. Par-4 is unique in the sense it can selectively induce apoptosis in cancer cells. For this, caspase-dependent intracellular cleavage of Par-4 is essential to produce the functionally active fragment, cl-Par-4 (caspase-cleaved Par-4). The cl-Par-4 protein inhibits the NF-κB-mediated cell survival pathway and causes selective apoptosis in various tumor cells.

Our laboratory is interested in determining the structure of cl-Par-4 and understanding it’s interaction with various …

The Development Of Inhibitors For Sars-Cov-2 Orf8, My Thanh Thao Nguyen

CSB and SJU Distinguished Thesis

An unexpected outbreak of SARS-CoV-2 caused a worldwide pandemic in 2020. Many repurposed drugs were tested, but there are currently only three FDA approved antivirals (Merck’s antiviral Molnupiravir, Pfizer’s antiviral Paxlovid, and Remdisivir).1 Most of the antiviral drugs tested SARS-CoV-2 main protease and RNA-dependent RNA polymerase. However, it is important to explore different drug targets of SARS-CoV-2 to prepare for the virus mutations of the future. This research looks at an alternative approach in which SARSCoV- 2 Open Reading Frame 8 (ORF8), which has been shown to be a rapidly evolving hypervariable gene, was chosen to be the protein of …

Sars-Cov-2 Main Protease Inhibitors Repurposed For Hiv-1 Protease Binding, Jacob Minkkinen

CSB and SJU Distinguished Thesis

Severe acute respiratory syndrome (SARS-CoV-2) led to the COVID-19 global pandemic, with over 460 million cases of infection and over 6 million deaths since the start of the pandemic. SARS-CoV-2 is a retrovirus that utilizes a main protease (Mpro). Mpro is a catalytic cys/his protease. Several treatments were proposed to stop the pandemic including repurposing drugs to inhibit the Mpro. Another retrovirus that uses a protease is human immunodeficiency virus (HIV-1) which has been a global epidemic for 40 years and is a devastating disease that attacks the immune system. HIV-1 has infected 79.5 million people and has killed an …

Case 71: Lactate Dehydrogenase As A Therapeutic Target To Treat Parasitic Disease, Dr. Kathleen Cornely

Chemistry & Biochemistry Case Studies

In this case study, researchers use their knowledge of lactate dehydrogenase in parasites and humans to investigate inhibitors that are selective for the parasite agent.

Effects Of Pore-Forming Peptides (Melittin And Magainin 2) On The Phospholipid Bilayer Interior, Elmukhtar Ehmed Alhatmi

Dissertations and Theses

Antimicrobial peptides (AMPs) are one of the most promising solutions to drug-resistant bacteria. Melittin and magainin 2 are two of the most representative and extensively studied AMPs. In this research, I investigated the interaction of these two AMPs with three models of cell membranes: 80% POPC 20% POPG, 40%POPC 40% POPE and 20% POPG, and 80%POPC 20%POPG plus 30% mole fraction of cholesterol. Time-resolved fluorescence emission and fluorescence anisotropy decays of the fluorescent probe 1,6-diphenyl-1,3,5-hexatriene (DPH) were analyzed to determine the effects of AMPs on the bilayer headgroup packing and changes in the interior of the phospholipid bilayer during the …

Structural And Biochemical Investigations Of The Initiation Of Dna Replication In Bacteriophage Lambda And Escherichia Coli, Jillian D. Chase

Dissertations, Theses, and Capstone Projects

Faithful transmission of genetic information is requisite for the propagation of all life. DNA replication in each of the three domains of life requires the separation of double stranded DNA (dsDNA) into single stranded DNA (ssDNA) which then serves as a template for genomic duplication of each original DNA strand. Initiation of replication events occurs by tightly regulated processes during which specialized proteins are loaded at a specific locus within the genome, termed the origin of replication, in preparation of bidirectional replication events. A replicative helicase must be loaded or assembled on both strands of DNA at the origin to …