Biophysics Commons^™

Complexation Of Glycoalkaloid Α- Tomatine With Sterols And Its Potential Application As An Anti-Cancer Drug, Bishal Nepal

Dissertations

Glycoalkaloids (GAs) are secondary metabolites found mostly in higher plant species and some marine invertebrates. They are known to form complexes with 3β-hydroxy sterols such as cholesterol causing membrane disruption. So far the visual evidence showcasing the complexes formed between glycoalkaloids and sterols has been mainly restricted to some earlier studies using Brewster angle microscopy. This study aimed to develop a method for topographic and morphological analysis of sterol-glycoalkaloid complexes. Langmuir-Blodgett (LB) transfer of monolayers comprising of glycoalkaloid tomatine, sterols, and lipids in varying molar ratios onto mica followed by AFM examination was performed. The AFM method used required minimal …

Lipoprotein-Induced Increases In Cholesterol And 7-Ketocholesterol Result In Opposite Molecular-Scale Biophysical Effects On Membrane Structure, Manuela A.A. Ayee, Irena Levitan

Faculty Work Comprehensive List

Under hypercholesterolemic conditions, exposure of cells to lipoproteins results in a subtle membrane increase in the levels of cholesterol and 7-ketocholesterol, as compared to normal conditions. The effect of these physiologically relevant concentration increases on multicomponent bilayer membranes was investigated using coarse-grained molecular dynamics simulations. Significant changes in the structural and dynamic properties of the bilayer membranes resulted from these subtle increases in sterol levels, with both sterol species inducing decreases in the lateral area and inhibiting lateral diffusion to varying extents. Cholesterol and 7-ketocholesterol, however, exhibited opposite effects on lipid packing and orientation. The results from this study indicate …

Characterizing Multivalent Interactions Between Folded Protein Domains And Intrinsically Disordered Regions Or Peptide Substrates, Tongyin Zheng

Dissertations - ALL

Protein-protein interactions (PPIs) play central roles in most biological processes. Studying PPIs is a fundamental step in understanding the molecular basis of cellular processes such as cell-cell contact, enzyme activity, and transient assembly of signaling complexes or cellular structures. In this work, we employed a combination of biophysical and biochemical methods to characterize PPIs, with a focus on interactions between structured domains and intrinsically disordered regions or peptide substrates.The subject of Chapter two is prolyl isomerase Ess1, which is an essential enzyme found in Saccharomyces cerevisiae. Ess1 regulates the transcription and co-transcriptional RNA processing by catalyzing the isomerization of serine-proline …

Medical Schools Ignore The Nature Of Consciousness At Great Cost, Anoop Kumar

Journal of Wellness

The essential question of the relationship between consciousness and matter is ignored in medical school curricula, leading to a machine-like view of the human being that contributes to physician burnout and intellectual dissatisfaction. The evidence suggesting that the brain may not be the seat of consciousness is generally ignored to preserve the worldview of the primacy of matter. By investigating new frameworks detailing the nature of consciousness at different levels of hierarchy, we can bring intellectual rigor to a once opaque subject that supports a fundamental reality about our experience: We are human beings, not only human bodies.

Case 51: Purification Of A Transferase Involved In The Production Of Physiologically Important Glycoproteins, Dr. Kathleen Cornely

Chemistry & Biochemistry Case Studies

A transferase involved in post-translational glycosylation of a physiologically important glycoprotein is purified and characterized.

Case 40: A Collection Of Collagen Cases, Dr. Kathleen Cornely

Chemistry & Biochemistry Case Studies

Factors important in the stability of collagen are examined.

Case 6: Hemoglobin Providence, Dr. Kathleen Cornely

Chemistry & Biochemistry Case Studies

A mutant hemoglobin variant, Hemoglobin Providence, exists in two forms in vivo.

Electrohydrodynamic Simulations Of Capsule Deformation Using A Dual Time-Stepping Lattice Boltzmann Scheme, Charles Leland Armstrong

Mathematics & Statistics Theses & Dissertations

Capsules are fluid-filled, elastic membranes that serve as a useful model for synthetic and biological membranes. One prominent application of capsules is their use in modeling the response of red blood cells to external forces. These models can be used to study the cell’s material properties and can also assist in the development of diagnostic equipment. In this work we develop a three dimensional model for numerical simulations of red blood cells under the combined influence of hydrodynamic and electrical forces. The red blood cell is modeled as a biconcave-shaped capsule suspended in an ambient fluid domain. Cell deformation occurs …

Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye

Biology: Faculty Publications and Other Works

Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in clinical practices. Via electromagnetic induction, a miniature-sized magnetic coil could provide focal stimulation to the ganglion neurons. Here we report that high-frequency stimulation with the miniature coil could reversibly block ganglion cell activity in marine mollusk Aplysia californica, regardless the firing frequency of the neurons, or concentration of potassium ions around the ganglion neurons. Presence of the ganglion sheath has minimal impact on the inhibitory effects of the coil. The inhibitory effect was local to the …

Flow Visualization And Aerosol Characterization Of Respiratory Jets Exhaled From A Mannequin Simulator, Sindhu Reddy Mutra

USF Tampa Graduate Theses and Dissertations

It is important to understand the airborne transmission of infectious diseases due to the COVID-19 pandemic. Physical experiments were conducted to understand the dispersion of aerosols emitted from a mannequin simulator replicating human tidal breathing through the nose and mouth with and without a protective face mask in an enclosed space. Flow patterns are observed via high-speed visualization, and the concentration and size distribution of the particles is measured as a function of distance from the mannequin using an optical particle sizer. Masks were shown to effectively reduce the horizontal dispersion of aerosol for both mouth and nose breathing. Further, …

Rapid Warming Events In A Small Coastal Upwelling Embayment, Tatjana E. Ellis

Physics

Temperature variability in the nearshore coastal ocean influences various biological processes and can drive changes in biodiversity and habitat range. Despite recent progress, there are still significant gaps in the understanding of drivers of temperature variability in upwelling bays, particularly at higher frequencies. In this study, we analyzed a decade of nearshore temperature measurements both inside and outside a small coastal embayment located in central California [San Luis Obispo (SLO) bay], as well as temperature data from satellites, to characterize rapid warming events. We found that rapid warming events, defined using rates of temperature change across different thresholds, occurred more …

Computational Modeling Of Water And Proteins In Drug Discovery, Anthony Cruz Balberdy

Dissertations, Theses, and Capstone Projects

This thesis aims to improve how structural and thermodynamic properties of water on protein surfaces can be exploited to aid early stage drug discovery and lead optimization. We first discuss our development of SSTMap, a public domain software suite that maps out the properties of water on biomolecular surfaces. We then show the utility of these maps in describing differences in binding affinities between congeneric pairs of ligands. We then discuss our use of solvation maps in the prospective discovery of novel binders to cytochrome C peroxidase. Finally, we present our creation and validation of a homology model of Interleukin-24 …

Designing A Reactive Warhead To Bind And Inhibit Pseudomonas Aeruginosa’S Periplasmic Protein, Inhibitor Of Vertebrate Lysozyme, Leah Greinke

Master of Science in Chemical Sciences Theses

Pseudomonas aeruginosa is a Gram-negative bacterium commonly found throughout the environment. It is a significant cause of disease and mortality in immunodeficient patients such as those suffering from cystic fibrosis (CF). Due to the emerging antibiotic resistance of P. aeruginosa, it is becoming increasingly more challenging to treat an infection by traditional means. Further complicating treatment, P. aeruginosa secretes a protein known as Inhibitor of Vertebrate Lysozyme (PaIVY) that binds to and inhibits C-type lysozyme, thus preventing the degradation of the bacterium. A reactive chemical warhead was synthesized from a rhenium(I) tricarbonyl derivative inorder to bind to and irreversibly …

Abhd5 Induced Morphological Changes On Model Membrane Systems, Nasser S. Junedi

Honors College Theses

Proper regulation of neutral lipid storage (lipogenesis) and release (lipolysis) are critical molecular processes localized to an organelle called the Lipid Droplet (LD). The LD consists of a core with neutral lipids such as triacylglycerols (TAGs) and sterol esters surrounded by a phospholipid monolayer. Dysregulation of the processes localized to the LD are involved in the pathology of various diseases such as Neutral Lipid Storage Disease, diabetes, stroke and cancer. The non-enzymatic protein ABHD5 (α-β Hydrolase Domain-Containing Protein 5), is thought to play a key role in the process of lipolysis by forming homo-oligomers on the surface of the LD …

Rna G-Quadruplex Structures: Functions In Noncoding Rnas And Disease, Emily Benner

Electronic Theses and Dissertations

Paraspeckles are a relatively newly identified subnuclear body whose function is still largely unknown. They are membraneless organelles found within mammalian nuclei originally identified as being comprised of different paraspeckle proteins (PSPs), and later proven to also contain RNA. This study investigates the long non-coding RNA nuclear enriched abundant transcript 1 (NEAT1), which has been found to be indispensable in the formation of paraspeckles, with each containing up to 50 NEAT1 molecules. NEAT1 has two isoforms, the shorter NEAT1_1, and the longer NEAT1_2. The focus of this work will be on the NEAT1_2, which acts as a scaffold in the …

New Applications For The Kinetic Exclusion Assay (Kinexa), Mark Harrison Smith

Boise State University Theses and Dissertations

This dissertation examines the fundamental principles and applicability of the kinetic exclusion assay (KinExA), developed and marketed by Sapidyne Instruments of Boise, Idaho, since 1995. Chapter One reviews and consolidates the manufacturer’s guidance and many early papers that delineate the practical and theoretical aspects of the technology. In brief, KinExA is a two stage analytical system. In stage one, a number of solutions are prepared, whereby one of the partners is kept constant (the constant binding partner, or CBP), while the other (the titrant) is varied, usually in serial dilution. As the titrant is increased, the free CBP decreases, and …

Biochemical Characterization Of Small Molecule Inhibitor Binding On A Ras Related Gtpase And Its Effector Interactions, Djamali Muhoza

Graduate Theses and Dissertations

The Ras superfamily of GTPases has 167 proteins that are involved in various cellular processes such as proliferation, transformation, migration, and inhibition of cell death. Mutations, abnormal expression, and function of these proteins are observed in many diseases, including several forms of cancer. Even though these GTPases were among the first discovered oncogenes, no successful Ras drug candidate has successfully passed clinical trials. Drugs targeting these proteins have failed mainly because of the complexity of their regulation, their high affinity to GTP, and their structure’s dynamic nature. Recently, novel promising targeting approaches have renewed interest in the Ras drug discovery …

Analyzing The Effects Of E-Hook Peptides On Kinesin-1, Ashton Ward Murrah, Baylee Hope Howard

Honors Theses

Cancer is the second leading cause of death in the United States. Cancerous growth is a result of oncogenes, or mutated genes that increase the rate of cell division in an uncontrolled manner. Cell division, which consists of mitosis and cytokinesis phases, is dependent upon the active movement of kinesin motor proteins along microtubules to rearrange the cytoskeleton for equitable distribution of genetic material to daughter cells. As kinesins are vital to this process, if we could prevent kinesin from binding to the microtubules, cell division would cease.

The goal of this study is to develop a method to prevent …

Applying Computational Methods To Study The Interactions Between Sars-Cov-2 And Hace2, Yixin Xie

Open Access Theses & Dissertations

The ongoing outbreak of COVID-19 has been a serious threat to human health worldwide. The virus SARS-CoV-2 initiates its infection to the human body via the interaction of its spike (S) protein with the human Angiotensin-Converting Enzyme 2 (ACE2) of the host cells. Here we implemented multi-scale computational approaches to study the binding mechanisms of human ACE2 and S proteins of both SARS-CoV and SARS-CoV-2. Electrostatic features, including electrostatic potential, electric field lines and electrostatic forces of SARS-CoV and SARS-CoV-2 were calculated and compared in detail. The results demonstrate that SARS-CoV and SARS-CoV-2 S proteins are both attractive to ACE2 …

The Hybridizing Ions Treatment (Hit) Method Development And Computational Study On Sars-Cov-2 E Protein., Shengjie Sun

Open Access Theses & Dissertations

Fast and accurate calculations of the electrostatic features for highly charged biomolecules such as DNA, RNA, highly charged proteins, are crucial but challenging tasks. Traditional implicit solvent methods calculate the electrostatic features fast, but they are not able to balance the high net charges in the biomolecules effectively. Explicit solvent methods add unbalanced ions to neutralize the highly charged biomolecules in molecular dynamic simulations, which require more expensive computing resources. Here we developed a novel method, the Hybridizing Ions Treatment (HIT) method, which hybridizes the implicit solvent method with the explicit method to realistically calculate the electrostatic potential for highly …