Biophysics Commons^™

Illuminating Function And Enabling Inhibition At The Protein-Membrane Interface Of Glutathione Peroxidase 4., Courtney L. Labrecque

Theses and Dissertations

Membrane proteins act as gateways to cells and are responsible not only for signaling, lipid transport, and cellular homeostasis, but they are also integral in disease pathologies. One class of membrane proteins, peripheral membrane proteins (PMPs), reside in aqueous compartments of the cell until they are recruited to the membrane to perform their function. Glutathione peroxidase 4 (GPx4) is a PMP enzyme responsible for engaging the membrane and reducing lipid hydroperoxides, thereby preventing cellular death via ferroptosis. Due to its central function surrounding ferroptosis, GPx4 is an interesting drug target that has recently gained interest for inflammatory diseases as well …

Compliance And Roughness In Relation To Gecko Locomotion, Brooklynn Campbell

Williams Honors College, Honors Research Projects

Geckos move efficiently through a variety of substrates, from swaying branches to wooden fences to the sides of structures. Previous studies have studied locomotion and adhesion on manmade and rough substrates; however, the work is limited when discussing locomotion and adhesion as a relationship of compliance and roughness. Ease of movement was quantified by speed, under the assumption that the faster a gecko moves, the easier it is for the gecko to cross the substrate. Gehyra oceanica geckos from Moorea, French Polynesia were tested on substrates varying in compliance and roughness with four different treatments in total. Compliance, roughness, and …

Mechanistic Analysis Of Four-Way Dna Junctions And Cytokine-Binding Aptamers For Therapeutic Interventions, Roaa S. Mahmoud

Theses and Dissertations

DNA is inherently dynamic and topologically diverse and can fold into many different structures. Besides the canonical Watson-Crick structure, other higher-order structures such as G-quadruplexes (G4), i-motifs (iM), and four-way DNA junctions are possible. Although these high-order DNA structures are known to form transiently, they are important due to the crucial roles they play in many cellular processes including DNA replication, recombination, and repair. Among these DNA structures, 4-way junctions (also known as Holliday junctions, HJ) which are formed during the repair of double-strand DNA breaks (DSBs) and interact with proteins have garnered significant attention due to their central role …

Investigating Dynamics Of Electron Transfer Flavoprotein And Its Partner Flavodoxin Via Small Angle Neutron Scattering And Fluorine Nmr, Sharique Ahmad Khan

Theses and Dissertations--Chemistry

Anaerobic bacteria and archaea thrive in seemingly inhospitable environments because they are extremely energy efficient. Their capacity to fully utilize electrochemical energy is based in large part on their ability to conduct electron transfer bifurcation ('bifurcation') at strongly reducing potentials, thereby producing extremely potent reducing agents able to fix nitrogen and make molecular hydrogen. This chemistry is made possible by the use of a flavin as the site of bifurcation, supported by a specialized protein environment and mechanisms that control the flow of individual electrons.

Bifurcating electron transfer flavoproteins (Bf-ETFs) are versatile protein modules that provide the bifurcating capability associated …

Dna I-Motifs: Biophysical Characterization And Structure-Property Correlation As Foundation For Functional Material Design, Alexander Minasyan

Graduate Research Theses & Dissertations

Over the past decades, nucleic acids have emerged as crucial frameworks with significance in biological systems and functional material engineering. Cytosine-rich deoxyribonucleotide sequences can form quadruplex structures a.k.a. i-motifs. Recently, i-motifs have attracted scientific interest in biological and material design areas.

In this work, we systematically investigate an effect of structured and unstructured modifications such as hairpins, stems, loops and overhangs on the kinetic and thermodynamic properties of DNA i-motifs. We demonstrate that the modifications can influence i-motif’s stability and folding/unfolding rates: thus, double stranded stems and hairpins are the best at stabilizing i-motifs and increasing kinetic rates of folding. …

Synthesis And Biophysical Analysis Of Modified Cell-Penetrating Peptides, Joel Mitchell

Theses and Dissertations (Comprehensive)

Cell-penetrating peptides (CPPs) are a family of peptides that have the ability to penetrate biological membranes. They were discovered in the late 1980s and have been the topic of many studies. Much of the interest in CPPs has been due to their ability to translocate biological membranes, and the possibility that they could offer a novel drug delivery method by conjugation to biologically active molecules. Linear CPPs can be modified to form cyclic structures. This change in structure has been observed to enhance the stability and penetrative ability of the CPPs which have been studied. The current thesis focuses on …

The Study Of Ribosome-Amplified Metabolism, Rambo, Effect In Vitro And In Live Cells, Jianchao Yu

Electronic Theses & Dissertations (2024 - present)

Quinary interactions arise due to the extreme macromolecular crowding inside live cells. Quinary interactions affect intracellular protein stability, activity, and homeostasis. Ribosomes, traditionally known for their role in protein synthesis, have been found to engage in quinary interactions with metabolic enzymes, modulating their activity and thereby revealing a potential regulatory role for ribosomes in cellular metabolism. This phenomenon, termed the Ribosome-Amplified MetaBOlism (RAMBO) effect, was investigated in this dissertation through a series of in vitro and in vivo studies using primarily Nuclear Magnetic Resonance (NMR) spectroscopy.

Firstly, an NMR-based direct enzyme assay compatible with ribosome was developed and validated using …

Transparent And Conductive Gallium Oxide Electrode For Simultaneous Recording And Optogenetic Stimulation, Christopher Patrick Carey

Graduate Theses, Dissertations, and Problem Reports (ETD)

Neural electrode technology has been around for centuries since the times of Galvani. In early electrophysiology experiments metal wires were used to induce contractions in dissected animals. The metal wire electrode has since been a standard tool to both stimulate and record neural activity. In the past two decades, a new strategy for neural stimulation has been formulated based on the emergent field of optogenetics. Optogenetics refers to the use of light-sensitive proteins genetically imbedded in the membrane of a neuron to elicit neural activity. This technique offers more selectivity in the stimulation of neurons. Typical optogenetic neural electrodes, or …

Quantitative Raman Analysis Of Human Blood Serum Of Glaucoma Patients Supplemented With Macular Pigment Carotenoids., Joy Udensi, Ekaterina Loskutova, James Loughman, Hugh J. Byrne

Datasets

Carotenoids have been widely studied for their high dietary, antioxidant, and vision protection roles in the human body. Blood contains all major dietary carotenoids and hence presents as a suitable and efficient substrate for the estimation of dietary carotenoids in vivo. Following the 18-month supplementation of open angle glaucoma patients with macula pigment carotenoids (Lutein, Zeaxanthin and Meso-Zeaxanthin) in the European Nutrition in Glaucoma Management (ENIGMA) trial, Raman spectroscopic analysis of the pre-supplementation baseline and 18-month supplemented blood serum carotenoids from participants was carried out, to investigate the systemic impact of supplementation in the blood and explore a more direct …