Physical Sciences and Mathematics Commons^™

The Development Of Tailored Amphiphilic Copolymers For Detergent-Free Integral Membrane Protein Extraction, Cameron Edward Workman

Doctoral Dissertations

Integral membrane proteins are prolific targets for the design, development, and delivery of pharmaceuticals. In fact, over 60% of all currently available drugs target these proteins to accomplish their therapeutic effect. However, integral membrane proteins remain the least characterized class of all proteins, accounting for only ~2% of all solved protein structures. One of the primary reasons for this low number of solved protein structures is that many membrane proteins lose their native conformation when extracted using conventional methods (e.g. detergents), convoluting accurate structure determination. In contrast, amphiphilic styrene-maleic acid copolymers (SMAs) were recently discovered to readily isolate membrane proteins …

Analytical Considerations And Methods For Comprehensive Analysis Of Bacterial Phospholipidomics Using Hilic-Ms/Ms, David Thomas Reeves

Doctoral Dissertations

Omics technologies have rapidly evolved over the last half century through vast improvements in efficient extraction methodologies, advances in instrumentation for data collection, and a wide assortment of informatics tools to help deconvolute sample data sets. However, there are still untapped pools of molecules that warrant further analytical attention. As the frontline defense of the cell against exterior influences, the phospholipid membrane is key in structure, defense, and signaling, but current omics studies are only just now catching up to the potential hidden within cellular lipid profiles. Examination of shifts in phospholipid speciation and character could provide researchers with a …

Synthetic Heterosynaptic Plasticity Enhances The Versatility Of Memristive Systems Emulating Bio-Synapse Structure And Function, William T. Mcclintic

Doctoral Dissertations

Memristive systems occur in nature and are hallmarked via pinched hysteresis, the difference in the forward and reverse pathways for a given phenomenon. For example, neurons of the human brain are composed of synapses which apply the properties of memristance for neuronal communication, learning, and memory consolidation. Modern technology has much to gain from the characteristics of memristive systems, including lower power operation, on-chip memory, and bio-inspired computing. What is more, a relationship between memristive systems and synaptic plasticity exists and can be investigated focusing on homosynaptic and heterosynaptic plasticity. Where homosynaptic plasticity applies to interactions between neurons at a …

Probing Structure, Function And Dynamics In Bacterial Primary And Secondary Transporter-Associated Binding Proteins, Shantanu Shukla

Doctoral Dissertations

Substrate binding proteins (SBPs) are ubiquitous in all life forms and have evolved to perform diverse physiological functions, such as in membrane transport, gene regulation, neurotransmission, and quorum sensing. It is quite astounding to observe such functional diversity among the SBPs even when they are restricted by their fold space. Therefore, the SBPs are an excellent set of proteins that can reveal how proteins evolution novel function in a structurally conserved/constrained fold. This study attempts to understand the phenomenon of affinity and specificity evolution in SBPs by combining a set of biochemical, biophysical, and structural studies on the SBPs involved …

Using Second Harmonic Generation To Study Gram-Positive Bacterial Membranes, Lindsey N. Miller

Doctoral Dissertations

Understanding how small-molecules, such as drugs, interact with bacterial membranes can quickly unravel into much more perplexing questions. No two bacterial species are alike, especially when comparing their membrane compositions which can even be altered by incorporating fatty acids from their surrounding environment into their lipid-membrane composition. To further complicate the comparison, discrete alterations in small-molecule structures can result in vastly different membrane-interaction outcomes, giving rise to the need for more "label-free" studies when analyzing drug mechanisms. The work presented in this dissertation highlights the benefits to using nonlinear spectroscopy and microscopy techniques for probing small-molecule interactions in living bacteria. …

Design And Synthesis Of Analogs Of Myo-Inositol, Serine, And Cysteine To Enable Chemical Biology Studies, Tanei J. Ricks

Doctoral Dissertations

Phosphorylated myo-inositol compounds including inositol phosphates (InsPs) as well as the phosphatidylinositol polyphosphate lipids (PIP_ns) are critical biomolecules that regulate many of the most important biological processes and pathways. They are aberrant in many disease states due to their regulatory function. The same is true of the phospholipid phosphatidylserine (PS) which can serve as a marker to begin apoptosis. However, the full scope of activities of these structures is not clear, particularly since techniques that enable global detection and analysis of the production of these compounds spatially and temporally are lacking. With all of these obstacles in …

Biophysical Studies Of Cell Division Protein Localization Mechanisms In Escherichia Coli, Matthew Wayne Bailey

Doctoral Dissertations

How nanometer-scale proteins position accurately within micron-scale bacteria has intrigued both biologists and physicists alike. A critical process requiring precise protein localization is cell division. In most bacteria, cell division starts with the self-assembly of the FtsZ proteins into filaments that form a ring-like structure encircling the cell at its middle, the Z-ring. The Z-ring is a scaffold for additional proteins that synthesize the lateral cell wall which separates the two daughter cells. If division planes are misplaced relative to bacterial chromosomes, also called nucleoids, daughter cells with incomplete genetic material can be produced. In Escherichia coli, research carried out …

Engineering Photosystem I Complexes For Use In Bio-Hybrid Dye-Sensitized Solar Cells, Richard Franklin Simmerman

Doctoral Dissertations

Increasing global population, growing per capita energy needs, diminishing fossil fuels, and climate change collectively will require new, innovative, and sustainable alternatives to meet the world’s growing energy needs. One of the most promising yet simple approaches are dye-sensitized solar cells (DSSCs). However, conventional DSSCs use semi-conductor anodes sensitized with complex synthetic organometallic dyes. Most dyes utilize ruthenium complexes to absorb photons, which upon excitation, inject electrons into the anode, while holes migrate to the cathode via liquid electrolyte. However, these dyes are expensive, difficult to make, and resource-limited. This dissertation focuses on replacing synthetic dyes with the naturally occurring, …

Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega

Doctoral Dissertations

The combination of physics, biology, chemistry, and computer science constitutes the promising field of computational molecular biophysics. This field studies the molecular properties of DNA, protein lipids and biomolecules using computational methods. For this dissertation, I approached four problems involving the chemotaxis pathway, the set of proteins that function as the navigation system of bacteria and lower eukaryotes.

In the first chapter, I used a special-purpose machine for molecular dynamics simulations, Anton, to simulate the signaling domain of the chemoreceptor in different signaling states for a total of 6 microseconds. Among other findings, this study provides enough evidence to propose …

Quorum Sensing And Metabolism In Marine Environments, Amanda May

Doctoral Dissertations

Quorum sensing (QS) is a phenomenon that allows bacteria to communicate with each other. Small molecules known as autoinducers are synthesized and released by bacteria, and once enough members of the community are around to ensure survival, i.e. quorum, a phenotype, e.g. bioluminescence, is expressed. There are two types of QS molecules, intra- and inter-species.

S-4,5-Dihydroxy-2,3-pentanedione (DPD) is a byproduct of the activated methyl cycle which recycles methionine. This has led to the discussion as to whether DPD is a metabolic byproduct or is the interspecies signal as proposed previously. The detection and quantitation of DPD however, has not …

Towards A Unification Of Supercomputing, Molecular Dynamics Simulation And Experimental Neutron And X-Ray Scattering Techniques, Benjamin Lindner

Doctoral Dissertations

Molecular dynamics simulation has become an essential tool for scientific discovery and investigation. The ability to evaluate every atomic coordinate for each time instant sets it apart from other methodologies, which can only access experimental observables as an outcome of the atomic coordinates. Here, the utility of molecular dynamics is illustrated by investigating the structure and dynamics of fundamental models of cellulose fibers. For that, a highly parallel code has been developed to compute static and dynamical scattering functions efficiently on modern supercomputing architectures. Using state of the art supercomputing facilities, molecular dynamics code and parallelization strategies, this work also …

Synthesis, Characterization And Self-Assembly Of Amphiphilic Block Copolymers, Xiaojun Wang

Doctoral Dissertations

This dissertation presents a review on state-of-the-art research of well-defined charged block copolymers, including synthesis, characterization, bulk morphology and self-assembly in aqueous solution of amphiphilic block polyelectrolytes. In Chapter 1, as a general introduction, experimental observations and theoretical calculations devoted towards understanding morphological behavior in charged block copolymer systems are reviewed along with some of the new emerging research directions. Further investigation of charged systems is urged in order to fully understand their morphological behavior and to directly target structures for the tremendous potential in technological applications. Following this background, in Chapters 2, 3, 4 and 5 are presented the …

Development And Application Of Liquid Chromatography-Tandem Mass Spectrometry Methods To The Understanding Of Metabolism And Cell-Cell Signaling In Several Biological Systems, Jessica Renee Gooding

Doctoral Dissertations

Liquid chromatography tandem mass spectrometry has become a powerful tool for investigating biological systems. Herein we describe the development of both isotope dilution mass spectrometry methods and targeted metabolomics methods for the study of metabolic and cell-cell signaling applications.

A putative yeast enzyme was characterized by discovery metabolite profiling, kinetic flux profiling, transcriptomics and structural biology. These experiments demonstrated that the enzyme shb17 was a sedoheptulose bisphosphatase that provides a thermodynamically dedicated step towards riboneogenesis, leading to the redefinition of the canonical pentose phosphate pathway.

An extension of metabolic profiling and kinetic flux profiling methods was developed for a set …

A Time-And-Space Parallelized Algorithm For The Cable Equation, Chuan Li

Doctoral Dissertations

Electrical propagation in excitable tissue, such as nerve fibers and heart muscle, is described by a nonlinear diffusion-reaction parabolic partial differential equation for the transmembrane voltage $V(x,t)$, known as the cable equation. This equation involves a highly nonlinear source term, representing the total ionic current across the membrane, governed by a Hodgkin-Huxley type ionic model, and requires the solution of a system of ordinary differential equations. Thus, the model consists of a PDE (in 1-, 2- or 3-dimensions) coupled to a system of ODEs, and it is very expensive to solve, especially in 2 and 3 dimensions.

In order to …

Adaptation And Stochasticity Of Natural Complex Systems, Roy David Dar

Doctoral Dissertations

The methods that fueled the microscale revolution (top-down design/fabrication, combined with application of forces large enough to overpower stochasticity) constitute an approach that will not scale down to nanoscale systems. In contrast, in nanotechnology, we strive to embrace nature’s quite different paradigms to create functional systems, such as self-assembly to create structures, exploiting stochasticity, rather than overwhelming it, in order to create deterministic, yet highly adaptable, behavior. Nature’s approach, through billions of years of evolutionary development, has achieved self-assembling, self-duplicating, self-healing, adaptive systems. Compared to microprocessors, nature’s approach has achieved eight orders of magnitude higher memory density and three orders …

Human Decomposition Ecology At The University Of Tennessee Anthropology Research Facility, Franklin Edward Damann

Doctoral Dissertations

The University of Tennessee Anthropology Research Facility (ARF) is well known for its unique history as a site of human decomposition research in a natural environment. It has been integral to our understanding of the processes of human decomposition. Over the last 30 years 1,089 bodies have decomposed at this 1.28 acre facility, producing a density of 850 corpses per acre of land. This project evaluated the abiotic and biotic characteristics of the soil exposed to various levels of human decomposition in order to determine the effect on the physicochemical properties and the indigenous bacterial communities.

Specifically, 75 soil samples …