Biochemistry, Biophysics, and Structural Biology Commons^™

Interactions Between The Organellar Pol1a, Pol1b, And Twinkle Dna Replication Proteins And Their Role In Plant Organelle Dna Replication, Stewart Anthony Morley

Theses and Dissertations

Plants maintain organelle genomes that are descended from ancient microbes. Ages ago, these ancient microbes were engulfed by larger cells, beginning a process of co-evolution we now call the endo-symbiotic theory. Over time, DNA from the engulfed microbe was transferred to the genome of the larger engulfing cell, eventually losing the ability to be free-living, and establishing a permanent residency in the larger cell. Similarly, the larger cell came to rely so much on the microbe it had engulfed, that it too lost its ability to survive without it. Thus, mitochondria and plastids were born. Nearly all multicellular eukaryotes possess …

Ribosomally Synthesized And Post-Translationally Modified Peptides As Potential Scaffolds For Peptide Engineering, Devan Bursey

Theses and Dissertations

Peptides are small proteins that are crucial in many biological pathways such as antimicrobial defense, hormone signaling, and virulence. They often exhibit tight specificity for their targets and therefore have great therapeutic potential. Many peptide-based therapeutics are currently available, and the demand for this type of drug is expected to continue to increase. In order to satisfy the growing demand for peptide-based therapeutics, new engineering approaches to generate novel peptides should be developed. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a group of peptides that have the potential to be effective scaffolds for in vivo peptide engineering projects. These …

Synthesis Of Candidate Natural Killer T Cell Ligands, Teron Haynie, Shenglou Deng, Paul B. Savage

Undergraduate Honors Theses

Natural Killer T (NKT) cells are a subset of T cells that express an invariant T cell receptor (TCR) that recognizes lipid antigens in context of the CD1d molecule. CD1d presents both exogenous and endogenous glycolipids on the surface of antigen presenting cells (APCs). Multiple exogenous lipids capable of NKT cell stimulation have been characterized, but confirmed endogenous ligands are relatively few in number. Recently, a-galactosylceramides were shown to be endogenous NKT cell ligands. We have observed that a-galactosylceramides cyclize in acidic conditions. Since the biosynthetic pathway of lipid presentation via CD1d likely passes through the acidic lysosome, we propose …

An Introductory Study Of Solid Materials For Capture And Catalysis Of Waste Stream Chemicals, Steven Kyle Butler

Theses and Dissertations

Heterogeneous catalysts are key materials in research and industry. Herein we study two materials in different stages of development toward being applied as heterogeneous catalysts. First, MoO3SnO2 was synthesized and studied as a catalytic system similar to Sn-beta zeolites. While the Mo-based catalyst did not show similar activity to Sn-beta, it did show interesting reactivity in activating carbonyls and oxidizing organic substrates. Second, a method was developed for grafting amines onto carboxylic acid functionalized carbon nanotubes for CO2 capture. The method was successful for grafting monomer ethylamine groups onto CNT and can be further developed to allow for polymeric amine …

Progress Toward Synthetically Simplified Natural Anticancer Peptide, David W. Kastner, Steven L. Castle

Library/Life Sciences Undergraduate Poster Competition 2018

Yaku’amide A was isolated in late 2010 from the deep-sea sponge Ceratopsion sp. and exhibits potent inhibitory activity against 39 human cancer cell lines via a potentially novel mode of action. However, the total synthesis requires many steps and produces low yields. In this study, we determined two simpler YA analogues that may retain its anticancer properties and can be synthesized in larger quantities. The analogues replace dehydroisoleucine with either dehydroethylnorvaline or dehydrovaline.

Contribution Of Bulky <&Alpha>,<&Beta>-Dehydroamino Acids To The Proteolytic Stability Andenhanced Folding Of <&Beta>-Hairpins And Progress Towards The Total Synthesis Of Yaku<'>Amide A, Ankur Jalan

Theses and Dissertations

This dissertation primarily covers the impact of bulky ,-dehydroamino acids on the proteolytic stability and enhanced folding of -hairpins. It partly describes the progress towards the total synthesis of yakuamide A, a potent anticancer peptide with an IC50 value of 14 ng/mL against leukemia cells. Proteins and peptides are a very attractive source of potential medicinal agents as they can target various protein“protein interactions that are implicated in several diseases and disorders. The global sales of peptide drugs in 2013 were estimated to be about $28 billion and are constantly rising at an appreciable rate. However, peptide drugs have a …

Capacity Of Human Immunodeficiency Virus Targeting Chimeric Antigen Receptor T Cells To Eliminate Follicular Dendritic Cells Bearing Human Immunodeficiency Virus Immune Complexes, Matthew T. Ollerton

Theses and Dissertations

An important obstacle to a functional cure for HIV/AIDS is the persistence of viral reservoirs found throughout the body in various cells and tissues. Reservoirs can be latently infected cells, or in the case of follicular dendritic cells (FDC), non-infected cells that trap infectious virus on their surface through immune complexes (HIV-IC). Although several strategies have been employed to target and eliminate viral reservoirs, they are short-lived and ineffective. In an attempt to provide a long-term approach, chimeric antigen receptor T (CAR-T) cells were designed to eliminate native HIV on FDCs. Although effective at eliminating HIV-infected cells, and halting spreading …

Electronic Structure And Quassiclassical Dynamics Of [2+2] Tetrafluoroethylene Cycloaddition Reactions, Steven Jones, Daniel Ess

Journal of Undergraduate Research

Cycloaddition reactions are key reactions used to construct complex cyclic scaffolds (large networks of carbon atoms that can be used in catalysis, synthesis, etc.). While classical reactions that form 6-membered rings are well-known and generally have a one-step reaction mechanism, 4-member ring-forming reactions are much less used, but could be very valuable for the construction of cyclobutane structures.

Tetrafluoroethylene (TFE) is used on a large scale by Dow and other chemical companies to form hydrofluoro compounds such as teflon. The current understanding of the mechanism of cycloaddition reactions with TFE is limited. Standard hydrocarbon reactions proceed via a welldocumented, concerted …

Development And Application Of Minimum Energy Crossing Point Software Suite For Organometallic Reactions, Justin Snyder, Daniel H. Ess

Journal of Undergraduate Research

Computational studies are critical to the field of organometallic chemistry since many highly reactive and unstable compounds cannot be isolated or observed experimentally. It is well-known that many organometallic reaction mechanisms involve spin intersystem crossing, e.g. singlet to triplet conversion. To estimate the rate of intersystem crossing it is useful to calculate electronic structures where spin states and their energies are degenerate, which is called a “minimum energy crossing point (MECP).” Prior to the completion of this project, there was only one working program that interfaced with the Gaussian 09 electronic structure package for the calculation of minimum energy which …

Quantifying The Efficiency Of Heterobimetallic Complexes, Ryjul Stokes, David Michaelis

Journal of Undergraduate Research

Transition metal catalysts have revolutionized the efficiency by which pharmaceuticals and other value added products are synthesized due to their unique ability to activate small molecules and drive the formation of new C-C and C-N bonds. In particular, the direct functionalization of olefins with transition metal catalysts is a powerful method of converting simple, cheap building blocks into more complex molecules. The challenge is that many ligands that control reaction selectivity often decrease the electrophilicity of the catalyst. Heterobimetallic complexes containing an early/late transition metal pair could provide a solution to this challenge by providing a new way to activate …

Microwave Promoted Iminyl Radical Cyclization, Aaron Kubosumi, Steven L. Castle

Journal of Undergraduate Research

Pyrrolidines and their derivatives are found in many biologically active compounds, such as Lipitor and Atorvastatin, which possess a wide variety of remarkable pharmaceutical properties. Therefore, the efficient synthesis of functionalized pyrrolidines is of great value to organic chemists. Multiple attempts have been made to synthesize compounds containing pyrrolidine ring systems. Walton 1 utilized radical cyclization, via microwave heating, to transform Ophenyl oximes with terminal alkenes to dihydropyrroles, compounds closely related to pyrrolidines. Similarly, Sammis 2 proposed a method involving radical cyclizations of azidederived aminyl radicals onto silyl enol ethers. Unfortunately, the method proposed by Sammis requires highly toxic and …

Determining The Structure Of The Bbbsome, Grant Ludlam, Barry Willardson

Journal of Undergraduate Research

Bardet-Biedl Syndrome (BBS) occurs when an eight-protein complex called the BBSome is improperly assembled and can no longer function. The BBSome is responsible for trafficking membrane proteins to cilia, a projection from the cell surface packed with receptors that allow the cell to sense its surroundings. Loss of BBSome function causes malformation of cilia and leads to vision loss, obesity, kidney disease and mental retardation.

The Total Synthesis Of Yaku’Mide A, Shi Luo, Steven Castle

Journal of Undergraduate Research

Yaku’amide A (YA) has potent toxicity against cancer cells (IC50 = 14 ng/ml against P388 murine leukemia cells). Ueoka et al.1 first reported the isolation of YA from a marine sponge in the East China Sea. They used spectroscopy and chemical degradations to analyze its structure. YA contains unique dehydroamino acids (See Figure 1). In the growth inhibition study, YA showed unique activity against 39 cancer cell lines, indicating a novel mode of action. The unusual structure of YA and its prominent biological activity has attracted research groups from around the world to address its synthesis.

Using Three Incommensurate Wave Components To Generate Terahertz Radiation, Jacob Bagley, Jeremy Johnson

Journal of Undergraduate Research

Electromagnetic radiation is a wave composed of an electric field and a magnetic field. Examples of electromagnetic radiation include visible light, ultraviolet light, Xrays, infrared light, microwaves, and more. Electromagnetic radiation is an indispensable tool for both controlling and studying matter and is applied to countless fields such as electronics manufacturing and medical imaging. Over the past two decades terahertz (THz) radiation, a form of electromagnetic radiation, has become an intense area of research. This surge in activity in due in part to technological advances in generating THz radiation, but is also due to the myriad of potential applications of …

Anthrax, Matrix Biology, And Angiogenesis: Capillary Morphogenesis Gene 2 Mediates Activity And Uptake Of Type Iv Collagen-Derived Anti-Angiogenic Peptides, Jordan Grant Finnell

Theses and Dissertations

Capillary Morphogenesis Gene 2 (CMG2) is a type I transmembrane, integrin-like receptor. It was originally identified as one of several genes upregulated during capillary formation. It was subsequently identified as one of two physiological anthrax toxin receptors, where CMG2 serves as a cell-surface receptor for anthrax toxin and mediates entry of the toxin into cells via clathrin-dependent endocytosis. Additionally, loss-of-function mutations in CMG2 cause the genetic disorder hyaline fibromatosis syndrome (HFS), where the core symptom is dysregulation of extracellular matrix homeostasis (ECM), including excessive accumulation of proteinaceous hyaline material; HFS clearly indicates that CMG2 plays an essential function in ECM …

Enzyme Encapsulation, Biosensing Endocrine Disrupting Chemicals, And Bio-Therapeutic Expression Platforms Using Cell-Free Protein Synthesis, Seung Ook Yang

Theses and Dissertations

Cell-free protein synthesis (CFPS) is a powerful protein expression platform where protein synthesis machinery is borrowed from living organisms. Target proteins are synthesized in a reaction tube together with cell extract, amino acids, energy source, and DNA. This reaction is versatile, and dynamic optimizations of the reaction conditions can be performed. The "œopen" nature of CFPS makes it a compelling candidate for many technologies and applications. This dissertation reports new and innovative applications of CFPS including 1) enzyme encapsulation in a virus-like particle, 2) detection of endocrine disrupting chemicals in the presence of blood and urine, and 3) expression of …

Production Of Commodity Chemicals With A Glycerol Feedstock, Zachary Pribyl, Kara Stowers

Journal of Undergraduate Research

In recent years there has been a growing interest to move away from petroleum feedstocks and instead use renewable fuel sources. As this interest has increased and biofuel has been used in greater volume, glycerol (a byproduct of biofuel production) has become over-produced in the world market because it has limited commercial use as a non-edible oxygenated hydrocarbon. The ability to utilize this by-product in commercial bulk chemicals would correspondingly increase the demand for biofuel, promoting a greater shift toward renewable sources.

Development And Application Of Quassiclassical Direct Dynamics Program For Organic And Organometallic Reactions, Nathan Wohlgemuth, Dan Ess

Journal of Undergraduate Research

Organic and organometallic reactions are generally assumed to follow statistical mechanical models of reactivity and selectivity that correspond to transition state theory. However, in recent years there have been several organic reactions that have been shown to be controlled by post-transition state reaction dynamics. While some direct dynamics programs are available (VENUS, ProgDyn, etc.) they are generally difficult to use and have little documentation. To overcome this problem, we created a molecular dynamics software suite (called DynSuite) that interfaces with the electronic structure program Gaussian 09. We used this software to perform known examples of direct dynamics simulations for organic …

Utilizing Microfluidics Devices To Monitor Endothelial Cell Migration., Tsz Ming Jeremy Tsang, Jacob Lefler, Charles Voyton, Kenneth Christensen

Biomedical Engineering Western Regional Conference

Utilizing microfluidics devices to monitor endothelial cell migration.

Engineering Fret Biosensors For Microrna Presence/Absence Analysis, Nicholas E. Larkey, Sean M. Burrows

Biomedical Engineering Western Regional Conference

No abstract provided.

Deuterateer: A Tool For Quantifying Peptide Isotope Precision And Kinetic Proteomics, Bradley C. Naylor, Michael T. Porter, Elise Wilson, Adam Herring, Spencer Lofthouse, Austin Hannemann, Stephen R. Piccolo, Alan L. Rockwood, John C. Price

Faculty Publications

Motivation

Using mass spectrometry to measure the concentration and turnover of the individual proteins in a proteome, enables the calculation of individual synthesis and degradation rates for each protein. Software to analyze concentration is readily available, but software to analyze turnover is lacking. Data analysis workflows typically don’t access the full breadth of information about instrument precision and accuracy that is present in each peptide isotopic envelope measurement. This method utilizes both isotope distribution and changes in neutromer spacing, which benefits the analysis of both concentration and turnover.

Results

We have developed a data analysis tool, DeuteRater, to measure protein …

Placental ‘€˜Omics’€™ Study To Understand The Pathogenesis Of Preeclampsia, Komal Kedia

Theses and Dissertations

Preeclampsia (PE) is a potentially fatal complication of pregnancy characterized by an increase in blood pressure (>140/90 mmHg) and proteinuria (>300 mg/24 hrs), often accompanied by edema. Symptoms of PE start after 20 weeks of gestation. If PE remains untreated, it can lead to eclampsia, grand-mal seizures responsible for most fatalities. PE is believed to affect 2-10% of pregnancies worldwide, and claims the lives of over 75,000 mothers and 500,000 newborns yearly. No therapeutic agents have been developed to prevent or cure PE. Part of the reason for this is the absence of a complete understanding of the …

Development And Application Of New Solid-State Models For Low-Energy Vibrations, Lattice Defects, Entropies Of Mixing, And Magnetic Properties, Jacob M. Schliesser

Theses and Dissertations

Low-temperature heat capacity data contain information on the physical properties of materials, and new models continue to be developed to aid in the analysis and interpretation of heat capacity data into physically meaningful properties. This work presents the development of two such models and their application to real material systems. Equations describing low-energy vibrational modes with a gap in the density of states (DOS) have been derived and tested on several material systems with known gaps in the DOS, and the origins of such gaps in the DOS are presented. Lattice vacancies have been shown to produce a two-level system …

14-3-3Ζ Regulation Of Metastasis Through Mediation Of Liprin-Α And Liprin-Β, Rachel Hynes

Theses and Dissertations

Cancer is a set of varied and diverse diseases that share common characteristics, such as active proliferation, increased replicative potential, and tissue invasion or metastasis. One protein, 14-3-3ζ, is shown to be upregulated in a number of different cancers and also correlates with poor patient prognosis, recurrence, and mortality. This protein comes from a family of adapter proteins known for their scaffolding ability, pro- and anti-oncogenic capabilities, and affinity for phosphorylated substrates. It has been shown previously to participate in cancer progression, subversion of apoptosis, and to increase chemoresistance. Herein we will discuss the ability of 14-3-3ζ to promote distant-site …

Targeting Superoxide Dismutase-¬1 In Cancer, Laura Oh, Josh Andersen

Journal of Undergraduate Research

SOD1 is overexpressed in many cancers such as lung adenocarcinoma, non-­ small-­cell lung cancer, and 70% of primary breast cancers. Traditionally, SOD1 is known as an antioxidant in the human body, but only 1% of SOD1 expressed in cells is necessary to keep superoxide radicals below cytotoxic levels, suggesting that SOD1 may have undiscovered functions. One of the known trademarks of cancer is the Warburg Effect defined by up-­regulated glycolysis and down-­ regulated respiration. It is thought that this unique mode of metabolism promotes cancer cell growth. A recent study demonstrated that SOD1 functions to repress respiration through the casein …

Developing A Microfluidic Lab-On-A-Chip Device To Assess The Correlation Between The Ratio Of H And L Ferritin In Maternal Serum And Preterm Birth, Kaitlyn Brower, Adam Woolley

Journal of Undergraduate Research

Preterm birth is the leading cause of death in children under the age of 5¹ and is defined by the Centers for Disease Control as birth before 37 weeks gestation.² It is estimated that 15 million babies are born premature annually and that PTB kills nearly 1 million babies every year. Currently, accurate detection of PTB risk isn’t possible and extrauterine treatments and interventions are insufficient.

Learning Chemistry Through Experimentation, Kyle Long, Jennifer Nielson

Journal of Undergraduate Research

For the past five years, Dr. Jennifer Nielson has conducted research in Kampala, Uganda, located in south-central Africa. I have been able to join her for two of the five years, including this past year for nearly three weeks in August. Our research focuses on teaching basic chemistry principle that are difficult to comprehend by using experiments that demonstrate the general concept of atomic structures and functions.

Software Package For Mass Spectrometry Isotope Analysis And Extraction, Michael Porter, Dr. John Price

Journal of Undergraduate Research

Proteins are involved in nearly every cellular process. They transport molecules, replicate DNA, catalyze reactions, respond to stimuli, and form the structural framework of the cell. The diversity of protein function has led to an interest in understanding the cellular production and control of individual proteins which in turn is key to understanding how the cell responds to the environment and what occurs on a molecular level during disease.

Solving The Structure Of The Raptor-Cct Complex, Grant Ludlam, Barry Willardson

Journal of Undergraduate Research

The protein Raptor is an essential component of the mechanistic target of rapamycin (mTOR) cell signaling complex 1 (mTORC1) (1). The mTORC1 complex is a master regulator of cell growth, making it a high-priority target in cancer and inflammation research (2). Before Raptor can be assembled into the mTORC1, it is first folded by the chaperone protein cytosolic chaperonin containing TCP1 (CCT). CCT is composed of two rings of 8 different subunits, which together form a barrel shape. CCT substrates are folded in the 85 Å wide folding cavity inside the barrel.

Microbial Pretreatment Of Waste For Anaerobic Digestion, Braden Myers, Jaron Hansen

Journal of Undergraduate Research

The aim of this research was to demonstrate Caldicellulosiruptor bescii is a feasible microbial pretreatment of lignocellulose for enhanced production of biogas when coupled with secondary anaerobic digestion. Before anaerobic digestion of waste can reach its maximum energy production potential, economically sound methods for pretreatments that allow increased digestion of waste materials must be developed. Many types of waste cannot be broken down sufficiently by anaerobic digestion alone. Overcoming this hurdle through successful feedstock pretreatment would unlock a vast potential supply of renewable energy feedstock materials.