Biochemistry, Biophysics, and Structural Biology Commons^™

Mechanisms Of Oxidant Generation By Catalase, Diane E. Heck, Michael Shakarjian, Hong-Duck Kim, Jeffrey Laskin, Anna M. Vetrano

NYMC Faculty Publications

The enzyme catalase converts solar radiation into reactive oxidant species (ROS). In this study, we report that several bacterial catalases (hydroperoxidases, HP), including Escherichia coli HP-I and HP-II also generate reactive oxidants in response to ultraviolet B light (UVB). HP-I and HP-II are identical except for the presence of NADPH. We found that only one of the catalases, HPI, produces oxidants in response to UVB light, indicating a potential role for the nucleotide in ROS production. This prompts us to speculate that NADPH may act as a cofactor regulating ROS generation by mammalian catalases. Structural analysis of the NADPH domains …

The Marine Sponge Metabolite Mycothiazole: A Novel Prototype Mitochondrial Complex I Inhibitor., J Brian Morgan, Fakhri Mahdi, Yang Liu, Veena Coothankandaswamy, Mika B. Jekabsons, Tyler A. Johnson, Koneni V. Sashidhara, Phillip Crews, Dale G. Nagle, Yu-Dong Zhou

Natural Sciences and Mathematics | Faculty Scholarship

A natural product chemistry-based approach was applied to discover small-molecule inhibitors of hypoxia-inducible factor-1 (HIF-1). A Petrosaspongia mycofijiensis marine sponge extract yielded mycothiazole (1), a solid tumor selective compound with no known mechanism for its cell line-dependent cytotoxic activity. Compound 1 inhibited hypoxic HIF-1 signaling in tumor cells (IC(50) 1nM) that correlated with the suppression of hypoxia-stimulated tumor angiogenesis in vitro. However, 1 exhibited pronounced neurotoxicity in vitro. Mechanistic studies revealed that 1 selectively suppresses mitochondrial respiration at complex I (NADH-ubiquinone oxidoreductase). Unlike rotenone, MPP(+), annonaceous acetogenins, piericidin A, and other complex I inhibitors, mycothiazole is a mixed polyketide/peptide-derived compound …

Synthesis And Characterization Of An Oligothiophene-Ruthenium Complex And Synthesis And Optical Properties Of Oligothiophene-Ruthenium Complexes Bound To Cdse Nanoparticles, Nathan A. Bair

Theses and Dissertations

Oligothiophenes are of increasing interest in organic based electronic devices in part due to their high electron and hole mobilities. In an organic photovoltaic (OPV) device, the electronic properties of oligothiophenes make them advantageous as charge transfer junctions. To serve as charge transfer junctions, oligothiophenes must be functionalized to bind to the donor and acceptor parts of the device. The donor and acceptor parts are different materials and the synthesis of asymmetric oligothiophenes is of great interest. Previous researchers in our lab synthesized four asymmetric oligothiophenes, two with two thiophene subunits and two with four. Each set of oligothiophenes contained …

Exploring Zirconia As A Column Packing Material, Tushar Ghugare

Masters Theses & Specialist Projects

Zirconia is one of the most promising column packing materials for High Performance Liquid Chromatography (HPLC). The perfect HPLC support material should be energetically homogenous, have a high surface area on which different chemical species can reversibly attach and be physically and chemically stable over a wide range of pH, temperature and solvent conditions. Most existing supports do not have all of these properties. This project is also focused on a proteomics study. Zirconia, hafnium oxide and titanium oxide which are some of the more promising materials currently available, can be used for the separation and analysis of phosphorylated proteins. …

Properties Of Microbes In Natural Fire Burn Soils, Holly Anderson

Undergraduate Honors Capstone Projects

Soil underlying a natural fire develops a hydrophobic soil sub-layer. This hydrophobicity decreases with time although the mechanisms are unresolved, but are thought to be biotic and abiotic. Some of the compounds accounting for hydrophobicity are polycyclic aromatic hydrocarbons (PAHs) of which pyrene is an example.

Bacteria that grew on pyrene were isolated from burned soils at two sites in Utah in order to analyze the biotic microbial degradation of the hydrophobic soil sub-layer. The two sites were Wood Camp (Logan, UT) and Milford Flats (Central UT). Identifications of the genera of nine isolated bacteria were made through l6S rRNA …

Study Of The Efficacy, Biodistribution, And Safety Profile Of Therapeutic Gutless Adenovirus Vectors As A Prelude To A Phase I Clinical Trial For Glioblastoma, Akm Ghulam Muhammad, Mariana Puntel, Marianela Candolfi, A Salem, Kader Yagiz, C Farrokhi, Kurt Kroeger, Weidong Xiong, James Curtin, Chunyan Liu, K Lawrence, Niyati Bondale, Jonathan Lerner, G Baker, David Foulad, Robert Pechnick, Donna Palmer, Philip Ng, Pedro Lowenstein, Maria Castro

Articles

Glioblastoma multiforme (GBM) is the most common and most aggressive primary brain tumor in humans. Systemic immunity against gene therapy vectors has been shown to hamper therapeutic efficacy; however, helper-dependent high-capacity adenovirus (HC-Ad) vectors elicit sustained transgene expression, even in the presence of systemic anti-adenoviral immunity. We engineered HC-Ads encoding the conditional cytotoxic herpes simplex type 1 thymidine kinase (TK) and the immunostimulatory cytokine fms-like tyrosine kinase ligand 3 (Flt3L). Flt3L expression is under the control of the regulatable Tet-ON system. In anticipation of a phase I clinical trial for GBM, we assessed the therapeutic efficacy, biodistribution, and clinical and …

Aryl Boronic Acid Inhibition Of Synthetic Melanin Polymerization, Jason M. Belitsky

Faculty & Staff Scholarship

Inhibitors of melanin formation are sought after for a range of applications. Boronophenylalanine is known to inhibit melanogenesis via boronic acid-catechol interactions. A spectroscopic assay was developed to study the polymerization of L-dopa to synthetic melanin in the presence of para-substituted aryl boronic acids. The best inhibition was observed for aryl boronic acids with electron-withdrawing substituents. The IC50 values exhibit a correlation with the Hammett sigma(p) parameter (rho = 0.97, r(2) = 0.92).

Poxa, Yjek And Elongation Factor P Coordinately Modulate Virulence And Drug Resistance In Salmonella Enterica, William Wiley Navarre, Shicong Zou, Hervé Roy, Jinglin Lucy Xie, Alexei Savchenko, Alexander Singer, Elena Edvokimova, Lynne R. Prost, Runjun Kumar, Michael Ibba, Ferric C. Fang

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We report an interaction between poxA, encoding a paralog of lysyl tRNA-synthetase, and the closely linked yjeK gene, encoding a putative 2,3-β-lysine aminomutase, that is critical for virulence and stress resistance in Salmonella enterica. Salmonella poxA and yjeK mutants share extensive phenotypic pleiotropy, including attenuated virulence in mice, an increased ability to respire under nutrient-limiting conditions, hypersusceptibility to a variety of diverse growth inhibitors, and altered expression of multiple proteins, including several encoded on the SPI-1 pathogenicity island. PoxA mediates posttranslational modification of bacterial elongation factor P (EF-P), analogous to the modification of the eukaryotic EF-P homolog, eIF5A, with …

Measurement Of Hono, Hnco, And Other Inorganic Acids By Negative-Ion Proton-Transfer Chemical-Ionization Mass Spectrometry (Ni-Pt-Cims): Application To Biomass Burning Emissions, J. M. Roberts, P. Veres, C. Warneke, J. A. Neuman, R. A. Washenfelder, S. S. Brown, M. Baasandorj, J. B. Burkholder, I. R. Burling, T. J. Johnson, Robert J. Yokelson, J. De Gouw

Chemistry and Biochemistry Faculty Publications

A negative-ion proton-transfer chemical ionization mass spectrometric technique (NI-PT-CIMS), using acetate as the reagent ion, was applied to the measurement of volatile inorganic acids of atmospheric interest: hydrochloric (HCl), nitrous (HONO), nitric (HNO(3)), and isocyanic (HNCO) acids. Gas phase calibrations through the sampling inlet showed the method to be intrinsically sensitive (6-16 cts/pptv), but prone to inlet effects for HNO(3) and HCl. The ion chemistry was found to be insensitive to water vapor concentrations, in agreement with previous studies of carboxylic acids. The inlet equilibration times for HNCO and HONO were 2 to 4s, allowing for measurement in biomass burning …

2,4,6-Triphenyl­Aniline, Onome Ugono, Stephanie Cowin, Alicia Beatty

Chemistry & Biochemistry Faculty Works

Individual mol­ecules of the title compound, C24H19N, do not participate in hydrogen-bonding inter­actions due to the steric bulk of the phenyl rings ortho to the amine. The dihedral angles between the central ring and the pendant rings are 68.26 (10), 55.28 (10) and 30.61 (11)°.

Synthesis Of Glycolipids And Evaluation Of Their Nkt Cell Stimulatory Properties, Yang Liu

Theses and Dissertations

Natural killer T (NKT) cells are a subset of T cells that modify a variety of immune responses. NKT cells recognize glycolipid antigen presented by a molecule called CD1d, a nonclassical antigen-presenting molecule. The best known subset of CD1d-dependent NKT cells expresses an invariant T cell receptor Vα (TCR-α) chain. These are referred to as type I or invariant NKT (iNKT) cells. When stimulated by a glycolipid, NKT cells rapidly release large amounts of cytokines. Cytokines released by NKT cells can induce either Th1 or Th2 responses. Th1 cytokines are effective in regulating bacterial, parasitic, and viral infections. But Th1 …

Release Of Hmgb1 In Response To Pro-Apoptotic Glioma Killing Strategies: Efficacy And Neurotoxicity, Marianela Candolfi, Kader Yagiz, David Foulad, Gabrielle Alzadeh, Matthew Tesarfreund, Akm Ghulam Muhammad, Mariana Puntel, Kurt Kroeger, Chunyan Liu, Sharon Lee, James Curtin, Gwendalyn D. King, Jonathan Lerner, Katsuaki Sato, Yohei Mineharu, Weidong Xiong, Pedro R. Lowenstein, Maria Castro

Articles

Purpose In preparation for a Phase I clinical trial utilizing a combined cytotoxic/immunotherapeutic strategy using adenoviruses expressing Flt3L (Ad-Flt3L) and thymidine kinase (Ad-TK) to treat glioblastoma (GBM), we tested the hypothesis that Ad-TK+GCV would be the optimal tumor killing agent in relation to efficacy and safety when compared to other pro-apoptotic approaches. Experimental Design and Results The efficacy and neurotoxicity of Ad-TK+GCV was compared with Ads encoding the pro-apoptotic cytokines (TNF-α, TRAIL, FasL), alone or in combination with Ad-Flt3L. In rats bearing small GBMs (day 4), only Ad-TK+GCV or Ad-FasL improved survival. In rats bearing large GBMs (day 9), the …

Short-Chain Carboxylic Acids From Gray Catbird (Dumetella Carolinensis) Uropygial Secretions Vary With Testosterone Levels And Photoperiod, Rebecca J. Whelan, Tera C. Levin, Mary C. Garvin

Faculty & Staff Scholarship

The uropygial gland of birds produces secretions that are important in maintaining the health and structural integrity of feathers. Non-volatile components of uropygial secretions are believed to serve a number of functions including waterproofing and conditioning the feathers. Volatile components have been characterized in fewer species, but are particularly interesting because of their potential importance in olfactory interactions within and across species. We used solid-phase microextraction headspace sampling with gas chromatography-mass spectrometry to detect and identify volatiles in uropygial secretions of gray catbirds (Dumetella carolinensis), a North American migratory bird. We consistently detected the following carboxylic acids: acetic, …

Targeting Complex Cyclic Peptides For Synthesis: The Celogentin And Theonellamide Families, Joshua Wayne Robinson

Theses and Dissertations

Celogentin C and theonellamide F are a class of natural products that have potential antimitotic behavior. They both contain interesting bicyclic structures with unusual linkages within a central moiety. Celogentin C's highly functionalized tryptophan moiety has two unusual linkages, a β-substituted Leu connection to the C6 of the indole structure that makes up the left-hand ring, and a τ-N connection of the imidazole to the C2 of the indole constructing the right-hand ring. This right-hand ring connection was solved via a novel oxidative coupling procedure developed in our group and the left-hand ring was initially constructed via a radical conjugated …

Redox Status Affects The Catalytic Activity Of Glutamyl-Trna Synthetase, Assaf Katz, Ranat Banerjee, Merly De Armas, Michael Ibba, Omar Orellana

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Glutamyl-tRNA synthetases (GluRS) provide Glu-tRNA for different processes including protein synthesis, glutamine transamidation and tetrapyrrole biosynthesis. Many organisms contain multiple GluRSs, but whether these duplications solely broaden tRNA specificity or also play additional roles in tetrapyrrole biosynthesis is not known. Previous studies have shown that GluRS1, one of two GluRSs from the extremophile Acidithiobacillus ferrooxidans, is inactivated when intracellular heme is elevated suggesting a specific role for GluRS1 in the regulation of tetrapyrrole biosynthesis. We now show that, in vitro, GluRS1 activity is reversibly inactivated upon oxidation by hemin and hydrogen peroxide. The targets for oxidation-based inhibition were …

Celogentin C And Thioviridamide: Synthetic And Structural Studies, Dmitry Nikolayevich Litvinov

Theses and Dissertations

Project I Celogentin C, isolated by Kobayashi from the seeds of Celosia argentea in 2001 exhibits strong inhibitory behavior towards polymerization of tubulin – globular protein, which plays crucial role during the cell division cycle. We have attempted synthesis of the left-hand ring of celogentin C via the intramolecular alkylation and the Knoevenagel condensation strategies. Utilizing synthetic methodologies in the field of nitroacetyl chemistry, developed by Kornblum and Rajappa we have successfully prepared the intermolecular Knoevenagel condensation product – the late-stage precursor to the left-hand ring of celogentin C. Synthesis of this key intermediate subsequently led to the preparation of …

Ricin B Chain-Insulin Fusion Protein Immunomodulation Of Type 1 Diabetes, James Edward Carter Iii

Loma Linda University Electronic Theses, Dissertations & Projects

Type 1 diabetes mellitus (T1D) is a debilitating chronic inflammatory disease of the insulin-producing pancreatic islet β-cells that results from a combination of genetic and environmental factors. Attempts to suppress Th1-mediated autoimmune diseases such as T1D by mucosal delivery of autoantigens for immunotolerization have yielded only partial success. Attainment of satisfactory levels of sustained immunological tolerance remains to be accomplished. To restore self-tolerance requires delivery of sufficient amounts of autoantigen to stimulate regulatory T helper cells that function to survey the gut and induce tolerance to consumed antigens such as food. Oral delivery of autoantigens has previously been shown to …

Poisonous Rangeland Plants In San Luis Obispo County, Sara Litten, Amanda Ou

Animal Science

Poisonous Rangeland Plants in San Luis Obispo County is a comprehensive educational guide to rangeland plants that are toxic to domestic livestock. This guide begins with an exploration of how the biological systems are affected by the poisonous plant toxins. The biochemistry behind these toxins is included in the discussion. Next, reference material for fourteen plants that inhabit San Luis Obispo County is provided. This information includes specific toxins found in poisonous plants, affected animals, symptoms of poisoning, stages of growth, lethal dose, and distribution of the plant in California. This section of the guide is filled with helpful photos …

Mimosa: A System For Minimotif Annotation, Jay Vyas, Ronald J. Nowling, Thomas Meusburger, David P. Sargeant, Krishna Kadaveru, Michael R. Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran, Martin Schiller

Life Sciences Faculty Research

BACKGROUND:

Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature.

RESULTS:

We have built the MimoSA application for minimotif annotation. The application supports management of …

Overexpression And Partial Purification Of Recombinant Human Serine Hydroxymethyltransferase: A Potential Anticancer Target, Suprit Singh Deol

Chemistry and Biochemistry

Serine Hydroxymethyltransferase (SHMT) is a member of the thymidylate synthase cycle that provides pyrimidine nucleotides to actively dividing cells, including cancer cells. The other two enzymes involved in this cycle have been targets for clinical anticancer drugs, suggesting that inhibitors of SHMT may also be used as clinical anticancer drugs. In order to test potential inhibitors against SHMT, human SHMT has been overexpressed in E. coli and partially purified by selective ammonium sulfate fractionation followed by anion-exchange fast protein liquid chromatography. A coupled assay using L-allo-threonine and alcohol dehydrogenase was used to identify active fractions, which were analyzed …

Terminal Deoxynucleotidyl Transferase: The Story Of A Misguided Dna Polymerase, Edward A. Motea, Anthony J. Berdis

Chemistry Faculty Publications

Nearly every DNA polymerase characterized to date exclusively catalyzes the incorporation of mononucleotides into a growing primer using a DNA or RNA template as a guide to direct each incorporation event. There is, however, one unique DNA polymerase designated terminal deoxynucleotidyl transferase that performs DNA synthesis using only single-stranded DNA as the nucleic acid substrate. In this chapter, we review the biological role of this enigmatic DNA polymerase and the biochemical mechanism for its ability to perform DNA synthesis in the absence of a templating strand. We compare and contrast the molecular events for template-independent DNA synthesis catalyzed by terminal …

Non-Natural Nucleotides As Probes For The Mechanism And Fidelity Of Dna Polymerases, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

DNA is a remarkable macromolecule that functions primarily as the carrier of the genetic information of organisms ranging from viruses to bacteria to eukaryotes. The ability of DNA polymerases to efficiently and accurately replicate genetic material represents one of the most fundamental yet complex biological processes found in nature. The central dogma of DNA polymerization is that the efficiency and fidelity of this biological process is dependent upon proper hydrogen-bonding interactions between an incoming nucleotide and its templating partner. However, the foundation of this dogma has been recently challenged by the demonstration that DNA polymerases can effectively and, in some …

Conformational Motion Associated With Catalysis In Indole-3-Glycerol Phosphate Synthase From S. Solfataricus, Tomasz Kurcon

Theses, Dissertations and Culminating Projects

Indole-3-glycerol phosphate synthase from Sulfolobus solfataricus (SsIGPS) belongs to a broad family of (βα)₈-barrel enzymes. It catalyzes the fifth step in tryptophan biosynthesis, converting l-(o-carboxylphenylamino)-l-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP). Site selective mutagenesis was used to introduce a single cysteine in two loops near the active site, generating two recombinant proteins, each containing a single cysteine handle. The two construct were labeled, each with two different thiol-reactive probes generating four labeled constructs that were used for this study. Steady-state kinetic parameters of the labeled mutants and the wild type SsIGPS were well characterized using fluorescence spectroscopy. Subsequent experiments …

A Novel Filarial Parasite (B. Malayi) Stress-Activated Protein Kinase As A Potential Drug Target, Akruti Patel

Theses, Dissertations and Culminating Projects

Lymphatic filariasis (or elephantiasis) is a major neglected disease with an estimated 120 million individuals infected and approximately 1.5 billion at risk in endemic regions. It is a highly disfiguring and debilitating disease and one of the major causes of global morbidity. Treatment options for this disease are few and new drug targets and therapies need to be identified. We have identified a protein kinase ortholog of human p38 mitogen-activated protein kinase (p38) expressed in the filarial parasite, Brugia malayi (B. malayi), one of three causative agent of lymphatic filariasis. We hypothesize that this protein kinase, BmMPKl, is important for …

Investigation Of Near-Infrared Fluorescence And Photobleaching Of Human Volar Side Fingertips In Vivo: Antioxidants And Melanin, Colin Wright

Renée Crown University Honors Thesis Projects - All

Noninvasive in vivo blood glucose determination in the skin of volar side of human fingertips by near-infrared (NIR) Raman spectroscopy relies on fluorescence to quantify blood volume. Fluorescence does not only come from blood, which is composed of plasma and red blood cells; in fact, most fluorescence produced by human fingertips originates in the static tissues, e.g. skin, interstitial fluid, etc.. It will soon be possible to quantify the precise contributions of red blood cells, plasma, and static tissue to the overall fluorescence emission. Observations reveal a systematic decay in fluorescence, which, if not caused by blood movement, challenges our …

The Role Of Cuticular Hydrocarbons In The Pre-Mating Isolation Of Two Pissodes Species, Stephanie L. Teale

Renée Crown University Honors Thesis Projects - All

Pissodes strobi and P. nemorensis are weevils (Coleoptera, Curculionidae) that infest pines (Pinus spp.) and spruces (Picea spp.). Previous studies indicate that they are able to hybridize. In the spring, breeding site specificity maintains reproductive isolation, but in the late summer, both species occupy lateral branches of host trees. Aggregation pheromones for P. nemorensis have been identified but the mechanism for late summer isolation is unknown. Cuticular hydrocarbons have been shown to play a role in the chemical recognition of species, sex, kin, and caste in many groups of insects. The large number of possible compounds and the …

Mtor In Cell Signaling And Size Enlargement As A Target For The Chemico-Physical Therapy Of Cancer, Gabriela Krawiec

Renée Crown University Honors Thesis Projects - All

mTOR is a kinase protein meaning it phosphorylates target proteins affecting their cell signaling properties¹. The drug Rapamycin, analogs of Rapamycin, and cell signaling proteins that interact with mTOR control the activities mediated by mTOR¹. mTOR is located in the cytoplasm at a convergent point of many signaling pathways that regulate a multiplicity of cellular processes including metabolism that precede cell enlargement (cell “growth”), cell proliferation (cell division), and angiogenesis^1,2. Cells with mTOR inappropriately activated can proceed with cell enlargement and cell proliferation in the absence of normal cell signaling². Rapamycin and …

The Effect Of Exogenous Estrogens On Primordial Follicle Assembly In Vivo, Jenna Rose Karavan

Renée Crown University Honors Thesis Projects - All

During embryogenesis in the mouse, primordial germ cells develop, move to the genital ridge of the embryo, and form germline cysts as the ovary develops. The cells in these cysts are linked by intercellular bridges. The cysts then undergo a breakdown process which ultimately results in primordial follicles, each of which consists of a single oocyte surrounded by somatic cells called granulosa cells. During this cyst breakdown process, approximately one-third of the original oocytes become enclosed in primordial follicles, the amount of which is representative of the number of eggs a female will have available to her during her reproductive …

Dna Polymerases: Perfect Enzymes For An Imperfect World, Anthony J. Berdis

Chemistry Faculty Publications

This Special Thematic Issue explores the molecular properties of DNA polymerases as extraordinary biological catalysts. In this short introductory chapter, I briefly highlight some of the most important concepts from the articles contained within this Special Issue. The contents of this Special Issue are arranged into distinct sub-categories corresponding to mechanistic studies of faithful DNA polymerization, studies of "specialized" DNA polymerases that function on damaged DNA, and DNA polymerases that are of therapeutic importance against various diseases. Emphasis is placed on understanding the dynamic cellular roles and biochemical functions of DNA polymerases, and how their structure and mechanism impact their …

Role Of Secondary Interactions (Π, Agostic) As Well As Solvent Influence On Alkali Metal Complexes, Elizabeth D. Nagle

Renée Crown University Honors Thesis Projects - All

We here attempt to synthesize heterobimetallic alkali metal complexes with bulky phenolate ligands via solid state direct metallation. The solid state route may offer a facile method of producing these heterobimetallic species. Synthesis of heterobimetallic alkali metal compounds remains a challenge, as the homometallic complexes are generally favored over formation of the heterobimetallic species. Previous work has shown that the alkali metals have a strong solvent dependency; the recrystallization of heterobimetallic products from toluene yields the heterobimetallic, while recrystallization from THF yields the homometallic. However, the ability for phenolate ligands to stabilize metal centers through secondary interactions, such as M∙∙∙π …