Biochemistry Commons^™

Metabolomics Reveals New Mechanisms For Pathogenesis In Barth Syndrome And Introduces Novel Roles For Cardiolipin In Cellular Function, Yana Sandlers, Kelly Mercier, Wimal Pathmasiri, Jim Carlson, Susan Mcritchie, Susan Sumner, Hilary J. Vernon

Chemistry Faculty Publications

Barth Syndrome is the only known Mendelian disorder of cardiolipin remodeling, with characteristic clinical features of cardiomyopathy, skeletal myopathy, and neutropenia. While the primary biochemical defects of reduced mature cardiolipin and increased monolysocardiolipin are well-described, much of the downstream biochemical dysregulation has not been uncovered, and biomarkers are limited. In order to further expand upon the knowledge of the biochemical abnormalities in Barth Syndrome, we analyzed metabolite profiles in plasma from a cohort of individuals with Barth Syndrome compared to age-matched controls via ¹H nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry. A clear distinction between metabolite profiles of …

Uplc–Qtof–Ms And Nmr Analyses Of Graviola (Annona Muricata) Leaves, Ingrid De Moraes, Paulo Ribeiro, Flávio Schmidt, Kirley Canuto, Guilherme Zocolo, Edy De Brito, Rensheng Luo, Kristy Richards, Kevin Tran, Robert Smith

Chemistry & Biochemistry Faculty Works

No abstract provided.

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 …

Potential Regulation Of Deadly Water-Borne Shigella Bacteria Pathogenesis Through The Shigella Infection Protein Spa47, Jamie Kingsford

Research on Capitol Hill

• Shigella is a gram-negative, bacterial pathogen typically found in contaminated water sources.
• Each year, Shigella is responsible for over 90 million infections and 100,000 deaths stemming from symptoms of severe dysentery, fever, nausea and vomiting.
• A needle-like apparatus found on the surface of Shigella allows the bacterium to infect host cells.
• Each needle-apparatus has an associated ATPase, a protein that can hydrolyze ATP into ADP and P_i.
• The Shigella needle-apparatus ATPase Spa47 is predicted to provide the energy for infection.
• Spa47 has been shown to be essential for infection – without Spa47, no infection will occur.
• We were …

The Dual Regulatory Role Of Amino Acids Leu480 And Gln481 Of Prothrombin, Joesph R. Wiencek, Jamila Hirbawi, Vivien C. Yee, Michael Kalafatis

Chemistry Faculty Publications

Prothrombin (FII) is activated to α-thrombin (IIa) by prothrombinase. Prothrombinase is composed of a catalytic subunit, factor Xa (fXa), and a regulatory subunit, factor Va (fVa), assembled on a membrane surface in the presence of divalent metal ions. We constructed, expressed, and purified several mutated recombinant FII (rFII) molecules within the previously determined fVa-dependent binding site for fXa (amino acid region 473–487 of FII). rFII molecules bearing overlapping deletions within this significant region first established the minimal stretch of amino acids required for the fVa-dependent recognition exosite for fXa in prothrombinase within the amino acid sequence Ser⁴⁷⁸–Val^{479 …}

Kdac8 With High Basal Velocity Is Not Activated By N-Acetylthioureas, Tasha B. Toro, Subramanya Pingali, Thao P. Nguyen, Destane S. Garrett, Kyra A. Dodson, Kyara A. Nichols, Rashad A. Haynes, Florastina Payton-Stewart, Terry J. Watt

Faculty and Staff Publications

Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Recently, a series of N-acetylthioureas were synthesized and reported to enhance the activity of KDAC8 with a fluorogenic substrate. To determine if the activation was general, we synthesized three of the most potent N-acetylthioureas and measured their effect with peptide substrates and the fluorogenic substrate under multiple reaction conditions and utilizing two enzyme purification approaches. No activation was observed for any of the three N-acetylthioureas under any assayed conditions. Further characteriza- tion of KDAC8 kinetics with the fluorogenic substrate yielded a k cat /K M of 164 …

C-Reactive Protein Interactions With Cellular Membranes And Supported Lipid Bilayers, Aml Abd Alhamed Alnaas

Electronic Theses and Dissertations

C-reactive protein (CRP) is a serum protein that binds to damaged membranes and initiates the complement immune response. Different forms of CRP are thought to alter how the body responds to inflammation and the degradation of foreign material. Despite knowing that a modified form of CRP(mCRP) binds to downstream protein binding partners better than the native pentameric form, the role of CRP conformation on lipid binding is yet unknown. In this work, three main assays were performed to characterize how conformation affects CRP-membrane interactions. The first assay utilized supported lipid bilayers that mimic the plasma membrane of apoptotic cells. The …

Source Apportionment Of Atmospheric Particulate Matter In Developing Countries Using Trace Elements And Stable Metal Isotope Ratios, Nitika Dewan

Electronic Theses and Dissertations

The work presented herein details the source apportionment of atmospheric particulate matter in developing countries (Kyrgyzstan in Central Asia, metropolitan cities in Northern India, and Shenzhen in China) using trace elements and stable metal isotope ratios. The first study focused on the development of a novel method for the concomitant separation of rare-earth elements in environmental samples of any geological origin. The separation procedure is based on three extraction chromatographic materials, referred to as Sr.Spec, TRU.Spec, and Ln.Spec. This triple column arrangement enables the simultaneous isolation of pure Sr and Nd fractions in less than one day and with great …

Towards Structural Determination Of Human Α1-Glycine Receptor Allostery, Rathna Jyothi Veeramachaneni

Electronic Theses and Dissertations

Recent advances in technology have led to the determination of numerous notable structures of membrane proteins. While they provide valuable information about the structure of membrane proteins these studies often provide static images with potentially limited dynamics, and structural determination often requires truncation of flexible regions, and often utilizes bacterial homologs given the need for stable, heterologous overexpression. In order to better understand allostery at a molecular level, state-dependent crosslinking studies coupled with multidimensional mass spectrometry (MS) were conducted on glycine receptor (GlyR) stabilized in different allosteric states. Predominant allosteric states were stabilized using wild type or mutated receptor in …

Water Soluble Cationic Porphyrin Sensor For Detection Of Hg2+, Pb2+, Cd2+, And Cu2+, Matibur Zamadar, Christopher Orr, Miranda Uherek

Faculty Publications

Here we report the sensing properties of the aqueous solution of meso-tetra(N-methyl-4-pyridyl)porphine tetrachloride (1) for simultaneous detection of toxic metal ions by using UV-vis spectroscopy. Cationic porphyrin 1 displayed different electronic absorptions in UV-vis region upon interacting with Hg2+, Pb2+, Cd2+, and Cu2+ ions in neutral water solution at room temperature. Quite interestingly, the porphyrin 1 showed that it can function as a single optical chemical sensor and/or metal ion receptor capable of detecting two or more toxic metal ions, particularly Hg2+, Pb2+, and Cd2+ ions coexisting in a water sample. Porphyrin 1 in an aqueous solution provides a unique …

Agricultural Fires In The Southeastern U.S. During Seac4Rs: Emissions Of Trace Gases And Particles And Evolution Of Ozone, Reactive Nitrogen, And Organic Aerosol, Xiaoxi Liu, Y. Zhang, L. G. Huey, R. J. Yokelson, Y. Wang, J. L. Jimenez, P. Campuzano-Jost, A. J. Beyersdorf, D. R. Blake, Y. Choi, J. M. St. Clair, J. D. Crounse, D. A. Day, G. S. Diskin, A. Ried, S. R. Hall, T. F. Hanisco, L. E. King, S. Meinardi, T. Mikoviny, B. B. Palm, J. Peischl, A. E. Perring, I. B. Pollack, T. B. Ryerson, G. Sachse, J. P. Schwarz, I. J. Simpson, D. J. Tanner, K. L. Thornhil, K. Ullmann, R. J. Weber, P. O. Wennberg

Chemistry and Biochemistry Faculty Publications

Emissions from 15 agricultural fires in the southeastern U.S. were measured from the NASA DC-8 research aircraft during the summer 2013 Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) campaign. This study reports a detailed set of emission factors (EFs) for 25 trace gases and 6 fine particle species. The chemical evolution of the primary emissions in seven plumes was examined in detail for ~1.2 h. A Lagrangian plume cross-section model was used to simulate the evolution of ozone (O3), reactive nitrogen species, and organic aerosol (OA). Observed EFs are generally consistent with previous …

Planning, Implementation, And Scientific Goals Of The Studies Of Emissions And Atmospheric Composition, Clouds And Climate Coupling By Regional Surveys (Seac4Rs) Field Mission, Owen B. Toon, Hal Maring, Jack Dibb, Richard Ferrare, Daniel J. Jacob, Eric J. Jensen, Z. Johnny Luo, Gerald G. Mace, Laura L. Pan, Lenny Pfister, Karen H. Rosenlof, Jens Redemann, Jeffrey S. Reid, Hanwant B. Singh, Anne M. Thompson, Robert Yokelson, Patrick Minnis, Gao Chen, Kenneth W. Jucks, Alex Pszenny

Chemistry and Biochemistry Faculty Publications

The Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) fieldmission based at Ellington Field, Texas, during August and September 2013 employed the most comprehensive airborne payload to date to investigate atmospheric composition over North America. The NASA ER-2, DC-8, and SPEC Inc. Learjet flew 57 science flights fromthe surface to 20 km. The ER-2 employed seven remote sensing instruments as a satellite surrogate and eight in situ instruments. The DC-8 employed 23 in situ and five remote sensing instruments for radiation, chemistry, and microphysics. The Learjet used 11 instruments to explore cloud microphysics. SEAC4RS …

Ice-Nucleating Particle Emissions From Biomass Combustion And The Potential Importance Of Soot Aerosol, E. J.T. Levin, G. R. Mcmeeking, P. J. Demott, C. S. Mccluskey, C. M. Carrico, S. Nakao, T. Jayarathne, E. A. Stone, C. E. Stockwell, R. J. Yokelson, S. M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Ice-nucleating particles (INPs) are required for initial ice crystal formation in clouds at temperatures warmer than about -36°C and thus play a crucial role in cloud and precipitation formation. Biomass burning has been found to be a source of INPs in previous studies and is also a major contributor to atmospheric black carbon (BC) concentrations. This study focuses on isolating the BC contribution to the INP population associated with biomass combustion. Emissions of condensation mode INPs from a number of globally relevant biomass fuels were measured at -30°C and above water saturation as fires progressed from ignition to extinguishment in …

Rapidly Evolving Ultrafine And Fine Mode Biomass Smoke Physical Properties: Comparing Laboratory And Field Results, Christian M. Carrico, Anthony J. Prenni, Sonia M. Kreidenweis, Ezra J.T. Levin, Christina S. Mccluskey, Paul J. Demott, Gavin R. Mcmeeking, Shunsuke Nakao, Chelsea Stockwell, Robert J. Yokelson

Chemistry and Biochemistry Faculty Publications

Combining field and laboratory results, we present biomass smoke physical properties. We report sub-0.56 µm diameter (Dp) particle sizing (fast mobility particle sizer, FMPS) plus light absorption and scattering at 870nm (photoacoustic extinctiometer). For Dp<200 >nm, the FMPS characterized sizing within ±20% compared to standards. As compared to the traditional scanning mobility particle sizer, the FMPS responded most accurately to single-mode polydispersions with mean Dp<200 >nm, which characterized the smoke sampled here. Smoke was measured from laboratory fresh emissions (seconds to hours old), the High Park Fire (hours to<1 >day), and from regional biomass burning (several days). During a High …

Development Of Gamma-Modified Atp Analogs To Study Kinase-Catalyzed Phosphorylations, Ahmed Eid Fouda

Wayne State University Dissertations

Kinase-catalyzed protein phosphorylation is one of the most important post-translational modifications that controls cascades of biochemical reactions. Irregularities in phosphorylation result in many diseases, such as diabetes mellitus, Parkinsons, and cancer. The development of new methods to monitor kinase-catalyzed phosphorylation is needed to decipher details of normal and diseased cell signaling. The Pflum lab recently developed several -modified ATP analogs to study kinase catalyzed phosphorylation reactions. The -modified ATP analogs have different tags, such as biotin for substrate labeling or aryl-azide for kinase substrates identification. Unfortunately, use of -modified ATP analogs was limited to in vitro studies due to the …

The Development Of Peptide Ligands To Target H69 Rrna, Danielle Nicole Dremann

Wayne State University Dissertations

ABSTRACT

THE DEVELOPMENT OF PEPTIDE LIGANDS TO TARGET H69

by

DANIELLE NICOLE DREMANN

December 2015

Advisor: Prof. Christine S. Chow

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

In the development of peptide ligands to target H69, SPPS and ESI MS was used to determine if 1) peptides could bind to modified H69 and 2) if increased affinity for the target RNA could be enhanced with modification. An alanine and arginine scan was synthesized and tested for this determination. Selected peptides were then tested using biophysical techniques such as circular dichroism and isothermal titration calorimetry. An assay was also designed to …

The Unusual Substrate Specificity Of A Virulence Associated Serine Hydrolase From The Highly Toxic Bacterium, Francisella Tularensis, Alexander M. Farberg, Whitney K. Hart, R. Jeremy Johnson

Scholarship and Professional Work - LAS

Francisella tularensis is the causative agent of the highly, infectious disease, tularemia. Amongst the genes identified as essential to the virulence of F. tularensis was the proposed serine hydrolase FTT0941c. Herein, we purified FTT0941c to homogeneity and then characterized the folded stability, enzymatic activity, and substrate specificity of FTT0941c. Based on phylogenetic analysis, FTT0941c was classified within a divergent Francisella subbranch of the bacterial hormone sensitive lipase (HSL) superfamily, but with the conserved sequence motifs of a bacterial serine hydrolase. FTT0941c showed broad hydrolase activity against diverse libraries of ester substrates, including significant hydrolytic activity across alkyl ester substrates from …

Substrate Specificity Of The Lipn Hydrolase From Mycobacterium Ulcerans, Stephanie Raynor

Undergraduate Honors Thesis Collection

Mycobacterium ulcerans is the causative agent of Buruli ulcer, a tropical skin disease that affects thousands of individuals annually. Recent studies have revealed that lipolytic enzymes are involved in the pathogenicity processes of mycobacterium and could be potential targets for novel antibiotics. LipN is one proposed serine hydrolase in Mycobacterium ulcerans that contains the conserved α/β hydrolase protein fold and utilizes the conserved catalytic traid of serine, histidine, and aspartate/glutamate. The physiological substrate and biological role of LipN from M. ulcerans have not yet been determined. In this study, LipN was cloned into a pET28a plasmid and overexpressed in an …

Functional Effects Of Calcium Regulation Of Thin Filaments At Single Particle Resolution, Christopher Solis-Ocampo

Electronic Theses and Dissertations

Heart disease is the leading cause of death in the United States. Understanding heart function at the molecular level is critical for developing of more effective treatments. In the cardiac muscle, the thin filament is composed by troponin (Tn), tropomyosin (Tm), and F-actin. It provides Ca2+-dependent regulation of contraction by modulating myosin attachment and force generation in a cooperative scheme. However, this mechanism remains unclear. To understand thin filament activation, we studied the binding and functional properties of Tn and Tm to F-actin at single particle resolution by employing fluorescence image colocalization, in vitro motility assays, and Förster resonance energy …

It Is All About (U)Biquitin: Role Of Altered Ubiquitin-Proteasome System And Uchl1 In Alzheimer Disease, Antonella Tramutola, Fabio Di Domenico, Eugenio Barone, Marzia Perluigi, D. Allan Butterfield

Chemistry Faculty Publications

Free radical-mediated damage to macromolecules and the resulting oxidative modification of different cellular components are a common feature of aging, and this process becomes much more pronounced in age-associated pathologies, including Alzheimer disease (AD). In particular, proteins are particularly sensitive to oxidative stress-induced damage and these irreversible modifications lead to the alteration of protein structure and function. In order to maintain cell homeostasis, these oxidized/damaged proteins have to be removed in order to prevent their toxic accumulation. It is generally accepted that the age-related accumulation of “aberrant” proteins results from both the increased occurrence of damage and the decreased efficiency …

Identifying Non-Classical Active Sites As A Tool For Enzyme Inhibition, Marisol Serrano

Open Access Theses & Dissertations

Chagas disease, caused by the parasite Trypanosoma cruzi, is an endemic life-threatening disease that affects mainly the heart. It remains the leading cause of heart failure in Latin American countries. Since current treatments against this parasite are highly toxic and somewhat ineffective, novel and more efficacious types of interventions are desired. Cruzain, identified as the major cathepsin for T. cruzi, plays a major role in the parasite's life cycle; making this enzyme very attractive for potential trypanocidal drugs discovery. The recombinant cruzain is synthesized as a zymogenic pro-protein (PCZN) which possesses a pro domain and a catalytic domain. In this …

Study On Dioxygen Binding To Heme Using Scan Functional, Zegnet Yimer Muhammed

Open Access Theses & Dissertations

Density functional theory, a quantum mechanical based electronic structure method with GGA-PBE and MGG-SCAN functionals, are used to investigate the structure and energies of singlet, triplet, and quintet spin states of FeP (iron Porphyrin), FePIm (imidazole iron porphyrin), and FePImO2 (dioxygen imidazole iron porphyrin) systems. The binding and release of dioxygen to and from hemoglobin (Hb) are the most crucial reaction takes place in human body to sustain the existence of life. FePImO2 is used to model this phenomenon. When O2 binds to FePIm, the system undergoes a conformational change. i.e. from domed structure of FePIm in which the Fe …

The Characterization Of A Recombinant Virophage Integrase, Martin Christopher Chacon

Open Access Theses & Dissertations

Virophages are satellite-like dsDNA viruses that parasitize giant viruses of the family Mimiviridae. Mavirus is the second virophage discovered that associates with its host virus Cafeteria roenbergensis Virus (CroV). When co-infecting their common host cell Cafeteria roenbergensis, a marine zooplankton that is widely spread throughout the oceans, mavirus will inhibit CroV's replication. In addition, mavirus was shown to share high similarities to the Maverick/Polinton eukaryotic DNA transposons. A coding sequence in mavirus genome (MV02) reveals high homology to retroviral integrases such as those found in HIVs. The putative integrase MV02 is predicted to integrate mavirus DNA into the host genome. …

The Chemistry Of New Garlic-Derived Organosulfur Compounds And The Molecular Basis Of Olfaction, Berenice Dethier

Legacy Theses & Dissertations (2009 - 2024)

Garlic is a very popular condiment that has been used around the world for centuries. It is also a source of a remarkably extensive range of organosulfur compounds, whose chemistry is the focus of this thesis. The central reaction in formation of these compounds is the enzymatic cleavage of alk(en)yl cysteine sulfoxides by alliinases, which leads to sulfenic acids. The latter can then undergo condensation and rearrangement into various organosulfur compounds. Three aspects of the chemistry of garlic have been investigated in this thesis.

Study Of Protein-Protein Interaction By Using In-Cell Nmr In Human Cells, Asma Salem M Aldousary

Legacy Theses & Dissertations (2009 - 2024)

We developed a new technology to study protein-protein interaction in mammalian cells. This technology is based high resolution of Nucleic Magnetic Resonance (NMR) spectroscopy. Using this technology we studied interaction between the receptor for advanced glycation endproducts (RAGE). RAGE- is a multiligand receptor of immunoglobulin receptor family that is activated by a multitude of ligands. Activation of RAGE results in signal transduction that leads to the inflammatory response implicated in the complications of Diabetes. RAGE is an emergent drug target that has been explored for the variety of pathologist including cancers, neurological disorders, inflammatory disease, and diabetes. and Intracellular effector …

The Use Of Ion Mobility Spectrometry-Mass Spectrometry For The Structural Elucidation Of Progressively Larger Nucleic Acids, Jennifer Lynn Lippens

Legacy Theses & Dissertations (2009 - 2024)

The biomedical community and pharmaceutical industry have come to rely in ever

A Disease Spectrum For Itpa Variation: Advances In Biochemical And Clinical Research, Nicholas E. Burgis

Chemistry and Biochemistry Faculty Publications

Human ITPase (encoded by the ITPA gene) is a protective enzyme which acts to exclude noncanonical (deoxy) nucleoside triphosphates ((d)NTPs) such as (deoxy)inosine 5′-triphosphate ((d)ITP), from (d)NTP pools. Until the last few years, the importance of ITPase in human health and disease has been enigmatic. In 2009, an article was published demonstrating that ITPase deficiency in mice is lethal. All homozygous null offspring died before weaning as a result of cardiomyopathy due to a defect in the maintenance of quality ATP pools. More recently, a whole exome sequencing project revealed that very rare, severe human ITPA mutation results in early …

The Development Of Colorimetric Assays To Determine The Identity And Frequency Of Specific Nucleobases In Dna Oligomers, Elizabeth Marie Thomas

Theses and Dissertations--Chemistry

Colorimetric methods combined with color-changing chemical probes are widely used as simple yet effective tools for identifying and quantifying a wide variety of molecules in solution. For nucleic acids (DNA and RNA), perhaps the most commonly used colorimetric probe is potassium permanganate, which can be used to identify single-stranded pyrimidines (thymine and cytosine) in polymers. Unfortunately, permanganate is not an effective probe for identifying purines (adenine and guanine), especially in the presence of the more reactive pyrimidines. Therefore, robust methods for discriminating between the purines remain elusive, thereby creating a barrier toward developing more complex colorimetric applications. In this dissertation, …

Probing Allosteric, Partial Inhibition Of Thrombin Using Novel Anticoagulants, Stephen S. Verespy Iii

Theses and Dissertations

Thrombin is the key protease that regulates hemostasis; the delicate balance between procoagulation and anticoagulation of blood. In clotting disorders, like deep vein thrombosis or pulmonary embolism, procoagulation is up-regulated, but propagation of clotting can be inhibited with drugs targeting the proteases involved, like thrombin. Such drugs however, have serious side effects (e.g., excessive bleeding) and some require monitoring during the course of treatment. The reason for these side effects is the mechanism by which the drugs’ act. The two major mechanisms are direct orthosteric and indirect allosteric inhibition, which will completely abolish the protease’s activity. Herein we sought an …