DOCSLIB.ORG

Heme Biosynthesis: Structure-Activity Studies of Murine Ferrochelatase Zhen Shi University of South Florida

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Heme Biosynthesis: Structure-Activity Studies of Murine Ferrochelatase Zhen Shi University of South Florida University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 2006 Heme biosynthesis: structure-activity studies of murine ferrochelatase Zhen Shi University of South Florida Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the American Studies Commons Scholar Commons Citation Shi, Zhen, "Heme biosynthesis: structure-activity studies of murine ferrochelatase" (2006). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/2699 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Heme Biosynthesis: Structure–Activity Studies of Murine Ferrochelatase by Zhen Shi A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Biochemistry and Molecular Biology College of Medicine University of South Florida Major Professor: Gloria Ferreira, Ph.D. Michael Barber, Ph.D. Huntington Potter, Ph.D. George Blanck, Ph.D. Peter Medveczky, Ph.D. Kenton Rodgers, Ph.D. Date of Approval: February 10, 2006 Keywords: porphyrin, iron, resonance Raman, continuous assay, random mutagenesis © Copyright 2006, Zhen Shi ACKNOWLEDGEMENTS I wish to express my deep gratitude to the members of my committee, Dr. Michael Barber, Dr. Huntington Potter, Dr. George Blanck, Dr. Peter Medveczky, and most of all, to Dr. Gloria Ferreria, for their consistent guidance, understanding and support throughout the course of my graduate work. I am thankful to all the professors and colleagues in the Department of Biochemistry, the members of Dr. Ferreira lab, as well as the lab group of Dr. John Shelnutt at the University of New Mexico for their help and advice during the studies. I would like to acknowledge the financial support from the American Heart Association for a pre-doctoral fellowship from 2000 to 2002, and from the Institute of Biomolecular Sciences for a graduate fellowship from 1998 to 2000. I wish to express my appreciation to Ms. Kathy Zahn and Susan Chapman at the Office of Research and Graduate Affairs for their continuous administrative assistance. I am forever grateful to my family for their enduring understanding and encouragement. NOTE TO THE READER The original of this document contains color that is necessary for understanding the data. The original dissertation is on file with the USF library in Tampa, Florida. TABLE OF CONTENTS LIST OF TABLES iv LIST OF FIGURES v LIST OF ABBREVIATIONS vii ABSTRACT ix CHAPTER ONE INTRODUCTION 1 The importance of heme in biological systems 1 Enzymes in the heme biosynthetic pathway 7 Aminolevulinic acid synthase 7 Porphobilinogen synthase 13 Porphobilinogen deaminase 18 Uroporphyrinogen III synthase 22 Uroporphyrinogen III decarboyxlase 27 Coproporphyrinogen III oxidase 32 Protoporphyrinogen IX oxidase 37 Ferrochelatase 42 CHAPTER TWO MATERIALS AND METHODS 55 Materials 55 Experimental Methods 57 Media preparation for bacterial cultures 57 Competent cell preparation and bacterial transformation 58 Glycerol stock preparation for bacterial cells 59 Plasmid DNA purification 60 Sodium dodecyl sulfate-polyacylamide gel electrophoresis and protein concentration determination 60 Construction of a random library and genetic selection of functional ferrochelatase loop variants 61 Large-scale purification of the wild-type ferrochelatase and loop variants 65 UV-visible absorbance spectra of purified ferrochelatase 67 Metal content analysis of purified ferrochelatase 68 Pyridine-hemochromogen assay 68 Continuous assay of ferrochelatase activity 69 Steady-state kinetic analysis of the loop variants 71 i Homology modeling of murine ferrochelatase 72 Resonance Raman spectroscopy of porphyrin binding to the wild-type ferrochelatase and loop variants 72 Profiling the active variants by high-throughput protein purification 74 Liposomal binding assays of ferrochelatase variants 75 Inhibition assay of ferrochelatase by N-methyl protoporphyrin on agar plates 76 Quantification of N-methyl protoporphyrin binding to ferrochelatase by fluorescence quenching measurements 77 Transient kinetic analysis of ferrochelatase activity 78 Ligand binding pocket size measurement 79 Enzymatic activity of ferrochelatase in the absence of FeS cluster synthesis 80 Molecular mass assessment of purified ferrochelatase 81 Electron paramagnetic resonance spectroscopy of purified ferrochelatase 82 CHAPTER THREE RESULTS 83 Purification of recombinant ferrochelatase 83 Large-scale purification of wild-type ferrochelatase and loop variants 83 Small-scale purification of ferrochelatase loop variants 84 Developing a continuous assay for steady-state kinetic analysis of ferrochelatase 87 Characterization of the functional ferrochelatase loop variants 92 Biological selection of the active loop variants 92 Distribution of the functional amino acid substitutions 96 Steady-state kinetic analysis of the active loop variants 96 Homology modeling of wild-type murine ferrochelatase and selected loop variants 98 Interaction of ferrochelatase with mitochondrial membrane lipids 103 Resonance Raman spectroscopic analysis of porphyrin binding in the loop variants 105 Binding of substrate protoporphyrin to the variants 105 Binding of hemin to the variants 108 Binding of nickel-protoporphyrin to the variants 108 Inhibition of ferrochelatase by N-methyl protoporphyrin 112 Equilibrium binding of inhibitor to ferrochelatase 114 Kinetic pathway of inhibition 114 Size measurement of the active site pocket 119 FeS cluster and oligomeric assembly in ferrochelatase variants 121 UV-visible absorbance spectra of the variants 121 Metal content analysis 123 Dependence of enzymatic activity on FeS cluster synthesis 123 Subunit assembly of purified ferrochelatase 125 Electron paramagnetic resonance spectra of ferrochelatase 128 CHAPTER FOUR DISCUSSION 131 Continuous assay for ferrochelatase activity 131 Characterization of the active site loop variants 135 Resonance Raman spectroscopy analysis of ferrochelatase-induced porphyrin distortion 142 ii Inhibition of ferrochelatase by N-methyl protoporphyrin 151 FeS cluster assembly and oligomeric organization in ferrochelatase 155 REFERENCES 161 APPENDICES 205 ABOUT THE AUTHOR END PAGE iii LIST OF TABLES Table 1. Steady-state kinetic parameters of wild-type ferrochelatase and selected loop variants 99 Table 2. Comparison of the steady-state kinetic parameters of ferrochelatase determined by various assay methods 134 Table 3. Results of simulation for the low-frequency resonance Raman spectra of ferrochelatase-bound protoporphyrin 145 iv LIST OF FIGURES Figure 1. The heme biosynthetic pathway in animal cells 3 Figure 2. The heme degradation pathway in mammalian cells 6 Figure 3. The reaction catalyzed by ferrochelatase 43 Figure 4. Random mutagenesis of the ferrochelatase active site loop motif and biological selection of the functional variants 62 Figure 5. The UV-visible absorbance spectra of purified wild-type murine ferrochelatase and selected loop variants 85 Figure 6. SDS-polyacrylamide gel electrophoresis of purified ferrochelatase 86 Figure 7. The fluorescence spectra of protoporphyrin 88 Figure 8. Time course for the disappearance of protoporphyrin in the ferrochelatase-catalyzed reaction 89 Figure 9. Dependence of the initial rate of protoporphyrin consumption on ferrochelatase concentration 90 Figure 10. Determination of the steady-state kinetic parameters of wild-type murine ferrochelatase 91 Figure 11. Sequence alignment of the loop motif in ferrochelatase 93 Figure 12. Activity assessment and distribution of the number of the functional loop variants 95 Figure 13. Spectrum and frequency of amino acid substitutions in the functional loop variants 97 Figure 14. Molecular modeling of wild-type murine ferrochelatase and selected loop variants 101 v Figure 15. Interaction between ferrochelatase and the mitochondrial membrane lipids 104 Figure 16. The resonance Raman spectra of protoporphyrin incubated with ferrochelatase at a porphyrin-to-protein molar ratio of 0.1 106 Figure 17. The resonance Raman spectra of hemin incubated with ferrochelatase at a hemin-to-protein molar ratio of 0.1 109 Figure 18. The resonance Raman spectra of nickel-protoporphyrin incubated with ferrochelatase at a porphyrin-to-protein molar ratio of 0.1 111 Figure 19. The structural diagram of N-methyl protoporphyrin 113 Figure 20. The intrinsic fluorescence of ferrochelatase 115 Figure 21. Binding curves generated from protein fluorescence quenching measurements following titration with N-methyl protoporphyrin 116 Figure 22. Transient kinetic analysis of the ferrochelatase-catalyzed reaction 118 Figure 23. Dependence of the rate constants for ferrochelatase binding on N- methyl protoporphyrin concentration 120 Figure 24. The UV-visible absorbance spectra of purified wild-type ferrochelatase and variants 122 Figure 25. Dependence of ferrochelatase activity on FeS cluster synthesis 124 Figure 26. Molecular weight assessment of purified wild-type ferrochelatase and variants by gel filtration chromatography 126 Figure 27. Molecular size determination of purified wild-type ferrochelatase and variants by dynamic light scattering 127 Figure 28. EPR spectra of purified wild-type ferrochelatase and variants 129 Figure 29. Temperature-dependence of the EPR signal intensity for a purified ferrochelatase variant
Load more

Recommended publications
  • Hyperbilirubinemia
    Porphyrins Porphyrins (Porphins) are cyclic tetrapyrol compounds formed by the linkage )). of four pyrrole rings through methenyl bridges (( HC In the reduced porphyrins (Porphyrinogens) the linkage of four pyrrole rings (tetrapyrol) through methylene bridges (( CH2 )) The characteristic property of porphyrins is the formation of complexes with the metal ion bound to nitrogen atoms of the pyrrole rings. e.g. Heme (iron porphyrin). Proteins which contain heme ((hemoproteins)) are widely distributed e.g. Hemoglobin, Myoglobin, Cytochromes, Catalase & Tryptophan pyrrolase. Natural porphyrins have substituent side chains on the eight hydrogen atoms numbered on the pyrrole rings. These side chains are: CH 1-Methyl-group (M)… (( 3 )) 2-Acetate-group (A)… (( CH2COOH )) 3-Propionate-group (P)… (( CH2CH2COOH )) 4-Vinyl-group (V)… (( CH CH2 )) Porphyrins with asymmetric arrangement of the side chains are classified as type III porphyrins while those with symmetric arrangement of the side chains are classified as type I porphyrins. Only types I & III are present in nature & type III series is more important because it includes heme. 1 Heme Biosynthesis Heme biosynthesis occurs through the following steps: 1-The starting reaction is the condensation between succinyl-CoA ((derived from citric acid cycle in the mitochondria)) & glycine, this reaction is a rate limiting reaction in the hepatic heme synthesis, it occurs in the mitochondria & is catalyzed by ALA synthase (Aminolevulinate synthase) enzyme in the presence of pyridoxal phosphate as a cofactor. The product of this reaction is α-amino-β-ketoadipate which is rapidly decarboxylated to form δ-aminolevulinate (ALA). 2-In the cytoplasm condensation reaction between two molecules of ALA is catalyzed by ALA dehydratase enzyme to form two molecules of water & one 2 molecule of porphobilinogen (PBG) which is a precursor of pyrrole.
    [Show full text]
  • Porphyrins & Bile Pigments
    Bio. 2. ASPU. Lectu.6. Prof. Dr. F. ALQuobaili Porphyrins & Bile Pigments • Biomedical Importance These topics are closely related, because heme is synthesized from porphyrins and iron, and the products of degradation of heme are the bile pigments and iron. Knowledge of the biochemistry of the porphyrins and of heme is basic to understanding the varied functions of hemoproteins in the body. The porphyrias are a group of diseases caused by abnormalities in the pathway of biosynthesis of the various porphyrins. A much more prevalent clinical condition is jaundice, due to elevation of bilirubin in the plasma, due to overproduction of bilirubin or to failure of its excretion and is seen in numerous diseases ranging from hemolytic anemias to viral hepatitis and to cancer of the pancreas. • Metalloporphyrins & Hemoproteins Are Important in Nature Porphyrins are cyclic compounds formed by the linkage of four pyrrole rings through methyne (==HC—) bridges. A characteristic property of the porphyrins is the formation of complexes with metal ions bound to the nitrogen atom of the pyrrole rings. Examples are the iron porphyrins such as heme of hemoglobin and the magnesium‐containing porphyrin chlorophyll, the photosynthetic pigment of plants. • Natural Porphyrins Have Substituent Side Chains on the Porphin Nucleus The porphyrins found in nature are compounds in which various side chains are substituted for the eight hydrogen atoms numbered in the porphyrin nucleus. As a simple means of showing these substitutions, Fischer proposed a shorthand formula in which the methyne bridges are omitted and a porphyrin with this type of asymmetric substitution is classified as a type III porphyrin.
    [Show full text]
  • UROPORPHYRINOGEN HII COSYNTHETASE in HUMAN Hemolysates from Five Patientswith Congenital Erythropoietic Porphyriawas Much Lower
    UROPORPHYRINOGEN HII COSYNTHETASE IN HUMAN CONGENITAL ERYTHROPOIETIC PORPHYRIA * BY GIOVANNI ROMEO AND EPHRAIM Y. LEVIN DEPARTMENT OF PEDIATRICS, THE JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE Communicated by William L. Straus, Jr., April 24, 1969 Abstract.-Activity of the enzyme uroporphyrinogen III cosynthetase in hemolysates from five patients with congenital erythropoietic porphyria was much lower than the activity in control samples. The low cosynthetase activity in patients was not due to the presence of a free inhibitor or some competing en- zymatic activity, because hemolysates from porphyric subjects did not interfere either with the cosynthetase activity of hemolysates from normal subjects or with cosynthetase prepared from hematopoietic mouse spleen. This partial deficiency of cosynthetase in congenital erythropoietic porphyria corresponds to that shown previously in the clinically similar erythropoietic porphyria of cattle and explains the overproduction of uroporphyrin I in the human disease. Erythropoietic porphyria is a rare congenital disorder of man and cattle, characterized by photosensitivity, erythrodontia, hemolytic anemia, and por- phyrinuria.1 Many of the clinical manifestations of the disease can be explained by the production in marrow, deposition in tissues, and excretion in the urine and feces, of large amounts of uroporphyrin I and coproporphyrin I, which are products of the spontaneous oxidation of uroporphyrinogen I and its decarboxyl- ated derivative, coproporphyrinogen I. In cattle, the condition is inherited
    [Show full text]
  • Noncanonical Coproporphyrin-Dependent Bacterial Heme Biosynthesis Pathway That Does Not Use Protoporphyrin
    Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin Harry A. Daileya,b,c,1, Svetlana Gerdesd, Tamara A. Daileya,b,c, Joseph S. Burcha, and John D. Phillipse aBiomedical and Health Sciences Institute and Departments of bMicrobiology and cBiochemistry and Molecular Biology, University of Georgia, Athens, GA 30602; dMathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439; and eDivision of Hematology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132 Edited by J. Clark Lagarias, University of California, Davis, CA, and approved January 12, 2015 (received for review August 25, 2014) It has been generally accepted that biosynthesis of protoheme of a “primitive” pathway in Desulfovibrio vulgaris (13). This path- (heme) uses a common set of core metabolic intermediates that way, named the “alternative heme biosynthesis” path (or ahb), has includes protoporphyrin. Herein, we show that the Actinobacteria now been characterized by Warren and coworkers (15) in sulfate- and Firmicutes (high-GC and low-GC Gram-positive bacteria) are reducing bacteria. In the ahb pathway, siroheme, synthesized unable to synthesize protoporphyrin. Instead, they oxidize copro- from uroporphyrinogen III, can be further metabolized by suc- porphyrinogen to coproporphyrin, insert ferrous iron to make Fe- cessive demethylation and decarboxylation to yield protoheme (14, coproporphyrin (coproheme), and then decarboxylate coproheme 15) (Fig. 1 and Fig. S1). A similar pathway exists for protoheme- to generate protoheme. This pathway is specified by three genes containing archaea (15, 16). named hemY, hemH, and hemQ. The analysis of 982 representa- Current gene annotations suggest that all enzymes for pro- tive prokaryotic genomes is consistent with this pathway being karyotic heme synthetic pathways are now identified.
    [Show full text]
  • Metabolism of the Stimulated Rat Spleen: I. Ferrochelatase Activity As an Index of Tissue Erythropoiesis
    Metabolism of the stimulated rat spleen: I. Ferrochelatase activity as an index of tissue erythropoiesis Abraham Mazur J Clin Invest. 1968;47(10):2230-2238. https://doi.org/10.1172/JCI105908. Assay of the enzyme ferrochelatase in marrow, liver, spleen, and red cells has been employed to assess the extent of erythropoietic stimulation in animals bearing the Walker 256 carcinosarcoma and in rats treated by administration of phenylhydrazine, cobalt chloride, human urinary erythropoietin, or chronic blood loss. In all instances, the spleen sustains the most marked increase of ferrochelatase activity, per gram of tissue. Spleen erythropoietic activity stimulation was confirmed by quantitative measurements in respiring slices of 59Fe and 14C incorporation into hemoglobin and ferritin. Increased spleen ferrochelatase activity in cobalt chloride-treated rats is prevented by actinomycin D, indicating that stimulated synthesis of the enzyme is associated with the metabolism of RNA. Find the latest version: https://jci.me/105908/pdf Metabolism of the Stimulated Rat Spleen I. FERROCHELATASE ACTIVITY AS AN INDEX OF TISSUE ERYTHROPOIESIS ABRAHAM MAZUR From The New York Blood Center, New York 10021 A B S TR A C T Assay of the enzyme ferrochelatase examination or the measurement of incorporation in marrow, liver, spleen, and red cells has been of injected 59Fe into the tissues (4). In addition, employed to assess the extent of erythropoietic other splenic cells (reticuloendothelial cells) may stimulation in animals bearing the Walker 256 car- hypertrophy, e.g., in response to phenylhydrazine cinosarcoma and in rats treated by administration administration (5). of phenylhydrazine, cobalt chloride, human urinary Because the entire spleen is readily available, erythropoietin, or chronic blood loss.
    [Show full text]
  • Some Biochemical Changes in Heme Synthesis in Iron Deficiency
    Indian J Physiol Pharmacol 2000; 44 (4): 491-494 SOME BIOCHEMICAL CHANGES IN HEME SYNTHESIS IN IRON DEFICIENCY D. C. SHARMA* AND RATI MATHUR Department of Biochemistry, S. M. S. Medical College, Jaipur - 302 004 (Received on January 18, 2000) Abstract: Some enzymes and intermediates of heme synthesis were determined in blood and urine of 26 women with severe iron deficiency anemia (IDA). Erythrocyte free protoporphyrin was almost doubled and delta-aminolevulinate dehydrase significantly raised. But urinary excretion of delta-aminolevulinic acid and reticulocyte ferrochelatase were significantly reduced in iron deficiency anemia. Hence these could serve as useful indices of iron deficiency and consequent anemia. Key words: iron deficiency anemia delta-aminolevulinate dehydrase protoporphyrin ferrochelatase delta-aminolevulinic acid INTRODUCTION iron incorporation at the level of ferrochelatase. However, this enzyme was Anemia is the chief manifestation of never measured in blood in IDA, despite iron deficiency. Several parameters are reports of its decrease in human leucocytes available for diagnosis of iron deficiency (3) and pig heart muscle (4). Therefore, we anemia (IDA). These include classical decided to estimate it. parameters, like, erythrocyte morphology, red cell indices, bone marrow iron, Another enzyme of heme biosynthesis-­ serum iron, iron binding capacity, delta aminolevulinate dehydrase (ALAD) has transferrin saturation, and more recent been studied in IDA in the past but the tests-erythrocyte protoporphyrin, serum reports were conflicting; ranging from ferritin, transferrin receptors (1) and zinc normal (5) to higher (6-8) or reduced (3). protoporphyrin (2). Similar contradiction was also seen in the reported excretion of delta-aminolevulinic Iron is known to affect synthesis of heme acid (ALA) in urine by iron deficient anemic and free protoporphyrin accumulates in persons in this study.
    [Show full text]
  • Biochemistry I Enzymes
    BIOCHEMISTRY I 3rd. Stage Lec. ENZYMES Biomedical Importance: Enzymes, which catalyze the biochemical reactions, are essential for life. They participate in the breakdown of nutrients to supply energy and chemical building blocks; the assembly of those building blocks into proteins, DNA, membranes, cells, and tissues; and the harnessing of energy to power cell motility, neural function, and muscle contraction. The vast majority of enzymes are proteins. Notable exceptions include ribosomal RNAs and a handful of RNA molecules imbued with endonuclease or nucleotide ligase activity known collectively as ribozymes. The ability to detect and to quantify the activity of specific enzymes in blood, other tissue fluids, or cell extracts provides information that complements the physician’s ability to diagnose and predict the prognosis of many diseases. Further medical applications include changes in the quantity or in the catalytic activity of key enzymes that can result from genetic defects, nutritional deficits, tissue damage, toxins, or infection by viral or bacterial pathogens (eg, Vibrio cholerae). Medical scientists address imbalances in enzyme activity by using pharmacologic agents to inhibit specific enzymes and are investigating gene therapy as a means to remedy deficits in enzyme level or function. In addition to serving as the catalysts for all metabolic processes, their impressive catalytic activity, substrate specificity, and stereospecificity enable enzymes to fulfill key roles in additional processes related to human health and well-being. Proteases and amylases augment the capacity of detergents to remove dirt and stains, and enzymes play important roles in producing or enhancing the nutrient value of food products for both humans and animals.
    [Show full text]
  • Michael Koch Strukturanalyse Der Mitochondrialen
    Michael Koch Strukturanalyse der mitochondrialen Protoporphyrinogen IX Oxidase aus Nicotiana tabacum und von zwei weiteren Proteinen: Blaues Cupredoxin Umecyanin aus Meerrettich (Armoracia rusticana) Lumazinsynthase-W27Y-Mutante aus Spalthefe (Schizosaccharomyces pombe) Technische Universität München Max-Planck-Institut für Biochemie Abteilung Strukturforschung Strukturanalyse der mitochondrialen Protoporphyrinogen IX Oxidase aus Nicotiana tabacum und von zwei weiteren Proteinen: Umecyanin und Lumazinsynthase-W27Y-Mutante Michael Koch Vollständiger Abdruck der von der Fakultät für Chemie der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. W. Hiller Prüfer der Dissertation 1. apl. Prof. Dr. Dr. h. c. R. Huber 2. Univ.-Prof. Dr. Dr. A. Bacher Die Dissertation wurde am 24.02.2004 bei der Technischen Universität München eingereicht und durch die Fakultät für Chemie am 23.03.2004 angenommen. Dissertation Michael Koch Seite 3 Teile der Arbeit sind zur Veröffentlichung eingereicht bzw. wurden bereits veröffentlicht in: Koch, M., Breithaupt, C., Kiefersauer, R., Freigang, J., Huber, R., Messerschmidt, A. Crystal Structure of Protoporphyrinogen IX Oxidase: A key enzyme in heme and chlorophyll biosynthesis (EMBO J., online veröffentlicht 1. April 2004) Koch, M., Breithaupt, C., Kiefersauer, R., Freigang, J., Huber, R. and Messerschmidt, A. (2004). Crystal Structure of Protoporphyrinogen IX Oxidase. Jahrestagung der Deutschen Gesellschaft für Kristallographie 2004, Jena (Vortrag) Koch, M., Kiefersauer, R., Huber, R. (2002) Improvement of freezing protein crystals by accurately controlled humidity changes. Poster presentation at the XIX Congress and general assembly of the International Union of Crystallography, Geneva, Switzerland (Posterpräsentation) Koch, M., Velarde, M., Echt, S., Harrison, M., Dennison, C., Messerschmidt, A.
    [Show full text]
  • Model Name: "Jamshidi2007
    SBML Model Report Model name: “Jamshidi2007 - Genome-scale metabolic network of Mycobacterium tuberculosis (iNJ661)” 2LATEX July 28, 2015 1 General Overview This is a document in SBML Level 3 Version 1 format. Table1 shows an overview of the quantities of all components of this model. Table 1: Number of components in this model, which are described in the following sections. Element Quantity Element Quantity compartment types 0 compartments 2 species types 0 species 826 events 0 constraints 0 reactions 1025 function definitions 0 global parameters 19 unit definitions 1 rules 0 initial assignments 0 Model Notes Jamshidi2007 - Genome-scale metabolic networkof Mycobacterium tuberculosis (iNJ661) This model is described in the article:Investigating the metabolic capabilities of Mycobac- terium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug tar- gets.Jamshidi N, Palsson B.BMC Syst Biol 2007; 1: 26 Abstract: Produced by SBML2LATEX 1 BACKGROUND: Mycobacterium tuberculosis continues to be a major pathogen in the third world, killing almost 2 million people a year by the most recent estimates. Even in industrialized countries, the emergence of multi-drug resistant (MDR) strains of tuberculosis hails the need to develop additional medications for treatment. Many of the drugs used for treatment of tuber- culosis target metabolic enzymes. Genome-scale models can be used for analysis, discovery, and as hypothesis generating tools, which will hopefully assist the rational drug development process. These models need to be able to assimilate data from large datasets and analyze them. RESULTS: We completed a bottom up reconstruction of the metabolic network of Mycobac- terium tuberculosis H37Rv.
    [Show full text]
  • A Framework for Application of Metabolic Modeling in Yeast to Predict the Effects of Nssnv in Human Orthologs Hayley Dingerdissen George Washington University
    Himmelfarb Health Sciences Library, The George Washington University Health Sciences Research Commons Biochemistry and Molecular Medicine Faculty Biochemistry and Molecular Medicine Publications 6-3-2014 A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs Hayley Dingerdissen George Washington University Daniel S. Weaver SRI International Menlo Park, Menlo Park, CA Peter D. Karp SRI International Menlo Park, Menlo Park, CA Yang Pan George Washington University Vahan Simonyan US Food and Drug Administration, Rockville, MD See next page for additional authors Follow this and additional works at: http://hsrc.himmelfarb.gwu.edu/smhs_biochem_facpubs Part of the Biochemistry, Biophysics, and Structural Biology Commons Recommended Citation Dingerdissen, H., Weaver, D.S., Karp, P.D., Pan, Y., Simonyan, V. et al. (2014). A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs. Biology Direct, 9:9. This Journal Article is brought to you for free and open access by the Biochemistry and Molecular Medicine at Health Sciences Research Commons. It has been accepted for inclusion in Biochemistry and Molecular Medicine Faculty Publications by an authorized administrator of Health Sciences Research Commons. For more information, please contact [email protected]. Authors Hayley Dingerdissen, Daniel S. Weaver, Peter D. Karp, Yang Pan, Vahan Simonyan, and Raja Mazumder This journal article is available at Health Sciences Research Commons: http://hsrc.himmelfarb.gwu.edu/smhs_biochem_facpubs/
    [Show full text]
  • The Nematode Transcriptome Resource
    International Journal for Parasitology 41 (2011) 881–894 Contents lists available at ScienceDirect International Journal for Parasitology journal homepage: www.elsevier.com/locate/ijpara NEMBASE4: The nematode transcriptome resource ⇑ Benjamin Elsworth a, James Wasmuth b, Mark Blaxter a, a Institute of Evolutionary Biology, The University of Edinburgh, EH9 3JT, UK b Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, 3330, Hospital Drive, University of Calgary, Calgary, Alberta, Canada T2N 4N1 article info abstract Article history: Nematode parasites are of major importance in human health and agriculture, and free-living species Received 21 December 2010 deliver essential ecosystem services. The genomics revolution has resulted in the production of many Received in revised form 11 March 2011 datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, Accepted 14 March 2011 but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally anno- Available online 21 April 2011 tated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal para- sites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available Keywords: ESTs for each species into a high-quality set of putative transcripts. These transcripts have been trans- Nematode lated to produce a protein sequence resource and each is annotated with functional information derived Transcriptome Genome from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nem- Expressed sequence tag atode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein Database family assignment for each translation.
    [Show full text]
  • Biliverdin Reductase: a Major Physiologic Cytoprotectant
    Biliverdin reductase: A major physiologic cytoprotectant David E. Baran˜ ano*, Mahil Rao*, Christopher D. Ferris†, and Solomon H. Snyder*‡§¶ Departments of *Neuroscience, ‡Pharmacology and Molecular Sciences, and §Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205; and †Department of Medicine, Division of Gastroenterology, C-2104 Medical Center North, Vanderbilt University Medical Center, Nashville, TN 37232-2279 Contributed by Solomon H. Snyder, October 16, 2002 Bilirubin, an abundant pigment that causes jaundice, has long hypothesize that bilirubin acts in a catalytic fashion whereby lacked any clear physiologic role. It arises from enzymatic reduction bilirubin oxidized to biliverdin is rapidly reduced back to bili- by biliverdin reductase of biliverdin, a product of heme oxygenase rubin, a process that could readily afford 10,000-fold amplifica- activity. Bilirubin is a potent antioxidant that we show can protect tion (13). Here we establish that a redox cycle based on BVRA cells from a 10,000-fold excess of H2O2. We report that bilirubin is activity provides physiologic cytoprotection as BVRA depletion a major physiologic antioxidant cytoprotectant. Thus, cellular de- exacerbates the formation of reactive oxygen species (ROS) and pletion of bilirubin by RNA interference markedly augments tissue augments cell death. levels of reactive oxygen species and causes apoptotic cell death. Depletion of glutathione, generally regarded as a physiologic Methods antioxidant cytoprotectant, elicits lesser increases in reactive ox- All chemicals were obtained from Sigma unless otherwise ygen species and cell death. The potent physiologic antioxidant indicated. actions of bilirubin reflect an amplification cycle whereby bilirubin, acting as an antioxidant, is itself oxidized to biliverdin and then Cell Culture and Viability Measurements.
    [Show full text]