DOCSLIB.ORG

Regulation of Oxidoreductase Enzymes During Inflammation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Regulation of Oxidoreductase Enzymes During Inflammation Regulation of oxidoreductase enzymes during inflammation Sonia Louise Ingram September 2018 A thesis submitted to the University of Brighton and the University of Sussex for a programme of study undertaken at the Brighton and Sussex Medical School for the degree of Doctor of Philosophy 1 Abstract Autoimmune diseases such as rheumatoid arthritis (RA) occur when immune responses erroneously target host cells and proteins. The triggers for this dysregulated inflammation are unknown, but Toll-like receptors (TLRs) and oxidative stress are contributing factors (1, 2). Peroxiredoxin (PRDX) and thioredoxin (TXN) are intracellular protein thiol-disulphide oxidoreductase enzymes which link the TLRs to oxidative stress. These enzymes are induced during inflammation and oxidative stress, and are released from cells following inflammatory stimuli. In the extracellular environment they can act as danger signals, triggering TLR activation and perpetuating inflammation. However, knowledge of oxidoreductase regulation and release is limited. The hypotheses of this study were that responses of oxidoreductases vary depending on the TLR stimulated, and that serum oxidoreductases could be used as biomarkers for RA. To investigate TLR-induced oxidoreductase responses, concentrations of TLR agonists required to induce release were examined and tested for effects on tumour necrosis factor (TNF) production and cell viability in RAW 264.7 cells. Cells were stimulated with optimised concentrations in serum free OptiMEM (24h) for cell lysate and supernatant gel electrophoresis and Western blot experiments, and cell culture media (6-18h) for real time Taqman qPCR. PRDX1 and TXN1 release was found to occur primarily following TLR3 and TLR4 stimulation. Each oxidoreductase had a different pattern of gene expression to the TLRs: PRDX1 only increased with TLR4 stimulation, whilst TXN reductase (TXNRD1) increased with TLR4, TLR7 and TLR8, and heme oxygenase (HO1) increased with these TLRs plus TLR1/2 and TLR3. To investigate the role of reactive oxygen and nitrogen species (ROS and RNS respectively) on oxidoreductase release, RAW 264.7 cells were stimulated with PMA or interferon (IFN)γ + lipopolysaccharide (LPS). Griess assay was used to assess nitrite production. IFNγ+LPS increased TXN1 release but abrogated PRDX1 release. PRDX1 protein underwent NO-mediated proteasomal degradation following IFNγ+LPS stimulation. Gene expression of all oxidoreductases investigated increased with IFNγ+LPS stimulation compared to LPS alone, and inhibition of protein synthesis prevented PRDX1 gene expression, suggesting a secondary signal protein is required. 2 To investigate serum PRDX2, serum was isolated from whole blood from RA patients and healthy donors. ELISA was used to quantify both PRDX2 and the inflammatory marker C-reactive protein (CRP). No difference was found between RA and healthy serums, and PRDX2 did not correlate with CRP. The findings from this project show that oxidoreductase regulation and responses are fine-tuned depending on the TLR stimuli, and that serum PRDX2 is not a suitable biomarker for RA. 3 Courage doesn’t always roar. Sometimes courage is the little voice at the end of the day that says “I’ll try again tomorrow” - Mary Anne Radmacher 4 Contents Abstract .............................................................................................................................................. 2 Contents ............................................................................................................................................ 5 List of figures ..................................................................................................................................... 9 List of tables .................................................................................................................................... 12 Abbreviations .................................................................................................................................. 13 Acknowledgements ........................................................................................................................ 16 Declaration ...................................................................................................................................... 17 1. Introduction ................................................................................................................................. 19 1.1 Inflammation and immunity ................................................................................................ 19 1.1.1 The Immune System .................................................................................................... 19 1.1.2 Rheumatoid Arthritis .................................................................................................... 24 1.1.3 Biomarkers of disease ................................................................................................. 27 1.1.4 Inflammation .................................................................................................................. 29 1.1.5 Macrophages ................................................................................................................ 35 1.1.6 Toll-like receptors ......................................................................................................... 38 1.1.7 NF-κB ............................................................................................................................. 46 1.1.8 Nrf2 ................................................................................................................................. 50 1.1.9 Nrf2 and NF-κB cross-signalling ................................................................................ 55 1.2 Reduction-Oxidation (Redox) Biology .............................................................................. 57 1.2.1 Reactive oxygen species ............................................................................................ 57 1.2.2 Reactive nitrogen species ........................................................................................... 61 1.2.3 Reactive sulphur species ............................................................................................ 62 1.2.4 Cysteine and the free thiol .......................................................................................... 63 1.2.5 The reactive species interactome .............................................................................. 65 1.3 Oxidoreductase enzymes ................................................................................................... 66 1.3.1 Thioredoxin .................................................................................................................... 68 1.3.2 Thioredoxin reductase ................................................................................................. 71 1.3.3 Peroxiredoxin ................................................................................................................ 75 1.3.4 Redox and inflammation.............................................................................................. 78 1.3.5 Oxidoreductases and inflammation ........................................................................... 79 Aims .................................................................................................................................................. 82 2. Methods and Materials .............................................................................................................. 84 2.1 Materials ................................................................................................................................ 84 2.1.1 Instruments .................................................................................................................... 84 5 2.1.2 Chemicals and Kits ...................................................................................................... 85 2.1.3 Plastics .......................................................................................................................... 87 2.1.4 Solutions, Buffers and Media ..................................................................................... 87 2.2 Software and Analysis ........................................................................................................ 88 2.2.1 ImageJ 1.48v ................................................................................................................ 88 2.2.2 Microsoft Excel 2010 ................................................................................................... 88 2.2.3 GraphPad Prism 7.03 .................................................................................................. 88 2.3 Cell culture and stimulation ................................................................................................ 89 2.3.1 RAW 264.7 cells ........................................................................................................... 89 2.3.2 RAW 264.7 cell culture ................................................................................................ 89 2.3.3 Cell stimulations ........................................................................................................... 89 2.3.4 Cell viability assay ........................................................................................................ 92 2.4 Ethical approvals, patients and recruitment ...................................................................
Load more

Recommended publications
  • Oxidative Pentose Phosphate Pathway Enzyme 6-Phosphogluconate Dehydrogenase Plays a Key Role in Breast Cancer Metabolism
    biology Article Oxidative Pentose Phosphate Pathway Enzyme 6-Phosphogluconate Dehydrogenase Plays a Key Role in Breast Cancer Metabolism Ibrahim H. Polat 1,2,3 ,Míriam Tarrado-Castellarnau 1,4 , Rohit Bharat 1, Jordi Perarnau 1 , Adrian Benito 1,5 , Roldán Cortés 1, Philippe Sabatier 2 and Marta Cascante 1,4,* 1 Department of Biochemistry and Molecular Biomedicine and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; [email protected] (I.H.P.); [email protected] (M.T.-C.); [email protected] (R.B.); [email protected] (J.P.); [email protected] (A.B.); [email protected] (R.C.) 2 Equipe Environnement et Prédiction de la Santé des Populations, Laboratoire TIMC (UMR 5525), CHU de Grenoble, Université Grenoble Alpes, 38700 CEDEX La Tronche, France; [email protected] 3 Department of Medicine, Hematology/Oncology, Goethe-University Frankfurt, 60590 Frankfurt, Germany 4 Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), 28001 Madrid, Spain 5 Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London W12 0NN, UK * Correspondence: [email protected] Simple Summary: Cancer cells alter their metabolism to maintain their high need for energy, produce Citation: Polat, I.H.; enough macromolecules for biosynthesis, and preserve their redox status. The investigation of Tarrado-Castellarnau, M.; Bharat, R.; cancer cell-specific metabolic alterations has vital importance to identify targets to be exploited for Perarnau, J.; Benito, A.; Cortés, R.; therapeutic development. The pentose phosphate pathway (PPP) is often highly activated in tumor Sabatier, P.; Cascante, M.
    [Show full text]
  • Lecture 7 - the Calvin Cycle and the Pentose Phosphate Pathway
    Lecture 7 - The Calvin Cycle and the Pentose Phosphate Pathway Chem 454: Regulatory Mechanisms in Biochemistry University of Wisconsin-Eau Claire 1 Introduction The Calvin cycle Text The dark reactions of photosynthesis in green plants Reduces carbon from CO2 to hexose (C6H12O6) Requires ATP for free energy and NADPH as a reducing agent. 2 2 Introduction NADH versus Text NADPH 3 3 Introduction The Pentose Phosphate Pathway Used in all organisms Glucose is oxidized and decarboxylated to produce reduced NADPH Used for the synthesis and degradation of pentoses Shares reactions with the Calvin cycle 4 4 1. The Calvin Cycle Source of carbon is CO2 Text Takes place in the stroma of the chloroplasts Comprises three stages Fixation of CO2 by ribulose 1,5-bisphosphate to form two 3-phosphoglycerate molecules Reduction of 3-phosphoglycerate to produce hexose sugars Regeneration of ribulose 1,5-bisphosphate 5 5 1. Calvin Cycle Three stages 6 6 1.1 Stage I: Fixation Incorporation of CO2 into 3-phosphoglycerate 7 7 1.1 Stage I: Fixation Rubisco: Ribulose 1,5- bisphosphate carboxylase/ oxygenase 8 8 1.1 Stage I: Fixation Active site contains a divalent metal ion 9 9 1.2 Rubisco Oxygenase Activity Rubisco also catalyzes a wasteful oxygenase reaction: 10 10 1.3 State II: Formation of Hexoses Reactions similar to those of gluconeogenesis But they take place in the chloroplasts And use NADPH instead of NADH 11 11 1.3 State III: Regeneration of Ribulose 1,5-Bisphosphosphate Involves a sequence of transketolase and aldolase reactions. 12 12 1.3 State III:
    [Show full text]
  • RESPIRATION Pentose Phosphate Pathway Or Hexose Monophosphate Pathway
    RESPIRATION Pentose Phosphate Pathway or Hexose Monophosphate Pathway Pentose phosphate pathway or hexose monophosphate pathway (HMP pathway) is the other common pathway to break down glucose to pyruvate and operates in both aerobic and anaerobic conditions. This pathway produces NADPH, which carries chemical energy in the form of reducing power and is used almost universally as the reductant in anabolic (energy utilization) pathways (e.g., fatty acid biosynthesis, cholesterol biosynthesis, nucleotide biosynthesis) and detoxification pathways (e.g., reduction of oxidized glutathione, cytochrome P450 monooxygenases). Also, the pentose phosphate pathway generates pentose sugar ribose and its derivatives, which are necessary for the biosynthesis of nucleic acids (DNA and RNA) as well as ATP, NADH, FAD, and coenzyme A. In this way, though the pentose phosphate pathway may be a source of energy in many microorganisms, it is more often of greater importance in various biosynthetic pathways. Pentose phosphate pathway consists of two phases: the oxidative phase and the non-oxidative phase. Oxidative Phase: The oxidative phase of the pentose phosphate pathway initiates with the conversion of glucose 6- phosphate to 6-Phosphogluconate. NADP+ is the electron acceptor yielding NADPH during this reaction. 6-Phosphogluconate, a six-carbon sugar, is then oxidativelydecarboxylated to yield ribulose 5-phosphate, a five-carbon sugar. NADP+ is again the electron acceptor yielding NADPH. In the final step of oxidative phase, there is isomerisation of ribulose 5-phosphatc to ribose 5- phosphate by phosphopentose isomerase and the conversion of ribulose 5-phosphate into its epimerxylulose 5-phosphate by phosphopentose epimerase for the transketolase reaction in non- oxidative phase.
    [Show full text]
  • Transaldolase B of Escherichia Coli K-12: Cloning of Its Gene, Talb, and Characterization of the Enzyme from Recombinant Strains
    JOURNAL OF BACTERIOLOGY, Oct. 1995, p. 5930–5936 Vol. 177, No. 20 0021-9193/95/$04.0010 Copyright q 1995, American Society for Microbiology Transaldolase B of Escherichia coli K-12: Cloning of Its Gene, talB, and Characterization of the Enzyme from Recombinant Strains GEORG A. SPRENGER,* ULRICH SCHO¨ RKEN, GERDA SPRENGER, AND HERMANN SAHM Institut fu¨r Biotechnologie 1, Forschungszentrum Ju¨lich GmbH, D-52425 Ju¨lich, Germany Received 7 June 1995/Accepted 7 August 1995 A previously recognized open reading frame (T. Yura, H. Mori, H. Nagai, T. Nagata, A. Ishihama, N. Fujita, K. Isono, K. Mizobuchi, and A. Nakata, Nucleic Acids Res. 20:3305–3308) from the 0.2-min region of the Escherichia coli K-12 chromosome is shown to encode a functional transaldolase activity. After cloning of the gene onto high-copy-number vectors, transaldolase B (D-sedoheptulose-7-phosphate:D-glyceraldehyde-3-phos- phate dihydroxyacetone transferase; EC 2.2.1.2) was overexpressed up to 12.7 U mg of protein21 compared with less than 0.1 U mg of protein21 in wild-type homogenates. The enzyme was purified from recombinant E. coli K-12 cells by successive ammonium sulfate precipitations (45 to 80% and subsequently 55 to 70%) and two anion-exchange chromatography steps (Q-Sepharose FF, Fractogel EMD-DEAE tentacle column; yield, 130 mg of protein from 12 g of cell wet weight) and afforded an apparently homogeneous protein band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a subunit size of 35,000 6 1,000 Da. As the enzyme had a molecular mass of 70,000 Da by gel filtration, transaldolase B is likely to form a homodimer.
    [Show full text]
  • PENTOSE PHOSPHATE PATHWAY — Restricted for Students Enrolled in MCB102, UC Berkeley, Spring 2008 ONLY
    Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY Bryan Krantz: University of California, Berkeley MCB 102, Spring 2008, Metabolism Lecture 5 Reading: Ch. 14 of Principles of Biochemistry, “Glycolysis, Gluconeogenesis, & Pentose Phosphate Pathway.” PENTOSE PHOSPHATE PATHWAY This pathway produces ribose from glucose, and it also generates 2 NADPH. Two Phases: [1] Oxidative Phase & [2] Non-oxidative Phase + + Glucose 6-Phosphate + 2 NADP + H2O Ribose 5-Phosphate + 2 NADPH + CO2 + 2H ● What are pentoses? Why do we need them? ◦ DNA & RNA ◦ Cofactors in enzymes ● Where do we get them? Diet and from glucose (and other sugars) via the Pentose Phosphate Pathway. ● Is the Pentose Phosphate Pathway just about making ribose sugars from glucose? (1) Important for biosynthetic pathways using NADPH, and (2) a high cytosolic reducing potential from NADPH is sometimes required to advert oxidative damage by radicals, e.g., ● - ● O2 and H—O Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY Two Phases of the Pentose Pathway Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY NADPH vs. NADH Metabolism Lecture 5 — PENTOSE PHOSPHATE PATHWAY — Restricted for students enrolled in MCB102, UC Berkeley, Spring 2008 ONLY Oxidative Phase: Glucose-6-P Ribose-5-P Glucose 6-phosphate dehydrogenase. First enzymatic step in oxidative phase, converting NADP+ to NADPH. Glucose 6-phosphate + NADP+ 6-Phosphoglucono-δ-lactone + NADPH + H+ Mechanism. Oxidation reaction of C1 position. Hydride transfer to the NADP+, forming a lactone, which is an intra-molecular ester.
    [Show full text]
  • A Deeply Glimpse Into Protein Fold Recognition
    International Journal of Sciences Research Article (ISSN 2305-3925) Volume 2, Issue June 2013 http://www.ijSciences.com A Deep Glimpse into Protein Fold Recognition Ahmed Sharaf Eldin1, Taysir Hassan A. Soliman2, Mohammed Ebrahim Marie3, Marwa Mohamed M. Ghareeb4 1Information Systems Department, Faculty of Computers and Information, Helwan University, Cairo, Egypt 2Supervisor of Information Systems Department, Faculty of Computers and Information, Assiut University, Assiut, Egypt 3Information Systems Department, Faculty of Computers and Information, Helwan University, Cairo, Egypt 4Assistant Lecturer, Information Systems Department, Modern Academy, Cairo, Egypt Abstract: The rapid growth in genomic and proteomic data causes a lot of challenges that are raised up and need powerful solutions. It is worth noting that UniProtKB/TrEMBL database Release 28-Nov-2012 contains 28,395,832 protein sequence entries, while the number of stored protein structures in Protein Data Bank (PDB, 4- 12-2012) is 65,643. Thus, the need of extracting structural information through computational analysis of protein sequences has become very important, especially, the prediction of the fold of a query protein from its primary sequence has become very challenging. The traditional computational methods are not powerful enough to address theses challenges. Researchers have examined the use of a lot of techniques such as neural networks, Monte Carlo, support vector machine and data mining techniques. This paper puts a spot on this growing field and covers the main approaches and perspectives to handle this problem. Keywords: Protein fold recognition, Neural network, Evolutionary algorithms, Meta Servers. research has been conducted towards this goal in the I. INTRODUCTION late years. Especially, the prediction of the fold of a Proteins transport oxygen to cells, prevent harmful query protein from its primary sequence has become infections, convert chemical energy into mechanical very challenging.
    [Show full text]
  • Synthesis and Cell Survival Under Stress Conditions . the PPP
    Pentose phosphate pathway Significance of Pentose Phosphate Pathway To generate reducing equivalents, in the form of NADPH, which is needed for fatty acid synthesis and cell survival under stress conditions . To provide the cell with ribose-5-phosphate (R5P) for the synthesis of the nucleotides and nucleic acids. No ATP is generated in this pathway. So glucose can be metabolized through this pathway even when energy requirement is low. Location of the pathway • The enzymes are located in the cytosol. The tissues such as liver, adipose tissue, adrenal gland, erythrocytes, testes & lactating mammary gland, are highly active in the oxidative phase of HMP shunt. Rapidly dividing cells have a high activity of the non-oxidative phase. *It is called the pentose phosphate shunt because the pathway allows for carbon atoms from glucose 6-phosphate to take a shunt before they proceed down the glycolytic pathway. The PPP comprises two irreversible oxidative reactions followed by a series of reversible interconversions. The PPP is thus divided into two biochemical branches: An oxidative and a non-oxidative branch. The oxidative branch converts glucose 6-phosphate (G6P) into ribulose-5-phosphate (Ru5P), CO2 and NADPH. NADPH is vital to maintain the reduction-oxidation (redox) balance under stress conditions and allows cells to proliferate rapidly. The non-oxidative branch yields the glycolytic intermediates fructose 6-phosphate (F6P), glyceraldehyde 3-phosphate (G3P) and sedoheptulose sugars, resulting in the production of sugar phosphate precursors for amino acid synthesis and ribose-5-phosphate (R5P), which is essential for nucleic acid synthesis. Oxidative Phase of the Pentose Phosphate Pathway Glucose 6-phosphate is oxidized to 6-phosphoglucono-δ-lactone to generate one molecule of NADPH.
    [Show full text]
  • Modeling and Predicting Super-Secondary Structures of Transmembrane Beta-Barrel Proteins Thuong Van Du Tran
    Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins Thuong van Du Tran To cite this version: Thuong van Du Tran. Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins. Bioinformatics [q-bio.QM]. Ecole Polytechnique X, 2011. English. NNT : 2011EPXX0104. pastel-00711285 HAL Id: pastel-00711285 https://pastel.archives-ouvertes.fr/pastel-00711285 Submitted on 23 Jun 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THESE` pr´esent´ee pour obtenir le grade de DOCTEUR DE L’ECOLE´ POLYTECHNIQUE Sp´ecialit´e: INFORMATIQUE par Thuong Van Du TRAN Titre de la th`ese: Modeling and Predicting Super-secondary Structures of Transmembrane β-barrel Proteins Soutenue le 7 d´ecembre 2011 devant le jury compos´ede: MM. Laurent MOUCHARD Rapporteurs Mikhail A. ROYTBERG MM. Gregory KUCHEROV Examinateurs Mireille REGNIER M. Jean-Marc STEYAERT Directeur Laboratoire d’Informatique UMR X-CNRS 7161 Ecole´ Polytechnique, 91128 Plaiseau CEDEX, FRANCE Composed with LATEX !c Thuong Van Du Tran. All rights reserved. Contents Introduction 1 1Fundamentalreviewofproteins 5 1.1 Introduction................................... 5 1.2 Proteins..................................... 5 1.2.1 Aminoacids............................... 5 1.2.2 Properties of amino acids .
    [Show full text]
  • Final List of NGF Publications (2001-2007)
    Final List of NGF Publications (2001-2007) (1) Abahuni N, Gispert S, Bauer P, Riess O, Krüger R, Becker T, Auburger G. Mitochondrial translation initiation factor 3 gene polymorphism associated with Parkinson's disease. Neurosci Lett. 2007 Mar 6;414(2):126-9. (2) Abarca C, Albrecht U, Spanagel R. Cocaine sensitization and reward are influenced by circadian genes and rhythm. Proc. Natl. Acad. Sci. USA 2002; 99, 9026-9030 (3) Abdelaziz AI, Segaric J, Bartsch H, Petzhold D, Schlegel WP, Kott M, Seefeldt I, Klose J, Bader M, Haase H, Morano I. Functional characterization of the human atrial essential myosin light chain (hALC-1) in a transgenic rat model. J Mol Med. 2004 Apr;82(4):265-74. (4) Abdollahi A, Hahnfeldt P, Maercker C, Grone HJ, Debus J, Ansorge W, Folkman J, Hlatky L, Huber PE. Endostatin's antiangiogenic signaling network. Mol Cell. 2004 Mar 12;13(5):649-63. (5) Abe K, Fuchs H, Lisse T, Hans W, de Angelis MH. New ENU-induced semidominant mutation, Ali18, causes inflammatory arthritis, dermatitis, and osteoporosis in the mouse. Mamm Genome. 2006 Sep 8; [Epub ahead of print] (6) Abe M, Westermann F, Nakagawara A, Takato T, Schwab M, Ushijima T. Marked and independent prognostic significance of the CpG island methylator phenotype in neuroblastomas. Cancer Lett. 2007 Mar 18;247(2):253- 258. (7) Abeysinghe SS, Chuzhanova N, Krawczak M, Ball EV, Cooper DN. Translocation and gross deletion breakpoints in human inherited disease and cancer I. Nucleotide composition and recombination-associated motifs. Hum Mutat. 2003; 22:229-244 (8) Abeysinghe SS, Stenson PD, Krawczak M, Cooper DN.
    [Show full text]
  • A Tri-Gram Based Feature Extraction Technique Using Linear Probabilities of Position Specific Scoring Matrix for Protein Fold Recognition
    A Tri-Gram Based Feature Extraction Technique Using Linear Probabilities of Position Specific Scoring Matrix for Protein Fold Recognition Author Paliwal, Kuldip K, Sharma, Alok, Lyons, James, Dehzangi, Abdollah Published 2014 Journal Title IEEE Transactions on NanoBioscience DOI https://doi.org/10.1109/TNB.2013.2296050 Copyright Statement © 2014 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. Downloaded from http://hdl.handle.net/10072/67288 Griffith Research Online https://research-repository.griffith.edu.au A Tri-gram Based Feature Extraction Technique Using Linear Probabilities of Position Specific Scoring Matrix for Protein Fold Recognition Kuldip K. Paliwal, Member, IEEE, Alok Sharma, Member, IEEE, James Lyons, Abdollah Dhezangi, Member, IEEE protein structure in a reasonable amount of time. Abstract— In biological sciences, the deciphering of a three The prime objective of protein fold recognition is to find the dimensional structure of a protein sequence is considered to be an fold of a protein sequence. Assigning of protein fold to a important and challenging task. The identification of protein folds protein sequence is a transitional stage in the recognition of from primary protein sequences is an intermediate step in three dimensional structure of a protein. The protein fold discovering the three dimensional structure of a protein. This can be done by utilizing feature extraction technique to accurately recognition broadly covers feature extraction task and extract all the relevant information followed by employing a classification task.
    [Show full text]
  • The Classification of Chemical Compounds Should Preferably Be Of
    PROTEINS OF THE NERVOUS SYSTEM: CONSIDERED IN THE LIGHT OF THE PREVAILING HYPOTHESES ON PROTEIN STRUCTURE* RICHARD J. BLOCK THE CLASSIFICATION OF THE PROTEINS The classification of chemical compounds should preferably be based on definite chemical and physical properties of the individual substances. However, at the present time such treatment of most of the proteins is, impossible. Only a few groups-protamines, keratins, globins, collagens, and homologous tissue proteins-can be thus definitely classified. But, in order to have a better understand- ing of the hypotheses on the structure of the proteins, this discussion will be introduced by a brief summary of a scheme by means of which the proteins can be grouped.45 THE PROTEINS I. Simple Proteins yield on hydrolysis only amino acids or their derivatives. A. Albumins are soluble in water, coagulable by heat, and are usually deficient in glycine.t B. Globulins are insoluble in water, soluble in strong acids and alkalis, in neutral salts, and usually contain glycine.:: C. Prolamines are soluble in 70-80 per cent ethyl alcohol, yield large amounts of proline and amide nitrogen (indicative of consider- *From the Department of Chemistry, New York State Psychiatric Institute and Hospital, New York City. t Apparently the solubility of native proteins depends on the distribution of the surface charges. If the number of positive and negative groups on the surface are equal, these unite to form protein aggregates which then precipitate. The positive and negative groups in the interior of the protein globules are claimed to have no effect on the solubility, except after denaturation when some are transferred to the surface causing precipitation at the isoelectric point (cf.
    [Show full text]
  • Pentose Phosphate Pathway Biochemistry, Metabolism and Inherited Defects
    Pentose phosphate pathway biochemistry, metabolism and inherited defects Amsterdam 2008 Mirjam M.C. Wamelink The research described in this thesis was carried out at the Department of Clinical Chemistry, Metabolic Unit, VU University Medical Center, Amsterdam, The Netherlands. The publication of this thesis was financially supported by: Department of Clinical Chemistry, VU University Medical Center Amsterdam E.C. Noyons Stichting ter bevordering van de Klinische Chemie in Nederland J.E. Jurriaanse Stichting te Rotterdam Printed by: Printpartners Ipskamp BV, Enschede ISBN: 978-90-9023415-1 Cover: Representation of a pathway of sugar Copyright Mirjam Wamelink, Amsterdam, The Netherlands, 2008 2 VRIJE UNIVERSITEIT Pentose phosphate pathway biochemistry, metabolism and inherited defects ACADEMISCH PROEFSCHRIFT ter verkrijging van de graad Doctor aan de Vrije Universiteit Amsterdam, op gezag van de rector magnificus prof.dr. L.M. Bouter, in het openbaar te verdedigen ten overstaan van de promotiecommissie van de faculteit der Geneeskunde op donderdag 11 december 2008 om 13.45 uur in de aula van de universiteit, De Boelelaan 1105 door Mirjam Maria Catharina Wamelink geboren te Alkmaar 3 promotor: prof.dr.ir. C.A.J.M. Jakobs copromotor: dr. E.A. Struijs 4 Abbreviations 6PGD 6-phosphogluconate dehydrogenase ADP adenosine diphosphate ATP adenosine triphosphate CSF cerebrospinal fluid DHAP dihydroxyacetone phosphate G6PD glucose-6-phosphate dehydrogenase GA glyceraldehyde GAPDH glyceraldehyde-3-phosphate dehydrogenase GSG oxidized glutathione
    [Show full text]