Structure and Function of Microsomal Prostaglandin E Synthase-1
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Comparative Modeling and Functional Characterization of Two Enzymes of the Cyclooxygenase Pathway in Drosophila Melanogaster
City University of New York (CUNY) CUNY Academic Works All Dissertations, Theses, and Capstone Projects Dissertations, Theses, and Capstone Projects 2-2014 Comparative Modeling and Functional Characterization of Two Enzymes of the Cyclooxygenase Pathway in Drosophila melanogaster Yan Qi Graduate Center, City University of New York How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/gc_etds/94 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Comparative Modeling and Functional Characterization of Two Enzymes of the Cyclooxygenase Pathway in Drosophila melanogaster by Yan Qi A dissertation submitted to the Graduate Faculty in Biology in partial fulfillment of the requirements for the degree of Doctor of Philosophy, The City University of New York 2014 i © 2014 Yan Qi All Rights Reserved ii This manuscript has been read and accepted for the Graduate Faculty in Biology in satisfaction of the dissertation requirement for the degree of Doctor of Philosophy. _______ ______________________ Date Chair of Examining Committee Dr. Shaneen Singh, Brooklyn College _______ ______________________ Date Executive Officer Dr. Laurel A. Eckhardt ______________________ Dr. Peter Lipke, Brooklyn College ______________________ Dr. Shubha Govind, City College ______________________ Dr. Richard Magliozzo, Brooklyn College ______________________ Dr. Evros Vassiliou, Kean University Supervising Committee The City University of New York iii Abstract Comparative Modeling and Functional Characterization of Two Enzymes of the Cyclooxygenase Pathway in Drosophila melanogaster by Yan Qi Mentor: Shaneen Singh Eicosanoids are biologically active molecules oxygenated from twenty carbon polyunsaturated fatty acids. -
The Endocannabinoid 2-Arachidonoylglycerol Negatively Regulates Habituation by Suppressing Excitatory Recurrent Network Activity
3588 • The Journal of Neuroscience, February 20, 2013 • 33(8):3588–3601 Cellular/Molecular The Endocannabinoid 2-Arachidonoylglycerol Negatively Regulates Habituation by Suppressing Excitatory Recurrent Network Activity and Reducing Long-Term Potentiation in the Dentate Gyrus Yuki Sugaya,1 Barbara Cagniard,1 Maya Yamazaki,2 Kenji Sakimura,2 and Masanobu Kano1 1Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan and 2Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan Endocannabinoids are known to mediate retrograde suppression of synaptic transmission, modulate synaptic plasticity, and influence learning and memory. The 2-arachidonoylglycerol (2-AG) produced by diacylglycerol lipase ␣ (DGL␣) is regarded as the major endo- cannabinoid that causes retrograde synaptic suppression. To determine how 2-AG signaling influences learning and memory, we sub- jected DGL␣ knock-out mice to two learning tasks. We tested the mice using habituation and odor-guided transverse patterning tasks that are known to involve the dentate gyrus and the CA1, respectively, of the hippocampus. We found that DGL␣ knock-out mice showed significantly faster habituation to an odor and a new environment than wild-type littermates with normal performance in the transverse patterning task. In freely moving animals, long-term potentiation (LTP) induced by theta burst stimulation was significantly larger at perforantpath–granulecellsynapsesinthedentategyrusofDGL␣knock-outmice.Importantly,priorinductionofsynapticpotentiation -
Supplementary Materials
Supplementary Materials Figure S1. Bioinformatics evaluation of dystrophin isoform Dp427 and its central position in the molecular pathogenesis of X-linked muscular dystrophy. In order to generate a protein interaction map with known and predicted protein associations that include direct physical and indirect functional protein linkages, the bioinformatics STRING database [1,2] was used to analyse mass spectrometrically-identified proteins with a changed abundance in mdx-4cv skeletal muscles (Tables 1 and 2). S2 Figure S2. Focus of the bioinformatics evaluation of dystrophin isoform Dp427 and its central position in the molecular pathogenesis of X-linked muscular dystrophy. Shown is the middle part of the interaction map of altered muscle-associated proteins from mdx-4cv hind limb muscles, focusing on the central position of the dystrophin protein Dp427 (marked in yellow). In order to generate a protein interaction map with known and predicted protein associations that include direct physical and indirect functional protein linkages, the bioinformatics STRING database [1,2] was used to analyse mass spectrometrically-identified proteins with a changed abundance in mdx-4cv skeletal muscles (Tables 1 and 2). S3 Table S1. List of identified proteins that exhibit a significantly altered concentration in crude mdx-4cv hind limb muscle preparations as revealed by label-free LC-MS/MS analysis. This table contains the statistical q-values of the proteins listed in Tables 1 and 2. Accession Peptide Max Fold Highest Mean Description q Value Number -
S42003-021-02488-1.Pdf
ARTICLE https://doi.org/10.1038/s42003-021-02488-1 OPEN In situ imaging reveals disparity between prostaglandin localization and abundance of prostaglandin synthases ✉ Kyle D. Duncan 1,5, Xiaofei Sun 2,3,5, Erin S. Baker 4, Sudhansu K. Dey 2,3 & Ingela Lanekoff 1 Prostaglandins are important lipids involved in mediating many physiological processes, such as allergic responses, inflammation, and pregnancy. However, technical limitations of in-situ prostaglandin detection in tissue have led researchers to infer prostaglandin tissue dis- tributions from localization of regulatory synthases, such as COX1 and COX2. Herein, we apply a novel mass spectrometry imaging method for direct in situ tissue localization of 1234567890():,; prostaglandins, and combine it with techniques for protein expression and RNA localization. We report that prostaglandin D2, its precursors, and downstream synthases co-localize with the highest expression of COX1, and not COX2. Further, we study tissue with a conditional deletion of transformation-related protein 53 where pregnancy success is low and confirm that PG levels are altered, although localization is conserved. Our studies reveal that the abundance of COX and prostaglandin D2 synthases in cellular regions does not mirror the regional abundance of prostaglandins. Thus, we deduce that prostaglandins tissue localization and abundance may not be inferred by COX or prostaglandin synthases in uterine tissue, and must be resolved by an in situ prostaglandin imaging. 1 Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden. 2 Division of Reproductive Sciences, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA. 3 College of Medicine, University of Cincinnati, Cincinnati, OH 45221, USA. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
GT Lauram.Sc Thesis (FINAL)
OPTIMIZATION OF OVER-EXPRESSION AND PURIFICATION OF HUMAN LEUKOTRIENE C4 SYNTHASE MUTANT R104A FOR STRUCTURE-FUNCTION STUDIES BY TWO-DIMENSIONAL CRYSTALLIZATION AND ELECTRON CRYSTALLOGRAPHY A Thesis Presented to The Academic Faculty by Laura Yaunhee Kim In Partial Fulfillment of the Requirements for the Degree Master of Science in the School of Biology Georgia Institute of Technology December 2012 OPTIMIZATION OF OVER-EXPRESSION AND PURIFICATION OF HUMAN LEUKOTRIENE C4 SYNTHASE MUTANT R104A FOR STRUCTURE-FUNCTION STUDIES BY TWO-DIMENSIONAL CRYSTALLIZATION AND ELECTRON CRYSTALLOGRAPHY Approved by: Dr. Ingeborg Schmidt-Krey, Advisor School of Biology School of Chemistry and Biochemistry Georgia Institute of Technology Dr. Thomas DiChristina School of Biology Georgia Institute of Technology Dr. Raquel L. Lieberman School of Chemistry and Biochemistry Georgia Institute of Technology Date Approved: July 24, 2012 I dedicate this work to my father Sun Dong Kim, mother In Ok Kim, and sister Esther Kim, who have supported me from the very beginning. This work could not have been completed without your love and encouragement. ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. Inga Schmidt-Krey, for guiding and supporting me throughout my academic studies. I would like to thank her for her consistent availability and scientific input during every step of research. Without her guidance this work would not have been possible. I am in debt to my family and friends for their unflinching support and encouragement, without which none of this would be possible. I am also very grateful to all the Schmidt-Krey lab members, especially Matthew Johnson and Maureen Metcalfe, for their support and input into this work. -
Development of Potent and Selective Inhibitors of Aldo−Keto Reductase
Article pubs.acs.org/jmc Development of Potent and Selective Inhibitors of Aldo−Keto Reductase 1C3 (Type 5 17β-Hydroxysteroid Dehydrogenase) Based on N-Phenyl-Aminobenzoates and Their Structure−Activity Relationships † § ‡ § † † † ‡ Adegoke O. Adeniji, , Barry M. Twenter, , Michael C. Byrns, Yi Jin, Mo Chen, Jeffrey D. Winkler,*, † and Trevor M. Penning*, † Department of Pharmacology and Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, 130C John Morgan Building, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104-6084, United States ‡ Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States *S Supporting Information ABSTRACT: Aldo−keto reductase 1C3 (AKR1C3; type 5 17β-hydroxy- steroid dehydrogenase) is overexpressed in castration resistant prostate cancer (CRPC) and is implicated in the intratumoral biosynthesis of testosterone and 5α-dihydrotestosterone. Selective AKR1C3 inhibitors are required because compounds should not inhibit the highly related AKR1C1 and AKR1C2 isoforms which are involved in the inactivation of 5α-dihydrotestosterone. NSAIDs, N-phenylanthranilates in particular, are potent but nonselective AKR1C3 inhibitors. Using flufenamic acid, 2-{[3-(trifluoromethyl)phenyl]amino}- benzoic acid, as lead compound, five classes of structural analogues were synthesized and evaluated for AKR1C3 inhibitory potency and selectivity. Structure−activity relationship (SAR) studies revealed that a meta-carboxylic acid group relative to the amine conferred pronounced AKR1C3 selectivity without loss of potency, while electron withdrawing groups on the phenylamino B-ring were optimal for AKR1C3 inhibition. Lead compounds did not inhibit COX-1 or COX-2 but blocked the AKR1C3 mediated production of testosterone in LNCaP-AKR1C3 cells. These compounds offer promising leads toward new therapeutics for CRPC. -
9 Glutathione S-Transferases
Enzyme Systems that Metabolise Drugs and Other Xenobiotics. Edited by Costas Ioannides Copyright # 2001 John Wiley & Sons Ltd ISBNs: 0-471-894-66-4 %Hardback); 0-470-84630-5 %Electronic) 9 Glutathione S-transferases Philip J. Sherratt and John D. Hayes University of Dundee, UK Introduction Glutathione S-transferase GST; EC 2.5.1.18) isoenzymes are ubiquitously distributed in nature, being found in organisms as diverse as microbes, insects, plants, ®sh, birds andmammals Hayes andPulford1995). The transferases possess various activities andparticipate in several differenttypes of reaction. Most of these enzymes can catalyse the conjugation of reduced glutathione GSH) with compounds that contain an electrophilic centre through the formation of a thioether bondbetween the sulphur atom of GSH and the substrate Chasseaud 1979; Mannervik 1985). In addition to conjugation reactions, a number of GST isoenzymes exhibit other GSH-dependent catalytic activities including the reduction of organic hydroperoxides Ketterer et al. 1990) andisomerisation of various unsaturatedcompoundsBenson et al. 1977; Jakoby andHabig 1980). These enzymes also have several non-catalytic functions that relate to the sequestering of carcinogens, intracellular transport of a wide spectrum of hydrophobic ligands, and modulation of signal transduction pathways Listowsky 1993; Adler et al. 1999; Cho et al. 2001). Glutathione S-transferases represent a complex grouping of proteins. Two entirely distinct superfamilies of enzyme have evolved that possess transferase activity Hayes andStrange 2000). The ®rst enzymes to be characterisedwere the cytosolic, or soluble, GSTs BoylandandChasseaud1969; Mannervik 1985). To dateat least 16 members of this superfamily have been identi®ed in humans Board et al. 1997, 2000; Hayes and Strange 2000). -
Crystal Structure of Microsomal Prostaglandin E2 Synthase Provides Insight Into Diversity in the MAPEG Superfamily
Crystal structure of microsomal prostaglandin E2 synthase provides insight into diversity in the MAPEG superfamily Tove Sjögrena,1, Johan Nordb, Margareta Eka, Patrik Johanssona, Gang Liub, and Stefan Geschwindnera,1 aDiscovery Sciences, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden; and bDepartment of Neuroscience, AstraZeneca R&D Södertälje, S-151 85 Södertälje, Sweden Edited by R. Michael Garavito, Michigan State University, East Lansing, MI, and accepted by the Editorial Board January 17, 2013 (received for review October 24, 2012) fl Prostaglandin E2 (PGE2) is a key mediator in in ammatory re- with mPGES-1. Leukotriene C4 (LTC4) synthase, 5-lipoxygenase sponse. The main source of inducible PGE2, microsomal PGE2 syn- activating protein (FLAP), MGST2, and MGST3 are more dis- thase-1 (mPGES-1), has emerged as an interesting drug target for tantly related with a sequence identity of 15–30%. Initial struc- treatment of pain. To support inhibitor design, we have deter- tural characterization of the MAPEG family was done using mined the crystal structure of human mPGES-1 to 1.2 Å resolution. electron crystallography and showed that the members contain The structure reveals three well-defined active site cavities within four transmembrane helices and are organized as trimers (8, 9). the membrane-spanning region in each monomer interface of This was later confirmed by the X-ray crystal structures of FLAP the trimeric structure. An important determinant of the active (10) and LTC4 synthase (11, 12). There are also low-resolution site cavity is a small cytosolic domain inserted between trans- 3D electron crystallography structures of MGST1 and mPGES-1 membrane helices I and II. -
Mechanism of Enzymes Involved in Leukotriene C4 Biosynthesis
From Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm, Sweden MECHANISM OF ENZYMES INVOLVED IN LEUKOTRIENE C4 BIOSYNTHESIS H. R. Shabbir Ahmad Stockholm 2016 All previously published papers were reproduced with permission from the publisher. Published by Karolinska Institutet. Printed by E-Print AB © H. R. Shabbir Ahmad, 2016 ISBN 978-91-7676-368-1 Mechanism of Enzymes Involved in Leukotriene C4 Biosynthesis THESIS FOR DOCTORAL DEGREE (Ph.D.) By H. R. Shabbir Ahmad Opponent: Principal Supervisor: Tim Mantle, PhD Professor Jesper Z. Haeggström Trinity College Dublin Karolinska Institutet Ireland. Department of Medical Biochemistry and Biophysics Division of Chemistry II Examination Board: Co-supervisor(s): Professor Hans-Erik Claesson Karolinska Institutet Agnes Rinaldo-Matthis, PhD Department of Medicine, Solna. Karolinska Institutet Department of Medical Biochemistry and Professor Pia Ädelroth Biophysics Stockholm University Division of Chemistry II Department of Biochemistry and Biophysics Professor Ralf Morgenstern Docent Ylva Ivarsson Karolinska Institutet Uppsala University Institute of Environmental Medicine Department of Chemistry, BMC To my family ABSTRACT Cysteinyl leukotrienes (cys-LTs) are potent proinflammatory mediators associated with various diseases including asthma and allergic rhinitis. Leukotriene C4 synthase (LTC4S) and microsomal glutathione transferase 2 (MGST2) catalyze conjugation of the epoxide intermediate LTA4 with GSH to form LTC4, the parent compound of the cys-LTs. Both enzymes belong to the Membrane-Associated Proteins in Eicosanoid and Glutathione metabolism (MAPEG) super family of integral membrane proteins involved in the generation of lipid mediators and in the metabolism of xenobiotics. This thesis investigates the catalytic mechanism and regulation of LTC4S and MGST2. MGST2 can also catalyze conjugation of glutathione (GSH) with electrophilic substrates, such as 1-chloro-2,4-dinitrobenzene (CDNB) and also possesses GSH-dependent peroxidase activity. -
Cytochrome P450
Cytochrome P450 • R.T. Williams - in vivo, 1947. Brodie – in vitro, from late 40s till the 60s. • Cytochrome P450 enzymes (hemoproteins) play an important role in the intra-cellular metabolism. • Exist in prokaryotic and eukaryotic (plants insects fish and mammal, as well as microorganisms) • Different P450 enzymes can be found in almost any tissue: liver, kidney, lungs and even brain. • Plays important role in drugs metabolism and xenobiotics. P450 Reactions • Cytochrome P450 enzymes catalyze thousands of different reaction. • Oxidative reactions. SH + O2 + NADPH + H+ SOH + H2O + NADPH+ • The protein structure is believed to determines the catalytic specificity through complementarity to the transition state. General Features of Cytochrome P450 Catalysis 1. Substrate binding (presumably near the site of the heme ligand) 2. 1-electorn reduction of the iron by flavprotein NADPH cytochrome P450 reductase 3. Reaction of ferrous iron with O2 to yield an unstable FeO2 complex 4. Addition of the second electron from NADPH or cytochrome b5 5. Heterolytic scission of the FeO-O(H) bond to generate a formal (FeO)3+ 6. Oxidation of the substrate. 1. Formal abstraction of hydrogen atom or electron 2. Radical recombination 7. Release of the product. • Oxidative Reactions • Carbon Hydroxylation • Heteroatom Hydroxylation • Heteroatom Release • Rearangement Related to Heteroatom Oxidations • Oxidation of π-System • Hypervalent Oxygen substrate • Reductive Reactions Humans CYP450 -18 families, 43 subfamilies • CYP1 drug metabolism (3 subfamilies, 3 genes, -
Lifestyle-Induced Metabolic Inflexibility and Accelerated Ageing Syndrome: Insulin Resistance, Friend Or Foe?
Lifestyle-induced metabolic inflexibility and accelerated ageing syndrome: insulin resistance, friend or foe? Article Published Version Creative Commons: Attribution 3.0 (CC-BY) Nunn, A. V.W., Bell, J. D. and Guy, G. W. (2009) Lifestyle- induced metabolic inflexibility and accelerated ageing syndrome: insulin resistance, friend or foe? Nutrition & Metabolism, 6 (16). ISSN 1743-7075 doi: https://doi.org/10.1186/1743-7075-6-16 Available at http://centaur.reading.ac.uk/35369/ It is advisable to refer to the publisher’s version if you intend to cite from the work. See Guidance on citing . To link to this article DOI: http://dx.doi.org/10.1186/1743-7075-6-16 Publisher: BioMed Central Ltd All outputs in CentAUR are protected by Intellectual Property Rights law, including copyright law. Copyright and IPR is retained by the creators or other copyright holders. Terms and conditions for use of this material are defined in the End User Agreement . www.reading.ac.uk/centaur CentAUR Central Archive at the University of Reading Reading’s research outputs online Nutrition & Metabolism BioMed Central Commentary Open Access Lifestyle-induced metabolic inflexibility and accelerated ageing syndrome: insulin resistance, friend or foe? Alistair VW Nunn*1, Jimmy D Bell1 and Geoffrey W Guy2 Address: 1Metabolic and Molecular Imaging Group, MRC Clinical Sciences Centre, Hammersmith Hospital, Imperial College London, Du Cane Road, London, W12 OHS, UK and 2GW pharmaceuticals, Porton Down, Dorset, UK Email: Alistair VW Nunn* - [email protected]; Jimmy D Bell - [email protected]; Geoffrey W Guy - [email protected] * Corresponding author Published: 16 April 2009 Received: 12 August 2008 Accepted: 16 April 2009 Nutrition & Metabolism 2009, 6:16 doi:10.1186/1743-7075-6-16 This article is available from: http://www.nutritionandmetabolism.com/content/6/1/16 © 2009 Nunn et al; licensee BioMed Central Ltd.