Generate Metabolic Map Poster

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Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000702945Cyc: Clostridium sp. KNHs205 Cellular Overview Connections between pathways are omitted for legibility.

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Phosphorylation of Mcardle Phosphorylase Induces Activity (Human Skeletal Muscle/Protein Kinase) CESARE G
Proc. Nati. Acad. Sci. USA Vol. 78, No. 5, pp. 2688-2692, May 1981 Biochemistry Phosphorylation of McArdle phosphorylase induces activity (human skeletal muscle/protein kinase) CESARE G. CERRI AND JOSEPH H. WILLNER Department of Neurology and H. Houston Merritt Clinical Research Center for Muscular Dystrophy and Related Diseases, Columbia University College of Physicians and Surgeons, New York, New York 10032 Communicated by Harry Grundfest, January 7, 1981 ABSTRACT In McArdle disease, myophosphorylase defi- mediate between those of phosphorylases b and a. Karpatkin ciency, enzyme activity is absent but the presence of an altered et al. (19, 20) found that incubation of human platelets with enzyme protein can frequently be demonstrated. We have found MgATP+ resulted in an increase in total phosphorylase activity that phosphorylation of this protein in vitro can result in catalytic and concluded that the data were "consistent with the presence activity. We studied muscle of four patients; all lacked myophos- in human platelets of inactive dimer and monomer species of phorylase activity, but myophosphorylase protein was demon- phosphorylase, which require MgATP for activation." Because strated by immunodiffusion or gel electrophoresis. Incubation of activation of these isozymes was probably due to protein phos- muscle homogenate supernatants with cyclic AMP-dependent pro- phorylation and also because incomplete phosphorylation could tein kinase and ATP resulted in phosphorylase activity. The ac- tivated enzyme comigrated with normal human myophosphory- result in reduced activity, we evaluated the possibility that the lase in gel electrophoresis. Incubation with [y-32P]ATP resulted activity ofphosphorylase in McArdle muscle could be restored in incorporation of 32P into the band possessing phosphorylase by phosphorylation of the inactive phosphorylase protein pres- activity.
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Guaiacol As a Drug Candidate for Treating Adult Polyglucosan Body Disease
Guaiacol as a drug candidate for treating adult polyglucosan body disease Or Kakhlon, … , Wyatt W. Yue, H. Orhan Akman JCI Insight. 2018;3(17):e99694. https://doi.org/10.1172/jci.insight.99694. Research Article Metabolism Therapeutics Graphical abstract Find the latest version: https://jci.me/99694/pdf RESEARCH ARTICLE Guaiacol as a drug candidate for treating adult polyglucosan body disease Or Kakhlon,1 Igor Ferreira,2 Leonardo J. Solmesky,3 Netaly Khazanov,4 Alexander Lossos,1 Rafael Alvarez,5 Deniz Yetil,6 Sergey Pampou,7 Miguel Weil,3,8 Hanoch Senderowitz,4 Pablo Escriba,5 Wyatt W. Yue,2 and H. Orhan Akman9 1Department of Neurology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel. 2Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.3 Cell Screening Facility for Personalized Medicine, Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. 4Department of Chemistry, Bar Ilan University, Ramat Gan, Israel. 5Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain. 6Connecticut College, Newington, Connecticut USA. 7Columbia University Department of Systems Biology Irving Cancer Research Center, New York, New York, USA. 8Laboratory for Neurodegenerative Diseases and Personalized Medicine, Department of Cell Research and Immunology, The George S. Wise Faculty for Life Sciences, Sagol School of Neurosciences, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel. 9Columbia University Medical Center Department of Neurology, Houston Merritt Neuromuscular diseases research center, New York, New York, USA. Adult polyglucosan body disease (APBD) is a late-onset disease caused by intracellular accumulation of polyglucosan bodies, formed due to glycogen-branching enzyme (GBE) deficiency.
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A Genome Based Discovery of S. Mansoni Secretome to Identify Therapeutic Targets
ics om & B te i ro o P in f f o o Mandage et al. J Proteomics Bioinform 2011, 4:3 r l m a Journal of a n t r i c u DOI: 10.4172/jpb.1000168 s o J ISSN: 0974-276X Proteomics & Bioinformatics Research Article Article OpenOpen Access Access A Genome Based Discovery of S. mansoni Secretome to Identify Therapeutic Targets Mandage RH1*, Jadhavrao PK2, Wadnerkar AS1, Varsale AR1 and Kurwade KK1 1Dept of Bioinformatics, Centre for Advanced Life Sciences, Deogiri College, Aurangabad 431005, M.S. India 2Dept of Microbiology, Abeda Inamdar College, Pune 411001, M.S. India Abstract The motivation behind the large scale genome analysis of S. mansoni was to explore the possibility of discovering the secretome that is frequently secreted at the interface of parasite and host is supposed to play a crucial role in parasitism by suppressing the immune response, to aid the proliferation of infectivity. Here, we present an efficient pipeline of bioinformatics methodology to identify candidate parasitism proteins within S. mansoni secretome of immune responses in the infected host. The 3,700 proteins deduced from the S. mansoni genome were analysed for the presence or absence of secretory signal peptides. We identified 32 proteins carrying an N-terminal secreted signal peptide but deficient in extra membrane-anchoring moieties. Notably we identified proteins involved in ATP synthesis, redox balance, protein folding, gluconeogenesis, development and signaling, scavenging and nucleotide metabolic pathways, immune response modulation. Most of these proteins define their potential for immunological diagnosis and vaccine design. A systematic attempt has been made here to develop a general method for predicting secretory proteins of a parasite with high efficiency and accuracy.
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An Evolving Hierarchical Family Classification for Glycosyltransferases
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Chem331 Glycogen Metabolism
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Peroxisomes in Brain Development and Function☆
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Comparative Transcriptomics Reveals Lineage Specific Evolution of Cold
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(NMDA) Receptor Coactivation: Inhibition of D-Serine Synthesis by Converting Serine Racemase Into an Eliminase
A new strategy to decrease N-methyl-D-aspartate (NMDA) receptor coactivation: Inhibition of D-serine synthesis by converting serine racemase into an eliminase Roge´ rio Panizzutti*, Joari De Miranda*, Ca´ tia S. Ribeiro*, Simone Engelender†, and Herman Wolosker*‡ *Departamento de Bioquimica Medica, Instituto de Ciencias Biomedicas, and †Center for Neurodegenerative Diseases, Departamento de Anatomia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21491-590, Brazil Edited by Solomon H. Snyder, Johns Hopkins University School of Medicine, Baltimore, MD, and approved February 23, 2001 (received for review January 3, 2001) Serine racemase is a brain-enriched enzyme that synthesizes D- serine racemase genes (9, 10). The distribution of serine race- serine, an endogenous modulator of the glycine site of N-methyl- mase was closely similar to that of endogenous D-serine with the D-aspartate (NMDA) receptors. We now report that serine race- highest concentrations in the forebrain and negligible levels in mase catalyzes an elimination reaction toward a nonphysiological the brainstem. Both D-serine and serine racemase occur in substrate that provides a powerful tool to study its neurobiological astrocytes, in regions enriched in NMDA receptors, suggesting role and will be useful to develop selective enzyme inhibitors. that serine racemase physiologically synthesizes D-serine to Serine racemase catalyzes robust elimination of L-serine O-sulfate regulate NMDA receptor activity (9). that is 500 times faster than the physiological racemization reac- As an endogenous coagonist of NMDA receptors, D-serine tion, generating sulfate, ammonia, and pyruvate. This reaction may play a role in several pathological conditions related to provides the most simple and sensitive assay to detect the enzyme NMDA receptor dysfunction.
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Discovery of a Novel Amino Acid Racemase Through Exploration of Natural Variation in Arabidopsis Thaliana
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View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1822 (2012) 493–499 Contents lists available at SciVerse ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbadis Molecular pathogenesis of a new glycogenosis caused by a glycogenin-1 mutation Johanna Nilsson a,⁎, Adnan Halim b, Ali-Reza Moslemi a, Anders Pedersen c, Jonas Nilsson b, Göran Larson b, Anders Oldfors a a Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden b Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden c Swedish NMR Centre, Gothenburg, Sweden article info abstract Article history: Glycogenin-1 initiates the glycogen synthesis in skeletal muscle by the autocatalytic formation of a short ol- Received 27 June 2011 igosaccharide at tyrosine 195. Glycogenin-1 catalyzes both the glucose-O-tyrosine linkage and the α1,4 glu- Received in revised form 7 November 2011 cosidic bonds linking the glucose molecules in the oligosaccharide. We recently described a patient with Accepted 28 November 2011 glycogen depletion in skeletal muscle as a result of a non-functional glycogenin-1. The patient carried a Available online 9 December 2011 Thr83Met substitution in glycogenin-1. In this study we have investigated the importance of threonine 83 Keywords: for the catalytic activity of glycogenin-1. Non-glucosylated glycogenin-1 constructs, with various amino Glycogen acid substitutions in position 83 and 195, were expressed in a cell-free expression system and autoglucosy- Glycogenin lated in vitro.
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SI Appendix Index 1
SI Appendix Index Calculating chemical attributes using EC-BLAST ................................................................................ 2 Chemical attributes in isomerase reactions ............................................................................................ 3 Bond changes …..................................................................................................................................... 3 Reaction centres …................................................................................................................................. 5 Substrates and products …..................................................................................................................... 6 Comparative analysis …........................................................................................................................ 7 Racemases and epimerases (EC 5.1) ….................................................................................................. 7 Intramolecular oxidoreductases (EC 5.3) …........................................................................................... 8 Intramolecular transferases (EC 5.4) ….................................................................................................. 9 Supporting references …....................................................................................................................... 10 Fig. S1. Overview …............................................................................................................................
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Generate Metabolic Map Poster
Authors: Zheng Zhao, Delft University of Technology Marcel A. van den Broek, Delft University of Technology S. Aljoscha Wahl, Delft University of Technology Wilbert H. Heijne, DSM Biotechnology Center Roel A. Bovenberg, DSM Biotechnology Center Joseph J. Heijnen, Delft University of Technology An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Marco A. van den Berg, DSM Biotechnology Center Peter J.T. Verheijen, Delft University of Technology Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. PchrCyc: Penicillium rubens Wisconsin 54-1255 Cellular Overview Connections between pathways are omitted for legibility. Liang Wu, DSM Biotechnology Center Walter M. van Gulik, Delft University of Technology L-quinate phosphate a sugar a sugar a sugar a sugar multidrug multidrug a dicarboxylate phosphate a proteinogenic 2+ 2+ + met met nicotinate Mg Mg a cation a cation K + L-fucose L-fucose L-quinate L-quinate L-quinate ammonium UDP ammonium ammonium H O pro met amino acid a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar K oxaloacetate L-carnitine L-carnitine L-carnitine 2 phosphate quinic acid brain-specific hypothetical hypothetical hypothetical hypothetical
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