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Preclinical Evaluation of Protein Disulfide Isomerase Inhibitors for the Treatment of Glioblastoma by Andrea Shergalis
Preclinical Evaluation of Protein Disulfide Isomerase Inhibitors for the Treatment of Glioblastoma By Andrea Shergalis A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Medicinal Chemistry) in the University of Michigan 2020 Doctoral Committee: Professor Nouri Neamati, Chair Professor George A. Garcia Professor Peter J. H. Scott Professor Shaomeng Wang Andrea G. Shergalis [email protected] ORCID 0000-0002-1155-1583 © Andrea Shergalis 2020 All Rights Reserved ACKNOWLEDGEMENTS So many people have been involved in bringing this project to life and making this dissertation possible. First, I want to thank my advisor, Prof. Nouri Neamati, for his guidance, encouragement, and patience. Prof. Neamati instilled an enthusiasm in me for science and drug discovery, while allowing me the space to independently explore complex biochemical problems, and I am grateful for his kind and patient mentorship. I also thank my committee members, Profs. George Garcia, Peter Scott, and Shaomeng Wang, for their patience, guidance, and support throughout my graduate career. I am thankful to them for taking time to meet with me and have thoughtful conversations about medicinal chemistry and science in general. From the Neamati lab, I would like to thank so many. First and foremost, I have to thank Shuzo Tamara for being an incredible, kind, and patient teacher and mentor. Shuzo is one of the hardest workers I know. In addition to a strong work ethic, he taught me pretty much everything I know and laid the foundation for the article published as Chapter 3 of this dissertation. The work published in this dissertation really began with the initial identification of PDI as a target by Shili Xu, and I am grateful for his advice and guidance (from afar!). -
Of Candida Bombicola
Aerodynamically, the bumble bee shouldn't be able to fly, but the bumble bee doesn't know it so it goes on flying anyway. Mary Kay Ash Jury: Prof. Dr. ir. Norbert DE KIMPE Prof. Dr. ir. Nico BOON Lic. Dirk DEVELTER Prof. Dr. ir. Monica HÖFTE Prof. Dr. Andreas SCHMID Prof. Dr. Els VAN DAMME Prof. Dr. ir. Wim SOETAERT Prof. Dr. ir. Erick VANDAMME Promotors: Prof . Dr. ir. Erick VANDAMME Prof. Dr. ir. Wim SOETAERT Laboratory of Industrial Microbiology and Biocatalysis Department of Biochemical and Microbial Technology Ghent University Dean: Prof. Dr. ir. Herman VAN LANGENHOVE Rector: Prof. Dr. Paul VAN CAUWENBERGE Ir. Inge Van Bogaert was supported by Ecover Belgium NV (Malle, Belgium) and a fellowship of the Bijzonder Onderzoekfonds of Ghent University (BOF). The research was conducted at the Laboratory of Industrial Microbiology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University. ir. Inge Van Bogaert MICROBIAL SYNTHESIS OF SOPHOROLIPIDS BY THE YEAST CANDIDA BOMBICOLA Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences Titel van het doctoraatsproefschrift in het Nederlands: Microbiële synthese van sopohorolipiden door de gist Candida bombicola Cover illustration: Cadzand on a stormy day by Inge Van Bogaert Refer to this thesis: Van Bogaert INA (2008) Microbial synthesis of sophorolipids by the yeast Candida bombicola. PhD-thesis, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium, 239 p. ISBN-number: ISBN 978-90-5989-243-9 The author and the promotor give the authorisation to consult and to copy parts of this work for personal use only. -
Characterization of Ribose-5-Phosphate Isomerase B from Newly Isolated Strain Ochrobactrum Sp
J. Microbiol. Biotechnol. (2018), 28(7), 1122–1132 https://doi.org/10.4014/jmb.1802.02021 Research Article Review jmb Characterization of Ribose-5-Phosphate Isomerase B from Newly Isolated Strain Ochrobactrum sp. CSL1 Producing L-Rhamnulose from L-Rhamnose Min Shen1†, Xin Ju1†, Xinqi Xu2, Xuemei Yao1, Liangzhi Li1*, Jiajia Chen1, Cuiying Hu1, Jiaolong Fu1, and Lishi Yan1 1School of Chemistry, Biology, and Material Engineering, Suzhou University of Science and Technology, Suzhou 215009, P.R. China 2Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, P.R. China Received: February 14, 2018 Revised: April 12, 2018 In this study, we attempted to find new and efficient microbial enzymes for producing rare Accepted: April 13, 2018 sugars. A ribose-5-phosphate isomerase B (OsRpiB) was cloned, overexpressed, and First published online preliminarily purified successfully from a newly screened Ochrobactrum sp. CSL1, which could May 8, 2018 catalyze the isomerization reaction of rare sugars. A study of its substrate specificity showed *Corresponding author that the cloned isomerase (OsRpiB) could effectively catalyze the conversion of L-rhamnose to Phone: +86-512-68056493; L-rhamnulose, which was unconventional for RpiB. The optimal reaction conditions (50oC, Fax: +86-512-68418431; 2+ E-mail: [email protected] pH 8.0, and 1 mM Ca ) were obtained to maximize the potential of OsRpiB in preparing L-rhamnulose. The catalytic properties of OsRpiB, including Km, kcat, and catalytic efficiency † These authors contributed (k /K ), were determined as 43.47 mM, 129.4 sec-1, and 2.98 mM/sec. The highest conversion equally to this work. -
GLUCOSE ISOMERASE from an ARTHROBACTER SPECIES By
GLUCOSE ISOMERASE FROM AN ARTHROBACTER SPECIES by Christopher Andrew Smith A dissertation submitted to the University of London in candidature for the degree of Doctor of Philosophy. Imperial College, December 1979 University of London, London. SW7 2AZ Abstract C.A. Smith Glucose Isomerase from an Arthrobacter Species This dissertation describes the investigation of possible means of increasing the yield of glucose isomerase from a species of Arthro- bacter. Glucose isomerase catalyses the interconversion of D-glucose and D-fructose, although its natural substrate is D-xylose. The enzyme is of importance in the production of high fructose syrups for use as sweeteners in the food industry. The possibility of manipulating the normal pathways of glucose metabolism by mutation to make the enzymic conversion of glucose to fructose an essential step in glucose metabolism was explored. Since the activity of the enzyme towards glucose is low under physiological conditions, it would then be rate-limiting for growth on glucose. This would enable the selection of mutants producing either elevated levels of the wild type enzyme or an enzyme of increased specificity for glucose, by virtue of their faster growth in glucose limited chemo- stat culture. Evidence was obtained that this approach was not like- ly to be successful in the case of Arthrobacter. No activity able to phosphorylate intracellular fructose could be detected. The enzyme was purified from a strain constitutive for its syn- thesis and was found already to account for at least ten percent of the soluble cell protein. The activity of the purified enzyme towards various potential substrates was determined, to evaluate the possibility of using grat- uitous substrates other than glucose to select for mutants with elev- ated levels of the isomerase. -
Microorganism Expressing Xylose Isomerase Mikroorganismus Welcher Xylose Isomerase Exprimiert Micro-Organisme Exprimant De Xylose Isomerase
(19) TZZ ¥¥Z_T (11) EP 2 376 630 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 9/92 (2006.01) C12N 15/81 (2006.01) 20.04.2016 Bulletin 2016/16 C12P 7/06 (2006.01) C12P 19/24 (2006.01) (21) Application number: 09787397.0 (86) International application number: PCT/IB2009/055652 (22) Date of filing: 10.12.2009 (87) International publication number: WO 2010/070549 (24.06.2010 Gazette 2010/25) (54) MICROORGANISM EXPRESSING XYLOSE ISOMERASE MIKROORGANISMUS WELCHER XYLOSE ISOMERASE EXPRIMIERT MICRO-ORGANISME EXPRIMANT DE XYLOSE ISOMERASE (84) Designated Contracting States: WO-A1-2010/000464 WO-A1-2010/001363 AT BE BG CH CY CZ DE DK EE ES FI FR GB GR WO-A2-2009/120731 HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO SE SI SK SM TR • VAN MARIS A J A ET AL: "Development of Designated Extension States: Efficient Xylose Fermentation in Saccharomyces AL BA RS cerevisiae: Xylose Isomerase as a Key Component" ADVANCES IN BIOCHEMICAL (30) Priority: 16.12.2008 GB 0822937 ENGINEERING, BIOTECHNOLOGY, SPRINGER, 17.12.2008 US 138293 P BERLIN, DE, vol. 108, 1 January 2007 (2007-01-01), pages 179-204, XP008086128 ISSN: (43) Date of publication of application: 0724-6145 19.10.2011 Bulletin 2011/42 • KUYPER M ET AL: "Metabolic engineering of a xylose-isomerase-expressing Saccharomyces (73) Proprietor: Terranol A/S cerevisiae strain for rapid anaerobic xylose 2800 Lyngby (DK) fermentation" FEMS YEAST RESEARCH, WILEY-BLACKWELL PUBLISHING LTD, GB, NL (72) Inventors: LNKD- DOI:10.1016/J.FEMSYR.2004.09.010, vol. -
Production of Natural and Rare Pentoses Using Microorganisms and Their Enzymes
EJB Electronic Journal of Biotechnology ISSN: 0717-3458 Vol.4 No.2, Issue of August 15, 2001 © 2001 by Universidad Católica de Valparaíso -- Chile Received April 24, 2001 / Accepted July 17, 2001 REVIEW ARTICLE Production of natural and rare pentoses using microorganisms and their enzymes Zakaria Ahmed Food Science and Biochemistry Division Faculty of Agriculture, Kagawa University Kagawa 761-0795, Kagawa-Ken, Japan E-mail: [email protected] Financial support: Ministry of Education, Science, Sports and Culture of Japan under scholarship program for foreign students. Keywords: enzyme, microorganism, monosaccharides, pentose, rare sugar. Present address: Scientific Officer, Microbiology and Biochemistry Division, Bangladesh Jute Research Institute, Shere-Bangla Nagar, Dhaka- 1207, Bangladesh. Tel: 880-2-8124920. Biochemical methods, usually microbial or enzymatic, murine tumors and making them useful for cancer treatment are suitable for the production of unnatural or rare (Morita et al. 1996; Takagi et al. 1996). Recently, monosaccharides. D-Arabitol was produced from D- researchers have found many important applications of L- glucose by fermentation with Candida famata R28. D- arabinose in medicine as well as in biological sciences. In a xylulose can also be produced from D-arabitol using recent investigation, Seri et al. (1996) reported that L- Acetobacter aceti IFO 3281 and D-lyxose was produced arabinose selectively inhibits intestinal sucrase activity in enzymatically from D-xylulose using L-ribose isomerase an uncompetitive manner and suppresses the glycemic (L-RI). Ribitol was oxidized to L-ribulose by microbial response after sucrose ingestion by such inhibition. bioconversion with Acetobacter aceti IFO 3281; L- Furthermore, Sanai et al. (1997) reported that L-arabinose ribulose was epimerized to L-xylulose by the enzyme D- is useful in preventing postprandial hyperglycemia in tagatose 3-epimerase and L-lyxose was produced by diabetic patients. -
12) United States Patent (10
US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S. -
All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA -
Proteins Involved in Hdaci Induced Decay of ERBB2 Transcripts in Breast Cancer
Dominican Scholar Graduate Master's Theses, Capstones, and Culminating Projects Student Scholarship 5-2015 Proteins Involved in HDACi Induced Decay of ERBB2 Transcripts in Breast Cancer Sadaf Malik Dominican University of California https://doi.org/10.33015/dominican.edu/2015.bio.03 Survey: Let us know how this paper benefits you. Recommended Citation Malik, Sadaf, "Proteins Involved in HDACi Induced Decay of ERBB2 Transcripts in Breast Cancer" (2015). Graduate Master's Theses, Capstones, and Culminating Projects. 176. https://doi.org/10.33015/dominican.edu/2015.bio.03 This Master's Thesis is brought to you for free and open access by the Student Scholarship at Dominican Scholar. It has been accepted for inclusion in Graduate Master's Theses, Capstones, and Culminating Projects by an authorized administrator of Dominican Scholar. For more information, please contact [email protected]. Proteins Involved in HDACi Induced Decay of ERBB2 Transcripts in Breast Cancer A thesis submitted to the faculty of Dominican University of California and the Buck Institute for Research on Aging in partial fulfillment of the requirements for the degree Master of Science In Biology By Sadaf Z. Malik San Rafael, California May 2015 Copyright by Sadaf Z. Malik 2015 i CERTIFICATION OF APPROVAL I certify that I have read Proteins Involved in HDACi Induced Decay of ERBB2 Transcripts in Breast Cancer by Sadaf Malik, and I approved this thesis to be submitted in partial fulfillment of the requirements for the degree: Master of Sciences in Biology at Dominican University of California and the Buck Institute of Aging. Dr. Christopher Benz Signature on File Graduate Research Advisor Dr. -
Salvage of the 5-Deoxyribose Byproduct of Radical SAM Enzymes
ARTICLE DOI: 10.1038/s41467-018-05589-4 OPEN Salvage of the 5-deoxyribose byproduct of radical SAM enzymes Guillaume A.W. Beaudoin1, Qiang Li2, Jacob Folz3, Oliver Fiehn 3,4, Justin L. Goodsell2, Alexander Angerhofer2, Steven D. Bruner2 & Andrew D. Hanson 1 5-Deoxyribose is formed from 5′-deoxyadenosine, a toxic byproduct of radical S-adeno- sylmethionine (SAM) enzymes. The degradative fate of 5-deoxyribose is unknown. Here, we 1234567890():,; define a salvage pathway for 5-deoxyribose in bacteria, consisting of phosphorylation, iso- merization, and aldol cleavage steps. Analysis of bacterial genomes uncovers widespread, unassigned three-gene clusters specifying a putative kinase, isomerase, and sugar phosphate aldolase. We show that the enzymes encoded by the Bacillus thuringiensis cluster, acting together in vitro, convert 5-deoxyribose successively to 5-deoxyribose 1-phosphate, 5- deoxyribulose 1-phosphate, and dihydroxyacetone phosphate plus acetaldehyde. Deleting the isomerase decreases the 5-deoxyribulose 1-phosphate pool size, and deleting either the isomerase or the aldolase increases susceptibility to 5-deoxyribose. The substrate preference of the aldolase is unique among family members, and the X-ray structure reveals an unusual manganese-dependent enzyme. This work defines a salvage pathway for 5-deoxyribose, a near-universal metabolite. 1 Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA. 2 Department of Chemistry, University of Florida, Gainesville, FL 32611, USA. 3 NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California Davis, Davis, CA 95616, USA. 4 Biochemistry Department, King Abdulaziz University, Jeddah 21589, Saudi Arabia. These authors contributed equally: Guillaume A. W. Beaudoin, Qiang Li. -
(12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur Et Al
US 20150240226A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur et al. (43) Pub. Date: Aug. 27, 2015 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/16 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/02 (2006.01) CI2N 9/78 (2006.01) (71) Applicant: BP Corporation North America Inc., CI2N 9/12 (2006.01) Naperville, IL (US) CI2N 9/24 (2006.01) CI2O 1/02 (2006.01) (72) Inventors: Eric J. Mathur, San Diego, CA (US); CI2N 9/42 (2006.01) Cathy Chang, San Marcos, CA (US) (52) U.S. Cl. CPC. CI2N 9/88 (2013.01); C12O 1/02 (2013.01); (21) Appl. No.: 14/630,006 CI2O I/04 (2013.01): CI2N 9/80 (2013.01); CI2N 9/241.1 (2013.01); C12N 9/0065 (22) Filed: Feb. 24, 2015 (2013.01); C12N 9/2437 (2013.01); C12N 9/14 Related U.S. Application Data (2013.01); C12N 9/16 (2013.01); C12N 9/0061 (2013.01); C12N 9/78 (2013.01); C12N 9/0071 (62) Division of application No. 13/400,365, filed on Feb. (2013.01); C12N 9/1241 (2013.01): CI2N 20, 2012, now Pat. No. 8,962,800, which is a division 9/2482 (2013.01); C07K 2/00 (2013.01); C12Y of application No. 1 1/817,403, filed on May 7, 2008, 305/01004 (2013.01); C12Y 1 1 1/01016 now Pat. No. 8,119,385, filed as application No. PCT/ (2013.01); C12Y302/01004 (2013.01); C12Y US2006/007642 on Mar. 3, 2006. -
Springer Handbook of Enzymes
Dietmar Schomburg Ida Schomburg (Eds.) Springer Handbook of Enzymes Alphabetical Name Index 1 23 © Springer-Verlag Berlin Heidelberg New York 2010 This work is subject to copyright. All rights reserved, whether in whole or part of the material con- cerned, specifically the right of translation, printing and reprinting, reproduction and storage in data- bases. The publisher cannot assume any legal responsibility for given data. Commercial distribution is only permitted with the publishers written consent. Springer Handbook of Enzymes, Vols. 1–39 + Supplements 1–7, Name Index 2.4.1.60 abequosyltransferase, Vol. 31, p. 468 2.7.1.157 N-acetylgalactosamine kinase, Vol. S2, p. 268 4.2.3.18 abietadiene synthase, Vol. S7,p.276 3.1.6.12 N-acetylgalactosamine-4-sulfatase, Vol. 11, p. 300 1.14.13.93 (+)-abscisic acid 8’-hydroxylase, Vol. S1, p. 602 3.1.6.4 N-acetylgalactosamine-6-sulfatase, Vol. 11, p. 267 1.2.3.14 abscisic-aldehyde oxidase, Vol. S1, p. 176 3.2.1.49 a-N-acetylgalactosaminidase, Vol. 13,p.10 1.2.1.10 acetaldehyde dehydrogenase (acetylating), Vol. 20, 3.2.1.53 b-N-acetylgalactosaminidase, Vol. 13,p.91 p. 115 2.4.99.3 a-N-acetylgalactosaminide a-2,6-sialyltransferase, 3.5.1.63 4-acetamidobutyrate deacetylase, Vol. 14,p.528 Vol. 33,p.335 3.5.1.51 4-acetamidobutyryl-CoA deacetylase, Vol. 14, 2.4.1.147 acetylgalactosaminyl-O-glycosyl-glycoprotein b- p. 482 1,3-N-acetylglucosaminyltransferase, Vol. 32, 3.5.1.29 2-(acetamidomethylene)succinate hydrolase, p. 287 Vol.