By Human Neutrophils to Avoid Destruction Staphylococcus Aureus
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Generate Metabolic Map Poster
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_001591825Cyc: Bacillus vietnamensis NBRC 101237 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari sn-glycerol phosphate phosphate pro phosphate phosphate phosphate thiamine molybdate D-xylose D-ribose glutathione 3-phosphate D-mannitol L-cystine L-djenkolate lanthionine α,β-trehalose phosphate phosphate [+ 3 more] α,α-trehalose predicted predicted ABC ABC FliY ThiT XylF RbsB RS10935 UgpC TreP PutP RS10200 PstB PstB RS10385 RS03335 RS20030 RS19075 transporter transporter of molybdate of phosphate α,β-trehalose 6-phosphate L-cystine D-xylose D-ribose sn-glycerol D-mannitol phosphate phosphate thiamine glutathione α α phosphate phosphate phosphate phosphate L-djenkolate 3-phosphate , -trehalose 6-phosphate pro 1-phosphate lanthionine molybdate phosphate [+ 3 more] Metabolic Regulator Amino Acid Degradation Amine and Polyamine Biosynthesis Macromolecule Modification tRNA-uridine 2-thiolation Degradation ATP biosynthesis a mature peptidoglycan a nascent β an N-terminal- -
Supporting Information High-Throughput Virtual Screening
Supporting Information High-Throughput Virtual Screening of Proteins using GRID Molecular Interaction Fields Simone Sciabola, Robert V. Stanton, James E. Mills, Maria M. Flocco, Massimo Baroni, Gabriele Cruciani, Francesca Perruccio and Jonathan S. Mason Contents Table S1 S2-S21 Figure S1 S22 * To whom correspondence should be addressed: Simone Sciabola, Pfizer Research Technology Center, Cambridge, 02139 MA, USA Phone: +1-617-551-3327; Fax: +1-617-551-3117; E-mail: [email protected] S1 Table S1. Description of the 990 proteins used as decoy for the Protein Virtual Screening analysis. PDB ID Protein family Molecule Res. (Å) 1n24 ISOMERASE (+)-BORNYL DIPHOSPHATE SYNTHASE 2.3 1g4h HYDROLASE 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE 1.8 1cel HYDROLASE(O-GLYCOSYL) 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I 1.8 1vyf TRANSPORT PROTEIN 14 KDA FATTY ACID BINDING PROTEIN 1.85 1o9f PROTEIN-BINDING 14-3-3-LIKE PROTEIN C 2.7 1t1s OXIDOREDUCTASE 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE 2.4 1t1r OXIDOREDUCTASE 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE 2.3 1q0q OXIDOREDUCTASE 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE 1.9 1jcy LYASE 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE 1.9 1fww LYASE 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE 1.85 1uk7 HYDROLASE 2-HYDROXY-6-OXO-7-METHYLOCTA-2,4-DIENOATE 1.7 1v11 OXIDOREDUCTASE 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT 1.95 1x7w OXIDOREDUCTASE 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT 1.73 1d0l TRANSFERASE 35KD SOLUBLE LYTIC TRANSGLYCOSYLASE 1.97 2bt4 LYASE 3-DEHYDROQUINATE DEHYDRATASE -
Generate Metabolic Map Poster
Authors: Pallavi Subhraveti Ron Caspi Quang Ong 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_900114035Cyc: Amycolatopsis sacchari DSM 44468 Cellular Overview Connections between pathways are omitted for legibility. -
The Crystal Structure of Novel Chondroitin Lyase ODV-E66, A
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 587 (2013) 3943–3948 journal homepage: www.FEBSLetters.org The crystal structure of novel chondroitin lyase ODV-E66, a baculovirus envelope protein ⇑ Yoshirou Kawaguchi a, Nobuo Sugiura b, Koji Kimata c, Makoto Kimura a,d, Yoshimitsu Kakuta a,d, a Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan b Institute for Molecular Science of Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi 480-1195, Japan c Research Complex for the Medicine Frontiers, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi 480-1195, Japan d Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan article info abstract Article history: Chondroitin lyases have been known as pathogenic bacterial enzymes that degrade chondroitin. Received 5 August 2013 Recently, baculovirus envelope protein ODV-E66 was identified as the first reported viral chondroi- Revised 1 October 2013 tin lyase. ODV-E66 has low sequence identity with bacterial lyases at <12%, and unique characteris- Accepted 15 October 2013 tics reflecting the life cycle of baculovirus. To understand ODV-E66’s structural basis, the crystal Available online 26 October 2013 structure was determined and it was found that the structural fold resembled that of polysaccharide Edited by Christian Griesinger lyase 8 proteins and that the catalytic residues were also conserved. This structure enabled discus- sion of the unique substrate specificity and the stability of ODV-E66 as well as the host specificity of baculovirus. -
Manual D'estil Per a Les Ciències De Laboratori Clínic
MANUAL D’ESTIL PER A LES CIÈNCIES DE LABORATORI CLÍNIC Segona edició Preparada per: XAVIER FUENTES I ARDERIU JAUME MIRÓ I BALAGUÉ JOAN NICOLAU I COSTA Barcelona, 14 d’octubre de 2011 1 Índex Pròleg Introducció 1 Criteris generals de redacció 1.1 Llenguatge no discriminatori per raó de sexe 1.2 Llenguatge no discriminatori per raó de titulació o d’àmbit professional 1.3 Llenguatge no discriminatori per raó d'ètnia 2 Criteris gramaticals 2.1 Criteris sintàctics 2.1.1 Les conjuncions 2.2 Criteris morfològics 2.2.1 Els articles 2.2.2 Els pronoms 2.2.3 Els noms comuns 2.2.4 Els noms propis 2.2.4.1 Els antropònims 2.2.4.2 Els noms de les espècies biològiques 2.2.4.3 Els topònims 2.2.4.4 Les marques registrades i els noms comercials 2.2.5 Els adjectius 2.2.6 El nombre 2.2.7 El gènere 2.2.8 Els verbs 2.2.8.1 Les formes perifràstiques 2.2.8.2 L’ús dels infinitius ser i ésser 2.2.8.3 Els verbs fer, realitzar i efectuar 2.2.8.4 Les formes i l’ús del gerundi 2.2.8.5 L'ús del verb haver 2.2.8.6 Els verbs haver i caldre 2.2.8.7 La forma es i se davant dels verbs 2.2.9 Els adverbis 2.2.10 Les locucions 2.2.11 Les preposicions 2.2.12 Els prefixos 2.2.13 Els sufixos 2.2.14 Els signes de puntuació i altres signes ortogràfics auxiliars 2.2.14.1 La coma 2.2.14.2 El punt i coma 2.2.14.3 El punt 2.2.14.4 Els dos punts 2.2.14.5 Els punts suspensius 2.2.14.6 El guionet 2.2.14.7 El guió 2.2.14.8 El punt i guió 2.2.14.9 L’apòstrof 2.2.14.10 L’interrogant 2 2.2.14.11 L’exclamació 2.2.14.12 Les cometes 2.2.14.13 Els parèntesis 2.2.14.14 Els claudàtors 2.2.14.15 -
The Effect of Skin Fatty Acids on Staphylococcus Aureus
Arch Microbiol (2015) 197:245–267 DOI 10.1007/s00203-014-1048-1 ORGINAL PAPER The effect of skin fatty acids on Staphylococcus aureus Yvonne Neumann · Knut Ohlsen · Stefanie Donat · Susanne Engelmann · Harald Kusch · Dirk Albrecht · Michael Cartron · Alexander Hurd · Simon J. Foster Received: 23 July 2014 / Revised: 19 September 2014 / Accepted: 6 October 2014 / Published online: 18 October 2014 © The Author(s) 2014. This article is published with open access at Springerlink.com Abstract Staphylococcus aureus is a commensal of the hlgBC) was reduced, whereas that of host defence evasion human nose and skin. Human skin fatty acids, in particular components (cap, sspAB, katA) was increased. In particular, cis-6-hexadecenoic acid (C-6-H), have high antistaphylococ- members of the SaeRS regulon had highly reduced expres- cal activity and can inhibit virulence determinant production. sion, and the use of specific mutants revealed that the effect Here, we show that sub-MIC levels of C-6-H result in induc- on toxin production is likely mediated via SaeRS. tion of increased resistance. The mechanism(s) of C-6-H activity was investigated by combined transcriptome and Keywords S. aureus · Skin fatty acid · C-6-H · proteome analyses. Proteome analysis demonstrated a pleio- Resistance tropic effect of C-6-H on virulence determinant production. In response to C-6-H, transcriptomics revealed altered expres- sion of over 500 genes, involved in many aspects of virulence Introduction and cellular physiology. The expression of toxins (hla, hlb, The Gram-positive bacterium Staphylococcus aureus is able to survive as a commensal organism in the anterior nares and Communicated by Djamel DRIDER. -
Active Site of Chondroitin AC Lyase Revealed by the Structure Of
Biochemistry 2001, 40, 2359-2372 2359 Active Site of Chondroitin AC Lyase Revealed by the Structure of Enzyme-Oligosaccharide Complexes and Mutagenesis†,‡ Weijun Huang,§ Lorena Boju,§ Lydia Tkalec,|,⊥ Hongsheng Su,|,# Hyun-Ok Yang,3 Nur Sibel Gunay,3 Robert J. Linhardt,3 Yeong Shik Kim,O Allan Matte,§ and Miroslaw Cygler*,§ Biotechnology Research Institute, 6100 Royalmount AVenue, Montre´al, Que´bec H4P 2R2 Canada, Montreal Joint Centre for Structural Biology, Montre´al, Que´bec, Canada, IBEX Technologies Inc., 5485 Pare Street, Montre´al, Que´bec H4P 1P7 Canada, Department of Chemistry, DiVision of Medicinal Chemistry and Department of Chemical and Biochemical Engineering, The UniVersity of Iowa, 115 South Grand AVenue, PHAR S328, Iowa City, Iowa 52242-1112, and Natural Products Research Institute, Seoul National UniVersity, Seoul 110-460, Korea ReceiVed October 17, 2000; ReVised Manuscript ReceiVed December 18, 2000 ABSTRACT: The crystal structures of FlaVobacterium heparinium chondroitin AC lyase (chondroitinase AC; EC 4.2.2.5) bound to dermatan sulfate hexasaccharide (DShexa), tetrasaccharide (DStetra), and hyaluronic acid tetrasaccharide (HAtetra) have been refined at 2.0, 2.0, and 2.1 Å resolution, respectively. The structure of the Tyr234Phe mutant of AC lyase bound to a chondroitin sulfate tetrasaccharide (CStetra) has also been determined to 2.3 Å resolution. For each of these complexes, four (DShexa and CStetra) or two (DStetra and HAtetra) ordered sugars are visible in electron density maps. The lyase AC DShexa and CStetra complexes reveal binding at four subsites, -2, -1, +1, and +2, within a narrow and shallow protein channel. We suggest that subsites -2 and -1 together represent the substrate recognition area, +1 is the catalytic subsite and +1 and +2 together represent the product release area. -
Wo 2008/127291 A2
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date PCT (10) International Publication Number 23 October 2008 (23.10.2008) WO 2008/127291 A2 (51) International Patent Classification: Jeffrey, J. [US/US]; 106 Glenview Drive, Los Alamos, GOlN 33/53 (2006.01) GOlN 33/68 (2006.01) NM 87544 (US). HARRIS, Michael, N. [US/US]; 295 GOlN 21/76 (2006.01) GOlN 23/223 (2006.01) Kilby Avenue, Los Alamos, NM 87544 (US). BURRELL, Anthony, K. [NZ/US]; 2431 Canyon Glen, Los Alamos, (21) International Application Number: NM 87544 (US). PCT/US2007/021888 (74) Agents: COTTRELL, Bruce, H. et al.; Los Alamos (22) International Filing Date: 10 October 2007 (10.10.2007) National Laboratory, LGTP, MS A187, Los Alamos, NM 87545 (US). (25) Filing Language: English (81) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of national protection available): AE, AG, AL, AM, AT,AU, AZ, BA, BB, BG, BH, BR, BW, BY,BZ, CA, CH, (30) Priority Data: CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, 60/850,594 10 October 2006 (10.10.2006) US ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, (71) Applicants (for all designated States except US): LOS LR, LS, LT, LU, LY,MA, MD, ME, MG, MK, MN, MW, ALAMOS NATIONAL SECURITY,LLC [US/US]; Los MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PG, PH, PL, Alamos National Laboratory, Lc/ip, Ms A187, Los Alamos, PT, RO, RS, RU, SC, SD, SE, SG, SK, SL, SM, SV, SY, NM 87545 (US). -
ABSTRACT BOZDAG, AHMET. Investigation of Methanol and Formaldehyde Metabolism in Bacillus Methanolicus
ABSTRACT BOZDAG, AHMET. Investigation of Methanol and Formaldehyde Metabolism in Bacillus methanolicus.(Under the direction of Prof. Michael C. Flickinger). Bacillus methanolicus is a Gram-positive aerobic methylotroph growing optimally at 50-53 °C. Wild-type strains of B. methanolicus have been reported to secrete 58 g/l of L- glutamate in fed-batch cultures. Mutants of B. methanolicus created via classical mutangenesis can secrete 37 g/l of L-lysine, at 50 °C. The genes required for methylotrophyin B. methanolicus are encoded by an endogenous plasmid, pBM19 in strain MGA3, except for hexulose phosphate synthase (hps) and phosphohexuloisomerase (phi) which are encoded on the chromosome.It is a promising candidate for industrial production of chemical intermediates or amino acids from methanol. B. methanolicus employs the ribulose monophospate (RuMP) pathway to assimilate the carbon derived from the methanol, but enzymes that dissimilate carbon are not identified, although formaldehyde and formate were identified as intermediates by 13C NMR. It is important to understand how methanol is oxidized to formaldehyde and then, to formate and carbon dioxide. This study aims to elucidate the methanol dissimilation pathway of B. methanolicus. Growth rates of B. methanolicus MGA3 were assessed on methanol, mannitol, and glucose as a substrate. B. methanolicus achieved maximum growth rate, µmax, when growing on 25 mM methanol, 0.65±0.007 h-1, and it gradually decreased to 0.231±0.004 h-1 at 2Mmethanol concentration which demonstrates substrate inhibition. The maximum growth rates (µmax) of B. methanolicus MGA3 on mannitol and glucose are 0.532±0.002 and 0.336±0.003 h-1, respectively. -
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. -
Conditioned Medium Compared to ∆Agr Biofilm-Conditioned Medium
Table S1. Proteins identified to be in greater abundance in WT S. aureus biofilm- conditioned medium compared to ∆agr biofilm-conditioned medium Magnitude Category Protein Identity 14.32 Translation RL5 Ribosomal protein 4.73 Translation Syn Asparagine-tRNA ligase 4.09 Translation RL13 Ribosomal protein 3.32 Translation RL332 Ribosomal protein 2.90 Translation EF-TU Elongation factor 2.72 Translation RL27 Ribosomal protein 2.56 Translation GatB Aspartyl/glutamyl-tRNA amidotransferase subunit B 2.42 Translation RS7 Ribosomal protein 2.1 Translation RL16 Ribosomal protein 2.01 Translation RL10 Ribosomal protein 25.93 Metabolism CysK Cysteine synthase 6.92 Metabolism CarB Carbamoyl phosphate synthetase subunit B 4.37 Metabolism OtcC Ornithine carbamoyltransferase 3.91 Metabolism KpyK Pyruvate kinase 3.63 Metabolism Pur8 Adenylosuccinate lyase 3.07 Metabolism HutG Formimidoylglutamase 2.87 Metabolism Pgk Phosphoglycerate kinase 2.50 Metabolism GlmS Glutamine--fructose-6-phosphate aminotransferase 2.42 Metabolism OdpB Pyruvate dehydrogenase E1 component subunit beta 2.29 Metabolism Ldh1 L-lactate dehydrogenase 1 42.01 Protease SplB Serine-like protease a 33.61 Protease SplD Serine-like protease 24.78 Protease SspA Serine protease 24.78 Protease SspB Cysteine protease 14.23 Protease SspP Cysteine protease 9.02 Protease SplA Serine-like protease 6.48 Protease SplC Serine-like protease 2.17 Protease SplE Serine-like protease 11.97 Virulence LukDV/HlgB Leukocidin component 10.59 Virulence HlgA Gamma-hemolysin component A 9.71 Virulence Hld Delta-hemolysin -
Supplementary Materials
Supplementary Materials OH 8 H H8 H C N OH 3 7 3 2 4 H1 1 5 O H4 O 6 H6’ H3 OH H6 H1’ H2 H5 3.9 3.8 3.7 3.6 3.5 3.4 3.3 3.2 ppm 4.0 3.8 3.6 3.4 3.2 3.0 2.8 2.6 2.4 2.2 ppm Figure S1. 1D 1H spectrum of 1-dglcnac and signal assignments ppm 2.0 H8 2.5 OH 8 H H C N OH 3 7 3 2 4 3.0 1 5 H1 O H5 O 6 H4 H3 OH 3.5 H6 H2 H6’ H1’ 4.0 4.0 3.8 3.6 3.4 3.2 3.0 2.8 2.6 2.4 2.2 2.0 ppm Figure S2. 1H-1H TOCSY 2D NMR spectra for 1-dglcnac and signal assignments ppm 3.0 H1 3.2 H5 H4 3.4 H3 3.6 H6 H6’ H2 3.8 H1’ 4.0 4.1 4.0 3.9 3.8 3.7 3.6 3.5 3.4 3.3 3.2 3.1 3.0 ppm Figure S3. 1H-1H COSY 2D NMR spectra for 1-dglcnac and signal assignment ppm -0.02 -0.01 0.00 0.01 0.02 H1’ H6’ H2 H6 H3 H4 H5 H1 3.9 3.8 3.7 3.6 3.5 3.4 3.3 3.2 3.1 ppm Figure S4. 1H-1H JRES 2D NMR spectra for 1-dglcnac and signal assignments ppm 20 C8(22.9) 40 OH 8 H H C N OH C2(53.2) 3 7 3 2 4 60 1 5 C6(63.2) C6(63.2) O 6 C1(69.2) C1(69.2) O C4(72.6) C3(77.0) OH 80 C5(82.7) 100 4.0 3.8 3.6 3.4 3.2 3.0 2.8 2.6 2.4 2.2 2.0 ppm Figure S5.