Proceedings of the NATIONAL ACADEMY of SCIENCES
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
A Little Sugar Goes a Long Way: the Cell Biology of O-Glcnac
Published March 30, 2015 JCB: Review A little sugar goes a long way: The cell biology of O-GlcNAc Michelle R. Bond and John A. Hanover Unlike the complex glycans decorating the cell surface, the to nucleocytoplasmic kinases and phosphatases. In fact, there are O-linked -N-acetyl glucosamine (O-GlcNAc) modifica- many parallels between phosphorylation and O-GlcNAcylation: O-GlcNAc is added to Ser and Thr residues; the modification tion is a simple intracellular Ser/Thr-linked monosaccha- rapidly cycles on and off modified proteins at a rate faster than ride that is important for disease-relevant signaling and protein turnover; and like kinases and phosphatases, OGT and enzyme regulation. O-GlcNAcylation requires uridine OGA are phosphorylated (Fig. 1 B; Butkinaree et al., 2010; diphosphate–GlcNAc, a precursor responsive to nutrient Hanover et al., 2010). Many target proteins are modified by both status and other environmental cues. Alternative splicing O-GlcNAc and phosphate at exposed regions, suggesting the of the genes encoding the O-GlcNAc cycling enzymes presence of shared or coexisting recognition motifs. However, although the sites of protein phosphorylation can often be identified Downloaded from O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) by primary sequence alone, O-GlcNAcylation is not associated yields isoforms targeted to discrete sites in the nucleus, cy- with a clear consensus motif. toplasm, and mitochondria. OGT and OGA also partner OGT uses UDP-GlcNAc, a nucleotide sugar derived from with cellular effectors and act in tandem with other post- the nutrient-dependent hexosamine biosynthetic pathway (HBP), translational modifications. The enzymes of O-GlcNAc to catalyze O-GlcNAc addition (Fig. -
SUPPY Liglucosexlmtdh
US 20100314248A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/0314248 A1 Worden et al. (43) Pub. Date: Dec. 16, 2010 (54) RENEWABLE BOELECTRONIC INTERFACE Publication Classification FOR ELECTROBOCATALYTC REACTOR (51) Int. Cl. (76) Inventors: Robert M. Worden, Holt, MI (US); C25B II/06 (2006.01) Brian L. Hassler, Lake Orion, MI C25B II/2 (2006.01) (US); Lawrence T. Drzal, Okemos, GOIN 27/327 (2006.01) MI (US); Ilsoon Lee, Okemo s, MI BSD L/04 (2006.01) (US) C25B 9/00 (2006.01) (52) U.S. Cl. ............... 204/403.14; 204/290.11; 204/400; Correspondence Address: 204/290.07; 427/458; 204/252: 977/734; PRICE HENEVELD COOPER DEWITT & LIT 977/742 TON, LLP 695 KENMOOR, S.E., PO BOX 2567 (57) ABSTRACT GRAND RAPIDS, MI 495.01 (US) An inexpensive, easily renewable bioelectronic device useful for bioreactors, biosensors, and biofuel cells includes an elec (21) Appl. No.: 12/766,169 trically conductive carbon electrode and a bioelectronic inter face bonded to a surface of the electrically conductive carbon (22) Filed: Apr. 23, 2010 electrode, wherein the bioelectronic interface includes cata lytically active material that is electrostatically bound directly Related U.S. Application Data or indirectly to the electrically conductive carbon electrode to (60) Provisional application No. 61/172,337, filed on Apr. facilitate easy removal upon a change in pH, thereby allowing 24, 2009. easy regeneration of the bioelectronic interface. 7\ POWER 1 - SUPPY|- LIGLUCOSEXLMtDH?till pi 6.0 - esses&aaaas-exx-xx-xx-xx-xxxxixax-e- Patent Application Publication Dec. 16, 2010 Sheet 1 of 18 US 2010/0314248 A1 Potential (nV) Patent Application Publication Dec. -
N-Acetyl-D-Glucosamine Kinase Is a Component of Nuclear Speckles and Paraspeckles
Mol. Cells 2015; 38(5): - http://dx.doi.org/10.14348/molcells.2015.2242 Molecules and Cells http://molcells.org Established in 1990 N-Acetyl-D-Glucosamine Kinase is a Component of Nuclear Speckles and Paraspeckles Syeda Ridita Sharif1,4, HyunSook Lee2,4, Md. Ariful Islam1, Dae-Hyun Seog3, and Il Soo Moon1,2,* Protein O-GlcNAcylation, dictated by cellular UDP-N- conformational change in which the two domains close around acetylglucosamine (UDP-GlcNAc) levels, plays a crucial role the nucleotide (Hurley, 1996). N-acetylglucosamine kinase in posttranslational modifications. The enzyme GlcNAc (GlcNAc kinase or NAGK; E.C. 2.7.1.59), an enzyme of the sug- kinase (NAGK, E.C. 2.7.1.59) catalyzes the formation of ar-kinase/Hsp70/actin super family (Berger et al., 2002), was first GlcNAc-6-phosphate, which is a major substrate for the identified in 1970 (Datta, 1970). NAGK is a prominent enzyme in biosynthesis of UDP-GlcNAc. Recent studies have revealed amino sugar metabolism where it catalyzes the conversion of the expression of NAGK in different types of cells especially GlcNAc to GlcNAc-6-phosphate. This metabolic pathway even- in neuronal dendrites. Here, by immunocytochemistry (ICC) tually yields to UDP-GlcNAc, which is utilized in the synthesis of and immunonucleochemistry (INC) of cultured rat hippo- O-/N-glycans and sialic acid. UDP-GlcNAc is also a substrate for campal neurons, HEK293T and GT1-7 cells we have showed O-GlcNAc transferase, which modifies cytosolic and nuclear that NAGK immuno-reactive punctae being present in the proteins at serine or threonine residues by adding a single nucleoplasm colocalized with small nuclear ribonucleoprotein- GlcNAc. -
Conserved Phosphoryl Transfer Mechanisms Within Kinase Families
Kenyon et al. BMC Research Notes 2012, 5:131 http://www.biomedcentral.com/1756-0500/5/131 RESEARCHARTICLE Open Access Conserved phosphoryl transfer mechanisms within kinase families and the role of the C8 proton of ATP in the activation of phosphoryl transfer Colin P Kenyon*, Robyn L Roth, Chris W van der Westhuyzen and Christopher J Parkinson Abstract Background: The kinome is made up of a large number of functionally diverse enzymes, with the classification indicating very little about the extent of the conserved kinetic mechanisms associated with phosphoryl transfer. It has been demonstrated that C8-H of ATP plays a critical role in the activity of a range of kinase and synthetase enzymes. Results: A number of conserved mechanisms within the prescribed kinase fold families have been identified directly utilizing the C8-H of ATP in the initiation of phosphoryl transfer. These mechanisms are based on structurally conserved amino acid residues that are within hydrogen bonding distance of a co-crystallized nucleotide. On the basis of these conserved mechanisms, the role of the nucleotide C8-H in initiating the formation of a pentavalent intermediate between the g-phosphate of the ATP and the substrate nucleophile is defined. All reactions can be clustered into two mechanisms by which the C8-H is induced to be labile via the coordination of a backbone carbonyl to C6-NH2 of the adenyl moiety, namely a “push” mechanism, and a “pull” mechanism, based on the protonation of N7. Associated with the “push” mechanism and “pull” mechanisms are a series of proton transfer cascades, initiated from C8-H, via the tri-phosphate backbone, culminating in the formation of the pentavalent transition state between the g-phosphate of the ATP and the substrate nucleophile. -
THE DEVELOPMENT of CHEMICAL METHODS to DISCOVER KINASE SUBSTRATES and MAP CELL SIGNALING with GAMMA-MODIFIED ATP ANALOG-DEPENDENT KINASE-CATALYZED PHOSPHORYLATION By
Wayne State University Wayne State University Dissertations 1-1-2017 The evelopmeD nt Of Chemical Methods To Discover Kinase Substrates And Map Cell Signaling With Gamma-Modified Atp Analog- Dependent Kinase-Catalyzed Phosphorylation Dissanayaka Mudiyanselage Maheeka Madhubashini Embogama Wayne State University, Follow this and additional works at: https://digitalcommons.wayne.edu/oa_dissertations Part of the Analytical Chemistry Commons, and the Biochemistry Commons Recommended Citation Embogama, Dissanayaka Mudiyanselage Maheeka Madhubashini, "The eD velopment Of Chemical Methods To Discover Kinase Substrates And Map Cell Signaling With Gamma-Modified Atp Analog-Dependent Kinase-Catalyzed Phosphorylation" (2017). Wayne State University Dissertations. 1698. https://digitalcommons.wayne.edu/oa_dissertations/1698 This Open Access Dissertation is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Dissertations by an authorized administrator of DigitalCommons@WayneState. THE DEVELOPMENT OF CHEMICAL METHODS TO DISCOVER KINASE SUBSTRATES AND MAP CELL SIGNALING WITH GAMMA-MODIFIED ATP ANALOG-DEPENDENT KINASE-CATALYZED PHOSPHORYLATION by DISSANAYAKA M. MAHEEKA M. EMBOGAMA DISSERTATION Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY 2017 MAJOR: CHEMISTRY (Biochemistry) Approved By: Advisor Date DEDICATION To my beloved mother, father, husband, daughter and sister. ii ACKNOWLEGEMENTS Many people have helped me during the past five years of earning my PhD. I would like to take this opportunity to convey my gratitude to them. First and foremost, I would like to thank my research supervisor Dr. Mary Kay Pflum for being the greatest mentor that I have met so far. -
(12) Patent Application Publication (10) Pub. No.: US 2010/0158968 A1 Panitch Et Al
US 20100158968A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/0158968 A1 Panitch et al. (43) Pub. Date: Jun. 24, 2010 (54) CELL-PERMEANT PEPTIDE-BASED Publication Classification INHIBITOR OF KINASES (51) Int. Cl. (76) Inventors: Alyssa Panitch, West Lafayette, IN st e8 CR (US); Brandon Seal, West ( .01) Lafayette, IN (US) A638/10 (2006.01) s A638/16 (2006.01) Correspondence Address: A6IP 43/00 (2006.01) GREENBERG TRAURIG, LLP (52) U.S. Cl. ................ 424/422:514/15: 514/13: 514/14 200 PARKAVE., P.O. BOX 677 FLORHAMPARK, NJ 07932 (US) (57) ABSTRACT The described invention provides kinase inhibiting composi (21) Appl. No.: 12/634,476 tions containing a therapeutic amount of a therapeutic inhibi (22) Filed: Dec. 9, 2009 torpeptide that inhibits at least one kinase enzyme, methods e 19 for treating an inflammatory disorder whose pathophysiology comprises inflammatory cytokine expression, and methods Related U.S. Application Data for treating an inflammatory disorder whose pathophysiology (60) Provisional application No. 61/121,396, filed on Dec. comprises inflammatory cytokine expression using the kinase 10, 2008. inhibiting compositions. 20 { ki> | 0: & c s - --- 33- x: SE PEPELE, ics 1.-- E- X K. AAA 22.9 --- KKK. Y.A., 3.2; C. -r { AAEASA. A. E. i : A X AAAAAAA; ; ; ; :-n. 4:-: is SEEKESAN.ARESA, 3523 -- -- Yili.A.R.AKA: 5,342 3. {{RCE: Rix i: Patent Application Publication US 2010/0158968A1 & ******** NO s ***** · Patent Application Publication Jun. 24, 2010 Sheet 2 of 11 US 2010/0158968A1 it, O Peptide: Cso: g E 100 WRRKAWRRKANRO, GWAA. -
High Constitutive Cytokine Release by Primary Human Acute Myeloid Leukemia Cells Is Associated with a Specific Intercellular Communication Phenotype
Supplementary Information High Constitutive Cytokine Release by Primary Human Acute Myeloid Leukemia Cells Is Associated with a Specific Intercellular Communication Phenotype Håkon Reikvam 1,2,*, Elise Aasebø 1, Annette K. Brenner 2, Sushma Bartaula-Brevik 1, Ida Sofie Grønningsæter 2, Rakel Brendsdal Forthun 2, Randi Hovland 3,4 and Øystein Bruserud 1,2 1 Department of Clinical Science, University of Bergen, 5020, Bergen, Norway 2 Department of Medicine, Haukeland University Hospital, 5021, Bergen, Norway 3 Department of Medical Genetics, Haukeland University Hospital, 5021, Bergen, Norway 4 Institute of Biomedicine, University of Bergen, 5020, Bergen, Norway * Correspondence: [email protected]; Tel.: +55-97-50-00 J. Clin. Med. 2019, 8, x 2 of 36 Figure S1. Mutational studies in a cohort of 71 AML patients. The figure shows the number of patients with the various mutations (upper), the number of mutations in for each patient (middle) and the number of main classes with mutation(s) in each patient (lower). 2 J. Clin. Med. 2019, 8, x; doi: www.mdpi.com/journal/jcm J. Clin. Med. 2019, 8, x 3 of 36 Figure S2. The immunophenotype of primary human AML cells derived from 62 unselected patients. The expression of the eight differentiation markers CD13, CD14, CD15, CD33, CD34, CD45, CD117 and HLA-DR was investigated for 62 of the 71 patients included in our present study. We performed an unsupervised hierarchical cluster analysis and identified four patient main clusters/patient subsets. The mutational profile for each f the 62 patients is also given (middle), no individual mutation of main class of mutations showed any significant association with any of the for differentiation marker clusters (middle). -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................ -
Supplementary Information
Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle. -
N-Acetyl-D-Glucosamine Kinase Interacts with Nudc and Lis1 in Dynein Motor Complex and Promotes Cell Migration
International Journal of Molecular Sciences Article N-Acetyl-D-Glucosamine Kinase Interacts with NudC and Lis1 in Dynein Motor Complex and Promotes Cell Migration Md. Ariful Islam 1,†, Ho Jin Choi 1, Raju Dash 1 , Syeda Ridita Sharif 1,‡, Diyah Fatimah Oktaviani 1 , Dae-Hyun Seog 2 and Il Soo Moon 1,3,* 1 Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea; [email protected] (M.A.I.); [email protected] (H.J.C.); [email protected] (R.D.); [email protected] (S.R.S.); [email protected] (D.F.O.) 2 Department of Biochemistry, Dementia and Neurodegenerative Disease Research Center, Inje University College of Medicine, Busan 47392, Korea; [email protected] 3 Dongguk Medical Institute, Dongguk University College of Medicine, Gyeongju 38066, Korea * Correspondence: [email protected]; Tel.: +82-54-770-2414; Fax: +82-54-770-2447 † Current address: Departments of Biological Sciences & Brain and Cognitive Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea. ‡ Current address: Department of Pharmacy, University of Science and Technology Chittagong, Chittagong 4202, Bangladesh. Abstract: Recently, we showed that N-acetylglucosamine kinase (NAGK), an enzyme of amino sugar metabolism, interacts with dynein light chain roadblock type 1 (DYNLRB1) and promotes the functions of dynein motor. Here, we report that NAGK interacts with nuclear distribution protein C (NudC) and lissencephaly 1 (Lis1) in the dynein complex. Yeast two-hybrid assays, pull-down assays, immunocy- tochemistry, and proximity ligation assays revealed NAGK–NudC–Lis1–dynein complexes around nuclei, at the leading poles of migrating HEK293T cells, and at the tips of migratory processes of cultured rat neuroblast cells. -
(12) STANDARD PATENT (11) Application No. AU 2015215937 B2 (19) AUSTRALIAN PATENT OFFICE
(12) STANDARD PATENT (11) Application No. AU 2015215937 B2 (19) AUSTRALIAN PATENT OFFICE (54) Title Metabolically engineered organisms for the production of added value bio-products (51) International Patent Classification(s) C12N 15/52 (2006.01) C12P 19/26 (2006.01) C12P 19/18 (2006.01) C12P 19/30 (2006.01) (21) Application No: 2015215937 (22) Date of Filing: 2015.08.21 (43) Publication Date: 2015.09.10 (43) Publication Journal Date: 2015.09.10 (44) Accepted Journal Date: 2017.03.16 (62) Divisional of: 2011278315 (71) Applicant(s) Universiteit Gent (72) Inventor(s) MAERTENS, Jo;BEAUPREZ, Joeri;DE MEY, Marjan (74) Agent / Attorney Griffith Hack, GPO Box 3125, Brisbane, QLD, 4001, AU (56) Related Art Trinchera, M. et al., 'Dictyostelium cytosolic fucosyltransferase synthesizes H type 1 trisaccharide in vitro', FEBS Letters, 1996, Vol. 395, pages 68-72 GenBank accession no. AF279134, 6 May 2002 van der Wel, H. et al., 'A bifunctional diglycosyltransferase forms the Fuc#1,2Gal#1,3-disaccharide on Skpl in the cytoplasm of Dictyostelium', The Journal of Biological Chemistry, 2002, Vol. 277, No. 48, pages 46527-46534 WO 2010/070104 Al Abstract The present invention relates to genetically engineered organisms, especially microorganisms such as bacteria and yeasts, for the production of added value bio-products such as specialty saccharide, activated saccharide, nucleoside, glycoside, glycolipid or glycoprotein. More specifically, the present invention relates to host cells that are metabolically engineered so that they can produce said valuable specialty products in large quantities and at a high rate by bypassing classical technical problems that occur in biocatalytical or fermentative production processes. -
Enzymatic Post‐Translational Modifications Linking
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Kanazawa University Repository for Academic Resources Enzymatic and non-enzymatic post-translational modifications linking diabetes and heart disease 著者 Yamamoto Yasuhiko, Yamamoto Hiroshi journal or Journal of Diabetes Investigation publication title volume 6 number 1 page range 16-17 year 2015-01-01 URL http://hdl.handle.net/2297/45821 doi: 10.1111/jdi.12248 COMMENTARY Enzymatic and non-enzymatic post-translational modifications linking diabetes and heart disease Diabetes-related morbidity and mortality has received considerable attention as a however, its flux is upregulated in dia- is evident in the increased prevalence of key factor in diabetic cardiac pathology2,3. betic cardiomyocytes4. The rate-limiting cardiovascular diseases and the high-risk In contrast to non-enzymatic glycation enzyme glutamine, fructose-6-phosphate of heart failure. Diabetic cardiomyopathy reactions, O-GlcNAc glycosylation is a aminotransferase (GFAT), converts fruc- is a well-known complication of diabetes, reversible and labile post-translational tose-6-phosphate to glucosamine-6-phos- and is defined as a ventricular dysfunc- modification. phate, which is then converted into tion independent of coronary heart After entering a cell, glucose is phos- UDP-GlcNAc and transferred onto target diseases and hypertension. The Framing- phorylated to glucose-6-phosphate (Fig- proteins by O-GlcNAc transferase ham study firmly established an epidemi- ure 1). It is further metabolized during (OGT). The enzyme, O-GlcNAcase, cata- ological link between diabetes and heart glycolysis to fructose-6-phosphate, which lyzes the removal of the O-GlcNAc failure1.Diabetescausesmetabolicdistur- leads to accessory pathways of glucose adduct from O-GlcNAcylated proteins bances, cardiac fibrosis, endothelial and metabolism; one such pathway is the (Figure 1)2.