Supplementary Table 6 . Pharmacophore Candidates

Total Page:16

File Type:pdf, Size:1020Kb

Supplementary Table 6 . Pharmacophore Candidates Supplementary Table 6. pharmacophore candidates identified by pharmMapper Pharma Model Norm Fit symple Name Uniplot 2p3g_v 0.9707 MAPKAPK2 MAP kinase-activated protein kinase 2 P49137 3gam_v 0.8849 NQO2 Ribosyldihydronicotinamide dehydrogenase [quinone] P16083 1shj_v 0.8818 CASP7 Caspase-7 CASP7_HUMAN 1e7a_v 0.8008 ALB Serum albumin ALBU_HUMAN 2zas_v 0.7294 ESRRG Estrogen-related receptor gamma P62508 2o65_v 0.702 PIM1 Proto-oncogene serine/threonine-protein kinase Pim-1 PIM1_HUMAN 2ipw_v 0.6914 AKR1B1 Aldose reductase ALDR_HUMAN 3fzk_v 0.6896 HSPA8 Heat shock cognate 71 kDa protein P11142 1fdu_v 0.6888 HSD17B1 Estradiol 17-beta-dehydrogenase 1 P14061 1j99_v 0.6846 SULT2A1 Bile salt sulfotransferase Q06520 1b6a_v 0.6528 METAP2 Methionine aminopeptidase 2 AMPM2_HUMAN 1j78_v 0.6505 VTDB Vitamin D-binding protein VTDB_HUMAN 2zaz_v 0.5891 MAPK14 Mitogen-activated protein kinase 14 Q16539 1mkd_v 0.5789 PDE4D cAMP-specific 3,5-cyclic phosphodiesterase 4D PDE4D_HUMAN 1oiz_v 0.5723 TTPA Alpha-tocopherol transfer protein P49638 1ctr_v 0.5687 Calmodulin Calmodulin CALM_HUMAN 1ype_v 0.5659 F2 Prothrombin THRB_HUMAN 2vww_v 0.5598 EPHB4 Ephrin type-B receptor 4 EPHB4_HUMAN 2aa5_v 0.5513 NR3C2 Mineralocorticoid receptor MCR_HUMAN 2fq9_v 0.5423 CTSS Cathepsin S CATS_HUMAN 1tbf_v 0.5371 PDE5A cGMP-specific 3,5-cyclic phosphodiesterase PDE5A_HUMAN 1a28_v 0.516 PGR Progesterone receptor PRGR_HUMAN 3ddp_v 0.5137 CDK2 Cell division protein kinase 2 P24941 3ekr_v 0.5123 HSP90AA1 Heat shock protein HSP 90-alpha P07900 2uwl_v 0.5119 FA10 Coagulation factor X FA10_HUMAN 19gs_v 0.5022 GSTP1 Glutathione S-transferase P GSTP1_HUMAN 1d3g_v 0.502 DHODH Dihydroorotate dehydrogenase, mitochondrial PYRD_HUMAN 1dvu_v 0.5 TTR Transthyretin TTHY_HUMAN 2j4a_v 0.4987 THRB Thyroid hormone receptor beta P10828 1xvp_v 0.4974 NR1I3 Nuclear receptor subfamily 1 group I member 3 NR1I3_HUMAN 2i6b_v 0.4952 ADK Adenosine kinase P55263 2rfn_v 0.4935 MET Hepatocyte growth factor receptor P08581 [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, 2bu5_v 0.4899 PDK2 PDK2_HUMAN mitochondrial 1gse_v 0.4894 GSTA1 Glutathione S-transferase A1 P08263 2zdz_v 0.4847 BACE1 Beta-secretase 1 P56817 1y2h_v 0.4796 PDE4B cAMP-specific 3,5-cyclic phosphodiesterase 4B PDE4B_HUMAN 1r7y_v 0.4763 ABO Histo-blood group ABO system transferase P16442 1kdk_v 0.4742 SHBG Sex hormone-binding globulin SHBG_HUMAN 3f7z_v 0.4722 GSK3B Glycogen synthase kinase-3 beta P49841 1t48_v 0.4712 PTPN1 Tyrosine-protein phosphatase non-receptor type 1 PTN1_HUMAN 1xqc_v 0.4608 ESR1 Estrogen receptor ESR1_HUMAN 1knu_v 0.4598 PPARG Peroxisome proliferator-activated receptor gamma PPARG_HUMAN 1sm2_v 0.4524 ITK Tyrosine-protein kinase ITK/TSK Q08881 1t4e_v 0.4511 MDM2 E3 ubiquitin-protein ligase Mdm2 MDM2_HUMAN 1h1b_v 0.4466 ELANE Leukocyte elastase ELNE_HUMAN 1qab_v 0.4449 RBP4 Retinol-binding protein 4 RET4_HUMAN 3d3e_v 0.4414 HSD11B1 Corticosteroid 11-beta-dehydrogenase isozyme 1 DHI1_HUMAN 1i7g_v 0.4338 PPARA Peroxisome proliferator-activated receptor alpha PPARA_HUMAN 1if5_v 0.4317 CA2 Carbonic anhydrase 2 CAH2_HUMAN 1xq3_v 0.4256 AR Androgen receptor ANDR_HUMAN 1fcz_v 0.4252 RARG Retinoic acid receptor gamma RARG_HUMAN 1mzn_v 0.4251 RXRA Retinoic acid receptor RXR-alpha RXRA_HUMAN 1tou_v 0.4243 FABP4 Fatty acid-binding protein, adipocyte FABP4_HUMAN 1upw_v 0.4227 NR1H2 Oxysterols receptor LXR-beta NR1H2_HUMAN 1w6k_v 0.4206 LSS Lanosterol synthase ERG7_HUMAN Protein farnesyltransferase/geranylgeranyltransferase 1sa4_v 0.4201 FNTA FNTA_HUMAN type-1 subunit alpha 1fe3_v 0.4191 FABP7 Fatty acid-binding protein, brain FABP7_HUMAN 1fls_v 0.4165 MMP13 Collagenase 3 MMP13_HUMAN 1q22_v 0.4152 SULT2B1 Sulfotransferase family cytosolic 2B member 1 O00204 1dxo_v 0.4106 NQO1 NAD(P)H dehydrogenase [quinone] 1 NQO1_HUMAN 2iw6_v 0.4093 CCNA2 Cyclin-A2 CCNA2_HUMAN 2j14_v 0.4073 PPARD Peroxisome proliferator-activated receptor delta PPARD_HUMAN 2hmb_v 0.4043 FABP3 Fatty acid-binding protein, heart FABPH_HUMAN 1uu7_v 0.4021 PDPK1 3-phosphoinositide-dependent protein kinase 1 PDPK1_HUMAN 1p62_v 0.4017 DCK Deoxycytidine kinase DCK_HUMAN 2o9i_v 0.4 NR1I2 Nuclear receptor subfamily 1 group I member 2 NR1I2_HUMAN 1rw8_v 0.3936 TGFBR1 TGF-beta receptor type-1 TGFR1_HUMAN 1g3m_v 0.3888 SULT1E1 Estrogen sulfotransferase ST1E1_HUMAN 3nos_v 0.3819 NOS3 Nitric oxide synthase, endothelial NOS3_HUMAN 2oqv_v 0.3807 DPP4 Dipeptidyl peptidase 4 DPP4_HUMAN 1tfg_v 0.3779 TGFB2 Transforming growth factor beta-2 TGFB2_HUMAN 1jqe_v 0.3716 HNMT Histamine N-methyltransferase P50135 2v11_v 0.3709 REN Renin RENI_HUMAN 1r9o_v 0.37 CYP2C9 Cytochrome P450 2C9 CP2C9_HUMAN 1nhz_v 0.3697 NR3C1 Glucocorticoid receptor GCR_HUMAN 1uym_v 0.3629 HSP90AB1 Heat shock protein HSP 90-beta P08238 1s19_v 0.3601 VDR Vitamin D3 receptor VDR_HUMAN 3c7q_v 0.3552 KDR Vascular endothelial growth factor receptor 2 P35968 1nmz_v 0.3542 DTYMK Thymidylate kinase KTHY_HUMAN 2gqg_v 0.3493 ABL1 Proto-oncogene tyrosine-protein kinase ABL1 P00519 1qpf_v 0.3479 FKBP1A Peptidyl-prolyl cis-trans isomerase FKBP1A FKB1A_HUMAN 1mmb_v 0.3467 MMP8 Neutrophil collagenase MMP8_HUMAN 2ofu_v 0.3458 LCK Proto-oncogene tyrosine-protein kinase LCK LCK_HUMAN 3fxv_v 0.3456 NR1H4 Bile acid receptor Q96RI1 1kqu_v 0.3351 PLA2G2A Phospholipase A2, membrane associated P14555 1lv2_v 0.3318 HNF4G Hepatocyte nuclear factor 4-gamma Q14541 3c4c_v 0.3316 BRAF B-Raf proto-oncogene serine/threonine-protein kinase BRAF1_HUMAN 1t64_v 0.3304 HDAC8 Histone deacetylase 8 HDAC8_HUMAN 1tfq_v 0.3298 XIAP Baculoviral IAP repeat-containing protein 4 XIAP_HUMAN 2fgi_v 0.3287 FGFR1 Basic fibroblast growth factor receptor 1 FGFR1_HUMAN Dual specificity mitogen-activated protein kinase kinase 1s9j_v 0.3246 MAP2K1 MP2K1_HUMAN 1 1xh5_v 0.3216 PRKACA cAMP-dependent protein kinase catalytic subunit alpha P00517 1i7b_v 0.321 AMD1 S-adenosylmethionine decarboxylase proenzyme DCAM_HUMAN 1gmy_v 0.3206 CTSB Cathepsin B CATB_HUMAN 2p4i_v 0.3156 TEK Angiopoietin-1 receptor TIE2_HUMAN 1rhr_v 0.314 CASP3 Caspase-3 CASP3_HUMAN 1itu_v 0.3137 DPEP1 Dipeptidase 1 DPEP1_HUMAN 2bk3_v 0.3099 MAOB Amine oxidase [flavin-containing] B AOFB_HUMAN 1t46_v 0.3087 KIT Mast/stem cell growth factor receptor KIT_HUMAN 3cbs_v 0.3086 CRABP2 Cellular retinoic acid-binding protein 2 P29373 3f7i_v 0.3028 BIRC7 Baculoviral IAP repeat-containing protein 7 Q96CA5 Serine/threonine-protein phosphatase PP1-gamma 1jk7_v 0.2996 PPP1CC P36873 catalytic subunit 1x0n_v 0.2912 GRB2 Growth factor receptor-bound protein 2 GRB2_HUMAN 1o43_v 0.2728 SRC Proto-oncogene tyrosine-protein kinase Src SRC_HUMAN 1s0x_v 0.2722 RORA Nuclear receptor ROR-alpha RORA_HUMAN 1njs_v 0.2636 GART Trifunctional purine biosynthetic protein adenosine-3 PUR2_HUMAN 3cda_v 0.2617 HMGCR 3-hydroxy-3-methylglutaryl-coenzyme A reductase HMDH_HUMAN 1h9u_v 0.2596 RXRB Retinoic acid receptor RXR-beta RXRB_HUMAN 1xap_v 0.2516 RARB Retinoic acid receptor beta RARB_HUMAN 2yxj_v 0.2502 BCL2L1 Bcl-2-like protein 1 Q07817 1p4m_v 0.2319 RFK Riboflavin kinase Q969G6 1ln3_v 0.2172 PCTP Phosphatidylcholine transfer protein Q9UKL6 1dug_v 0.2152 FGG Fibrinogen gamma chain FIBG_HUMAN 1l8j_v 0.2149 PROCR Endothelial protein C receptor EPCR_HUMAN 1ice_v 0.2067 CASP1 Caspase-1 CASP1_HUMAN 1xh0_v 0.1817 AMY2A Pancreatic alpha-amylase AMYP_HUMAN.
Recommended publications
  • Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases
    International Journal of Molecular Sciences Review Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases Peter Goettig Structural Biology Group, Faculty of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria; [email protected]; Tel.: +43-662-8044-7283; Fax: +43-662-8044-7209 Academic Editor: Cheorl-Ho Kim Received: 30 July 2016; Accepted: 10 November 2016; Published: 25 November 2016 Abstract: Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications. Keywords: secreted protease; sequon; N-glycosylation; O-glycosylation; core glycan; enzyme kinetics; substrate recognition; flexible loops; Michaelis constant; turnover number 1.
    [Show full text]
  • ONLINE SUPPLEMENTARY TABLE Table 2. Differentially Expressed
    ONLINE SUPPLEMENTARY TABLE Table 2. Differentially Expressed Probe Sets in Livers of GK Rats. A. Immune/Inflammatory (67 probe sets, 63 genes) Age Strain Probe ID Gene Name Symbol Accession Gene Function 5 WKY 1398390_at small inducible cytokine B13 precursor Cxcl13 AA892854 chemokine activity; lymph node development 5 WKY 1389581_at interleukin 33 Il33 BF390510 cytokine activity 5 WKY *1373970_at interleukin 33 Il33 AI716248 cytokine activity 5 WKY 1369171_at macrophage stimulating 1 (hepatocyte growth factor-like) Mst1; E2F2 NM_024352 serine-throenine kinase; tumor suppression 5 WKY 1388071_x_at major histocompatability antigen Mhc M24024 antigen processing and presentation 5 WKY 1385465_at sialic acid binding Ig-like lectin 5 Siglec5 BG379188 sialic acid-recognizing receptor 5 WKY 1393108_at major histocompatability antigen Mhc BM387813 antigen processing and presentation 5 WKY 1388202_at major histocompatability antigen Mhc BI395698 antigen processing and presentation 5 WKY 1371171_at major histocompatability antigen Mhc M10094 antigen processing and presentation 5 WKY 1370382_at major histocompatability antigen Mhc BI279526 antigen processing and presentation 5 WKY 1371033_at major histocompatability antigen Mhc AI715202 antigen processing and presentation 5 WKY 1383991_at leucine rich repeat containing 8 family, member E Lrrc8e BE096426 proliferation and activation of lymphocytes and monocytes. 5 WKY 1383046_at complement component factor H Cfh; Fh AA957258 regulation of complement cascade 4 WKY 1369522_a_at CD244 natural killer
    [Show full text]
  • University of California, San Diego
    UNIVERSITY OF CALIFORNIA, SAN DIEGO A Lipidomic Perspective on Inflammatory Macrophage Eicosanoid Signaling A Thesis submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Chemistry by Paul Christopher Norris Committee in charge: Professor Edward A. Dennis, Chair Professor Pieter C. Dorrestein Professor Partho Ghosh Professor Christopher K. Glass Professor Michael J. Sailor 2013 The Dissertation of Paul Christopher Norris is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2013 iii DEDICATION To my parents, Darrell and Kathy, for always allowing me to think (and choose) for myself. iv TABLE OF CONTENTS Signature page ............................................................................................................................ iii Dedication .................................................................................................................................. iv Table of contents ......................................................................................................................... v List of symbols and abbreviations ........................................................................................... viii List of figures ............................................................................................................................. xi List of tables ............................................................................................................................
    [Show full text]
  • Download Product Insert (PDF)
    PRODUCT INFORMATION FABP2 Polyclonal Antibody Item No. 10010019 Overview and Properties Contents: This vial contains 500 μl of peptide affinity-purified IgG. Synonyms: Fatty Acid Binding Protein 2, Intestinal-Fatty Acid Binding Protein, I-FABP Immunogen: Synthetic peptide from an internal region of human FABP2 Cross Reactivity: (+) FABP2; (-) FABP1, FABP3, FABP4, FABP5, FABP7 Species Reactivity: (+) Human, rat; other species not tested Uniprot No.: P12104 Form: Liquid Storage: -20°C (as supplied) Stability: ≥1 year Storage Buffer: TBS, pH 7.4, with with 50% glycerol, 0.1% BSA, and 0.02% sodium azide Applications: Western blot (WB); the recommended starting dilution is 1:200. Other applications were not tested, therefore optimal working concentration/dilution should be determined empirically. Image 1 2 3 4 5 6 7 · · · · · · · 16 kDa Lane 1: Rat Recombinant FABP1 (0.4 μg) Lane 2: Rat Recombinant FABP2 (0.025 μg) Lane 3: Rat Recombinant FABP2 (0.050 μg) Lane 4: Human Recombinant FABP3 (0.4 μg) Lane 5: Murine Recombinant FABP4 (0.4 μg) Lane 6: Murine Recombinant FABP5 (0.4 μg) Lane 7: Human Duodenum Homogenate (30 μg) WARNING CAYMAN CHEMICAL THIS PRODUCT IS FOR RESEARCH ONLY - NOT FOR HUMAN OR VETERINARY DIAGNOSTIC OR THERAPEUTIC USE. 1180 EAST ELLSWORTH RD SAFETY DATA ANN ARBOR, MI 48108 · USA This material should be considered hazardous until further information becomes available. Do not ingest, inhale, get in eyes, on skin, or on clothing. Wash thoroughly after handling. Before use, the user must review the complete Safety Data Sheet, which has been sent via email to your institution. PHONE: [800] 364-9897 WARRANTY AND LIMITATION OF REMEDY [734] 971-3335 Buyer agrees to purchase the material subject to Cayman’s Terms and Conditions.
    [Show full text]
  • The Association Between FABP7 Serum Levels with Survival And
    Karvellas et al. Ann. Intensive Care (2017) 7:99 DOI 10.1186/s13613-017-0323-0 RESEARCH Open Access The association between FABP7 serum levels with survival and neurological complications in acetaminophen‑induced acute liver failure: a nested case–control study Constantine J. Karvellas1* , Jaime L. Speiser2, Mélanie Tremblay3, William M. Lee4, Christopher F. Rose3 and For the US Acute Liver Failure Study Group Abstract Background: Acetaminophen (APAP)-induced acute liver failure (ALF) is associated with signifcant mortality due to intracranial hypertension (ICH), a result of cerebral edema (CE) and astrocyte swelling. Brain-type fatty acid-binding protein (FABP7) is a small (15 kDa) cytoplasmic protein abundantly expressed in astrocytes. The aim of this study was to determine whether serum FABP7 levels early (day 1) or late (days 3–5) level were associated with 21-day mortality and/or the presence of ICH/CE in APAP-ALF patients. Methods: Serum samples from 198 APAP-ALF patients (nested case–control study with 99 survivors and 99 non-sur- vivors) were analyzed by ELISA methods and assessed with clinical data from the US Acute Liver Failure Study Group (ALFSG) Registry (1998–2014). Results: APAP-ALF survivors had signifcantly lower serum FABP7 levels on admission (147.9 vs. 316.5 ng/ml, p 0.0002) and late (87.3 vs. 286.2 ng/ml, p < 0.0001) compared with non-survivors. However, a signifcant association between= 21-day mortality and increased serum FABP7 early [log FABP7 odds ratio (OR) 1.16, p 0.32] and late (log FABP7 ~ OR 1.34, p 0.21) was not detected after adjusting for signifcant covariates (MELD, vasopressor= use).
    [Show full text]
  • Proteomic Analysis of Exosome-Like Vesicles Derived from Breast Cancer Cells
    ANTICANCER RESEARCH 32: 847-860 (2012) Proteomic Analysis of Exosome-like Vesicles Derived from Breast Cancer Cells GEMMA PALAZZOLO1, NADIA NINFA ALBANESE2,3, GIANLUCA DI CARA3, DANIEL GYGAX4, MARIA LETIZIA VITTORELLI3 and IDA PUCCI-MINAFRA3 1Institute for Biomedical Engineering, Laboratory of Biosensors and Bioelectronics, ETH Zurich, Switzerland; 2Department of Physics, University of Palermo, Palermo, Italy; 3Centro di Oncobiologia Sperimentale (C.OB.S.), Oncology Department La Maddalena, Palermo, Italy; 4Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland FHNW, Muttenz, Switzerland Abstract. Background/Aim: The phenomenon of membrane that vesicle production allows neoplastic cells to exert different vesicle-release by neoplastic cells is a growing field of interest effects, according to the possible acceptor targets. For instance, in cancer research, due to their potential role in carrying a vesicles could potentiate the malignant properties of adjacent large array of tumor antigens when secreted into the neoplastic cells or activate non-tumoral cells. Moreover, vesicles extracellular medium. In particular, experimental evidence show could convey signals to immune cells and surrounding stroma that at least some of the tumor markers detected in the blood cells. The present study may significantly contribute to the circulation of mammary carcinoma patients are carried by knowledge of the vesiculation phenomenon, which is a critical membrane-bound vesicles. Thus, biomarker research in breast device for trans cellular communication in cancer. cancer can gain great benefits from vesicle characterization. Materials and Methods: Conditioned medium was collected The phenomenon of membrane release in the extracellular from serum starved MDA-MB-231 sub-confluent cell cultures medium has long been known and was firstly described by and exosome-like vesicles (ELVs) were isolated by Paul H.
    [Show full text]
  • MALE Protein Name Accession Number Molecular Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean H Mean PDAC Mean T-Test PDAC Vs. H T-Test
    MALE t-test t-test Accession Molecular H PDAC PDAC vs. PDAC vs. Protein Name Number Weight CP1 CP2 H1 H2 PDAC1 PDAC2 CP Mean Mean Mean H CP PDAC/H PDAC/CP - 22 kDa protein IPI00219910 22 kDa 7 5 4 8 1 0 6 6 1 0.1126 0.0456 0.1 0.1 - Cold agglutinin FS-1 L-chain (Fragment) IPI00827773 12 kDa 32 39 34 26 53 57 36 30 55 0.0309 0.0388 1.8 1.5 - HRV Fab 027-VL (Fragment) IPI00827643 12 kDa 4 6 0 0 0 0 5 0 0 - 0.0574 - 0.0 - REV25-2 (Fragment) IPI00816794 15 kDa 8 12 5 7 8 9 10 6 8 0.2225 0.3844 1.3 0.8 A1BG Alpha-1B-glycoprotein precursor IPI00022895 54 kDa 115 109 106 112 111 100 112 109 105 0.6497 0.4138 1.0 0.9 A2M Alpha-2-macroglobulin precursor IPI00478003 163 kDa 62 63 86 72 14 18 63 79 16 0.0120 0.0019 0.2 0.3 ABCB1 Multidrug resistance protein 1 IPI00027481 141 kDa 41 46 23 26 52 64 43 25 58 0.0355 0.1660 2.4 1.3 ABHD14B Isoform 1 of Abhydrolase domain-containing proteinIPI00063827 14B 22 kDa 19 15 19 17 15 9 17 18 12 0.2502 0.3306 0.7 0.7 ABP1 Isoform 1 of Amiloride-sensitive amine oxidase [copper-containing]IPI00020982 precursor85 kDa 1 5 8 8 0 0 3 8 0 0.0001 0.2445 0.0 0.0 ACAN aggrecan isoform 2 precursor IPI00027377 250 kDa 38 30 17 28 34 24 34 22 29 0.4877 0.5109 1.3 0.8 ACE Isoform Somatic-1 of Angiotensin-converting enzyme, somaticIPI00437751 isoform precursor150 kDa 48 34 67 56 28 38 41 61 33 0.0600 0.4301 0.5 0.8 ACE2 Isoform 1 of Angiotensin-converting enzyme 2 precursorIPI00465187 92 kDa 11 16 20 30 4 5 13 25 5 0.0557 0.0847 0.2 0.4 ACO1 Cytoplasmic aconitate hydratase IPI00008485 98 kDa 2 2 0 0 0 0 2 0 0 - 0.0081 - 0.0
    [Show full text]
  • Vertebrate Fatty Acid and Retinoid Binding Protein Genes and Proteins: Evidence for Ancient and Recent Gene Duplication Events
    In: Advances in Genetics Research. Volume 11 ISBN: 978-1-62948-744-1 Editor: Kevin V. Urbano © 2014 Nova Science Publishers, Inc. Chapter 7 Vertebrate Fatty Acid and Retinoid Binding Protein Genes and Proteins: Evidence for Ancient and Recent Gene Duplication Events Roger S. Holmes Eskitis Institute for Drug Discovery and School of Biomolecular and Physical Sciences, Griffith University, Nathan, QLD, Australia Abstract Fatty acid binding proteins (FABP) and retinoid binding proteins (RBP) are members of a family of small, highly conserved cytoplasmic proteins that function in binding and facilitating the cellular uptake of fatty acids, retinoids and other hydrophobic compounds. Several human FABP-like genes are expressed in the body: FABP1 (liver); FABP2 (intestine); FABP3 (heart and skeletal muscle); FABP4 (adipocyte); FABP5 (epidermis); FABP6 (ileum); FABP7 (brain); FABP8 (nervous system); FABP9 (testis); and FABP12 (retina and testis). A related gene (FABP10) is expressed in lower vertebrate liver and other tissues. Four RBP genes are expressed in human tissues: RBP1 (many tissues); RBP2 (small intestine epithelium); RBP5 (kidney and liver); and RBP7 (kidney and heart). Comparative FABP and RBP amino acid sequences and structures and gene locations were examined using data from several vertebrate genome projects. Sequence alignments, key amino acid residues and conserved predicted secondary and tertiary structures were also studied, including lipid binding regions. Vertebrate FABP- and RBP- like genes usually contained 4 coding exons in conserved locations, supporting a common evolutionary origin for these genes. Phylogenetic analyses examined the relationships and evolutionary origins of these genes, suggesting division into three FABP gene classes: 1: FABP1, FABP6 and FABP10; 2: FABP2; and 3, with 2 groups: 3A: FABP4, FABP8, FABP9 and FABP12; and 3B: and FABP3, FABP5 and FABP7.
    [Show full text]
  • Bonded His93 As a Sensitive Probe for Identifying Inhibitors of the Endocannabinoid Transport Protein FABP7
    Chem Biol Drug Des 2015; 85: 534–540 Research Article Hydrogen-Bonded His93 As a Sensitive Probe for Identifying Inhibitors of the Endocannabinoid Transport Protein FABP7 Sergiy Tyukhtenko1, Karrie Chan1, Rubin Jiang1, receptor-mediated signal transduction (2). The biosynthesis Han Zhou1, Richard W. Mercier1, De-Ping Yang2, and physiology of AEA are well understood (3,4), but its Alexandros Makriyannis1 and Jason J. Guo1,* mechanism of uptake has been elusive. Despite intensive studies on the AEA transport process (5–9), the question 1Center for Drug Discovery, Department of Pharmaceutical remains on how the uncharged lipophilic endocannabinoid Sciences and Department of Chemistry and Chemical ligand AEA crosses the cellular membrane to access the Biology, Northeastern University, 360 Huntington Avenue, hydrophilic cytosol. Recently, it was reported (10,11) that a Boston, MA 02115, USA 2 group of carrier proteins, particularly fatty acid binding pro- Physics Department, College of the Holy Cross, 1 College teins (FABPs), can significantly enhance the cellular uptake Street, Worcester, MA 01610, USA and subsequent inactivation of AEA. The findings provide *Corresponding author: Jason J. Guo, [email protected] a potential new therapeutic modality to the treatment of pain, inflammation, and drug abuse through dual inhibition The human brain FABP (FABP7) has been shown to be an intracellular carrier protein that can significantly of the deactivating enzymes such as fatty acid amide potentiate the uptake of the endocannabinoid ananda- hydrolase (FAAH) (12) and the endocannabinoid transport mide. For this reason, there is a great interest in the proteins. discovery and development of FABP7 inhibitors for treating stress, pain, inflammation, and drug abuse.
    [Show full text]
  • Noncanonical Role of Transferrin Receptor 1 Is Essential for Intestinal Homeostasis
    Noncanonical role of transferrin receptor 1 is essential for intestinal homeostasis Alan C. Chena, Adriana Donovanb, Renee Ned-Sykesc, and Nancy C. Andrewsa,d,1 aDepartment of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 27705; bDivision of Pharmacology and Preclinical Biology, Scholar Rock, Cambridge, MA 02142; cDivision of Laboratory Systems, Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA 30333; and dDepartment of Pediatrics, Duke University School of Medicine, Durham, NC 27705 Contributed by Nancy C. Andrews, August 4, 2015 (sent for review June 16, 2015; reviewed by Jerry Kaplan and Ramesh A. Shivdasani) Transferrin receptor 1 (Tfr1) facilitates cellular iron uptake through Surprisingly, the mice showed marked induction of genes asso- receptor-mediated endocytosis of iron-loaded transferrin. It is ex- ciated with epithelial–mesenchymal transition in IECs, suggest- pressed in the intestinal epithelium but not involved in dietary iron ing that Tfr1 normally acts to suppress this cell fate change. absorption. To investigate its role, we inactivated the Tfr1 gene There was also abnormal accumulation of lipids, similar to mice selectively in murine intestinal epithelial cells. The mutant mice had lacking transcription factor Plagl2, and increased expression of severe disruption of the epithelial barrier and early death. There stem cell markers. was impaired proliferation of intestinal epithelial cell progenitors, aberrant lipid handling, increased mRNA expression of stem cell Results markers, and striking induction of many genes associated with Conditional Deletion of Tfr1 in IECs. We developed Tfr1fl/fl mice epithelial-to-mesenchymal transition. Administration of parenteral carrying loxP sites flanking Tfr1 exons 3–6(Fig.
    [Show full text]
  • NIH Public Access Author Manuscript Glia
    NIH Public Access Author Manuscript Glia. Author manuscript; available in PMC 2013 May 03. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Glia. 2008 July ; 56(9): 935–941. doi:10.1002/glia.20666. A BAC Transgenic Mouse Model to Analyze the Function of Astroglial SPARCL1 (SC1) in the Central Nervous System Jill M. Weimer1, Amelia Stanco1, Jr-Gang Cheng1, Ana C. Vargo1, Santhi Voora1, and E. S. Anton1,2,* 1UNC Neuroscience Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 2Department of Cell and Molecular Physiology, The University of North Carolina School of Medicine, Chapel Hill, North Carolina Abstract Extracellular matrix associated Sparc-like 1 (SC1/SPARCL1) can influence the function of astroglial cells in the developing and mature central nervous system (CNS). To examine SC1’s significance in the CNS, we generated a BAC transgenic mouse model in which Sc1 is expressed in radial glia and their astrocyte derivatives using the astroglial-specific Blbp (Brain-lipid binding protein; [Feng et al., (1994) Neuron 12:895–908]) regulatory elements. Characterization of these Blbf-Sc1 transgenic mice show elevated Sc1 transcript and protein in an astroglial selective pattern throughout the CNS. This model provides a novel in vivo system for evaluating the role of SC1 in brain development and function, in general, and for understanding SC1’s significance in the fate and function of astroglial cells, in particular. Keywords cerebral cortex; astroglia; SPARCL1; SC1; fatty acid binding protein 7; fabp7 INTRODUCTION SC1 is a member of the SPARC (Secreted Protein Acidic and Rich in Cysteine) family of extracellular matrix-associated proteins, which, in addition to SC1 and SPARC, includes testicans 1–3, tsc36, QR1, and SMOCs.
    [Show full text]
  • Novel Proteins Regulated by Mtor in Subependymal Giant Cell Astrocytomas of Patients with Tuberous Sclerosis Complex and New Therapeutic Implications
    The American Journal of Pathology, Vol. 176, No. 4, April 2010 Copyright © American Society for Investigative Pathology DOI: 10.2353/ajpath.2010.090950 Molecular Pathogenesis of Genetic and Inherited Diseases Novel Proteins Regulated by mTOR in Subependymal Giant Cell Astrocytomas of Patients with Tuberous Sclerosis Complex and New Therapeutic Implications Magdalena Ewa Tyburczy,* Katarzyna Kotulska,† and demonstrated an effective modulation of SEGA Piotr Pokarowski,‡ Jakub Mieczkowski,* growth by pharmacological inhibition of both Joanna Kucharska,* Wieslawa Grajkowska,† mTOR and extracellular signal-regulated kinase sig- Maciej Roszkowski,§ Sergiusz Jozwiak,† naling pathways, which could represent a novel ther- and Bozena Kaminska* apeutic approach. (Am J Pathol 2010, 176:1878–1890; DOI: 10.2353/ajpath.2010.090950) From the Laboratory of Transcription Regulation,* the Nencki Institute of Experimental Biology, Warsaw; the Departments of Neurology and Epileptology,† and Neurosurgery,§ the Children’s Subependymal giant cell astrocytomas (SEGAs) are rare, Memorial Health Institute, Warsaw; and the Faculty of low-grade brain tumors (World Health Organization Grade I) Mathematics, Informatics, and Mechanics,‡ University of of a mixed glioneuronal lineage.1,2 They are observed in Warsaw, Poland 10% to 20% of patients with tuberous sclerosis complex (TSC) and are the major cause of morbidity in children and young adults with TSC.3 The disease affects about one in Subependymal giant cell astrocytomas (SEGAs) are 6000 people, is characterized by the formation of benign rare brain tumors associated with tuberous sclerosis tumors in multiple organs (mainly brain, heart, kidneys, skin, complex (TSC), a disease caused by mutations in TSC1 or lungs), and is often associated with epilepsy, mental or TSC2, resulting in enhancement of mammalian retardation, and autism.4,5 Tuberous sclerosis complex is target of rapamycin (mTOR) activity, dysregulation of caused by mutation in one of two tumor suppressor genes, cell growth, and tumorigenesis.
    [Show full text]