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Nordqvist A, O'Mahony G, Fridén-Saxin M, Fredenwall M, Hogner A, Granberg KL, Aagaard A, Bäckström S, Gunnarsson A, Kaminski T, Xue Y, Dellsén A, Hansson E, Hansson P, Ivarsson I, Karlsson U, Bamberg K, Hermansson M, Georgsson J, Lindmark B, Edman K. Structure-Based Drug Design of Mineralocorticoid Receptor Antagonists to Explore Oxosteroid Receptor Selectivity. ChemMedChem 2016; 12:50-65. [DOI: 10.1002/cmdc.201600529] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/22/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Anneli Nordqvist
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 43183 Sweden
| | - Gavin O'Mahony
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 43183 Sweden
| | - Maria Fridén-Saxin
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 43183 Sweden
| | - Marlene Fredenwall
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 43183 Sweden
| | - Anders Hogner
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 43183 Sweden
| | - Kenneth L. Granberg
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 43183 Sweden
| | - Anna Aagaard
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Stefan Bäckström
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Anders Gunnarsson
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Tim Kaminski
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Yafeng Xue
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Anita Dellsén
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Eva Hansson
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Pia Hansson
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Ida Ivarsson
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Ulla Karlsson
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
| | - Krister Bamberg
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 43183 Sweden
| | - Majlis Hermansson
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 43183 Sweden
| | - Jennie Georgsson
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 43183 Sweden
| | - Bo Lindmark
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 43183 Sweden
| | - Karl Edman
- Discovery Sciences; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 43183 Mölndal Sweden
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2
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Xue Y, Olsson T, Johansson CA, Öster L, Beisel HG, Rohman M, Karis D, Bäckström S. Fragment Screening of Soluble Epoxide Hydrolase for Lead Generation-Structure-Based Hit Evaluation and Chemistry Exploration. ChemMedChem 2016; 11:497-508. [PMID: 26845235 DOI: 10.1002/cmdc.201500575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 12/20/2022]
Abstract
Soluble epoxide hydrolase (sEH) is involved in the regulation of many biological processes by metabolizing the key bioactive lipid mediator, epoxyeicosatrienoic acids. For the development of sEH inhibitors with improved physicochemical properties, we performed both a fragment screening and a high-throughput screening aiming at an integrated hit evaluation and lead generation. Followed by a joint dose-response analysis to confirm the hits, the identified actives were then effectively triaged by a structure-based hit-classification approach to three prioritized series. Two distinct scaffolds were identified as tractable starting points for potential lead chemistry work. The oxoindoline series bind at the right-hand side of the active-site pocket with hydrogen bonds to the protein. The 2-phenylbenzimidazole-4-sulfonamide series bind at the central channel with significant induced fit, which has not been previously reported. On the basis of the encouraging initial results, we envision that a new lead series with improved properties could be generated if a vector is found that could merge the cyclohexyl functionality of the oxoindoline series with the trifluoromethyl moiety of the 2-phenylbenzimidazole-4-sulfonamide series.
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Affiliation(s)
- Yafeng Xue
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Thomas Olsson
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Carina A Johansson
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Linda Öster
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Hans-Georg Beisel
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Mattias Rohman
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - David Karis
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Stefan Bäckström
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden.
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3
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Edman K, Hosseini A, Bjursell MK, Aagaard A, Wissler L, Gunnarsson A, Kaminski T, Köhler C, Bäckström S, Jensen TJ, Cavallin A, Karlsson U, Nilsson E, Lecina D, Takahashi R, Grebner C, Geschwindner S, Lepistö M, Hogner AC, Guallar V. Ligand Binding Mechanism in Steroid Receptors: From Conserved Plasticity to Differential Evolutionary Constraints. Structure 2015; 23:2280-2290. [DOI: 10.1016/j.str.2015.09.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 12/17/2022]
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4
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Edman K, Ahlgren R, Bengtsson M, Bladh H, Bäckström S, Dahmén J, Henriksson K, Hillertz P, Hulikal V, Jerre A, Kinchin L, Kåse C, Lepistö M, Mile I, Nilsson S, Smailagic A, Taylor J, Tjörnebo A, Wissler L, Hansson T. The discovery of potent and selective non-steroidal glucocorticoid receptor modulators, suitable for inhalation. Bioorg Med Chem Lett 2014; 24:2571-7. [PMID: 24755427 DOI: 10.1016/j.bmcl.2014.03.070] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 01/05/2023]
Abstract
We report the discovery of highly potent and selective non-steroidal glucocorticoid receptor modulators with PK properties suitable for inhalation. A high throughput screen of the AstraZeneca compound collection identified sulfonamide 3 as a potent non-steroidal glucocorticoid receptor ligand. Further optimization of this lead generated indazoles 30 and 48 that were progressed to characterization in in vivo models. X-ray crystallography was used to gain further insight into the binding mode of selected ligands.
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Affiliation(s)
- Karl Edman
- Discovery Sciences, Innovative Medicines, AstraZeneca R&D, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | | | | | - Håkan Bladh
- AstraZeneca R&D Lund, Scheelevägen 1, SE-221 87 Lund, Sweden
| | - Stefan Bäckström
- Discovery Sciences, Innovative Medicines, AstraZeneca R&D, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Jan Dahmén
- AstraZeneca R&D Lund, Scheelevägen 1, SE-221 87 Lund, Sweden
| | | | - Per Hillertz
- Discovery Sciences, Innovative Medicines, AstraZeneca R&D, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | | | - Anders Jerre
- AstraZeneca R&D Lund, Scheelevägen 1, SE-221 87 Lund, Sweden
| | - Liz Kinchin
- AstraZeneca R&D Lund, Scheelevägen 1, SE-221 87 Lund, Sweden
| | - Charlotte Kåse
- AstraZeneca R&D Lund, Scheelevägen 1, SE-221 87 Lund, Sweden
| | - Matti Lepistö
- Respiratory, Inflammation and Autoimmunity, Innovative Medicines, AstraZeneca R&D, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Irene Mile
- AstraZeneca R&D Lund, Scheelevägen 1, SE-221 87 Lund, Sweden
| | | | - Amir Smailagic
- Respiratory, Inflammation and Autoimmunity, Innovative Medicines, AstraZeneca R&D, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - John Taylor
- Respiratory, Inflammation and Autoimmunity, Innovative Medicines, AstraZeneca R&D, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Ann Tjörnebo
- AstraZeneca R&D Lund, Scheelevägen 1, SE-221 87 Lund, Sweden
| | - Lisa Wissler
- Discovery Sciences, Innovative Medicines, AstraZeneca R&D, Pepparedsleden 1, SE-431 83 Mölndal, Sweden
| | - Thomas Hansson
- Respiratory, Inflammation and Autoimmunity, Innovative Medicines, AstraZeneca R&D, Pepparedsleden 1, SE-431 83 Mölndal, Sweden.
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Johansson P, Bernström J, Gorman T, Oster L, Bäckström S, Schweikart F, Xu B, Xue Y, Schiavone LH. FAM3B PANDER and FAM3C ILEI represent a distinct class of signaling molecules with a non-cytokine-like fold. Structure 2013; 21:306-13. [PMID: 23333428 DOI: 10.1016/j.str.2012.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 12/13/2012] [Accepted: 12/14/2012] [Indexed: 01/06/2023]
Abstract
The FAM3 superfamily is predicted to contain classical four-helix bundle cytokines, featuring a typical up-up-down-down fold. Two members of FAM3 have been extensively studied. FAM3B PANDER has been shown to regulate glucose homeostasis and β cell function, whereas the homologous FAM3C ILEI has been shown to be involved in epithelial-mesenchymal transition and cancer. Here, we present a three-dimensional structure of a FAM3 protein, murine PANDER. Contrary to previous suggestions, PANDER exhibits a globular β-β-α fold. The structure is composed of two antiparallel β sheets lined by three short helices packing to form a highly conserved water-filled cavity. The fold shares no relation to the predicted four-helix cytokines but is conserved throughout the FAM3 superfamily. The available biological data and the unexpected new fold indicate that FAM3 PANDER and ILEI could represent a new structural class of signaling molecules, with a different mode of action compared to the traditional four-helix bundle cytokines.
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Affiliation(s)
- Patrik Johansson
- Structure and Biophysics, Discovery Sciences, AstraZeneca, Mölndal 431-83, Sweden
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6
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Jemt E, Farge G, Bäckström S, Holmlund T, Gustafsson CM, Falkenberg M. The mitochondrial DNA helicase TWINKLE can assemble on a closed circular template and support initiation of DNA synthesis. Nucleic Acids Res 2011; 39:9238-49. [PMID: 21840902 PMCID: PMC3241658 DOI: 10.1093/nar/gkr653] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial DNA replication is performed by a simple machinery, containing the TWINKLE DNA helicase, a single-stranded DNA-binding protein, and the mitochondrial DNA polymerase γ. In addition, mitochondrial RNA polymerase is required for primer formation at the origins of DNA replication. TWINKLE adopts a hexameric ring-shaped structure that must load on the closed circular mtDNA genome. In other systems, a specialized helicase loader often facilitates helicase loading. We here demonstrate that TWINKLE can function without a specialized loader. We also show that the mitochondrial replication machinery can assemble on a closed circular DNA template and efficiently elongate a DNA primer in a manner that closely resembles initiation of mtDNA synthesis in vivo.
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Affiliation(s)
- Elisabeth Jemt
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
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Atanassova N, Fusté JM, Wanrooij S, Macao B, Goffart S, Bäckström S, Farge G, Khvorostov I, Larsson NG, Spelbrink JN, Falkenberg M. Sequence-specific stalling of DNA polymerase γ and the effects of mutations causing progressive ophthalmoplegia. Hum Mol Genet 2011; 20:1212-23. [PMID: 21228000 DOI: 10.1093/hmg/ddq565] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A large number of mutations in the gene encoding the catalytic subunit of mitochondrial DNA polymerase γ (POLγA) cause human disease. The Y955C mutation is common and leads to a dominant disease with progressive external ophthalmoplegia and other symptoms. The biochemical effect of the Y955C mutation has been extensively studied and it has been reported to lower enzyme processivity due to decreased capacity to utilize dNTPs. However, it is unclear why this biochemical defect leads to a dominant disease. Consistent with previous reports, we show here that the POLγA:Y955C enzyme only synthesizes short DNA products at dNTP concentrations that are sufficient for proper function of wild-type POLγA. In addition, we find that this phenotype is overcome by increasing the dNTP concentration, e.g. dATP. At low dATP concentrations, the POLγA:Y955C enzyme stalls at dATP insertion sites and instead enters a polymerase/exonuclease idling mode. The POLγA:Y955C enzyme will compete with wild-type POLγA for primer utilization, and this will result in a heterogeneous population of short and long DNA replication products. In addition, there is a possibility that POLγA:Y955C is recruited to nicks of mtDNA and there enters an idling mode preventing ligation. Our results provide a novel explanation for the dominant mtDNA replication phenotypes seen in patients harboring the Y955C mutation, including the existence of site-specific stalling. Our data may also explain why mutations that disturb dATP pools can be especially deleterious for mtDNA synthesis.
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Affiliation(s)
- Neli Atanassova
- Division of Metabolic Diseases, Karolinska Institutet, Solna, SE-17177 Stockholm, Sweden
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8
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Zhang P, Too PHM, Samuelson JC, Chan SH, Vincze T, Doucette S, Bäckström S, Potamousis KD, Schramm TM, Forrest D, Schwartz DC, Xu SY. Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA. Protein Expr Purif 2009; 69:226-34. [PMID: 19747545 DOI: 10.1016/j.pep.2009.09.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 08/26/2009] [Accepted: 09/04/2009] [Indexed: 11/30/2022]
Abstract
BspQI is a thermostable Type IIS restriction endonuclease (REase) with the recognition sequence 5'GCTCTTC N1/N4 3'. Here we report the cloning and expression of the bspQIR gene for the BspQI restriction enzyme in Escherichia coli. Alanine scanning of the BspQI charged residues identified a number of DNA nicking variants. After sampling combinations of different amino acid substitutions, an Nt.BspQI triple mutant (E172A/E248A/E255K) was constructed with predominantly top-strand DNA nicking activity. Furthermore, a triple mutant of BspQI (Nb.BspQI, N235A/K331A/R428A) was engineered to create a bottom-strand nicking enzyme. In addition, we demonstrated the application of Nt.BspQI in optical mapping of single DNA molecules. Nt or Nb.BspQI-nicked dsDNA can be further digested by E. coli exonuclease III to create ssDNA for downstream applications. BspQI contains two potential catalytic sites: a top-strand catalytic site (Ct) with a D-H-N-K motif found in the HNH endonuclease family and a bottom-strand catalytic site (Cb) with three scattered Glu residues. BlastP analysis of proteins in GenBank indicated a putative restriction enzyme with significant amino acid sequence identity to BspQI from the sequenced bacterial genome Croceibacter atlanticus HTCC2559. This restriction gene was amplified by PCR and cloned into a T7 expression vector. Restriction mapping and run-off DNA sequencing of digested products from the partially purified enzyme indicated that it is an EarI isoschizomer with 6-bp recognition, which we named CatHI (CTCTTC N1/N4).
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Affiliation(s)
- Penghua Zhang
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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9
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Bäckström S, Elfving N, Nilsson R, Wingsle G, Björklund S. Purification of a plant mediator from Arabidopsis thaliana identifies PFT1 as the Med25 subunit. Mol Cell 2007; 26:717-29. [PMID: 17560376 DOI: 10.1016/j.molcel.2007.05.007] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 04/04/2007] [Accepted: 05/07/2007] [Indexed: 11/26/2022]
Abstract
Mediator, a central coregulator of transcription, has been identified as a large protein complex in eukaryotes ranging from yeast to man. It is therefore remarkable that Mediator has not yet been identified within the plant kingdom. Here we identify Mediator in a plant, Arabidopsis thaliana. The plant Mediator subunits typically show very low homology to other species, but our biochemical purification identifies 21 conserved and six A. thaliana-specific Mediator subunits. Most notably, we identify the A. thaliana proteins STRUWWELPETER (SWP) and PHYTOCHROME AND FLOWERING TIME 1 (PFT1) as the Med14 and Med25 subunits, respectively. These findings show that specific plant Mediator subunits are linked to the regulation of specialized processes such as the control of cell proliferation and the regulation of flowering time in response to light quality. The identification of the plant Mediator will provide new tools and insights into the regulation of transcription in plants.
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Affiliation(s)
- Stefan Bäckström
- Department of Medical Biochemistry and Biophysics, KBC, Umeå University, SE-901 87 Umeå, Sweden.
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10
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Lundberg E, Bäckström S, Sauer UH, Sauer-Eriksson AE. The transthyretin-related protein: structural investigation of a novel protein family. J Struct Biol 2006; 155:445-57. [PMID: 16723258 DOI: 10.1016/j.jsb.2006.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 04/03/2006] [Accepted: 04/04/2006] [Indexed: 11/30/2022]
Abstract
The transthyretin-related protein (TRP) family comprises proteins predicted to be structurally related to the homotetrameric transport protein transthyretin (TTR). The function of TRPs is not yet fully established, but recent data suggest that they are involved in purine catabolism. We have determined the three-dimensional structure of the Escherichia coli TRP in two crystal forms; one at 1.65 A resolution in the presence of zinc, and the other at 2.1 A resolution in the presence of zinc and bromide. The structures revealed five zinc-ion-binding sites per monomer. Of these, the zinc ions bound at sites I and II are coordinated in tetrahedral geometries to the side chains of residues His9, His96, His98, Ser114, and three water molecules at the putative ligand-binding site. Of these four residues, His9, His98, and Ser114 are conserved. His9 and His98 bind the central zinc (site I) together with two water molecules. The side chain of His98 also binds to the zinc ion at site II. Bromide ions bind at site I only, replacing one of the water molecules coordinated to the zinc ion. The C-terminal four amino acid sequence motif Y-[RK]-G-[ST] constitutes the signature sequence of the TRP family. Two Tyr111 residues form direct hydrogen bonds to each other over the tetramer interface at the area, which in TTR constitutes the rear part of its thyroxine-binding channel. The putative substrate/ligand-binding channel of TRP is consequently shallower and broader than its counterpart in TTR.
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Affiliation(s)
- Erik Lundberg
- Umeå Centre for Molecular Pathogenesis, Umeå University, SE-90187 Umeå, Sweden
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11
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Hallgren J, Bäckström S, Estrada S, Thuveson M, Pejler G. Histidines are critical for heparin-dependent activation of mast cell tryptase. J Immunol 2004; 173:1868-75. [PMID: 15265919 DOI: 10.4049/jimmunol.173.3.1868] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mast cell tryptase is a tetrameric serine protease that is stored in complex with negatively charged heparin proteoglycans in the secretory granule. Tryptase has potent proinflammatory properties and has been implicated in diverse pathological conditions such as asthma and fibrosis. Previous studies have shown that tryptase binds tightly to heparin, and that heparin is required in the assembly of the tryptase tetramer as well as for stabilization of the active tetramer. Because the interaction of tryptase with heparin is optimal at acidic pH, we investigated in this study whether His residues are of importance for the heparin binding, tetramerization, and activation of the tryptase mouse mast cell protease 6. Molecular modeling of mouse mast cell protease 6 identified four His residues, H35, H106, H108, and H238, that are conserved among pH-dependent tryptases and are exposed on the molecular surface, and these four His residues were mutated to Ala. In addition, combinations of different mutations were prepared. Generally, the single His-Ala mutations did not cause any major defects in heparin binding, activation, or tetramerization, although some effect of the H106A mutation was observed. However, when several mutations were combined, large defects in all of these parameters were observed. Of the mutants, the triple mutant H106A/H108A/H238A was the most affected with an almost complete inability to bind to heparin and to form active tryptase tetramers. Taken together, this study shows that surface-exposed histidines mediate the interaction of mast cell tryptase with heparin and are of critical importance in the formation of active tryptase tetramers.
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Affiliation(s)
- Jenny Hallgren
- Department of Molecular Biosciences, The Biomedical Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
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12
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Bäckström S, Wolf-Watz M, Grundström C, Härd T, Grundström T, Sauer UH. The RUNX1 Runt domain at 1.25A resolution: a structural switch and specifically bound chloride ions modulate DNA binding. J Mol Biol 2002; 322:259-72. [PMID: 12217689 DOI: 10.1016/s0022-2836(02)00702-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The evolutionarily conserved Runt homology domain is characteristic of the RUNX family of heterodimeric eukaryotic transcription factors, including RUNX1, RUNX2 and RUNX3. The genes for RUNX1, also termed acute myeloid leukemia protein 1, AML1, and its dimerization partner core-binding factor beta, CBFbeta, are essential for hematopoietic development and are together the most common targets for gene rearrangements in acute human leukemias. Here, we describe the crystal structure of the uncomplexed RUNX1 Runt domain at 1.25A resolution and compare its conformation to previously published structures in complex with DNA, CBFbeta or both. We find that complex formation induces significant structural rearrangements in this immunoglobulin (Ig)-like DNA-binding domain. Most pronounced is the movement of loop L11, which changes from a closed conformation in the free Runt structure to an open conformation in the CBFbeta-bound and DNA-bound forms. This transition, which we refer to as the S-switch, and accompanying structural movements that affect other parts of the Runt domain are crucial for sustained DNA binding. The closed to open transition can be induced by CBFbeta alone; suggesting that one role of CBFbeta is to trigger the S-switch and to stabilize the Runt domain in a conformation enhanced for DNA binding.A feature of the Runt domain hitherto unobserved in any Ig-like DNA-binding domain is the presence of two specifically bound chloride ions. One chloride ion is coordinated by amino acid residues that make direct DNA contact. In a series of electrophoretic mobility-shift analyses, we demonstrate a chloride ion concentration-dependent stimulation of the DNA-binding activity of Runt in the physiological range. A comparable DNA-binding stimulation was observed for negatively charged amino acid residues. This suggests a regulatory mechanism of RUNX proteins through acidic amino acid residues provided by activation domains during cooperative interaction with other transcription factors.
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Affiliation(s)
- Stefan Bäckström
- Biocrystallography Group, Umeå Centre for Molecular Pathogenesis (UCMP), Umeå University, SE-901 87 Umeå, Sweden
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13
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Bäckström S, Huang SH, Wolf-Watz M, Xie XQ, Härd T, Grundström T, Sauer UH. Crystallization and preliminary studies of the DNA-binding runt domain of AML1. Acta Crystallogr D Biol Crystallogr 2001; 57:269-71. [PMID: 11173476 DOI: 10.1107/s0907444900015791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2000] [Accepted: 10/31/2000] [Indexed: 11/10/2022]
Abstract
The acute myeloid leukaemia 1 (AML1) protein belongs to the Runx family of transcription factors and is crucial for haematopoietic development. The genes encoding Runx1 and its associated factor CBF beta are the most frequent targets for chromosomal rearrangements in acute human leukaemias. In addition, point mutations of Runx1 in acute leukaemias and in the familial platelet disorder FPD/AML cluster within the evolutionary conserved runt domain that binds both DNA and CBF beta. Here, the crystallization of the Runx1 runt domain is reported. Crystals belong to space groups C2 and R32 and diffract to 1.7 and 2.0 A resolution, respectively.
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Affiliation(s)
- S Bäckström
- Umeå Center for Molecular Pathogenesis, UCMP, Umeå University, SE-901 87, Umeå, Sweden
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Abstract
It is known that the DNA binding Runt domain of the AML1/Runx1 transcription factor coordinates Cl(-) ions. In this paper we have determined Cl(-) binding affinities of AML1 by (35)Cl nuclear magnetic resonance (NMR) linewidth analysis. The Runt domain binds Cl(-) with a dissociation constant (K(d,Cl)) of 34 mM. If CBFbeta is added to form a 1:1 complex, the K(d,Cl) value increases to 56 mM. Homology modeling suggests that a high occupancy Cl(-) binding site overlaps with the DNA binding surface. NMR data show that DNA displaces this Cl(-) ion. Possible biological roles of Cl(-) binding are discussed based on these findings.
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Affiliation(s)
- M Wolf-Watz
- Department of Biotechnology, Royal Institute of Technology, Center for Structural Biochemistry, Novum, Huddinge, Sweden
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Hamnér S, Olsson PA, Bäckström S, Lindholm D. 205 upregulation of nedl after ngf withdrawal from pc12 cells. Int J Dev Neurosci 1996. [DOI: 10.1016/0736-5748(96)80394-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Wikner C, Meshalkina L, Nilsson U, Bäckström S, Lindqvist Y, Schneider G. His103 in yeast transketolase is required for substrate recognition and catalysis. Eur J Biochem 1995; 233:750-5. [PMID: 8521838 DOI: 10.1111/j.1432-1033.1995.750_3.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Crystallographic studies of thiamin-diphosphate-dependent transketolase from Saccharomyces cerevisiae suggested the invariant active-site residue H103 as a possible enzymic group binding the C1 hydroxyl group of the donor substrate and stabilizing the reaction intermediate. To test this hypothesis, H103 was replaced by alanine, asparagine and phenylalanine using site-directed mutagenesis. The crystallographic analysis of the mutant transketolases verified that no structural changes occurred as a consequence of the side-chain replacements. The residual catalytic activities of the mutant enzymes were 4.3% for the H103A, 2.4% for the H103N and 0.1% for the H103F mutant transketolase. Further kinetic analysis of the H103A and H103N mutant enzymes showed that the Km values for the coenzyme were increased by about eightfold. The Km values for the acceptor substrate ribose 5-phosphate were similar to the Km value for wild-type transketolase. However, the Km value for the donor substrate, xylulose 5-phosphate is increased more than tenfold in these two mutants. Circular dichroism spectra of the mutant enzymes also indicated a weaker binding of the donor substrate and/or a less stable reaction intermediate. These observations provide further evidence in support of the proposed role for this invariant residue in recognition of the donor substrate by forming a hydrogen bond between the side chain of H103 and the C1 hydroxyl group of the sugar phosphate. The significant decrease in catalytic activity suggests that this residue also facilitates catalysis, possibly by maintaining the optimal orientation of the donor substrate and reaction intermediates.
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Affiliation(s)
- C Wikner
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Center, Uppsala, Sweden
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Bäckström S. [Passage of radioactive substances between a labelled graft and its unmarked host. Autoradiographic study of sea urchin embryo submitted to transplantation]. C R Acad Hebd Seances Acad Sci D 1969; 269:1684-5. [PMID: 4982841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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18
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Bäckström S. Basic proteins in parthenogenetically activated sea urchin eggs. Acta Embryol Morphol Exp 1966; 9:83-86. [PMID: 6013511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Bäckström S. A complex between basic proteins and acid polysaccharides in sea urchin oocytes and eggs. Acta Embryol Morphol Exp 1966; 9:37-43. [PMID: 6013505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Bäckström S. Basic proteins during sea urchin ovogenesis. (Psammechinus miliaris). Acta Embryol Morphol Exp 1965; 8:178-82. [PMID: 5898956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Bäckström S. Basic proteins in the sea urchin embryo (Paracentrotus lividus). Acta Embryol Morphol Exp 1965; 8:20-31. [PMID: 5898825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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