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  • Protein Binding  (278)
  • *Federal Government  (222)
  • Nature Publishing Group (NPG)  (500)
  • 2010-2014  (500)
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  • 1
    Publication Date: 2010-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feng, Jian -- England -- Nature. 2010 Sep 16;467(7313):271. doi: 10.1038/467271a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20844517" target="_blank"〉PubMed〈/a〉
    Keywords: Embryo Research/economics/ethics/*legislation & jurisprudence ; *Embryonic Stem Cells ; *Federal Government ; Financing, Government/*legislation & jurisprudence ; Humans ; *Religion and Science ; Research Support as Topic/*legislation & jurisprudence ; United States ; Zygote/cytology
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  • 2
    Publication Date: 2010-11-26
    Description: In physiological settings, nucleic-acid translocases must act on substrates occupied by other proteins, and an increasingly appreciated role of translocases is to catalyse protein displacement from RNA and DNA. However, little is known regarding the inevitable collisions that must occur, and the fate of protein obstacles and the mechanisms by which they are evicted from DNA remain unexplored. Here we sought to establish the mechanistic basis for protein displacement from DNA using RecBCD as a model system. Using nanofabricated curtains of DNA and multicolour single-molecule microscopy, we visualized collisions between a model translocase and different DNA-bound proteins in real time. We show that the DNA translocase RecBCD can disrupt core RNA polymerase, holoenzymes, stalled elongation complexes and transcribing RNA polymerases in either head-to-head or head-to-tail orientations, as well as EcoRI(E111Q), lac repressor and even nucleosomes. RecBCD did not pause during collisions and often pushed proteins thousands of base pairs before evicting them from DNA. We conclude that RecBCD overwhelms obstacles through direct transduction of chemomechanical force with no need for specific protein-protein interactions, and that proteins can be removed from DNA through active disruption mechanisms that act on a transition state intermediate as they are pushed from one nonspecific site to the next.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230117/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230117/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Finkelstein, Ilya J -- Visnapuu, Mari-Liis -- Greene, Eric C -- F32GM80864/GM/NIGMS NIH HHS/ -- GM074739/GM/NIGMS NIH HHS/ -- GM082848/GM/NIGMS NIH HHS/ -- R01 CA146940/CA/NCI NIH HHS/ -- R01 GM074739/GM/NIGMS NIH HHS/ -- R01 GM074739-01A1/GM/NIGMS NIH HHS/ -- R01 GM074739-05/GM/NIGMS NIH HHS/ -- R01 GM082848/GM/NIGMS NIH HHS/ -- R01 GM082848-01A1/GM/NIGMS NIH HHS/ -- R01 GM082848-04/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Dec 16;468(7326):983-7. doi: 10.1038/nature09561. Epub 2010 Nov 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21107319" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/genetics ; Biocatalysis ; DNA/genetics/*metabolism ; DNA, Viral/genetics/metabolism ; DNA-Binding Proteins/*metabolism ; DNA-Directed RNA Polymerases/chemistry/metabolism ; Deoxyribonuclease EcoRI/metabolism ; Escherichia coli/enzymology ; Exodeoxyribonuclease V/*metabolism ; Holoenzymes/chemistry/metabolism ; Lac Repressors/metabolism ; Microscopy, Fluorescence ; *Movement ; Nucleosomes/metabolism ; Promoter Regions, Genetic/genetics ; Protein Binding ; Quantum Dots ; Time Factors
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  • 3
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    Nature Publishing Group (NPG)
    Publication Date: 2010-09-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Sep 23;467(7314):368. doi: 10.1038/467368a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20864950" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*methods ; Animals ; Cattle ; Disease Reservoirs/microbiology/*statistics & numerical data/*veterinary ; *Federal Government ; Great Britain/epidemiology ; *Mustelidae/microbiology ; Reproducibility of Results ; Tuberculosis Vaccines ; Tuberculosis, Bovine/epidemiology/*prevention & control/transmission ; Vaccination/veterinary
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  • 4
    Publication Date: 2010-01-16
    Description: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX(2). RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX(2). As revealed by the structure of a RbcL(8)-(RbcX(2))(8) assembly intermediate, RbcX(2) acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL(8) core assembly. Finally, addition of RbcS results in RbcX(2) release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Cuimin -- Young, Anna L -- Starling-Windhof, Amanda -- Bracher, Andreas -- Saschenbrecker, Sandra -- Rao, Bharathi Vasudeva -- Rao, Karnam Vasudeva -- Berninghausen, Otto -- Mielke, Thorsten -- Hartl, F Ulrich -- Beckmann, Roland -- Hayer-Hartl, Manajit -- England -- Nature. 2010 Jan 14;463(7278):197-202. doi: 10.1038/nature08651.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075914" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Chaperonin 10/metabolism ; Chaperonin 60/metabolism ; Cryoelectron Microscopy ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Molecular Chaperones/chemistry/*metabolism ; Protein Binding ; *Protein Folding ; *Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Ribulose-Bisphosphate Carboxylase/*chemistry/*metabolism/ultrastructure ; Synechococcus/*chemistry/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2010-04-03
    Description: Jasmonoyl-isoleucine (JA-Ile) is a plant hormone that regulates a broad array of plant defence and developmental processes. JA-Ile-responsive gene expression is regulated by the transcriptional activator MYC2 that interacts physically with the jasmonate ZIM-domain (JAZ) repressor proteins. On perception of JA-Ile, JAZ proteins are degraded and JA-Ile-dependent gene expression is activated. The molecular mechanisms by which JAZ proteins repress gene expression remain unknown. Here we show that the Arabidopsis JAZ proteins recruit the Groucho/Tup1-type co-repressor TOPLESS (TPL) and TPL-related proteins (TPRs) through a previously uncharacterized adaptor protein, designated Novel Interactor of JAZ (NINJA). NINJA acts as a transcriptional repressor whose activity is mediated by a functional TPL-binding EAR repression motif. Accordingly, both NINJA and TPL proteins function as negative regulators of jasmonate responses. Our results point to TPL proteins as general co-repressors that affect multiple signalling pathways through the interaction with specific adaptor proteins. This new insight reveals how stress-related and growth-related signalling cascades use common molecular mechanisms to regulate gene expression in plants.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849182/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849182/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pauwels, Laurens -- Barbero, Gemma Fernandez -- Geerinck, Jan -- Tilleman, Sofie -- Grunewald, Wim -- Perez, Amparo Cuellar -- Chico, Jose Manuel -- Bossche, Robin Vanden -- Sewell, Jared -- Gil, Eduardo -- Garcia-Casado, Gloria -- Witters, Erwin -- Inze, Dirk -- Long, Jeff A -- De Jaeger, Geert -- Solano, Roberto -- Goossens, Alain -- R01 GM072764/GM/NIGMS NIH HHS/ -- R01 GM072764-06/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Apr 1;464(7289):788-91. doi: 10.1038/nature08854.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, B-9052 Gent, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360743" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/cytology/*drug effects/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Cyclopentanes/antagonists & inhibitors/*pharmacology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Models, Biological ; Oxylipins/antagonists & inhibitors/*pharmacology ; Plants, Genetically Modified ; Protein Binding ; Repressor Proteins/genetics/*metabolism ; Signal Transduction/*drug effects ; Two-Hybrid System Techniques
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  • 6
    Publication Date: 2010-10-12
    Description: Jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. The F-box protein CORONATINE INSENSITIVE 1 (COI1) mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor JAZ proteins. Despite its importance, the mechanism of jasmonate perception remains unclear. Here we present structural and pharmacological data to show that the true Arabidopsis jasmonate receptor is a complex of both COI1 and JAZ. COI1 contains an open pocket that recognizes the bioactive hormone (3R,7S)-jasmonoyl-l-isoleucine (JA-Ile) with high specificity. High-affinity hormone binding requires a bipartite JAZ degron sequence consisting of a conserved alpha-helix for COI1 docking and a loop region to trap the hormone in its binding pocket. In addition, we identify a third critical component of the jasmonate co-receptor complex, inositol pentakisphosphate, which interacts with both COI1 and JAZ adjacent to the ligand. Our results unravel the mechanism of jasmonate perception and highlight the ability of F-box proteins to evolve as multi-component signalling hubs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988090/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988090/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sheard, Laura B -- Tan, Xu -- Mao, Haibin -- Withers, John -- Ben-Nissan, Gili -- Hinds, Thomas R -- Kobayashi, Yuichi -- Hsu, Fong-Fu -- Sharon, Michal -- Browse, John -- He, Sheng Yang -- Rizo, Josep -- Howe, Gregg A -- Zheng, Ning -- P30 DK056341/DK/NIDDK NIH HHS/ -- P30 DK056341-10/DK/NIDDK NIH HHS/ -- R01 AI068718/AI/NIAID NIH HHS/ -- R01 AI068718-04/AI/NIAID NIH HHS/ -- R01 CA107134/CA/NCI NIH HHS/ -- R01 CA107134-07/CA/NCI NIH HHS/ -- R01 GM057795/GM/NIGMS NIH HHS/ -- R01 GM057795-12/GM/NIGMS NIH HHS/ -- R01AI068718/AI/NIAID NIH HHS/ -- R01GM57795/GM/NIGMS NIH HHS/ -- T32 GM07270/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Nov 18;468(7322):400-5. doi: 10.1038/nature09430. Epub 2010 Oct 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Box 357280, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20927106" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/chemistry/metabolism ; Arabidopsis/chemistry/metabolism ; Arabidopsis Proteins/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Cyclopentanes/chemistry/*metabolism ; F-Box Proteins/chemistry/metabolism ; Indenes/chemistry/metabolism ; Inositol Phosphates/*metabolism ; Isoleucine/analogs & derivatives/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxylipins/chemistry/*metabolism ; Peptide Fragments/chemistry/metabolism ; Plant Growth Regulators/chemistry/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/*metabolism ; Signal Transduction
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  • 7
    Publication Date: 2010-02-25
    Description: Tumours with mutant BRAF are dependent on the RAF-MEK-ERK signalling pathway for their growth. We found that ATP-competitive RAF inhibitors inhibit ERK signalling in cells with mutant BRAF, but unexpectedly enhance signalling in cells with wild-type BRAF. Here we demonstrate the mechanistic basis for these findings. We used chemical genetic methods to show that drug-mediated transactivation of RAF dimers is responsible for paradoxical activation of the enzyme by inhibitors. Induction of ERK signalling requires direct binding of the drug to the ATP-binding site of one kinase of the dimer and is dependent on RAS activity. Drug binding to one member of RAF homodimers (CRAF-CRAF) or heterodimers (CRAF-BRAF) inhibits one protomer, but results in transactivation of the drug-free protomer. In BRAF(V600E) tumours, RAS is not activated, thus transactivation is minimal and ERK signalling is inhibited in cells exposed to RAF inhibitors. These results indicate that RAF inhibitors will be effective in tumours in which BRAF is mutated. Furthermore, because RAF inhibitors do not inhibit ERK signalling in other cells, the model predicts that they would have a higher therapeutic index and greater antitumour activity than mitogen-activated protein kinase (MEK) inhibitors, but could also cause toxicity due to MEK/ERK activation. These predictions have been borne out in a recent clinical trial of the RAF inhibitor PLX4032 (refs 4, 5). The model indicates that promotion of RAF dimerization by elevation of wild-type RAF expression or RAS activity could lead to drug resistance in mutant BRAF tumours. In agreement with this prediction, RAF inhibitors do not inhibit ERK signalling in cells that coexpress BRAF(V600E) and mutant RAS.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178447/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178447/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poulikakos, Poulikos I -- Zhang, Chao -- Bollag, Gideon -- Shokat, Kevan M -- Rosen, Neal -- 1P01CA129243-02/CA/NCI NIH HHS/ -- 2R01EB001987/EB/NIBIB NIH HHS/ -- P01 CA129243-010002/CA/NCI NIH HHS/ -- R01 EB001987/EB/NIBIB NIH HHS/ -- U01 CA091178/CA/NCI NIH HHS/ -- U01 CA091178-01/CA/NCI NIH HHS/ -- England -- Nature. 2010 Mar 18;464(7287):427-30. doi: 10.1038/nature08902.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Molecular Pharmacology and Chemistry and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20179705" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Catalytic Domain ; Cell Line ; Cell Line, Tumor ; Enzyme Activation/drug effects ; Extracellular Signal-Regulated MAP Kinases/*metabolism ; Humans ; Indoles/pharmacology ; MAP Kinase Signaling System/*drug effects ; Mice ; Mitogen-Activated Protein Kinase Kinases/metabolism ; Models, Biological ; Neoplasms/drug therapy/enzymology/genetics/metabolism ; Phosphorylation ; Protein Binding ; Protein Kinase Inhibitors/metabolism/*pharmacology/therapeutic use ; Protein Multimerization ; Proto-Oncogene Proteins B-raf/antagonists & ; inhibitors/chemistry/genetics/*metabolism ; Sulfonamides/pharmacology ; Transcriptional Activation/*drug effects ; raf Kinases/*antagonists & inhibitors/chemistry/genetics/*metabolism ; ras Proteins/genetics/metabolism
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  • 8
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    Nature Publishing Group (NPG)
    Publication Date: 2010-02-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Qiu, Jane -- England -- Nature. 2010 Feb 25;463(7284):1012-3. doi: 10.1038/4631012a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20182485" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Data Collection ; *Federal Government ; Internet/legislation & jurisprudence/utilization ; *Research Personnel ; Search Engine/*legislation & jurisprudence/*utilization
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  • 9
    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tollefson, Jeff -- England -- Nature. 2010 Oct 14;467(7317):762. doi: 10.1038/467762a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944703" target="_blank"〉PubMed〈/a〉
    Keywords: Conservation of Energy Resources/legislation & jurisprudence ; Environmental Policy/*legislation & jurisprudence ; *Federal Government ; Global Warming/*legislation & jurisprudence/prevention & control ; *Politics ; United States
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  • 10
    Publication Date: 2010-10-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Hara, Kathryn -- England -- Nature. 2010 Sep 30;467(7315):501. doi: 10.1038/467501a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Carleton University. kathryn_ohara@carleton.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20881970" target="_blank"〉PubMed〈/a〉
    Keywords: *Access to Information ; Animals ; Canada ; *Communication ; *Federal Government ; *Freedom ; Global Warming ; Humans ; *Journalism ; Mass Media ; Policy Making ; Politics ; Public Sector ; *Research Personnel
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  • 11
    Publication Date: 2010-05-14
    Description: Copper is an essential trace element for eukaryotes and most prokaryotes. However, intracellular free copper must be strictly limited because of its toxic side effects. Complex systems for copper trafficking evolved to satisfy cellular requirements while minimizing toxicity. The factors driving the copper transfer between protein partners along cellular copper routes are, however, not fully rationalized. Until now, inconsistent, scattered and incomparable data on the copper-binding affinities of copper proteins have been reported. Here we determine, through a unified electrospray ionization mass spectrometry (ESI-MS)-based strategy, in an environment that mimics the cellular redox milieu, the apparent Cu(I)-binding affinities for a representative set of intracellular copper proteins involved in enzymatic redox catalysis, in copper trafficking to and within various cellular compartments, and in copper storage. The resulting thermodynamic data show that copper is drawn to the enzymes that require it by passing from one copper protein site to another, exploiting gradients of increasing copper-binding affinity. This result complements the finding that fast copper-transfer pathways require metal-mediated protein-protein interactions and therefore protein-protein specific recognition. Together with Cu,Zn-SOD1, metallothioneins have the highest affinity for copper(I), and may play special roles in the regulation of cellular copper distribution; however, for kinetic reasons they cannot demetallate copper enzymes. Our study provides the thermodynamic basis for the kinetic processes that lead to the distribution of cellular copper.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Banci, Lucia -- Bertini, Ivano -- Ciofi-Baffoni, Simone -- Kozyreva, Tatiana -- Zovo, Kairit -- Palumaa, Peep -- England -- Nature. 2010 Jun 3;465(7298):645-8. doi: 10.1038/nature09018. Epub 2010 May 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463663" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biocatalysis ; Carrier Proteins/*metabolism ; Cations, Monovalent/metabolism ; Copper/isolation & purification/*metabolism ; Cyclooxygenase 2/chemistry/metabolism ; Dithiothreitol/metabolism ; Glutathione/metabolism ; Humans ; Intracellular Space/*metabolism ; Ion Transport ; Kinetics ; Ligands ; Metallothionein/metabolism ; Mitochondria, Liver ; Oxidation-Reduction ; Protein Binding ; Rats ; Spectrometry, Mass, Electrospray Ionization ; Thermodynamics
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  • 12
    Publication Date: 2010-09-30
    Description: Cell-cell signalling of semaphorin ligands through interaction with plexin receptors is important for the homeostasis and morphogenesis of many tissues and is widely studied for its role in neural connectivity, cancer, cell migration and immune responses. SEMA4D and Sema6A exemplify two diverse vertebrate, membrane-spanning semaphorin classes (4 and 6) that are capable of direct signalling through members of the two largest plexin classes, B and A, respectively. In the absence of any structural information on the plexin ectodomain or its interaction with semaphorins the extracellular specificity and mechanism controlling plexin signalling has remained unresolved. Here we present crystal structures of cognate complexes of the semaphorin-binding regions of plexins B1 and A2 with semaphorin ectodomains (human PLXNB1(1-2)-SEMA4D(ecto) and murine PlxnA2(1-4)-Sema6A(ecto)), plus unliganded structures of PlxnA2(1-4) and Sema6A(ecto). These structures, together with biophysical and cellular assays of wild-type and mutant proteins, reveal that semaphorin dimers independently bind two plexin molecules and that signalling is critically dependent on the avidity of the resulting bivalent 2:2 complex (monomeric semaphorin binds plexin but fails to trigger signalling). In combination, our data favour a cell-cell signalling mechanism involving semaphorin-stabilized plexin dimerization, possibly followed by clustering, which is consistent with previous functional data. Furthermore, the shared generic architecture of the complexes, formed through conserved contacts of the amino-terminal seven-bladed beta-propeller (sema) domains of both semaphorin and plexin, suggests that a common mode of interaction triggers all semaphorin-plexin based signalling, while distinct insertions within or between blades of the sema domains determine binding specificity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587840/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587840/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janssen, Bert J C -- Robinson, Ross A -- Perez-Branguli, Francesc -- Bell, Christian H -- Mitchell, Kevin J -- Siebold, Christian -- Jones, E Yvonne -- 082301/Wellcome Trust/United Kingdom -- 083111/Wellcome Trust/United Kingdom -- 10976/Cancer Research UK/United Kingdom -- A10976/Cancer Research UK/United Kingdom -- A3964/Cancer Research UK/United Kingdom -- A5261/Cancer Research UK/United Kingdom -- G0700232/Medical Research Council/United Kingdom -- G0700232(82098)/Medical Research Council/United Kingdom -- G0900084/Medical Research Council/United Kingdom -- G9900061/Medical Research Council/United Kingdom -- G9900061(69203)/Medical Research Council/United Kingdom -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Oct 28;467(7319):1118-22. doi: 10.1038/nature09468. Epub 2010 Sep 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20877282" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD/chemistry/genetics/metabolism ; Binding Sites ; Cell Adhesion Molecules/*chemistry/genetics/*metabolism ; Cell Communication ; Crystallography, X-Ray ; Humans ; Ligands ; Mice ; Mice, Inbred C57BL ; Models, Molecular ; NIH 3T3 Cells ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Cell Surface/chemistry/genetics/metabolism ; Semaphorins/*chemistry/genetics/*metabolism ; *Signal Transduction ; Structure-Activity Relationship
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  • 13
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    Nature Publishing Group (NPG)
    Publication Date: 2010-09-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Inouye, David W -- England -- Nature. 2010 Sep 23;467(7314):400. doi: 10.1038/467400c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20864979" target="_blank"〉PubMed〈/a〉
    Keywords: American Recovery and Reinvestment Act/*economics ; *Federal Government ; Flowers/classification/physiology ; Peer Review, Research/*standards ; United States
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  • 14
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    Nature Publishing Group (NPG)
    Publication Date: 2010-06-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tollefson, Jeff -- England -- Nature. 2010 Jun 3;465(7298):535. doi: 10.1038/465535a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20520681" target="_blank"〉PubMed〈/a〉
    Keywords: Advisory Committees ; Disaster Planning/*organization & administration ; Ecosystem ; *Federal Government ; Fires ; Global Warming/*statistics & numerical data ; Public Policy/*legislation & jurisprudence ; *Social Planning ; United States ; Water Supply
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  • 15
    Publication Date: 2010-09-14
    Description: Messenger RNA lacking stop codons ('non-stop mRNA') can arise from errors in gene expression, and encode aberrant proteins whose accumulation could be deleterious to cellular function. In bacteria, these 'non-stop proteins' become co-translationally tagged with a peptide encoded by ssrA/tmRNA (transfer-messenger RNA), which signals their degradation by energy-dependent proteases. How eukaryotic cells eliminate non-stop proteins has remained unknown. Here we show that the Saccharomyces cerevisiae Ltn1 RING-domain-type E3 ubiquitin ligase acts in the quality control of non-stop proteins, in a process that is mechanistically distinct but conceptually analogous to that performed by ssrA: Ltn1 is predominantly associated with ribosomes, and it marks nascent non-stop proteins with ubiquitin to signal their proteasomal degradation. Ltn1-mediated ubiquitylation of non-stop proteins seems to be triggered by their stalling in ribosomes on translation through the poly(A) tail. The biological relevance of this process is underscored by the finding that loss of Ltn1 function confers sensitivity to stress caused by increased non-stop protein production. We speculate that defective protein quality control may underlie the neurodegenerative phenotype that results from mutation of the mouse Ltn1 homologue Listerin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988496/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988496/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bengtson, Mario H -- Joazeiro, Claudio A P -- R01 GM083060/GM/NIGMS NIH HHS/ -- R01 GM083060-03/GM/NIGMS NIH HHS/ -- R01GM083060/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Sep 23;467(7314):470-3. doi: 10.1038/nature09371. Epub 2010 Sep 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, The Scripps Research Institute, CB168, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20835226" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Codon, Terminator/genetics ; Mice ; Models, Biological ; Peptide Chain Termination, Translational ; Polylysine/biosynthesis/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Protein Binding ; Protein Biosynthesis/*physiology ; Ribosomes/*enzymology/*metabolism ; Saccharomyces cerevisiae/cytology/enzymology/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Stress, Physiological ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/deficiency/genetics/*metabolism ; *Ubiquitination
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  • 16
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    Nature Publishing Group (NPG)
    Publication Date: 2010-10-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Sep 30;467(7315):500. doi: 10.1038/467500a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20881969" target="_blank"〉PubMed〈/a〉
    Keywords: Advisory Committees/*economics/*organization & administration ; *Federal Government ; Great Britain ; Lobbying ; Organizations/*economics/*organization & administration ; Public Sector
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  • 17
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    Nature Publishing Group (NPG)
    Publication Date: 2010-11-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Nov 11;468(7321):133-4. doi: 10.1038/468133b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21068782" target="_blank"〉PubMed〈/a〉
    Keywords: California ; Canada ; *Climate Change/economics ; Environmental Policy/economics/*legislation & jurisprudence ; *Federal Government ; Leadership ; *State Government ; United States
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  • 18
    Publication Date: 2010-10-01
    Description: In most bacteria and all archaea, glutamyl-tRNA synthetase (GluRS) glutamylates both tRNA(Glu) and tRNA(Gln), and then Glu-tRNA(Gln) is selectively converted to Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. The mechanisms by which the two enzymes recognize their substrate tRNA(s), and how they cooperate with each other in Gln-tRNA(Gln) synthesis, remain to be determined. Here we report the formation of the 'glutamine transamidosome' from the bacterium Thermotoga maritima, consisting of tRNA(Gln), GluRS and the heterotrimeric amidotransferase GatCAB, and its crystal structure at 3.35 A resolution. The anticodon-binding body of GluRS recognizes the common features of tRNA(Gln) and tRNA(Glu), whereas the tail body of GatCAB recognizes the outer corner of the L-shaped tRNA(Gln) in a tRNA(Gln)-specific manner. GluRS is in the productive form, as its catalytic body binds to the amino-acid-acceptor arm of tRNA(Gln). In contrast, GatCAB is in the non-productive form: the catalytic body of GatCAB contacts that of GluRS and is located near the acceptor stem of tRNA(Gln), in an appropriate site to wait for the completion of Glu-tRNA(Gln) formation by GluRS. We identified the hinges between the catalytic and anticodon-binding bodies of GluRS and between the catalytic and tail bodies of GatCAB, which allow both GluRS and GatCAB to adopt the productive and non-productive forms. The catalytic bodies of the two enzymes compete for the acceptor arm of tRNA(Gln) and therefore cannot assume their productive forms simultaneously. The transition from the present glutamylation state, with the productive GluRS and the non-productive GatCAB, to the putative amidation state, with the non-productive GluRS and the productive GatCAB, requires an intermediate state with the two enzymes in their non-productive forms, for steric reasons. The proposed mechanism explains how the transamidosome efficiently performs the two consecutive steps of Gln-tRNA(Gln) formation, with a low risk of releasing the unstable intermediate Glu-tRNA(Gln).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ito, Takuhiro -- Yokoyama, Shigeyuki -- England -- Nature. 2010 Sep 30;467(7315):612-6. doi: 10.1038/nature09411.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20882017" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon/genetics ; Biocatalysis ; Crystallography, X-Ray ; Electrophoretic Mobility Shift Assay ; Glutamate-tRNA Ligase/*chemistry/*metabolism ; Models, Molecular ; Molecular Conformation ; Nitrogenous Group Transferases/*chemistry/*metabolism ; Protein Binding ; RNA, Transfer, Gln/biosynthesis/*chemistry/*metabolism ; RNA, Transfer, Glu/chemistry/metabolism ; Staphylococcus aureus/enzymology ; Substrate Specificity ; Thermotoga maritima/*enzymology
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  • 19
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    Nature Publishing Group (NPG)
    Publication Date: 2010-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiermeier, Quirin -- England -- Nature. 2010 Jun 24;465(7301):996. doi: 10.1038/465996a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20577180" target="_blank"〉PubMed〈/a〉
    Keywords: Budgets ; *Federal Government ; Financing, Government/*economics ; Germany ; Schools, Medical/economics ; Universities/*economics/organization & administration
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  • 20
    Publication Date: 2010-07-14
    Description: The NAD-dependent deacetylase Sir2 was initially identified as a mediator of replicative lifespan in budding yeast and was subsequently shown to modulate longevity in worms and flies. Its mammalian homologue, SIRT1, seems to have evolved complex systemic roles in cardiac function, DNA repair and genomic stability. Recent studies suggest a functional relevance of SIRT1 in normal brain physiology and neurological disorders. However, it is unknown if SIRT1 has a role in higher-order brain functions. We report that SIRT1 modulates synaptic plasticity and memory formation via a microRNA-mediated mechanism. Activation of SIRT1 enhances, whereas its loss-of-function impairs, synaptic plasticity. Surprisingly, these effects were mediated via post-transcriptional regulation of cAMP response binding protein (CREB) expression by a brain-specific microRNA, miR-134. SIRT1 normally functions to limit expression of miR-134 via a repressor complex containing the transcription factor YY1, and unchecked miR-134 expression following SIRT1 deficiency results in the downregulated expression of CREB and brain-derived neurotrophic factor (BDNF), thereby impairing synaptic plasticity. These findings demonstrate a new role for SIRT1 in cognition and a previously unknown microRNA-based mechanism by which SIRT1 regulates these processes. Furthermore, these results describe a separate branch of SIRT1 signalling, in which SIRT1 has a direct role in regulating normal brain function in a manner that is disparate from its cell survival functions, demonstrating its value as a potential therapeutic target for the treatment of central nervous system disorders.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928875/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928875/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gao, Jun -- Wang, Wen-Yuan -- Mao, Ying-Wei -- Graff, Johannes -- Guan, Ji-Song -- Pan, Ling -- Mak, Gloria -- Kim, Dohoon -- Su, Susan C -- Tsai, Li-Huei -- P01 AG027916/AG/NIA NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Aug 26;466(7310):1105-9. doi: 10.1038/nature09271. Epub 2010 Jul 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20622856" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain-Derived Neurotrophic Factor/metabolism ; CREB-Binding Protein/metabolism ; Electrical Synapses/genetics/pathology ; Gene Expression Regulation ; Gene Knockdown Techniques ; Long-Term Potentiation/genetics ; Male ; Memory/*physiology ; Memory Disorders/genetics/physiopathology ; Mice ; MicroRNAs/*genetics/*metabolism ; Neuronal Plasticity/*genetics ; Protein Binding ; Sequence Deletion ; Sirtuin 1/*genetics/*metabolism
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  • 21
    Publication Date: 2010-07-30
    Description: The post-translational methylation of alpha-amino groups was first discovered over 30 years ago on the bacterial ribosomal proteins L16 and L33 (refs 1, 2), but almost nothing is known about the function or enzymology of this modification. Several other bacterial and eukaryotic proteins have since been shown to be alpha-N-methylated. However, the Ran guanine nucleotide-exchange factor, RCC1, is the only protein for which any biological function of alpha-N-methylation has been identified. Methylation-defective mutants of RCC1 have reduced affinity for DNA and cause mitotic defects, but further characterization of this modification has been hindered by ignorance of the responsible methyltransferase. All fungal and animal N-terminally methylated proteins contain a unique N-terminal motif, Met-(Ala/Pro/Ser)-Pro-Lys, indicating that they may be targets of the same, unknown enzyme. The initiating Met is cleaved, and the exposed alpha-amino group is mono-, di- or trimethylated. Here we report the discovery of the first alpha-N-methyltransferase, which we named N-terminal RCC1 methyltransferase (NRMT). Substrate docking and mutational analysis of RCC1 defined the NRMT recognition sequence and enabled the identification of numerous new methylation targets, including SET (also known as TAF-I or PHAPII) and the retinoblastoma protein, RB. Knockdown of NRMT recapitulates the multi-spindle phenotype seen with methylation-defective RCC1 mutants, demonstrating the importance of alpha-N-methylation for normal bipolar spindle formation and chromosome segregation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939154/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939154/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tooley, Christine E Schaner -- Petkowski, Janusz J -- Muratore-Schroeder, Tara L -- Balsbaugh, Jeremy L -- Shabanowitz, Jeffrey -- Sabat, Michal -- Minor, Wladek -- Hunt, Donald F -- Macara, Ian G -- R01 GM050526/GM/NIGMS NIH HHS/ -- R01 GM050526-17/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Aug 26;466(7310):1125-8. doi: 10.1038/nature09343.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA. ces5g@virginia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20668449" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Cycle Proteins/*metabolism ; Cell Line ; Chromosome Segregation ; Gene Knockdown Techniques ; Guanine Nucleotide Exchange Factors/*metabolism ; HeLa Cells ; Histone Chaperones/metabolism ; Humans ; Methyltransferases/chemistry/genetics/*metabolism ; Models, Molecular ; Mutation/genetics ; Nuclear Proteins/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Retinoblastoma Protein/*metabolism ; Spindle Apparatus/metabolism ; Transcription Factors/metabolism
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  • 22
    Publication Date: 2010-12-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bonetta, Laura -- England -- Nature. 2010 Dec 9;468(7325):854. doi: 10.1038/468854a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21151000" target="_blank"〉PubMed〈/a〉
    Keywords: California ; Protein Binding ; Protein Interaction Mapping/*methods ; RNA, Transfer/metabolism ; Ribosomes/metabolism ; Sequence Analysis, DNA/methods ; Time Factors
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  • 23
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    Publication Date: 2010-05-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 May 13;465(7295):135. doi: 10.1038/465135a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463693" target="_blank"〉PubMed〈/a〉
    Keywords: *Federal Government ; Great Britain ; Politics ; Public Policy ; *Research Personnel/economics ; Science/economics/*legislation & jurisprudence/trends
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    Nature Publishing Group (NPG)
    Publication Date: 2010-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Macilwain, Colin -- England -- Nature. 2010 Sep 16;467(7313):269. doi: 10.1038/467269a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉cfmworldview@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20844513" target="_blank"〉PubMed〈/a〉
    Keywords: *Federal Government ; Financing, Government/*economics/statistics & numerical data/trends ; Great Britain ; Research Support as Topic/*economics/statistics & numerical data/trends ; Science/*economics/trends ; Universities/economics
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  • 25
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    Publication Date: 2010-04-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Borrell, Brendan -- England -- Nature. 2010 Apr 15;464(7291):971. doi: 10.1038/464971a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393533" target="_blank"〉PubMed〈/a〉
    Keywords: Clinical Trials as Topic/ethics ; *Ethicists ; Ethics Committees/*organization & administration ; *Federal Government ; Humans ; Stem Cells ; United States
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  • 26
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    Publication Date: 2010-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Apr 22;464(7292):1103-4. doi: 10.1038/4641103b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20414265" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Benzhydryl Compounds ; Chemical Industry/*legislation & jurisprudence/*standards ; *Evaluation Studies as Topic ; *Federal Government ; Guidelines as Topic ; Humans ; Phenols/adverse effects/toxicity ; Reproducibility of Results ; Safety/*legislation & jurisprudence/*standards ; *Toxicity Tests/methods/standards ; United States
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  • 27
    Publication Date: 2010-02-26
    Description: Despite the essential roles of sphingolipids both as structural components of membranes and critical signalling molecules, we have a limited understanding of how cells sense and regulate their levels. Here we reveal the function in sphingolipid metabolism of the ORM genes (known as ORMDL genes in humans)-a conserved gene family that includes ORMDL3, which has recently been identified as a potential risk factor for childhood asthma. Starting from an unbiased functional genomic approach in Saccharomyces cerevisiae, we identify Orm proteins as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. We also define a regulatory pathway in which phosphorylation of Orm proteins relieves their inhibitory activity when sphingolipid production is disrupted. Changes in ORM gene expression or mutations to their phosphorylation sites cause dysregulation of sphingolipid metabolism. Our work identifies the Orm proteins as critical mediators of sphingolipid homeostasis and raises the possibility that sphingolipid misregulation contributes to the development of childhood asthma.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877384/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877384/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Breslow, David K -- Collins, Sean R -- Bodenmiller, Bernd -- Aebersold, Ruedi -- Simons, Kai -- Shevchenko, Andrej -- Ejsing, Christer S -- Weissman, Jonathan S -- N01-HV-28179/HV/NHLBI NIH HHS/ -- P50 GM073210/GM/NIGMS NIH HHS/ -- P50 GM073210-06/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Feb 25;463(7284):1048-53. doi: 10.1038/nature08787.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20182505" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Asthma/metabolism ; Cell Line ; Conserved Sequence ; Fatty Acids, Monounsaturated/pharmacology ; HeLa Cells ; *Homeostasis ; Humans ; Molecular Sequence Data ; *Multigene Family ; Multiprotein Complexes/chemistry/metabolism ; Phosphoric Monoester Hydrolases/genetics/metabolism ; Phosphorylation ; Protein Binding ; Saccharomyces cerevisiae/drug effects/enzymology/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/classification/genetics/*metabolism ; Serine C-Palmitoyltransferase/genetics/metabolism ; Sphingolipids/biosynthesis/*metabolism
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  • 28
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    Nature Publishing Group (NPG)
    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kool, Richard -- England -- Nature. 2010 Oct 14;467(7317):788. doi: 10.1038/467788d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944722" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; Conservation of Natural Resources/legislation & jurisprudence ; Environmental Policy/legislation & jurisprudence ; *Federal Government ; *Politics ; *Science ; United States
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  • 29
    Publication Date: 2010-05-21
    Description: In protein synthesis initiation, the eukaryotic translation initiation factor (eIF) 2 (a G protein) functions in its GTP-bound state to deliver initiator methionyl-tRNA (tRNA(i)(Met)) to the small ribosomal subunit and is necessary for protein synthesis in all cells. Phosphorylation of eIF2 [eIF2(alphaP)] is critical for translational control in diverse settings including nutrient deprivation, viral infection and memory formation. eIF5 functions in start site selection as a GTPase accelerating protein (GAP) for the eIF2.GTP.tRNA(i)(Met) ternary complex within the ribosome-bound pre-initiation complex. Here we define new regulatory functions of eIF5 in the recycling of eIF2 from its inactive eIF2.GDP state between successive rounds of translation initiation. First we show that eIF5 stabilizes the binding of GDP to eIF2 and is therefore a bi-functional protein that acts as a GDP dissociation inhibitor (GDI). We find that this activity is independent of the GAP function and identify conserved residues within eIF5 that are necessary for this role. Second we show that eIF5 is a critical component of the eIF2(alphaP) regulatory complex that inhibits the activity of the guanine-nucleotide exchange factor (GEF) eIF2B. Together our studies define a new step in the translation initiation pathway, one that is critical for normal translational controls.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875157/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875157/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jennings, Martin D -- Pavitt, Graham D -- BB/E002005/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H010599/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBE0020051/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2010 May 20;465(7296):378-81. doi: 10.1038/nature09003.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20485439" target="_blank"〉PubMed〈/a〉
    Keywords: Basic-Leucine Zipper Transcription Factors/metabolism ; Eukaryotic Initiation Factor-2/antagonists & inhibitors/chemistry/*metabolism ; GTPase-Activating Proteins/metabolism ; Guanine Nucleotide Dissociation Inhibitors/chemistry/*metabolism ; Guanosine Diphosphate/metabolism ; Guanosine Triphosphate/metabolism ; *Peptide Chain Initiation, Translational ; Peptide Initiation Factors/chemistry/*metabolism ; Phosphorylation ; Protein Binding ; Protein Subunits/chemistry/metabolism ; RNA, Transfer, Met/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism
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  • 30
    Publication Date: 2010-06-22
    Description: Autophagy, the process by which proteins and organelles are sequestered in autophagosomal vesicles and delivered to the lysosome/vacuole for degradation, provides a primary route for turnover of stable and defective cellular proteins. Defects in this system are linked with numerous human diseases. Although conserved protein kinase, lipid kinase and ubiquitin-like protein conjugation subnetworks controlling autophagosome formation and cargo recruitment have been defined, our understanding of the global organization of this system is limited. Here we report a proteomic analysis of the autophagy interaction network in human cells under conditions of ongoing (basal) autophagy, revealing a network of 751 interactions among 409 candidate interacting proteins with extensive connectivity among subnetworks. Many new autophagy interaction network components have roles in vesicle trafficking, protein or lipid phosphorylation and protein ubiquitination, and affect autophagosome number or flux when depleted by RNA interference. The six ATG8 orthologues in humans (MAP1LC3/GABARAP proteins) interact with a cohort of 67 proteins, with extensive binding partner overlap between family members, and frequent involvement of a conserved surface on ATG8 proteins known to interact with LC3-interacting regions in partner proteins. These studies provide a global view of the mammalian autophagy interaction landscape and a resource for mechanistic analysis of this critical protein homeostasis pathway.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901998/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901998/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Behrends, Christian -- Sowa, Mathew E -- Gygi, Steven P -- Harper, J Wade -- R01 AG011085/AG/NIA NIH HHS/ -- R01 AG011085-18/AG/NIA NIH HHS/ -- R01 GM054137/GM/NIGMS NIH HHS/ -- R01 GM054137-14/GM/NIGMS NIH HHS/ -- R01 GM054137-14S1/GM/NIGMS NIH HHS/ -- R01 GM054137-15/GM/NIGMS NIH HHS/ -- R01 GM070565/GM/NIGMS NIH HHS/ -- R01 GM070565-05S1/GM/NIGMS NIH HHS/ -- R01 GM095567/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jul 1;466(7302):68-76. doi: 10.1038/nature09204. Epub 2010 Jun 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20562859" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/genetics/metabolism ; Autophagy/genetics/*physiology ; Homeostasis ; Humans ; Microfilament Proteins/genetics/metabolism ; Phagosomes ; Phosphorylation ; Protein Binding ; *Protein Interaction Mapping ; Proteomics ; RNA Interference ; Reproducibility of Results ; Ubiquitination
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  • 31
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    Nature Publishing Group (NPG)
    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Oct 14;467(7317):751. doi: 10.1038/467751a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944684" target="_blank"〉PubMed〈/a〉
    Keywords: American Recovery and Reinvestment Act ; Comparative Effectiveness Research/legislation & jurisprudence ; Electronic Health Records/legislation & jurisprudence ; Embryonic Stem Cells ; *Federal Government ; Greenhouse Effect/legislation & jurisprudence/prevention & control ; Humans ; *Politics ; Stem Cell Research/legislation & jurisprudence ; United States
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  • 32
    Publication Date: 2010-12-18
    Description: Recognition of modified histone species by distinct structural domains within 'reader' proteins plays a critical role in the regulation of gene expression. Readers that simultaneously recognize histones with multiple marks allow transduction of complex chromatin modification patterns into specific biological outcomes. Here we report that chromatin regulator tripartite motif-containing 24 (TRIM24) functions in humans as a reader of dual histone marks by means of tandem plant homeodomain (PHD) and bromodomain (Bromo) regions. The three-dimensional structure of the PHD-Bromo region of TRIM24 revealed a single functional unit for combinatorial recognition of unmodified H3K4 (that is, histone H3 unmodified at lysine 4, H3K4me0) and acetylated H3K23 (histone H3 acetylated at lysine 23, H3K23ac) within the same histone tail. TRIM24 binds chromatin and oestrogen receptor to activate oestrogen-dependent genes associated with cellular proliferation and tumour development. Aberrant expression of TRIM24 negatively correlates with survival of breast cancer patients. The PHD-Bromo of TRIM24 provides a structural rationale for chromatin activation through a non-canonical histone signature, establishing a new route by which chromatin readers may influence cancer pathogenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058826/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058826/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsai, Wen-Wei -- Wang, Zhanxin -- Yiu, Teresa T -- Akdemir, Kadir C -- Xia, Weiya -- Winter, Stefan -- Tsai, Cheng-Yu -- Shi, Xiaobing -- Schwarzer, Dirk -- Plunkett, William -- Aronow, Bruce -- Gozani, Or -- Fischle, Wolfgang -- Hung, Mien-Chie -- Patel, Dinshaw J -- Barton, Michelle Craig -- GM079641/GM/NIGMS NIH HHS/ -- GM081627/GM/NIGMS NIH HHS/ -- P01 GM081627/GM/NIGMS NIH HHS/ -- P01 GM081627-010003/GM/NIGMS NIH HHS/ -- P01 GM081627-020003/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- P30DK078392-01/DK/NIDDK NIH HHS/ -- T32 HD07325/HD/NICHD NIH HHS/ -- U54 RR025216/RR/NCRR NIH HHS/ -- UL1 TR000077/TR/NCATS NIH HHS/ -- England -- Nature. 2010 Dec 16;468(7326):927-32. doi: 10.1038/nature09542.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Program in Genes and Development, Graduate School of Biomedical Sciences, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21164480" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Breast Neoplasms/*genetics/*metabolism/pathology ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Line, Tumor ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; Crystallography, X-Ray ; Estrogen Receptor alpha/metabolism ; Estrogens/metabolism ; *Gene Expression Regulation, Neoplastic/genetics ; HEK293 Cells ; Histones/chemistry/*metabolism ; Humans ; Methylation ; Protein Array Analysis ; Protein Binding ; Protein Structure, Tertiary ; Substrate Specificity ; Survival Rate
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  • 33
    Publication Date: 2010-09-08
    Description: Cell cycle checkpoints are implemented to safeguard the genome, avoiding the accumulation of genetic errors. Checkpoint loss results in genomic instability and contributes to the evolution of cancer. Among G1-, S-, G2- and M-phase checkpoints, genetic studies indicate the role of an intact S-phase checkpoint in maintaining genome integrity. Although the basic framework of the S-phase checkpoint in multicellular organisms has been outlined, the mechanistic details remain to be elucidated. Human chromosome-11 band-q23 translocations disrupting the MLL gene lead to poor prognostic leukaemias. Here we assign MLL as a novel effector in the mammalian S-phase checkpoint network and identify checkpoint dysfunction as an underlying mechanism of MLL leukaemias. MLL is phosphorylated at serine 516 by ATR in response to genotoxic stress in the S phase, which disrupts its interaction with, and hence its degradation by, the SCF(Skp2) E3 ligase, leading to its accumulation. Stabilized MLL protein accumulates on chromatin, methylates histone H3 lysine 4 at late replication origins and inhibits the loading of CDC45 to delay DNA replication. Cells deficient in MLL showed radioresistant DNA synthesis and chromatid-type genomic abnormalities, indicative of S-phase checkpoint dysfunction. Reconstitution of Mll(-/-) (Mll also known as Mll1) mouse embryonic fibroblasts with wild-type but not S516A or DeltaSET mutant MLL rescues the S-phase checkpoint defects. Moreover, murine myeloid progenitor cells carrying an Mll-CBP knock-in allele that mimics human t(11;16) leukaemia show a severe radioresistant DNA synthesis phenotype. MLL fusions function as dominant negative mutants that abrogate the ATR-mediated phosphorylation/stabilization of wild-type MLL on damage to DNA, and thus compromise the S-phase checkpoint. Together, our results identify MLL as a key constituent of the mammalian DNA damage response pathway and show that deregulation of the S-phase checkpoint incurred by MLL translocations probably contributes to the pathogenesis of human MLL leukaemias.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940944/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940944/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Han -- Takeda, Shugaku -- Kumar, Rakesh -- Westergard, Todd D -- Brown, Eric J -- Pandita, Tej K -- Cheng, Emily H-Y -- Hsieh, James J-D -- CA119008/CA/NCI NIH HHS/ -- CA123232/CA/NCI NIH HHS/ -- CA129537/CA/NCI NIH HHS/ -- R01 CA119008/CA/NCI NIH HHS/ -- R01 CA119008-01/CA/NCI NIH HHS/ -- R01 CA119008-02/CA/NCI NIH HHS/ -- R01 CA119008-03/CA/NCI NIH HHS/ -- R01 CA119008-04/CA/NCI NIH HHS/ -- R01 CA119008-05/CA/NCI NIH HHS/ -- England -- Nature. 2010 Sep 16;467(7313):343-6. doi: 10.1038/nature09350. Epub 2010 Sep 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20818375" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Ataxia Telangiectasia Mutated Proteins ; Cell Cycle Proteins/*metabolism ; Cell Line ; Chromatin/metabolism ; DNA Damage ; DNA Replication/physiology ; Genes, Dominant/genetics ; Genomic Instability/physiology ; Histone-Lysine N-Methyltransferase ; Histones/chemistry/metabolism ; Humans ; Leukemia/genetics ; Lysine/metabolism ; Methylation ; Mice ; Myeloid Progenitor Cells/metabolism ; Myeloid-Lymphoid Leukemia Protein/chemistry/deficiency/genetics/*metabolism ; Phosphorylation ; Phosphoserine/metabolism ; Protein Binding ; Protein-Serine-Threonine Kinases/*metabolism ; S Phase/*physiology ; S-Phase Kinase-Associated Proteins/metabolism ; Signal Transduction ; Translocation, Genetic/genetics
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  • 34
    Publication Date: 2010-12-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bonetta, Laura -- England -- Nature. 2010 Dec 9;468(7325):851-4. doi: 10.1038/468851a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21150998" target="_blank"〉PubMed〈/a〉
    Keywords: Breast Neoplasms/diagnosis/metabolism/pathology ; Computational Biology ; Databases, Factual/trends ; False Negative Reactions ; False Positive Reactions ; Genes, Reporter ; Humans ; Immunoprecipitation ; Mass Spectrometry ; Protein Array Analysis ; Protein Binding ; Protein Interaction Mapping/*methods/*trends ; Proteome/genetics/metabolism ; Two-Hybrid System Techniques
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  • 35
    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wadman, Meredith -- England -- Nature. 2010 Oct 14;467(7317):761. doi: 10.1038/467761a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944702" target="_blank"〉PubMed〈/a〉
    Keywords: Budgets ; *Federal Government ; Humans ; National Institutes of Health (U.S.)/economics/*legislation & jurisprudence ; *Politics ; Research Support as Topic/economics/trends ; Stem Cell Research/economics/*legislation & jurisprudence ; United States
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  • 36
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    Nature Publishing Group (NPG)
    Publication Date: 2010-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mascarelli, Amanda -- England -- Nature. 2010 Jun 24;465(7301):993. doi: 10.1038/465993b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20577177" target="_blank"〉PubMed〈/a〉
    Keywords: *Disasters ; *Ecosystem ; *Federal Government ; Industry/*economics/*legislation & jurisprudence ; Mexico ; Oceans and Seas ; Petroleum/*adverse effects ; Research/*economics ; Seawater/*chemistry ; United States
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  • 37
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    Nature Publishing Group (NPG)
    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Greenberg, Daniel S -- England -- Nature. 2010 Oct 14;467(7317):781-2. doi: 10.1038/467781a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉danielg523@aol.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944714" target="_blank"〉PubMed〈/a〉
    Keywords: Age Factors ; Budgets/trends ; Conflict of Interest/legislation & jurisprudence ; *Federal Government ; Humans ; Military Science/economics/legislation & jurisprudence ; National Institutes of Health (U.S.)/economics ; Policy Making ; Research Support as Topic/*legislation & jurisprudence/*trends ; Science/economics/*legislation & jurisprudence/*trends ; United States
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  • 38
    Publication Date: 2010-07-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jorgensen, William L -- England -- Nature. 2010 Jul 1;466(7302):42-3. doi: 10.1038/466042a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20596009" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; *Computer-Aided Design ; Drug Design ; Drug Discovery/*methods ; Enzyme Inhibitors/*chemistry/*metabolism ; Flavonoids/chemistry/metabolism ; Ligands ; Luteolin/chemistry/metabolism ; Molecular Dynamics Simulation ; Plasmodium falciparum ; Protein Binding ; Protozoan Proteins/chemistry/metabolism ; Thermodynamics
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  • 39
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    Nature Publishing Group (NPG)
    Publication Date: 2010-08-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Aug 5;466(7307):667. doi: 10.1038/466667b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20686526" target="_blank"〉PubMed〈/a〉
    Keywords: *Federal Government ; Global Warming/*legislation & jurisprudence/*prevention & control ; *Politics ; United States
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  • 40
    Publication Date: 2010-08-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rose, April -- Schlieker, Christian -- England -- Nature. 2010 Aug 19;466(7309):929-30. doi: 10.1038/466929a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20725029" target="_blank"〉PubMed〈/a〉
    Keywords: Ataxia Telangiectasia Mutated Proteins ; Cell Cycle Proteins/antagonists & inhibitors/metabolism ; Chromatin/chemistry/*metabolism ; Cysteine Endopeptidases/deficiency/*metabolism ; *DNA Breaks, Double-Stranded ; DNA Repair/physiology ; DNA-Binding Proteins/antagonists & inhibitors/metabolism ; Humans ; Protein Binding ; Protein-Serine-Threonine Kinases/antagonists & inhibitors/metabolism ; Tumor Suppressor Proteins/antagonists & inhibitors/metabolism ; Ubiquitin/metabolism ; Ubiquitin-Conjugating Enzymes/antagonists & inhibitors/metabolism ; Ubiquitin-Protein Ligases/antagonists & inhibitors/metabolism ; Ubiquitination/*physiology
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  • 41
    Publication Date: 2010-09-17
    Description: Specialized cellular microenvironments, or 'niches', modulate stem cell properties, including cell number, self-renewal and fate decisions. In the adult brain, niches that maintain a source of neural stem cells (NSCs) and neural progenitor cells (NPCs) are the subventricular zone (SVZ) of the lateral ventricle and the dentate gyrus of the hippocampus. The size of the NSC population of the SVZ at any time is the result of several ongoing processes, including self-renewal, cell differentiation, and cell death. Maintaining the balance between NSCs and NPCs in the SVZ niche is critical to supply the brain with specific neural populations, both under normal conditions or after injury. A fundamental question relevant to both normal development and to cell-based repair strategies in the central nervous system is how the balance of different NSC and NPC populations is maintained in the niche. EGFR (epidermal growth factor receptor) and Notch signalling pathways have fundamental roles during development of multicellular organisms. In Drosophila and in Caenorhabditis elegans these pathways may have either cooperative or antagonistic functions. In the SVZ, Notch regulates NSC identity and self-renewal, whereas EGFR specifically affects NPC proliferation and migration. This suggests that interplay of these two pathways may maintain the balance between NSC and NPC numbers. Here we show that functional cell-cell interaction between NPCs and NSCs through EGFR and Notch signalling has a crucial role in maintaining the balance between these cell populations in the SVZ. Enhanced EGFR signalling in vivo results in the expansion of the NPC pool, and reduces NSC number and self-renewal. This occurs through a non-cell-autonomous mechanism involving EGFR-mediated regulation of Notch signalling. Our findings define a novel interaction between EGFR and Notch pathways in the adult SVZ, and thus provide a mechanism for NSC and NPC pool maintenance.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941915/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941915/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aguirre, Adan -- Rubio, Maria E -- Gallo, Vittorio -- K99NS057944/NS/NINDS NIH HHS/ -- P30HD40677/HD/NICHD NIH HHS/ -- R00 NS057944/NS/NINDS NIH HHS/ -- R01 DC006881/DC/NIDCD NIH HHS/ -- R01 DC006881-03/DC/NIDCD NIH HHS/ -- R01 DC006881-04/DC/NIDCD NIH HHS/ -- R01DC006881/DC/NIDCD NIH HHS/ -- R01NS045702/NS/NINDS NIH HHS/ -- R01NS056427/NS/NINDS NIH HHS/ -- R0O NS057944-03/NS/NINDS NIH HHS/ -- England -- Nature. 2010 Sep 16;467(7313):323-7. doi: 10.1038/nature09347.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neuroscience Research, Children's National Medical Center, Washington, District of Columbia 20010, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20844536" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Count ; Cell Division ; Humans ; Membrane Proteins/deficiency/genetics/metabolism ; Mice ; Mice, Inbred C57BL ; Nerve Tissue Proteins/deficiency/genetics/metabolism ; Neurons/*cytology ; Protein Binding ; Receptor, Epidermal Growth Factor/genetics/*metabolism ; Receptor, Notch1/metabolism ; Receptors, Notch/*metabolism ; *Signal Transduction ; Stem Cell Niche/cytology ; Stem Cells/*cytology ; Ubiquitination
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  • 42
    Publication Date: 2010-09-24
    Description: Symplekin (Pta1 in yeast) is a scaffold in the large protein complex that is required for 3'-end cleavage and polyadenylation of eukaryotic messenger RNA precursors (pre-mRNAs); it also participates in transcription initiation and termination by RNA polymerase II (Pol II). Symplekin mediates interactions between many different proteins in this machinery, although the molecular basis for its function is not known. Here we report the crystal structure at 2.4 A resolution of the amino-terminal domain (residues 30-340) of human symplekin in a ternary complex with the Pol II carboxy-terminal domain (CTD) Ser 5 phosphatase Ssu72 (refs 7, 10-17) and a CTD Ser 5 phosphopeptide. The N-terminal domain of symplekin has the ARM or HEAT fold, with seven pairs of antiparallel alpha-helices arranged in the shape of an arc. The structure of Ssu72 has some similarity to that of low-molecular-mass phosphotyrosine protein phosphatase, although Ssu72 has a unique active-site landscape as well as extra structural features at the C terminus that are important for interaction with symplekin. Ssu72 is bound to the concave face of symplekin, and engineered mutations in this interface can abolish interactions between the two proteins. The CTD peptide is bound in the active site of Ssu72, with the pSer 5-Pro 6 peptide bond in the cis configuration, which contrasts with all other known CTD peptide conformations. Although the active site of Ssu72 is about 25 A from the interface with symplekin, we found that the symplekin N-terminal domain stimulates Ssu72 CTD phosphatase activity in vitro. Furthermore, the N-terminal domain of symplekin inhibits polyadenylation in vitro, but only when coupled to transcription. Because catalytically active Ssu72 overcomes this inhibition, our results show a role for mammalian Ssu72 in transcription-coupled pre-mRNA 3'-end processing.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038789/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038789/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiang, Kehui -- Nagaike, Takashi -- Xiang, Song -- Kilic, Turgay -- Beh, Maia M -- Manley, James L -- Tong, Liang -- GM028983/GM/NIGMS NIH HHS/ -- GM077175/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 GM028983/GM/NIGMS NIH HHS/ -- R01 GM028983-31/GM/NIGMS NIH HHS/ -- R01 GM077175/GM/NIGMS NIH HHS/ -- R01 GM077175-04/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Oct 7;467(7316):729-33. doi: 10.1038/nature09391. Epub 2010 Sep 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, New York 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20861839" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Carrier Proteins/*chemistry/genetics/*metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Drosophila Proteins/chemistry ; Humans ; Models, Molecular ; Nuclear Proteins/*chemistry/genetics/*metabolism ; Phosphopeptides/chemistry/*metabolism ; Phosphoprotein Phosphatases/chemistry/genetics/metabolism ; Polyadenylation ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Polymerase II/*chemistry/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Substrate Specificity ; mRNA Cleavage and Polyadenylation Factors/chemistry
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  • 43
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    Nature Publishing Group (NPG)
    Publication Date: 2010-04-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Butler, Declan -- England -- Nature. 2010 Apr 8;464(7290):822-3. doi: 10.1038/464822a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20376119" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information/*legislation & jurisprudence ; *Federal Government ; Financing, Government/economics ; PubMed ; Public Sector/economics/trends ; Publishing/economics/*trends ; Research Support as Topic/economics ; *Science/economics ; United States
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  • 44
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2010-11-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dyke, Gareth -- England -- Nature. 2010 Nov 11;468(7321):173. doi: 10.1038/468173d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21068816" target="_blank"〉PubMed〈/a〉
    Keywords: *Federal Government ; *Financing, Government/trends ; Ireland ; Research/*economics/*standards ; Research Personnel/economics ; *Research Support as Topic/trends
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  • 45
    Publication Date: 2010-09-21
    Description: Centrioles are found in the centrosome core and, as basal bodies, at the base of cilia and flagella. Centriole assembly and duplication is controlled by Polo-like-kinase 4 (Plk4): these processes fail if Plk4 is downregulated and are promoted by Plk4 overexpression. Here we show that the centriolar protein Asterless (Asl; human orthologue CEP152) provides a conserved molecular platform, the amino terminus of which interacts with the cryptic Polo box of Plk4 whereas the carboxy terminus interacts with the centriolar protein Sas-4 (CPAP in humans). Drosophila Asl and human CEP152 are required for the centrosomal loading of Plk4 in Drosophila and CPAP in human cells, respectively. Depletion of Asl or CEP152 caused failure of centrosome duplication; their overexpression led to de novo centriole formation in Drosophila eggs, duplication of free centrosomes in Drosophila embryos, and centrosome amplification in cultured Drosophila and human cells. Overexpression of a Plk4-binding-deficient mutant of Asl prevented centriole duplication in cultured cells and embryos. However, this mutant protein was able to promote microtubule organizing centre (MTOC) formation in both embryos and oocytes. Such MTOCs had pericentriolar material and the centriolar protein Sas-4, but no centrioles at their core. Formation of such acentriolar MTOCs could be phenocopied by overexpression of Sas-4 in oocytes or embryos. Our findings identify independent functions for Asl as a scaffold for Plk4 and Sas-4 that facilitates self-assembly and duplication of the centriole and organization of pericentriolar material.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dzhindzhev, Nikola S -- Yu, Quan D -- Weiskopf, Kipp -- Tzolovsky, George -- Cunha-Ferreira, Ines -- Riparbelli, Maria -- Rodrigues-Martins, Ana -- Bettencourt-Dias, Monica -- Callaini, Giuliano -- Glover, David M -- 11431/Cancer Research UK/United Kingdom -- Cancer Research UK/United Kingdom -- England -- Nature. 2010 Oct 7;467(7316):714-8. doi: 10.1038/nature09445. Epub 2010 Sep 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK Cell Cycle Genetics Group, University of Cambridge, Department of Genetics, Downing Street, Cambridge CB2 3EH, UK. nsd23@cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20852615" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Cell Cycle Proteins/*metabolism ; Cell Line ; Centrioles/*metabolism ; Centrosome/metabolism ; Drosophila Proteins/chemistry/deficiency/genetics/*metabolism ; Drosophila melanogaster/cytology/embryology/genetics/metabolism ; Female ; Humans ; Microtubule-Associated Proteins/metabolism ; Microtubule-Organizing Center/metabolism ; Oocytes/cytology/metabolism ; Protein Binding ; Protein-Serine-Threonine Kinases/chemistry/deficiency/genetics/metabolism ; Proto-Oncogene Proteins c-myc/genetics/metabolism
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  • 46
    Publication Date: 2010-10-12
    Description: DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160814/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160814/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rubinson, Emily H -- Gowda, A S Prakasha -- Spratt, Thomas E -- Gold, Barry -- Eichman, Brandt F -- P30 CA068485/CA/NCI NIH HHS/ -- P30 ES000267/ES/NIEHS NIH HHS/ -- R01 CA029088/CA/NCI NIH HHS/ -- R01 CA29088/CA/NCI NIH HHS/ -- T32 ES007028/ES/NIEHS NIH HHS/ -- England -- Nature. 2010 Nov 18;468(7322):406-11. doi: 10.1038/nature09428. Epub 2010 Oct 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20927102" target="_blank"〉PubMed〈/a〉
    Keywords: Alkylation ; Bacillus cereus/*enzymology ; Base Sequence ; Biocatalysis ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; *DNA Damage ; DNA Glycosylases/*metabolism ; DNA Repair/*physiology ; Hydrolysis ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Solvents/chemistry ; Thermodynamics
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  • 47
    Publication Date: 2010-08-21
    Description: DNA double-strand breaks (DSBs) pose a potent threat to genome integrity. These lesions also contribute to the efficacy of radiotherapy and many cancer chemotherapeutics. DSBs elicit a signalling cascade that modifies the chromatin surrounding the break, first by ATM-dependent phosphorylation and then by RNF8-, RNF168- and BRCA1-dependent regulatory ubiquitination. Here we report that OTUB1, a deubiquitinating enzyme, is an inhibitor of DSB-induced chromatin ubiquitination. Surprisingly, we found that OTUB1 suppresses RNF168-dependent poly-ubiquitination independently of its catalytic activity. OTUB1 does so by binding to and inhibiting UBC13 (also known as UBE2N), the cognate E2 enzyme for RNF168. This unusual mode of regulation is unlikely to be limited to UBC13 because analysis of OTUB1-associated proteins revealed that OTUB1 binds to E2s of the UBE2D and UBE2E subfamilies. Finally, OTUB1 depletion mitigates the DSB repair defect associated with defective ATM signalling, indicating that pharmacological targeting of the OTUB1-UBC13 interaction might enhance the DNA damage response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakada, Shinichiro -- Tai, Ikue -- Panier, Stephanie -- Al-Hakim, Abdallah -- Iemura, Shun-Ichiro -- Juang, Yu-Chi -- O'Donnell, Lara -- Kumakubo, Ayako -- Munro, Meagan -- Sicheri, Frank -- Gingras, Anne-Claude -- Natsume, Tohru -- Suda, Toshio -- Durocher, Daniel -- MOP10703115/Canadian Institutes of Health Research/Canada -- MOP84314/Canadian Institutes of Health Research/Canada -- England -- Nature. 2010 Aug 19;466(7309):941-6. doi: 10.1038/nature09297.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center of Integrated Medical Research, School of Medicine, Keio University, 35 Shinano-machi, Shinjuku-ku, Tokyo, 160-8582, Japan. snakada@z3.keio.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20725033" target="_blank"〉PubMed〈/a〉
    Keywords: Ataxia Telangiectasia Mutated Proteins ; Cell Cycle Proteins/antagonists & inhibitors/metabolism ; Cell Line ; Cell Line, Tumor ; Chromatin/chemistry/*metabolism ; Cysteine Endopeptidases/deficiency/genetics/*metabolism ; *DNA Breaks, Double-Stranded ; DNA Repair/physiology ; DNA-Binding Proteins/antagonists & inhibitors/metabolism ; Humans ; Protein Binding ; Protein-Serine-Threonine Kinases/antagonists & inhibitors/metabolism ; Tumor Suppressor Proteins/antagonists & inhibitors/metabolism ; Ubiquitin/genetics/metabolism ; Ubiquitin-Conjugating Enzymes/antagonists & inhibitors/metabolism ; Ubiquitin-Protein Ligases/antagonists & inhibitors/genetics/metabolism ; Ubiquitination/*physiology
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  • 48
    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ledford, Heidi -- England -- Nature. 2010 Oct 14;467(7317):763. doi: 10.1038/467763b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944705" target="_blank"〉PubMed〈/a〉
    Keywords: Comparative Effectiveness Research/economics/*legislation & ; jurisprudence/organization & administration ; *Federal Government ; Humans ; Insurance, Health/economics ; Patient Protection and Affordable Care Act/*legislation & ; jurisprudence/organization & administration ; *Politics ; United States
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  • 49
    Publication Date: 2010-02-05
    Description: During their intraerythrocytic development, malaria parasites export hundreds of proteins to remodel their host cell. Nutrient acquisition, cytoadherence and antigenic variation are among the key virulence functions effected by this erythrocyte takeover. Proteins destined for export are synthesized in the endoplasmic reticulum (ER) and cleaved at a conserved (PEXEL) motif, which allows translocation into the host cell via an ATP-driven translocon called the PTEX complex. We report that plasmepsin V, an ER aspartic protease with distant homology to the mammalian processing enzyme BACE, recognizes the PEXEL motif and cleaves it at the correct site. This enzyme is essential for parasite viability and ER residence is essential for its function. We propose that plasmepsin V is the PEXEL protease and is an attractive enzyme for antimalarial drug development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826791/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826791/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Russo, Ilaria -- Babbitt, Shalon -- Muralidharan, Vasant -- Butler, Tamira -- Oksman, Anna -- Goldberg, Daniel E -- AI-047798/AI/NIAID NIH HHS/ -- R01 AI047798/AI/NIAID NIH HHS/ -- R01 AI047798-10/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Feb 4;463(7281):632-6. doi: 10.1038/nature08726.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Washington University School of Medicine, Department of Molecular Microbiology, St Louis, Missouri 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130644" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Antimalarials/pharmacology ; Aspartic Acid Endopeptidases/antagonists & ; inhibitors/chemistry/genetics/*metabolism ; Biocatalysis/drug effects ; Endoplasmic Reticulum/enzymology/metabolism ; Erythrocytes/cytology/*metabolism/parasitology ; Genes, Dominant ; Genes, Essential ; HIV Protease Inhibitors/pharmacology ; Humans ; Malaria, Falciparum/*blood/metabolism/*parasitology/pathology ; Multiprotein Complexes/metabolism ; Pepstatins/pharmacology ; Phenotype ; Plasmids/genetics ; Plasmodium falciparum/enzymology/genetics/*metabolism/pathogenicity ; Protein Binding ; Protein Sorting Signals ; Protein Structure, Tertiary ; Protein Transport ; Proteomics ; Protozoan Proteins/chemistry/*metabolism ; Substrate Specificity
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  • 50
    Publication Date: 2010-06-26
    Description: Tumour-necrosis factor (TNF) receptor-associated factor 2 (TRAF2) is a key component in NF-kappaB signalling triggered by TNF-alpha. Genetic evidence indicates that TRAF2 is necessary for the polyubiquitination of receptor interacting protein 1 (RIP1) that then serves as a platform for recruitment and stimulation of IkappaB kinase, leading to activation of the transcription factor NF-kappaB. Although TRAF2 is a RING domain ubiquitin ligase, direct evidence that TRAF2 catalyses the ubiquitination of RIP1 is lacking. TRAF2 binds to sphingosine kinase 1 (SphK1), one of the isoenzymes that generates the pro-survival lipid mediator sphingosine-1-phosphate (S1P) inside cells. Here we show that SphK1 and the production of S1P is necessary for lysine-63-linked polyubiquitination of RIP1, phosphorylation of IkappaB kinase and IkappaBalpha, and IkappaBalpha degradation, leading to NF-kappaB activation. These responses were mediated by intracellular S1P independently of its cell surface G-protein-coupled receptors. S1P specifically binds to TRAF2 at the amino-terminal RING domain and stimulates its E3 ligase activity. S1P, but not dihydro-S1P, markedly increased recombinant TRAF2-catalysed lysine-63-linked, but not lysine-48-linked, polyubiquitination of RIP1 in vitro in the presence of the ubiquitin conjugating enzymes (E2) UbcH13 or UbcH5a. Our data show that TRAF2 is a novel intracellular target of S1P, and that S1P is the missing cofactor for TRAF2 E3 ubiquitin ligase activity, indicating a new paradigm for the regulation of lysine-63-linked polyubiquitination. These results also highlight the key role of SphK1 and its product S1P in TNF-alpha signalling and the canonical NF-kappaB activation pathway important in inflammatory, antiapoptotic and immune processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946785/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946785/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alvarez, Sergio E -- Harikumar, Kuzhuvelil B -- Hait, Nitai C -- Allegood, Jeremy -- Strub, Graham M -- Kim, Eugene Y -- Maceyka, Michael -- Jiang, Hualiang -- Luo, Cheng -- Kordula, Tomasz -- Milstien, Sheldon -- Spiegel, Sarah -- R01 AI050094/AI/NIAID NIH HHS/ -- R01 AI050094-09/AI/NIAID NIH HHS/ -- R01 CA061774/CA/NCI NIH HHS/ -- R01 CA061774-15/CA/NCI NIH HHS/ -- R01 CA061774-16/CA/NCI NIH HHS/ -- R01AI50094/AI/NIAID NIH HHS/ -- R01CA61774/CA/NCI NIH HHS/ -- R37 GM043880/GM/NIGMS NIH HHS/ -- R37 GM043880-18/GM/NIGMS NIH HHS/ -- R37 GM043880-19/GM/NIGMS NIH HHS/ -- R37 GM043880-20/GM/NIGMS NIH HHS/ -- R37 GM043880-21/GM/NIGMS NIH HHS/ -- R37GM043880/GM/NIGMS NIH HHS/ -- U19 AI077435/AI/NIAID NIH HHS/ -- U19 AI077435-020004/AI/NIAID NIH HHS/ -- U19 AI077435-02S10004/AI/NIAID NIH HHS/ -- U19 AI077435-030004/AI/NIAID NIH HHS/ -- U19AI077435/AI/NIAID NIH HHS/ -- England -- Nature. 2010 Jun 24;465(7301):1084-8. doi: 10.1038/nature09128.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, 1101 E. Marshall Street, Richmond, Virginia 23298, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20577214" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biocatalysis ; Cell Line ; Enzyme Activation ; Humans ; I-kappa B Kinase/metabolism ; I-kappa B Proteins/metabolism ; Lysine/metabolism ; Lysophospholipids/biosynthesis/chemistry/*metabolism ; Mice ; Models, Molecular ; NF-kappa B/metabolism ; Phosphorylation ; Phosphotransferases (Alcohol Group Acceptor)/genetics/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Receptor-Interacting Protein Serine-Threonine Kinases/metabolism ; Sphingosine/*analogs & derivatives/biosynthesis/chemistry/metabolism ; Substrate Specificity ; TNF Receptor-Associated Factor 2/chemistry/*metabolism ; Tumor Necrosis Factor-alpha/pharmacology ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitin-Protein Ligases/*metabolism ; Ubiquitination/drug effects
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  • 51
    Publication Date: 2010-03-20
    Description: Cobalamin (Cbl, vitamin B(12)) is a bacterial organic compound and an essential coenzyme in mammals, which take it up from the diet. This occurs by the combined action of the gastric intrinsic factor (IF) and the ileal endocytic cubam receptor formed by the 460-kilodalton (kDa) protein cubilin and the 45-kDa transmembrane protein amnionless. Loss of function of any of these proteins ultimately leads to Cbl deficiency in man. Here we present the crystal structure of the complex between IF-Cbl and the cubilin IF-Cbl-binding-region (CUB(5-8)) determined at 3.3 A resolution. The structure provides insight into how several CUB (for 'complement C1r/C1s, Uegf, Bmp1') domains collectively function as modular ligand-binding regions, and how two distant CUB domains embrace the Cbl molecule by binding the two IF domains in a Ca(2+)-dependent manner. This dual-point model provides a probable explanation of how Cbl indirectly induces ligand-receptor coupling. Finally, the comparison of Ca(2+)-binding CUB domains and the low-density lipoprotein (LDL) receptor-type A modules suggests that the electrostatic pairing of a basic ligand arginine/lysine residue with Ca(2+)-coordinating acidic aspartates/glutamates is a common theme of Ca(2+)-dependent ligand-receptor interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andersen, Christian Brix Folsted -- Madsen, Mette -- Storm, Tina -- Moestrup, Soren K -- Andersen, Gregers R -- England -- Nature. 2010 Mar 18;464(7287):445-8. doi: 10.1038/nature08874.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry, Aarhus University, 8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237569" target="_blank"〉PubMed〈/a〉
    Keywords: Aspartic Acid/metabolism ; Binding Sites ; Calcium/metabolism ; Crystallography, X-Ray ; Glutamic Acid/metabolism ; Humans ; Intrinsic Factor/*chemistry/*metabolism ; Ligands ; Models, Molecular ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Cell Surface/*chemistry/*metabolism ; Static Electricity ; Vitamin B 12/*chemistry/*metabolism
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  • 52
    Publication Date: 2010-06-11
    Description: Regulation of the expression of the human immunodeficiency virus (HIV) genome is accomplished in large part by controlling transcription elongation. The viral protein Tat hijacks the host cell's RNA polymerase II elongation control machinery through interaction with the positive transcription elongation factor, P-TEFb, and directs the factor to promote productive elongation of HIV mRNA. Here we describe the crystal structure of the Tat.P-TEFb complex containing HIV-1 Tat, human Cdk9 (also known as CDK9), and human cyclin T1 (also known as CCNT1). Tat adopts a structure complementary to the surface of P-TEFb and makes extensive contacts, mainly with the cyclin T1 subunit of P-TEFb, but also with the T-loop of the Cdk9 subunit. The structure provides a plausible explanation for the tolerance of Tat to sequence variations at certain sites. Importantly, Tat induces significant conformational changes in P-TEFb. This finding lays a foundation for the design of compounds that would specifically inhibit the Tat.P-TEFb complex and block HIV replication.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885016/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885016/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tahirov, Tahir H -- Babayeva, Nigar D -- Varzavand, Katayoun -- Cooper, Jeffrey J -- Sedore, Stanley C -- Price, David H -- AI074392/AI/NIAID NIH HHS/ -- GM082923/GM/NIGMS NIH HHS/ -- GM35500/GM/NIGMS NIH HHS/ -- P30CA036727/CA/NCI NIH HHS/ -- P41 RR015301/RR/NCRR NIH HHS/ -- P41 RR015301-075443/RR/NCRR NIH HHS/ -- R01 GM035500/GM/NIGMS NIH HHS/ -- R01 GM035500-20/GM/NIGMS NIH HHS/ -- R01 GM035500-21/GM/NIGMS NIH HHS/ -- R01 GM035500-22/GM/NIGMS NIH HHS/ -- R01 GM035500-23/GM/NIGMS NIH HHS/ -- R01 GM035500-24/GM/NIGMS NIH HHS/ -- R01 GM082923/GM/NIGMS NIH HHS/ -- R01 GM082923-01A2/GM/NIGMS NIH HHS/ -- R01 GM082923-02/GM/NIGMS NIH HHS/ -- R01 GM082923-02S1/GM/NIGMS NIH HHS/ -- R21 AI074392/AI/NIAID NIH HHS/ -- R21 AI074392-01A1/AI/NIAID NIH HHS/ -- R21 AI074392-02/AI/NIAID NIH HHS/ -- R33 AI074392/AI/NIAID NIH HHS/ -- R33 AI074392-03/AI/NIAID NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- England -- Nature. 2010 Jun 10;465(7299):747-51. doi: 10.1038/nature09131.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-7696, USA. ttahirov@unmc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20535204" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Cyclin T/chemistry/metabolism ; Cyclin-Dependent Kinase 9/chemistry/metabolism ; Enzyme Activation ; HIV-1/*chemistry ; Humans ; Models, Molecular ; Molecular Sequence Data ; Positive Transcriptional Elongation Factor B/*chemistry/*metabolism ; Protein Binding ; Protein Conformation ; tat Gene Products, Human Immunodeficiency Virus/*chemistry/genetics/*metabolism
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  • 53
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    Nature Publishing Group (NPG)
    Publication Date: 2010-01-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ellis, R John -- England -- Nature. 2010 Jan 14;463(7278):164-5. doi: 10.1038/463164a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075906" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Cell Respiration/radiation effects ; Chaperonin 10/metabolism ; Chaperonin 60/metabolism ; Holoenzymes/chemistry/isolation & purification/metabolism ; Molecular Chaperones/chemistry/*metabolism ; Protein Binding ; *Protein Folding ; *Protein Multimerization ; Ribulose-Bisphosphate Carboxylase/*chemistry/isolation & purification/*metabolism ; Synechococcus/*chemistry/metabolism
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  • 54
    Publication Date: 2010-01-16
    Description: Rho is the essential RNA helicase that sets the borders between transcription units and adjusts transcriptional yield to translational needs in bacteria. Although Rho was the first termination factor to be discovered, the actual mechanism by which it reaches and disrupts the elongation complex (EC) is unknown. Here we show that the termination-committed Rho molecule associates with RNA polymerase (RNAP) throughout the transcription cycle; that is, it does not require the nascent transcript for initial binding. Moreover, the formation of the RNAP-Rho complex is crucial for termination. We show further that Rho-dependent termination is a two-step process that involves rapid EC inactivation (trap) and a relatively slow dissociation. Inactivation is the critical rate-limiting step that establishes the position of the termination site. The trap mechanism depends on the allosterically induced rearrangement of the RNAP catalytic centre by means of the evolutionarily conserved mobile trigger-loop domain, which is also required for EC dissociation. The key structural and functional similarities, which we found between Rho-dependent and intrinsic (Rho-independent) termination pathways, argue that the allosteric mechanism of termination is general and likely to be preserved for all cellular RNAPs throughout evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929367/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929367/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Epshtein, Vitaly -- Dutta, Dipak -- Wade, Joseph -- Nudler, Evgeny -- R01 GM058750/GM/NIGMS NIH HHS/ -- R01 GM058750-12/GM/NIGMS NIH HHS/ -- R01 GM072814/GM/NIGMS NIH HHS/ -- R01GM58750/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jan 14;463(7278):245-9. doi: 10.1038/nature08669.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, New York University School of Medicine, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075920" target="_blank"〉PubMed〈/a〉
    Keywords: *Allosteric Regulation ; Binding Sites ; Biocatalysis ; Catalytic Domain ; DNA-Directed RNA Polymerases/genetics/*metabolism ; Dicarboxylic Acids/pharmacology ; Escherichia coli/enzymology ; Kinetics ; Mutant Proteins/genetics/metabolism ; Mutation/genetics ; Organophosphorus Compounds/pharmacology ; Protein Binding ; Rho Factor/*metabolism ; Templates, Genetic ; Transcription, Genetic/drug effects/*physiology
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  • 55
    Publication Date: 2010-09-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cash, Gordon -- England -- Nature. 2010 Sep 16;467(7313):271. doi: 10.1038/467271b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20844515" target="_blank"〉PubMed〈/a〉
    Keywords: Embryo Research/economics/ethics/*legislation & jurisprudence ; *Embryonic Stem Cells ; *Federal Government ; Humans ; *Religion and Science ; Research Support as Topic/legislation & jurisprudence ; United States
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  • 56
    Publication Date: 2010-08-13
    Description: The eubacterial SOS system is a paradigm of cellular DNA damage and repair, and its activation can contribute to antibiotic resistance. Under normal conditions, LexA represses the transcription of many DNA repair proteins by binding to SOS 'boxes' in their operators. Under genotoxic stress, accumulating complexes of RecA, ATP and single-stranded DNA (ssDNA) activate LexA for autocleavage. To address how LexA recognizes its binding sites, we determined three crystal structures of Escherichia coli LexA in complex with SOS boxes. Here we report the structure of these LexA-DNA complexes. The DNA-binding domains of the LexA dimer interact with the DNA in the classical fashion of a winged helix-turn-helix motif. However, the wings of these two DNA-binding domains bind to the same minor groove of the DNA. These wing-wing contacts may explain why the spacing between the two half-sites of E. coli SOS boxes is invariant.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921665/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921665/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Adrianna P P -- Pigli, Ying Z -- Rice, Phoebe A -- GM058827/GM/NIGMS NIH HHS/ -- R01 GM058827/GM/NIGMS NIH HHS/ -- R01 GM058827-09/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Aug 12;466(7308):883-6. doi: 10.1038/nature09200.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703307" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Bacterial Proteins/*chemistry/*metabolism ; Base Sequence ; Crystallography, X-Ray ; DNA Damage ; DNA Repair/genetics ; DNA, Bacterial/chemistry/*genetics/*metabolism ; Electrophoretic Mobility Shift Assay ; *Escherichia coli/chemistry/genetics ; Escherichia coli Proteins/chemistry/genetics/metabolism ; Models, Molecular ; Protein Binding ; *Protein Multimerization ; Protein Structure, Tertiary ; Rec A Recombinases/metabolism ; Repressor Proteins/chemistry/metabolism ; SOS Response (Genetics)/*genetics ; Serine Endopeptidases/*chemistry/*metabolism ; Winged-Helix Transcription Factors/chemistry/metabolism
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  • 57
    Publication Date: 2010-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cattaneo, Elena -- Cerbai, Elisabetta -- Garagna, Silvia -- England -- Nature. 2010 Feb 11;463(7282):729. doi: 10.1038/463729c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20148012" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/economics/*legislation & jurisprudence ; *Embryonic Stem Cells ; *Federal Government ; Humans ; Italy ; *Research Personnel/legislation & jurisprudence
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  • 58
    Publication Date: 2010-01-22
    Description: Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834796/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834796/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Junjie -- Baker, Matthew L -- Schroder, Gunnar F -- Douglas, Nicholai R -- Reissmann, Stefanie -- Jakana, Joanita -- Dougherty, Matthew -- Fu, Caroline J -- Levitt, Michael -- Ludtke, Steven J -- Frydman, Judith -- Chiu, Wah -- P41 RR002250/RR/NCRR NIH HHS/ -- P41 RR002250-23/RR/NCRR NIH HHS/ -- P41 RR002250-237254/RR/NCRR NIH HHS/ -- P41 RR002250-24/RR/NCRR NIH HHS/ -- P41 RR002250-247897/RR/NCRR NIH HHS/ -- PN2 EY016525/EY/NEI NIH HHS/ -- PN2 EY016525-02S1/EY/NEI NIH HHS/ -- PN2 EY016525-03/EY/NEI NIH HHS/ -- PN2 EY016525-04/EY/NEI NIH HHS/ -- PN2 EY016525-05/EY/NEI NIH HHS/ -- R01 GM063817/GM/NIGMS NIH HHS/ -- R01 GM079429/GM/NIGMS NIH HHS/ -- R01 GM079429-03/GM/NIGMS NIH HHS/ -- R01 GM080139/GM/NIGMS NIH HHS/ -- R01 GM080139-03/GM/NIGMS NIH HHS/ -- R01 GM080139-04/GM/NIGMS NIH HHS/ -- R90 DK071504/DK/NIDDK NIH HHS/ -- R90 DK071504-03/DK/NIDDK NIH HHS/ -- T32 GM007276-30/GM/NIGMS NIH HHS/ -- T32 GM007276-31/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jan 21;463(7279):379-83. doi: 10.1038/nature08701.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090755" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/chemistry/metabolism/pharmacology ; Allosteric Regulation ; Binding Sites ; Cryoelectron Microscopy ; Group II Chaperonins/*chemistry/*metabolism/ultrastructure ; Hydrolysis/drug effects ; Methanococcus/*chemistry ; Models, Molecular ; Protein Binding ; Protein Conformation/drug effects ; *Protein Folding ; Protein Subunits/chemistry/metabolism ; Structure-Activity Relationship
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  • 59
    Publication Date: 2010-02-05
    Description: Heterozygous mutations in the gene encoding the CHD (chromodomain helicase DNA-binding domain) member CHD7, an ATP-dependent chromatin remodeller homologous to the Drosophila trithorax-group protein Kismet, result in a complex constellation of congenital anomalies called CHARGE syndrome, which is a sporadic, autosomal dominant disorder characterized by malformations of the craniofacial structures, peripheral nervous system, ears, eyes and heart. Although it was postulated 25 years ago that CHARGE syndrome results from the abnormal development of the neural crest, this hypothesis remained untested. Here we show that, in both humans and Xenopus, CHD7 is essential for the formation of multipotent migratory neural crest (NC), a transient cell population that is ectodermal in origin but undergoes a major transcriptional reprogramming event to acquire a remarkably broad differentiation potential and ability to migrate throughout the body, giving rise to craniofacial bones and cartilages, the peripheral nervous system, pigmentation and cardiac structures. We demonstrate that CHD7 is essential for activation of the NC transcriptional circuitry, including Sox9, Twist and Slug. In Xenopus embryos, knockdown of Chd7 or overexpression of its catalytically inactive form recapitulates all major features of CHARGE syndrome. In human NC cells CHD7 associates with PBAF (polybromo- and BRG1-associated factor-containing complex) and both remodellers occupy a NC-specific distal SOX9 enhancer and a conserved genomic element located upstream of the TWIST1 gene. Consistently, during embryogenesis CHD7 and PBAF cooperate to promote NC gene expression and cell migration. Our work identifies an evolutionarily conserved role for CHD7 in orchestrating NC gene expression programs, provides insights into the synergistic control of distal elements by chromatin remodellers, illuminates the patho-embryology of CHARGE syndrome, and suggests a broader function for CHD7 in the regulation of cell motility.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890258/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890258/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bajpai, Ruchi -- Chen, Denise A -- Rada-Iglesias, Alvaro -- Zhang, Junmei -- Xiong, Yiqin -- Helms, Jill -- Chang, Ching-Pin -- Zhao, Yingming -- Swigut, Tomek -- Wysocka, Joanna -- R01 CA126832/CA/NCI NIH HHS/ -- R01 CA126832-01A1/CA/NCI NIH HHS/ -- R01 DK082664/DK/NIDDK NIH HHS/ -- R01 DK082664-01/DK/NIDDK NIH HHS/ -- R01 HL085345/HL/NHLBI NIH HHS/ -- R01 HL085345-04/HL/NHLBI NIH HHS/ -- R01DK082664/DK/NIDDK NIH HHS/ -- R01HL085345/HL/NHLBI NIH HHS/ -- England -- Nature. 2010 Feb 18;463(7283):958-62. doi: 10.1038/nature08733. Epub 2010 Feb 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130577" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cell Line ; Cell Lineage ; Cell Movement ; Chromosomal Proteins, Non-Histone/genetics/*metabolism ; DNA Helicases/chemistry/deficiency/genetics/*metabolism ; DNA-Binding Proteins/chemistry/deficiency/genetics/*metabolism ; Embryo, Nonmammalian/cytology/embryology/metabolism ; Embryonic Stem Cells/cytology/metabolism ; Enhancer Elements, Genetic/genetics ; Gene Expression Regulation, Developmental ; Humans ; Multipotent Stem Cells/*cytology/*metabolism ; Neural Crest/*cytology/embryology/*metabolism ; Protein Binding ; SOX9 Transcription Factor/genetics/metabolism ; Syndrome ; Transcription Factors/genetics/*metabolism ; Transcription, Genetic ; Twist Transcription Factor/genetics/metabolism ; Xenopus Proteins/chemistry/deficiency/genetics/*metabolism ; Xenopus laevis/embryology/genetics/metabolism
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  • 60
    Publication Date: 2010-11-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sarewitz, Daniel -- England -- Nature. 2010 Nov 11;468(7321):135. doi: 10.1038/468135a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Arizona State University, USA. dsarewitz@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21068785" target="_blank"〉PubMed〈/a〉
    Keywords: *Budgets ; Cost-Benefit Analysis ; Economic Recession ; *Federal Government ; Financing, Government/*organization & administration ; Politics ; *Public Policy ; Science/*economics ; United States
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  • 61
    Publication Date: 2010-10-01
    Description: Semaphorins and their receptor plexins constitute a pleiotropic cell-signalling system that is used in a wide variety of biological processes, and both protein families have been implicated in numerous human diseases. The binding of soluble or membrane-anchored semaphorins to the membrane-distal region of the plexin ectodomain activates plexin's intrinsic GTPase-activating protein (GAP) at the cytoplasmic region, ultimately modulating cellular adhesion behaviour. However, the structural mechanism underlying the receptor activation remains largely unknown. Here we report the crystal structures of the semaphorin 6A (Sema6A) receptor-binding fragment and the plexin A2 (PlxnA2) ligand-binding fragment in both their pre-signalling (that is, before binding) and signalling (after complex formation) states. Before binding, the Sema6A ectodomain was in the expected 'face-to-face' homodimer arrangement, similar to that adopted by Sema3A and Sema4D, whereas PlxnA2 was in an unexpected 'head-on' homodimer arrangement. In contrast, the structure of the Sema6A-PlxnA2 signalling complex revealed a 2:2 heterotetramer in which the two PlxnA2 monomers dissociated from one another and docked onto the top face of the Sema6A homodimer using the same interface as the head-on homodimer, indicating that plexins undergo 'partner exchange'. Cell-based activity measurements using mutant ligands/receptors confirmed that the Sema6A face-to-face dimer arrangement is physiologically relevant and is maintained throughout signalling events. Thus, homodimer-to-heterodimer transitions of cell-surface plexin that result in a specific orientation of its molecular axis relative to the membrane may constitute the structural mechanism by which the ligand-binding 'signal' is transmitted to the cytoplasmic region, inducing GAP domain rearrangements and activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nogi, Terukazu -- Yasui, Norihisa -- Mihara, Emiko -- Matsunaga, Yukiko -- Noda, Masanori -- Yamashita, Naoya -- Toyofuku, Toshihiko -- Uchiyama, Susumu -- Goshima, Yoshio -- Kumanogoh, Atsushi -- Takagi, Junichi -- England -- Nature. 2010 Oct 28;467(7319):1123-7. doi: 10.1038/nature09473. Epub 2010 Sep 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20881961" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; HEK293 Cells ; Humans ; Ligands ; Mice ; Models, Molecular ; Molecular Sequence Data ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Cell Surface/*chemistry/genetics/*metabolism ; Semaphorins/*chemistry/genetics/*metabolism ; *Signal Transduction ; Structure-Activity Relationship
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  • 62
    Publication Date: 2010-08-21
    Description: Propionyl-coenzyme A carboxylase (PCC), a mitochondrial biotin-dependent enzyme, is essential for the catabolism of the amino acids Thr, Val, Ile and Met, cholesterol and fatty acids with an odd number of carbon atoms. Deficiencies in PCC activity in humans are linked to the disease propionic acidaemia, an autosomal recessive disorder that can be fatal in infants. The holoenzyme of PCC is an alpha(6)beta(6) dodecamer, with a molecular mass of 750 kDa. The alpha-subunit contains the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains, whereas the beta-subunit supplies the carboxyltransferase (CT) activity. Here we report the crystal structure at 3.2-A resolution of a bacterial PCC alpha(6)beta(6) holoenzyme as well as cryo-electron microscopy (cryo-EM) reconstruction at 15-A resolution demonstrating a similar structure for human PCC. The structure defines the overall architecture of PCC and reveals unexpectedly that the alpha-subunits are arranged as monomers in the holoenzyme, decorating a central beta(6) hexamer. A hitherto unrecognized domain in the alpha-subunit, formed by residues between the BC and BCCP domains, is crucial for interactions with the beta-subunit. We have named it the BT domain. The structure reveals for the first time the relative positions of the BC and CT active sites in the holoenzyme. They are separated by approximately 55 A, indicating that the entire BCCP domain must translocate during catalysis. The BCCP domain is located in the active site of the beta-subunit in the current structure, providing insight for its involvement in the CT reaction. The structural information establishes a molecular basis for understanding the large collection of disease-causing mutations in PCC and is relevant for the holoenzymes of other biotin-dependent carboxylases, including 3-methylcrotonyl-CoA carboxylase (MCC) and eukaryotic acetyl-CoA carboxylase (ACC).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925307/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925307/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Christine S -- Sadre-Bazzaz, Kianoush -- Shen, Yang -- Deng, Binbin -- Zhou, Z Hong -- Tong, Liang -- AI069015/AI/NIAID NIH HHS/ -- DK067238/DK/NIDDK NIH HHS/ -- GM071940/GM/NIGMS NIH HHS/ -- GM08281/GM/NIGMS NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 AI069015/AI/NIAID NIH HHS/ -- R01 AI069015-04/AI/NIAID NIH HHS/ -- R01 DK067238/DK/NIDDK NIH HHS/ -- R01 DK067238-07/DK/NIDDK NIH HHS/ -- R01 GM071940/GM/NIGMS NIH HHS/ -- R01 GM071940-05/GM/NIGMS NIH HHS/ -- T32 GM008281/GM/NIGMS NIH HHS/ -- T32 GM008281-23/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Aug 19;466(7309):1001-5. doi: 10.1038/nature09302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Columbia University, New York, New York 10027, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20725044" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl-CoA Carboxylase/chemistry/metabolism/ultrastructure ; Biocatalysis ; Biotin/metabolism ; Carbon-Nitrogen Ligases/chemistry/metabolism/ultrastructure ; Carrier Proteins/chemistry/metabolism/ultrastructure ; Catalytic Domain ; *Cryoelectron Microscopy ; Crystallography, X-Ray ; Fatty Acid Synthase, Type II ; Holoenzymes/*chemistry/genetics/metabolism/*ultrastructure ; Humans ; Methylmalonyl-CoA Decarboxylase/*chemistry/genetics/metabolism/*ultrastructure ; Models, Molecular ; Mutation/genetics ; Propionic Acidemia/enzymology/genetics ; Protein Binding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Rhodobacteraceae/enzymology ; Structure-Activity Relationship
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  • 63
    Publication Date: 2010-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fang, Janet -- Hand, Eric -- Monastersky, Richard -- Tollefson, Jeff -- Wadman, Meredith -- Waldrop, Mitchell -- England -- Nature. 2010 Feb 4;463(7281):594-5. doi: 10.1038/463594a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130620" target="_blank"〉PubMed〈/a〉
    Keywords: Budgets/*legislation & jurisprudence ; *Federal Government ; Global Warming/economics/prevention & control ; National Institutes of Health (U.S.)/economics ; Research Support as Topic/economics/legislation & jurisprudence ; Science/*economics/legislation & jurisprudence ; United States ; United States National Aeronautics and Space Administration/economics
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  • 64
    Publication Date: 2010-07-03
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518437/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518437/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Levine, Beth -- Ranganathan, Rama -- R01 CA109618/CA/NCI NIH HHS/ -- England -- Nature. 2010 Jul 1;466(7302):38-40. doi: 10.1038/466038a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20596005" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/genetics/metabolism ; Autophagy/genetics/*physiology ; Humans ; Microfilament Proteins/genetics/metabolism ; Protein Binding ; Protein Interaction Mapping/methods ; Proteomics/methods
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  • 65
    Publication Date: 2010-05-28
    Description: The Escherichia coli isocitrate dehydrogenase kinase/phosphatase (AceK) is a unique bifunctional enzyme that phosphorylates or dephosphorylates isocitrate dehydrogenase (ICDH) in response to environmental changes, resulting in the inactivation or, respectively, activation of ICDH. ICDH inactivation short-circuits the Krebs cycle by enabling the glyoxlate bypass. It was the discovery of AceK and ICDH that established the existence of protein phosphorylation regulation in prokaryotes. As a 65-kDa protein, AceK is significantly larger than typical eukaryotic protein kinases. Apart from the ATP-binding motif, AceK does not share sequence homology with any eukaryotic protein kinase or phosphatase. Most intriguingly, AceK possesses the two opposing activities of protein kinase and phosphatase within one protein, and specifically recognizes only intact ICDH. Additionally, AceK has strong ATPase activity. It has been shown that AceK kinase, phosphatase and ATPase activities reside at the same site, although the molecular basis of such multifunctionality and its regulation remains completely unknown. Here we report the structures of AceK and its complex with ICDH. The AceK structure reveals a eukaryotic protein-kinase-like domain containing ATP and a regulatory domain with a novel fold. As an AceK phosphatase activator and kinase inhibitor, AMP is found to bind in an allosteric site between the two AceK domains. An AMP-mediated conformational change exposes and shields ATP, acting as a switch between AceK kinase and phosphatase activities, and ICDH-binding induces further conformational change for AceK activation. The substrate recognition loop of AceK binds to the ICDH dimer, allowing higher-order substrate recognition and interaction, and inducing critical conformational change at the phosphorylation site of ICDH.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zheng, Jimin -- Jia, Zongchao -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2010 Jun 17;465(7300):961-5. doi: 10.1038/nature09088. Epub 2010 May 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20505668" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Escherichia coli/*enzymology/genetics ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Isocitrate Dehydrogenase ; *Models, Molecular ; Multienzyme Complexes/*chemistry/genetics/metabolism ; Mutation/genetics ; Protein Binding ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid
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  • 66
    Publication Date: 2010-03-20
    Description: Variation in transcriptional regulation is thought to be a major cause of phenotypic diversity. Although widespread differences in gene expression among individuals of a species have been observed, studies to examine the variability of transcription factor binding on a global scale have not been performed, and thus the extent and underlying genetic basis of transcription factor binding diversity is unknown. By mapping differences in transcription factor binding among individuals, here we present the genetic basis of such variation on a genome-wide scale. Whole-genome Ste12-binding profiles were determined using chromatin immunoprecipitation coupled with DNA sequencing in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains and their parental lines. We identified extensive Ste12-binding variation among individuals, and mapped underlying cis- and trans-acting loci responsible for such variation. We showed that most transcription factor binding variation is cis-linked, and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several proposed Ste12 cofactors. We also identified two trans-factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than ten genes under alpha-factor treatment. Neither of these two genes was previously known to regulate Ste12, and we suggest that they may be mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes, indicating that binding variation is functional. Many of the variable-bound genes are involved in cell wall organization and biogenesis. Overall, these studies identified genetic regulators of molecular diversity among individuals and provide new insights into mechanisms of gene regulation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941147/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941147/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zheng, Wei -- Zhao, Hongyu -- Mancera, Eugenio -- Steinmetz, Lars M -- Snyder, Michael -- P01 HG000205/HG/NHGRI NIH HHS/ -- P01 HG000205-10/HG/NHGRI NIH HHS/ -- R01 CA077808/CA/NCI NIH HHS/ -- R01 CA077808-09/CA/NCI NIH HHS/ -- R01 GM059507-09/GM/NIGMS NIH HHS/ -- R01 GM068717/GM/NIGMS NIH HHS/ -- R01 GM068717-08/GM/NIGMS NIH HHS/ -- RR19895/RR/NCRR NIH HHS/ -- England -- Nature. 2010 Apr 22;464(7292):1187-91. doi: 10.1038/nature08934. Epub 2010 Mar 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237471" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs/genetics ; Binding Sites/genetics ; Cell Cycle Proteins/genetics/metabolism ; Cell Wall/genetics/metabolism ; Gene Expression Regulation, Fungal ; Genes, Fungal/genetics ; Genetic Variation/*genetics ; Genome, Fungal/genetics ; Nuclear Proteins/genetics/metabolism ; Oligonucleotide Array Sequence Analysis ; Peptides/pharmacology ; Pheromones/pharmacology ; Polymorphism, Genetic/genetics ; Promoter Regions, Genetic/genetics ; Protein Binding ; Quantitative Trait Loci/genetics ; Reproducibility of Results ; Saccharomyces cerevisiae/drug effects/*genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*genetics/*metabolism ; Trans-Activators/genetics/metabolism ; Transcription Factors/chemistry/*genetics/*metabolism
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  • 67
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2010-09-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tollefson, Jeff -- England -- Nature. 2010 Sep 23;467(7314):376-7. doi: 10.1038/467376a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20864965" target="_blank"〉PubMed〈/a〉
    Keywords: Conservation of Energy Resources/economics/legislation & jurisprudence ; *Federal Government ; Fossil Fuels/economics ; Nuclear Energy/economics/legislation & jurisprudence/statistics & numerical data ; Nuclear Power Plants/economics/*legislation & jurisprudence/*statistics & ; numerical data ; Radioactive Waste/*legislation & jurisprudence/prevention & control ; United States
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  • 68
    Publication Date: 2010-04-07
    Description: Targeting of proteins to appropriate subcellular compartments is a crucial process in all living cells. Secretory and membrane proteins usually contain an amino-terminal signal peptide, which is recognized by the signal recognition particle (SRP) when nascent polypeptide chains emerge from the ribosome. The SRP-ribosome nascent chain complex is then targeted through its GTP-dependent interaction with SRP receptor to the protein-conducting channel on endoplasmic reticulum membrane in eukaryotes or plasma membrane in bacteria. A universally conserved component of SRP (refs 1, 2), SRP54 or its bacterial homologue, fifty-four homologue (Ffh), binds the signal peptides, which have a highly divergent sequence divisible into a positively charged n-region, an h-region commonly containing 8-20 hydrophobic residues and a polar c-region. No structure has been reported that exemplifies SRP54 binding of any signal sequence. Here we have produced a fusion protein between Sulfolobus solfataricus SRP54 (Ffh) and a signal peptide connected via a flexible linker. This fusion protein oligomerizes in solution through interaction between the SRP54 and signal peptide moieties belonging to different chains, and it is functional, as demonstrated by its ability to bind SRP RNA and SRP receptor FtsY. We present the crystal structure at 3.5 A resolution of an SRP54-signal peptide complex in the dimer, which reveals how a signal sequence is recognized by SRP54.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897128/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897128/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janda, Claudia Y -- Li, Jade -- Oubridge, Chris -- Hernandez, Helena -- Robinson, Carol V -- Nagai, Kiyoshi -- MC_U105184330/Medical Research Council/United Kingdom -- U.1051.04.016(78933)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2010 May 27;465(7297):507-10. doi: 10.1038/nature08870. Epub 2010 Apr 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20364120" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/metabolism ; Crystallography, X-Ray ; Mass Spectrometry ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Multimerization ; Protein Sorting Signals/*physiology ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Receptors, Cytoplasmic and Nuclear/metabolism ; Receptors, Virus/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; Signal Recognition Particle/*chemistry/*metabolism ; Structure-Activity Relationship ; Sulfolobus solfataricus/*chemistry
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  • 69
    Publication Date: 2010-02-12
    Description: How instructive cues present on the cell surface have their precise effects on the actin cytoskeleton is poorly understood. Semaphorins are one of the largest families of these instructive cues and are widely studied for their effects on cell movement, navigation, angiogenesis, immunology and cancer. Semaphorins/collapsins were characterized in part on the basis of their ability to drastically alter actin cytoskeletal dynamics in neuronal processes, but despite considerable progress in the identification of semaphorin receptors and their signalling pathways, the molecules linking them to the precise control of cytoskeletal elements remain unknown. Recently, highly unusual proteins of the Mical family of enzymes have been found to associate with the cytoplasmic portion of plexins, which are large cell-surface semaphorin receptors, and to mediate axon guidance, synaptogenesis, dendritic pruning and other cell morphological changes. Mical enzymes perform reduction-oxidation (redox) enzymatic reactions and also contain domains found in proteins that regulate cell morphology. However, nothing is known of the role of Mical or its redox activity in mediating morphological changes. Here we report that Mical directly links semaphorins and their plexin receptors to the precise control of actin filament (F-actin) dynamics. We found that Mical is both necessary and sufficient for semaphorin-plexin-mediated F-actin reorganization in vivo. Likewise, we purified Mical protein and found that it directly binds F-actin and disassembles both individual and bundled actin filaments. We also found that Mical utilizes its redox activity to alter F-actin dynamics in vivo and in vitro, indicating a previously unknown role for specific redox signalling events in actin cytoskeletal regulation. Mical therefore is a novel F-actin-disassembly factor that provides a molecular conduit through which actin reorganization-a hallmark of cell morphological changes including axon navigation-can be precisely achieved spatiotemporally in response to semaphorins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3215588/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3215588/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hung, Ruei-Jiun -- Yazdani, Umar -- Yoon, Jimok -- Wu, Heng -- Yang, Taehong -- Gupta, Nidhi -- Huang, Zhiyu -- van Berkel, Willem J H -- Terman, Jonathan R -- MH085923/MH/NIMH NIH HHS/ -- R01 MH085923/MH/NIMH NIH HHS/ -- R01 MH085923-01A1/MH/NIMH NIH HHS/ -- England -- Nature. 2010 Feb 11;463(7282):823-7. doi: 10.1038/nature08724.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Neuroscience Graduate Program, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20148037" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*chemistry/*metabolism ; Animals ; Cell Adhesion Molecules/metabolism ; Cell Shape/physiology ; Cytoskeleton/chemistry/metabolism ; DNA-Binding Proteins/deficiency/genetics/*metabolism ; Drosophila melanogaster/anatomy & histology/*cytology/enzymology/*metabolism ; Growth Cones/metabolism ; Nerve Tissue Proteins/metabolism ; Oxidation-Reduction ; Oxidoreductases/deficiency/genetics/metabolism ; Protein Binding ; Semaphorins/*metabolism
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  • 70
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2010-10-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zou, Lee -- England -- Nature. 2010 Oct 7;467(7316):667-8. doi: 10.1038/467667a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20930833" target="_blank"〉PubMed〈/a〉
    Keywords: Apoptosis Regulatory Proteins ; BRCA2 Protein/chemistry/*isolation & purification/*metabolism ; Chromosomal Instability ; DNA/chemistry/metabolism ; DNA Repair ; DNA, Single-Stranded/chemistry/metabolism ; Humans ; Protein Binding ; Rad51 Recombinase/*metabolism ; *Recombination, Genetic ; Replication Protein A/metabolism ; Sequence Homology, Nucleic Acid ; Substrate Specificity
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  • 71
    Publication Date: 2010-08-24
    Description: Mutation of the breast cancer susceptibility gene, BRCA2, leads to breast and ovarian cancers. Mechanistic insight into the functions of human BRCA2 has been limited by the difficulty of isolating this large protein (3,418 amino acids). Here we report the purification of full-length BRCA2 and show that it both binds RAD51 and potentiates recombinational DNA repair by promoting assembly of RAD51 onto single-stranded DNA (ssDNA). BRCA2 acts by targeting RAD51 to ssDNA over double-stranded DNA, enabling RAD51 to displace replication protein-A (RPA) from ssDNA and stabilizing RAD51-ssDNA filaments by blocking ATP hydrolysis. BRCA2 does not anneal ssDNA complexed with RPA, implying it does not directly function in repair processes that involve ssDNA annealing. Our findings show that BRCA2 is a key mediator of homologous recombination, and they provide a molecular basis for understanding how this DNA repair process is disrupted by BRCA2 mutations, which lead to chromosomal instability and cancer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952063/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952063/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jensen, Ryan B -- Carreira, Aura -- Kowalczykowski, Stephen C -- GM 62653/GM/NIGMS NIH HHS/ -- R01 GM062653/GM/NIGMS NIH HHS/ -- R01 GM062653-30/GM/NIGMS NIH HHS/ -- R01 GM062653-31/GM/NIGMS NIH HHS/ -- R37 GM062653/GM/NIGMS NIH HHS/ -- R37 GM062653-29/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Oct 7;467(7316):678-83. doi: 10.1038/nature09399.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of California, Davis, California 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20729832" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Apoptosis Regulatory Proteins ; BRCA2 Protein/chemistry/*isolation & purification/*metabolism ; Cell Cycle Proteins/metabolism ; Cell Line ; Chromosomal Instability ; DNA/chemistry/metabolism ; DNA Repair ; DNA, Single-Stranded/chemistry/metabolism ; DNA-Binding Proteins/metabolism ; Humans ; Mutation ; Protein Binding ; Rad51 Recombinase/*metabolism ; *Recombination, Genetic ; Replication Protein A/metabolism ; Sequence Homology, Nucleic Acid ; Substrate Specificity
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  • 72
    Publication Date: 2010-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scherrer, Klaus -- England -- Nature. 2010 Apr 29;464(7293):1266. doi: 10.1038/4641266a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20428140" target="_blank"〉PubMed〈/a〉
    Keywords: *Federal Government ; France ; Politics ; Research/economics/*legislation & jurisprudence
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  • 73
    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mann, Adam -- England -- Nature. 2010 Oct 14;467(7317):763. doi: 10.1038/467763a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944704" target="_blank"〉PubMed〈/a〉
    Keywords: Astronauts/trends ; *Federal Government ; Policy ; *Politics ; United States ; United States National Aeronautics and Space ; Administration/*economics/*legislation & jurisprudence
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  • 74
    Publication Date: 2010-08-27
    Description: Successful partition of replicated genomes at cell division requires chromosome attachment to opposite poles of mitotic spindle (bi-orientation). Any defects in this regulation bring about chromosomal instability, which may accelerate tumour progression in humans. To achieve chromosome bi-orientation at prometaphase, the chromosomal passenger complex (CPC), composed of catalytic kinase Aurora B and regulatory components (INCENP, Survivin and Borealin), must be localized to centromeres to phosphorylate kinetochore substrates. Although the CPC dynamically changes the subcellular localization, the regulation of centromere targeting is largely unknown. Here we isolated a fission yeast cyclin B mutant defective specifically in chromosome bi-orientation. Accordingly, we identified Cdk1 (also known as Cdc2)-cyclin-B-dependent phosphorylation of Survivin. Preventing Survivin phosphorylation impairs centromere CPC targeting as well as chromosome bi-orientation, whereas phosphomimetic Survivin suppresses the bi-orientation defect in the cyclin B mutant. Survivin phosphorylation promotes direct binding with shugoshin, which we now define as a conserved centromeric adaptor of the CPC. In human cells, the phosphorylation of Borealin has a comparable role. Thus, our study resolves the conserved mechanisms of CPC targeting to centromeres, highlighting a key role of Cdk1-cyclin B in chromosome bi-orientation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsukahara, Tatsuya -- Tanno, Yuji -- Watanabe, Yoshinori -- England -- Nature. 2010 Oct 7;467(7316):719-23. doi: 10.1038/nature09390. Epub 2010 Aug 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chromosome Dynamics, Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi, Tokyo 113-0032, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20739936" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Aurora Kinase B ; Aurora Kinases ; CDC2 Protein Kinase/*metabolism ; Carrier Proteins/genetics/metabolism ; Cell Cycle Proteins/genetics/metabolism ; Cell Line ; Centromere/metabolism ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosomes, Fungal/*metabolism ; Chromosomes, Human/*metabolism ; Cyclin B/genetics/metabolism ; Humans ; Inhibitor of Apoptosis Proteins ; Microtubule-Associated Proteins/metabolism ; Molecular Sequence Data ; Multiprotein Complexes/*chemistry/*metabolism ; Phosphorylation ; Protein Binding ; Protein-Serine-Threonine Kinases/genetics/metabolism ; Schizosaccharomyces/cytology/genetics/metabolism ; Schizosaccharomyces pombe Proteins/genetics/*metabolism ; Substrate Specificity
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  • 75
    Publication Date: 2010-01-16
    Description: The Polycomb group (PcG) proteins have an important role in controlling the expression of genes essential for development, differentiation and maintenance of cell fates. The Polycomb repressive complex 2 (PRC2) is believed to regulate transcriptional repression by catalysing the di- and tri-methylation of lysine 27 on histone H3 (H3K27me2/3). At present, it is unknown how the PcG proteins are recruited to their target promoters in mammalian cells. Here we show that PRC2 forms a stable complex with the Jumonji- and ARID-domain-containing protein, JARID2 (ref. 4). Using genome-wide location analysis, we show that JARID2 binds to more than 90% of previously mapped PcG target genes. Notably, we show that JARID2 is sufficient to recruit PcG proteins to a heterologous promoter, and that inhibition of JARID2 expression leads to a major loss of PcG binding and to a reduction of H3K27me3 levels on target genes. Consistent with an essential role for PcG proteins in early development, we demonstrate that JARID2 is required for the differentiation of mouse embryonic stem cells. Thus, these results demonstrate that JARID2 is essential for the binding of PcG proteins to target genes and, consistent with this, for the proper differentiation of embryonic stem cells and normal development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pasini, Diego -- Cloos, Paul A C -- Walfridsson, Julian -- Olsson, Linda -- Bukowski, John-Paul -- Johansen, Jens V -- Bak, Mads -- Tommerup, Niels -- Rappsilber, Juri -- Helin, Kristian -- 084229/Wellcome Trust/United Kingdom -- England -- Nature. 2010 Mar 11;464(7286):306-10. doi: 10.1038/nature08788.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075857" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cell Line ; Embryonic Stem Cells/*cytology/*metabolism ; Gene Expression Regulation ; HeLa Cells ; Humans ; Mice ; Nerve Tissue Proteins/genetics/*metabolism ; Polycomb Repressive Complex 2 ; Polycomb-Group Proteins ; Promoter Regions, Genetic ; Protein Binding ; Repressor Proteins/*metabolism
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  • 76
    Publication Date: 2010-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goldstein, Stephane -- England -- Nature. 2010 Feb 18;463(7283):876-7. doi: 10.1038/463876c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20164900" target="_blank"〉PubMed〈/a〉
    Keywords: *Federal Government ; Great Britain ; Politics ; *Research Personnel ; Science/education/*manpower
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  • 77
    Publication Date: 2010-05-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wadman, Meredith -- England -- Nature. 2010 May 27;465(7297):404-5. doi: 10.1038/465404b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20505700" target="_blank"〉PubMed〈/a〉
    Keywords: Biomedical Research/economics/legislation & jurisprudence ; *Federal Government ; National Institutes of Health (U.S.)/*economics/*legislation & jurisprudence ; Research Personnel ; Research Support as Topic/economics/legislation & jurisprudence ; United States
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  • 78
    Publication Date: 2010-08-21
    Description: Haemostasis in the arteriolar circulation mediated by von Willebrand factor (VWF) binding to platelets is an example of an adhesive interaction that must withstand strong hydrodynamic forces acting on cells. VWF is a concatenated, multifunctional protein that has binding sites for platelets as well as subendothelial collagen. Binding of the A1 domain in VWF to the glycoprotein Ib alpha subunit (GPIbalpha) on the surface of platelets mediates crosslinking of platelets to one another and the formation of a platelet plug for arterioles. The importance of VWF is illustrated by its mutation in von Willebrand disease, a bleeding diathesis. Here, we describe a novel mechanochemical specialization of the A1-GPIbalpha bond for force-resistance. We have developed a method that enables, for the first time, repeated measurements of the binding and unbinding of a receptor and ligand in a single molecule (ReaLiSM). We demonstrate two states of the receptor-ligand bond, that is, a flex-bond. One state is seen at low force; a second state begins to engage at 10 pN with a approximately 20-fold longer lifetime and greater force resistance. The lifetimes of the two states, how force exponentiates lifetime, and the kinetics of switching between the two states are all measured. For the first time, single-molecule measurements on this system are in agreement with bulk phase measurements. The results have important implications not only for how platelets bound to VWF are able to resist force to plug arterioles, but also how increased flow activates platelet plug formation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117310/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117310/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Jongseong -- Zhang, Cheng-Zhong -- Zhang, Xiaohui -- Springer, Timothy A -- HL-48675/HL/NHLBI NIH HHS/ -- P01 HL048675/HL/NHLBI NIH HHS/ -- England -- Nature. 2010 Aug 19;466(7309):992-5. doi: 10.1038/nature09295.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Immune Disease Institute, Children's Hospital Boston and Department of Pathology, Harvard Medical School, 3 Blackfan Circle, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20725043" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arterioles/cytology/*physiology ; Blood Coagulation/*physiology ; Blood Platelets/chemistry/cytology/*metabolism ; Cell Line ; Hemorheology ; Humans ; Kinetics ; Ligands ; Membrane Glycoproteins/chemistry/*metabolism ; Mice ; Models, Chemical ; Models, Molecular ; Platelet Glycoprotein GPIb-IX Complex ; Protein Binding ; Protein Structure, Tertiary ; Tensile Strength ; von Willebrand Factor/chemistry/*metabolism
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  • 79
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    Nature Publishing Group (NPG)
    Publication Date: 2010-04-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wadman, Meredith -- England -- Nature. 2010 Apr 15;464(7291):967. doi: 10.1038/464967a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393530" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; *Embryonic Stem Cells ; *Federal Government ; Humans ; National Institutes of Health (U.S.)/legislation & jurisprudence ; Research Support as Topic/*economics ; Time Factors ; United States
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  • 80
    Publication Date: 2014-08-15
    Description: The balance between stem cell self-renewal and differentiation is controlled by intrinsic factors and niche signals. In the Drosophila melanogaster ovary, some intrinsic factors promote germline stem cell (GSC) self-renewal, whereas others stimulate differentiation. However, it remains poorly understood how the balance between self-renewal and differentiation is controlled. Here we use D. melanogaster ovarian GSCs to demonstrate that the differentiation factor Bam controls the functional switch of the COP9 complex from self-renewal to differentiation via protein competition. The COP9 complex is composed of eight Csn subunits, Csn1-8, and removes Nedd8 modifications from target proteins. Genetic results indicated that the COP9 complex is required intrinsically for GSC self-renewal, whereas other Csn proteins, with the exception of Csn4, were also required for GSC progeny differentiation. Bam-mediated Csn4 sequestration from the COP9 complex via protein competition inactivated the self-renewing function of COP9 and allowed other Csn proteins to promote GSC differentiation. Therefore, this study reveals a protein-competition-based mechanism for controlling the balance between stem cell self-renewal and differentiation. Because numerous self-renewal factors are ubiquitously expressed throughout the stem cell lineage in various systems, protein competition may function as an important mechanism for controlling the self-renewal-to-differentiation switch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pan, Lei -- Wang, Su -- Lu, Tinglin -- Weng, Changjiang -- Song, Xiaoqing -- Park, Joseph K -- Sun, Jin -- Yang, Zhi-Hao -- Yu, Junjing -- Tang, Hong -- McKearin, Dennis M -- Chamovitz, Daniel A -- Ni, Jianquan -- Xie, Ting -- GM64428/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Oct 9;514(7521):233-6. doi: 10.1038/nature13562.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, 15 Da Tun Road, Beijing 100101, China [3]. ; 1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Department of Cell Biology and Anatomy, University of Kansas School of Medicine, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA [3]. ; 1] Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China [2]. ; Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA. ; 1] Department of Molecular Biology and Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9148, USA [2] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA. ; Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China. ; 1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, 15 Da Tun Road, Beijing 100101, China. ; Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, 15 Da Tun Road, Beijing 100101, China. ; Department of Plant Sciences, Tel Aviv University, Tel Aviv 69978, Israel. ; 1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Department of Cell Biology and Anatomy, University of Kansas School of Medicine, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25119050" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Binding, Competitive ; *Cell Differentiation ; Cell Proliferation ; DNA Helicases/metabolism ; Drosophila Proteins/metabolism ; Drosophila melanogaster/*cytology/*metabolism ; Female ; Intracellular Signaling Peptides and Proteins/metabolism ; Male ; Multiprotein Complexes/*chemistry/*metabolism ; Ovary/cytology ; Peptide Hydrolases/*chemistry/*metabolism ; Protein Binding ; Stem Cells/*cytology/*metabolism ; Ubiquitins/metabolism
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  • 81
    Publication Date: 2014-04-04
    Description: Autophagy, the process by which proteins and organelles are sequestered in double-membrane structures called autophagosomes and delivered to lysosomes for degradation, is critical in diseases such as cancer and neurodegeneration. Much of our understanding of this process has emerged from analysis of bulk cytoplasmic autophagy, but our understanding of how specific cargo, including organelles, proteins or intracellular pathogens, are targeted for selective autophagy is limited. Here we use quantitative proteomics to identify a cohort of novel and known autophagosome-enriched proteins in human cells, including cargo receptors. Like known cargo receptors, nuclear receptor coactivator 4 (NCOA4) was highly enriched in autophagosomes, and associated with ATG8 proteins that recruit cargo-receptor complexes into autophagosomes. Unbiased identification of NCOA4-associated proteins revealed ferritin heavy and light chains, components of an iron-filled cage structure that protects cells from reactive iron species but is degraded via autophagy to release iron through an unknown mechanism. We found that delivery of ferritin to lysosomes required NCOA4, and an inability of NCOA4-deficient cells to degrade ferritin led to decreased bioavailable intracellular iron. This work identifies NCOA4 as a selective cargo receptor for autophagic turnover of ferritin (ferritinophagy), which is critical for iron homeostasis, and provides a resource for further dissection of autophagosomal cargo-receptor connectivity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180099/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180099/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mancias, Joseph D -- Wang, Xiaoxu -- Gygi, Steven P -- Harper, J Wade -- Kimmelman, Alec C -- GM070565/GM/NIGMS NIH HHS/ -- GM095567/GM/NIGMS NIH HHS/ -- P50 CA127003/CA/NCI NIH HHS/ -- R01 CA157490/CA/NCI NIH HHS/ -- R01 GM070565/GM/NIGMS NIH HHS/ -- R01 GM095567/GM/NIGMS NIH HHS/ -- R01CA157490/CA/NCI NIH HHS/ -- England -- Nature. 2014 May 1;509(7498):105-9. doi: 10.1038/nature13148. Epub 2014 Mar 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Harvard Radiation Oncology Program, Boston, Massachusetts 02115, USA [4] Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA. ; Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA. ; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24695223" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; *Autophagy ; Biological Availability ; Ferritins/chemistry/*metabolism ; Homeostasis ; Humans ; Iron/metabolism ; Lysosomes/metabolism ; Microfilament Proteins/metabolism ; Nuclear Receptor Coactivators/deficiency/genetics/*metabolism ; Phagosomes/*metabolism ; Protein Binding ; Protein Transport ; *Proteomics ; Substrate Specificity
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  • 82
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    Nature Publishing Group (NPG)
    Publication Date: 2014-02-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mallapaty, Smriti -- England -- Nature. 2014 Feb 20;506(7488):279. doi: 10.1038/506279a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24553222" target="_blank"〉PubMed〈/a〉
    Keywords: *Fasting ; *Federal Government ; Humans ; Male ; Nepal ; *Politics ; Schools, Medical/organization & administration ; *Strikes, Employee ; Universities/*organization & administration
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  • 83
    Publication Date: 2014-06-05
    Description: Genome instability is central to ageing, cancer and other diseases. It is not only proteins involved in DNA replication or the DNA damage response (DDR) that are important for maintaining genome integrity: from yeast to higher eukaryotes, mutations in genes involved in pre-mRNA splicing and in the biogenesis and export of messenger ribonucleoprotein (mRNP) also induce DNA damage and genome instability. This instability is frequently mediated by R-loops formed by DNA-RNA hybrids and a displaced single-stranded DNA. Here we show that the human TREX-2 complex, which is involved in mRNP biogenesis and export, prevents genome instability as determined by the accumulation of gamma-H2AX (Ser-139 phosphorylated histone H2AX) and 53BP1 foci and single-cell electrophoresis in cells depleted of the TREX-2 subunits PCID2, GANP and DSS1. We show that the BRCA2 repair factor, which binds to DSS1, also associates with PCID2 in the cell. The use of an enhanced green fluorescent protein-tagged hybrid-binding domain of RNase H1 and the S9.6 antibody did not detect R-loops in TREX-2-depleted cells, but did detect the accumulation of R-loops in BRCA2-depleted cells. The results indicate that R-loops are frequently formed in cells and that BRCA2 is required for their processing. This link between BRCA2 and RNA-mediated genome instability indicates that R-loops may be a chief source of replication stress and cancer-associated instability.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhatia, Vaibhav -- Barroso, Sonia I -- Garcia-Rubio, Maria L -- Tumini, Emanuela -- Herrera-Moyano, Emilia -- Aguilera, Andres -- England -- Nature. 2014 Jul 17;511(7509):362-5. doi: 10.1038/nature13374. Epub 2014 Jun 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centro Andaluz de Biologia Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Avenida Americo Vespucio s/n, 41092 Seville, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24896180" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyltransferases/metabolism ; BRCA2 Protein/deficiency/genetics/*metabolism ; DNA Damage ; DNA Replication ; DNA, Single-Stranded/chemistry/*metabolism ; Exodeoxyribonucleases/chemistry/deficiency/*metabolism ; *Genomic Instability ; Histones/chemistry/metabolism ; Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Nuclear Proteins/*metabolism ; Nucleic Acid Conformation ; Phosphoproteins/chemistry/deficiency/*metabolism ; Proteasome Endopeptidase Complex/metabolism ; Protein Binding ; RNA/chemistry/*metabolism ; *RNA Transport ; Ribonuclease H/chemistry ; Ribonucleoproteins/biosynthesis/metabolism
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  • 84
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    Publication Date: 2010-02-25
    Description: Science in Canada cannot realize its full potential without clear direction from government.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Jan 14;463(7278):135. doi: 10.1038/463135a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075872" target="_blank"〉PubMed〈/a〉
    Keywords: Arctic Regions ; Canada ; *Federal Government ; Lobbying ; Public Policy/legislation & jurisprudence/trends ; Science/economics/legislation & jurisprudence/*organization & ; administration/*trends
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  • 85
    Publication Date: 2010-10-15
    Description: Bacillus anthracis is the causative agent of anthrax in humans and other mammals. In lethal systemic anthrax, proliferating bacilli secrete large quantities of the toxins lethal factor (LF) and oedema factor (EF), leading to widespread vascular leakage and shock. Whereas host targets of LF (mitogen-activated protein-kinase kinases) and EF (cAMP-dependent processes) have been implicated in the initial phase of anthrax, less is understood about toxin action during the final stage of infection. Here we use Drosophila melanogaster to identify the Rab11/Sec15 exocyst, which acts at the last step of endocytic recycling, as a novel target of both EF and LF. EF reduces levels of apically localized Rab11 and indirectly blocks vesicle formation by its binding partner and effector Sec15 (Sec15-GFP), whereas LF acts more directly to reduce Sec15-GFP vesicles. Convergent effects of EF and LF on Rab11/Sec15 inhibit expression of and signalling by the Notch ligand Delta and reduce DE-cadherin levels at adherens junctions. In human endothelial cells, the two toxins act in a conserved fashion to block formation of Sec15 vesicles, inhibit Notch signalling, and reduce cadherin expression at adherens junctions. This coordinated disruption of the Rab11/Sec15 exocyst by anthrax toxins may contribute to toxin-dependent barrier disruption and vascular dysfunction during B. anthracis infection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guichard, Annabel -- McGillivray, Shauna M -- Cruz-Moreno, Beatriz -- van Sorge, Nina M -- Nizet, Victor -- Bier, Ethan -- GM068524/GM/NIGMS NIH HHS/ -- R01 AI070654/AI/NIAID NIH HHS/ -- R01AI070654/AI/NIAID NIH HHS/ -- R01AI077780/AI/NIAID NIH HHS/ -- R01NS29870/NS/NINDS NIH HHS/ -- England -- Nature. 2010 Oct 14;467(7317):854-8. doi: 10.1038/nature09446.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0349, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944747" target="_blank"〉PubMed〈/a〉
    Keywords: Adherens Junctions/metabolism ; Animals ; Antigens, Bacterial/*pharmacology ; *Bacillus anthracis/chemistry/pathogenicity ; Bacterial Toxins/*pharmacology ; Cadherins ; Cell Line ; Drosophila Proteins/metabolism ; Drosophila melanogaster/cytology/drug effects/metabolism ; Drug Synergism ; Endocytosis/*drug effects ; Endothelial Cells/drug effects/metabolism ; Female ; GTP-Binding Proteins/*metabolism ; Humans ; Models, Animal ; Protein Binding ; Receptors, Notch/metabolism ; Signal Transduction/drug effects ; Transport Vesicles/drug effects/metabolism ; Vesicular Transport Proteins/metabolism ; rab GTP-Binding Proteins/*metabolism
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  • 86
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    Nature Publishing Group (NPG)
    Publication Date: 2010-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Feb 11;463(7282):709-10. doi: 10.1038/463709b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20147990" target="_blank"〉PubMed〈/a〉
    Keywords: Astronauts/economics ; Budgets/legislation & jurisprudence ; *Federal Government ; Private Sector/*economics ; Public-Private Sector Partnerships/economics/trends ; Space Flight/*economics/*trends ; Spacecraft/*economics ; United States ; United States National Aeronautics and Space Administration/economics/*trends
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  • 87
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    Nature Publishing Group (NPG)
    Publication Date: 2010-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Feb 4;463(7281):587-8. doi: 10.1038/463587b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130608" target="_blank"〉PubMed〈/a〉
    Keywords: Budgets/*legislation & jurisprudence ; *Federal Government ; Investments/economics ; Research Personnel/*economics/*standards ; Research Support as Topic/*economics ; Science/*economics/legislation & jurisprudence ; United States
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  • 88
    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reich, Eugenie Samuel -- England -- Nature. 2010 Oct 14;467(7317):760-1. doi: 10.1038/467760a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944701" target="_blank"〉PubMed〈/a〉
    Keywords: American Recovery and Reinvestment Act/economics ; Budgets ; *Federal Government ; *Politics ; Research Support as Topic/*economics/*legislation & jurisprudence ; Science/*economics/legislation & jurisprudence ; United States
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  • 89
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    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2010-04-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2010 Apr 29;464(7293):1254-5. doi: 10.1038/4641254a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20428132" target="_blank"〉PubMed〈/a〉
    Keywords: *Federal Government ; Great Britain ; Political Systems ; Politics ; Research Personnel ; Research Support as Topic/economics ; Science/*economics/trends
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  • 90
    Publication Date: 2010-08-27
    Description: The transcription factor p53 (also known as TP53) guards against tumour and virus replication and is inactivated in almost all cancers. p53-activated transcription of target genes is thought to be synonymous with the stabilization of p53 in response to oncogenes and DNA damage. During adenovirus replication, the degradation of p53 by E1B-55k is considered essential for p53 inactivation, and is the basis for p53-selective viral cancer therapies. Here we reveal a dominant epigenetic mechanism that silences p53-activated transcription, irrespective of p53 phosphorylation and stabilization. We show that another adenoviral protein, E4-ORF3, inactivates p53 independently of E1B-55k by forming a nuclear structure that induces de novo H3K9me3 heterochromatin formation at p53 target promoters, preventing p53-DNA binding. This suppressive nuclear web is highly selective in silencing p53 promoters and operates in the backdrop of global transcriptional changes that drive oncogenic replication. These findings are important for understanding how high levels of wild-type p53 might also be inactivated in cancer as well as the mechanisms that induce aberrant epigenetic silencing of tumour-suppressor loci. Our study changes the longstanding definition of how p53 is inactivated in adenovirus infection and provides key insights that could enable the development of true p53-selective oncolytic viral therapies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929938/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929938/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Soria, Conrado -- Estermann, Fanny E -- Espantman, Kristen C -- O'Shea, Clodagh C -- R01 CA137094/CA/NCI NIH HHS/ -- R01 CA137094-01/CA/NCI NIH HHS/ -- R01CA137094/CA/NCI NIH HHS/ -- England -- Nature. 2010 Aug 26;466(7310):1076-81. doi: 10.1038/nature09307.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037-1099, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20740008" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae/*metabolism ; Cell Proliferation ; Cells, Cultured ; Epigenesis, Genetic ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; *Gene Silencing ; HCT116 Cells ; Heterochromatin/*metabolism ; Histones/metabolism ; Humans ; Methylation ; Neoplasms/metabolism/virology ; Oncogene Proteins, Viral/*metabolism ; Protein Binding ; Tumor Suppressor Protein p53/*genetics/*metabolism ; Virus Replication
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  • 91
    Publication Date: 2014-12-04
    Description: T-helper type 17 (TH17) cells that produce the cytokines interleukin-17A (IL-17A) and IL-17F are implicated in the pathogenesis of several autoimmune diseases. The differentiation of TH17 cells is regulated by transcription factors such as RORgammat, but post-translational mechanisms preventing the rampant production of pro-inflammatory IL-17A have received less attention. Here we show that the deubiquitylating enzyme DUBA is a negative regulator of IL-17A production in T cells. Mice with DUBA-deficient T cells developed exacerbated inflammation in the small intestine after challenge with anti-CD3 antibodies. DUBA interacted with the ubiquitin ligase UBR5, which suppressed DUBA abundance in naive T cells. DUBA accumulated in activated T cells and stabilized UBR5, which then ubiquitylated RORgammat in response to TGF-beta signalling. Our data identify DUBA as a cell-intrinsic suppressor of IL-17 production.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rutz, Sascha -- Kayagaki, Nobuhiko -- Phung, Qui T -- Eidenschenk, Celine -- Noubade, Rajkumar -- Wang, Xiaoting -- Lesch, Justin -- Lu, Rongze -- Newton, Kim -- Huang, Oscar W -- Cochran, Andrea G -- Vasser, Mark -- Fauber, Benjamin P -- DeVoss, Jason -- Webster, Joshua -- Diehl, Lauri -- Modrusan, Zora -- Kirkpatrick, Donald S -- Lill, Jennie R -- Ouyang, Wenjun -- Dixit, Vishva M -- England -- Nature. 2015 Feb 19;518(7539):417-21. doi: 10.1038/nature13979. Epub 2014 Dec 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, Genentech, 1 DNA Way, South San Francisco, California 94080, USA. ; Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, USA. ; Department of Protein Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, USA. ; Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, USA. ; Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, USA. ; Department of Pathology, Genentech, 1 DNA Way, South San Francisco, California 94080, USA. ; Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25470037" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Enzyme Stability ; Female ; Inflammation/genetics/pathology ; Interleukin-17/*biosynthesis ; Intestine, Small/metabolism/pathology ; Lymphocyte Activation ; Mice ; Mice, Inbred C57BL ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Protein Binding ; *Protein Biosynthesis ; Signal Transduction ; Substrate Specificity ; Th17 Cells/*metabolism ; Transforming Growth Factor beta/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitin-Specific Proteases/biosynthesis/deficiency/genetics/*metabolism ; Ubiquitination
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  • 92
    Publication Date: 2014-11-05
    Description: Plant stem cells in the shoot apical meristem (SAM) and root apical meristem are necessary for postembryonic development of aboveground tissues and roots, respectively, while secondary vascular stem cells sustain vascular development. WUSCHEL (WUS), a homeodomain transcription factor expressed in the rib meristem of the Arabidopsis SAM, is a key regulatory factor controlling SAM stem cell populations, and is thought to establish the shoot stem cell niche through a feedback circuit involving the CLAVATA3 (CLV3) peptide signalling pathway. WUSCHEL-RELATED HOMEOBOX 5 (WOX5), which is specifically expressed in the root quiescent centre, defines quiescent centre identity and functions interchangeably with WUS in the control of shoot and root stem cell niches. WOX4, expressed in Arabidopsis procambial cells, defines the vascular stem cell niche. WUS/WOX family proteins are evolutionarily and functionally conserved throughout the plant kingdom and emerge as key actors in the specification and maintenance of stem cells within all meristems. However, the nature of the genetic regime in stem cell niches that centre on WOX gene function has been elusive, and molecular links underlying conserved WUS/WOX function in stem cell niches remain unknown. Here we demonstrate that the Arabidopsis HAIRY MERISTEM (HAM) family of transcription regulators act as conserved interacting cofactors with WUS/WOX proteins. HAM and WUS share common targets in vivo and their physical interaction is important in driving downstream transcriptional programs and in promoting shoot stem cell proliferation. Differences in the overlapping expression patterns of WOX and HAM family members underlie the formation of diverse stem cell niche locations, and the HAM family is essential for all of these stem cell niches. These findings establish a new framework for the control of stem cell production during plant development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297503/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297503/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Yun -- Liu, Xing -- Engstrom, Eric M -- Nimchuk, Zachary L -- Pruneda-Paz, Jose L -- Tarr, Paul T -- Yan, An -- Kay, Steve A -- Meyerowitz, Elliot M -- GM056006/GM/NIGMS NIH HHS/ -- GM067837/GM/NIGMS NIH HHS/ -- GM094212/GM/NIGMS NIH HHS/ -- R01 GM056006/GM/NIGMS NIH HHS/ -- R01 GM067837/GM/NIGMS NIH HHS/ -- R01 GM104244/GM/NIGMS NIH HHS/ -- RC2 GM092412/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Jan 15;517(7534):377-80. doi: 10.1038/nature13853. Epub 2014 Oct 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA. ; Biology Department, College of William and Mary, Williamsburg, Virginia 23187-8795, USA. ; 1] Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA [2] Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA. ; Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA. ; University of Southern California, Molecular and Computational Biology, Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25363783" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*cytology/genetics/*metabolism ; Arabidopsis Proteins/*metabolism ; Cell Proliferation ; *Gene Expression Regulation, Plant ; Histone Acetyltransferases/metabolism ; Homeodomain Proteins/metabolism ; Plant Shoots/cytology/genetics ; Protein Binding ; Stem Cell Niche ; Stem Cells/*cytology/*metabolism ; *Transcription, Genetic
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  • 93
    Publication Date: 2014-12-04
    Description: Muscle contraction is initiated by the release of calcium (Ca(2+)) from the sarcoplasmic reticulum into the cytoplasm of myocytes through ryanodine receptors (RyRs). RyRs are homotetrameric channels with a molecular mass of more than 2.2 megadaltons that are regulated by several factors, including ions, small molecules and proteins. Numerous mutations in RyRs have been associated with human diseases. The molecular mechanism underlying the complex regulation of RyRs is poorly understood. Using electron cryomicroscopy, here we determine the architecture of rabbit RyR1 at a resolution of 6.1 A. We show that the cytoplasmic moiety of RyR1 contains two large alpha-solenoid domains and several smaller domains, with folds suggestive of participation in protein-protein interactions. The transmembrane domain represents a chimaera of voltage-gated sodium and pH-activated ion channels. We identify the calcium-binding EF-hand domain and show that it functions as a conformational switch allosterically gating the channel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Efremov, Rouslan G -- Leitner, Alexander -- Aebersold, Ruedi -- Raunser, Stefan -- England -- Nature. 2015 Jan 1;517(7532):39-43. doi: 10.1038/nature13916. Epub 2014 Dec 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany [2] Structural Biology Research Center, Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium [3] Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium. ; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland. ; 1] Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland [2] Faculty of Science, University of Zurich, 8057 Zurich, Switzerland. ; Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25470059" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation/drug effects ; Animals ; Calcium/deficiency/metabolism/pharmacology ; Cryoelectron Microscopy ; Cytoplasm/metabolism ; Hydrogen-Ion Concentration ; Inositol 1,4,5-Trisphosphate Receptors/chemistry ; Ion Channel Gating/drug effects ; Models, Molecular ; Protein Binding ; Protein Structure, Tertiary/drug effects ; Rabbits ; Ryanodine Receptor Calcium Release Channel/chemistry/*metabolism/*ultrastructure ; Tacrolimus Binding Protein 1A/chemistry/metabolism/ultrastructure
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  • 94
    Publication Date: 2010-07-31
    Description: Gain-of-function mutations in leucine-rich repeat kinase 2 (LRRK2) cause familial as well as sporadic Parkinson's disease characterized by age-dependent degeneration of dopaminergic neurons. The molecular mechanism of LRRK2 action is not known. Here we show that LRRK2 interacts with the microRNA (miRNA) pathway to regulate protein synthesis. Drosophila e2f1 and dp messenger RNAs are translationally repressed by let-7 and miR-184*, respectively. Pathogenic LRRK2 antagonizes these miRNAs, leading to the overproduction of E2F1/DP, previously implicated in cell cycle and survival control and shown here to be critical for LRRK2 pathogenesis. Genetic deletion of let-7, antagomir-mediated blockage of let-7 and miR-184* action, transgenic expression of dp target protector, or replacement of endogenous dp with a dp transgene non-responsive to let-7 each had toxic effects similar to those of pathogenic LRRK2. Conversely, increasing the level of let-7 or miR-184* attenuated pathogenic LRRK2 effects. LRRK2 associated with Drosophila Argonaute-1 (dAgo1) or human Argonaute-2 (hAgo2) of the RNA-induced silencing complex (RISC). In aged fly brain, dAgo1 protein level was negatively regulated by LRRK2. Further, pathogenic LRRK2 promoted the association of phospho-4E-BP1 with hAgo2. Our results implicate deregulated synthesis of E2F1/DP caused by the miRNA pathway impairment as a key event in LRRK2 pathogenesis and suggest novel miRNA-based therapeutic strategies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049892/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049892/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gehrke, Stephan -- Imai, Yuzuru -- Sokol, Nicholas -- Lu, Bingwei -- R01 AR054926/AR/NIAMS NIH HHS/ -- R01 AR054926-01A2/AR/NIAMS NIH HHS/ -- R01 MH080378/MH/NIMH NIH HHS/ -- R01 MH080378-01A2/MH/NIMH NIH HHS/ -- R01AR054926/AR/NIAMS NIH HHS/ -- R01MH080378/MH/NIMH NIH HHS/ -- R21 NS056878/NS/NINDS NIH HHS/ -- R21 NS056878-01A1/NS/NINDS NIH HHS/ -- R21NS056878/NS/NINDS NIH HHS/ -- England -- Nature. 2010 Jul 29;466(7306):637-41. doi: 10.1038/nature09191.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA. sgehrke@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20671708" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Argonaute Proteins ; Cell Line ; Dopamine/metabolism ; *Down-Regulation ; Drosophila Proteins/biosynthesis/genetics/metabolism ; Drosophila melanogaster ; E2F1 Transcription Factor/biosynthesis/genetics/metabolism ; Eukaryotic Initiation Factor-2/metabolism ; Eukaryotic Initiation Factors/biosynthesis/metabolism ; Female ; Humans ; Male ; MicroRNAs/antagonists & inhibitors/*genetics/*metabolism ; Neurons/cytology/metabolism ; Parkinson Disease/etiology/genetics/metabolism ; Protein Binding ; *Protein Biosynthesis ; Protein-Serine-Threonine Kinases/*genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA-Induced Silencing Complex/antagonists & inhibitors/chemistry/metabolism ; Trans-Activators/biosynthesis/genetics/metabolism ; Up-Regulation
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  • 95
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2010-10-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petherick, Anna -- England -- Nature. 2010 Sep 30;467(7315):511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20886665" target="_blank"〉PubMed〈/a〉
    Keywords: Brazil ; *Federal Government ; Forestry/statistics & numerical data ; *Politics ; Public Policy ; Research Support as Topic ; *Science/economics/standards/trends
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  • 96
    facet.materialart.
    Unknown
    Nature Publishing Group (NPG)
    Publication Date: 2010-07-31
    Description: The Canadian government should rethink its decision to change the way census data are collected.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Jul 29;466(7306):532. doi: 10.1038/466532a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20671665" target="_blank"〉PubMed〈/a〉
    Keywords: Canada ; *Censuses ; Data Collection/*trends ; *Federal Government ; Policy Making ; *Public Opinion ; Public Policy/trends ; Science/standards
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  • 97
    Publication Date: 2010-04-09
    Description: Recent studies have unequivocally associated the fat mass and obesity-associated (FTO) gene with the risk of obesity. In vitro FTO protein is an AlkB-like DNA/RNA demethylase with a strong preference for 3-methylthymidine (3-meT) in single-stranded DNA or 3-methyluracil (3-meU) in single-stranded RNA. Here we report the crystal structure of FTO in complex with the mononucleotide 3-meT. FTO comprises an amino-terminal AlkB-like domain and a carboxy-terminal domain with a novel fold. Biochemical assays show that these two domains interact with each other, which is required for FTO catalytic activity. In contrast with the structures of other AlkB members, FTO possesses an extra loop covering one side of the conserved jelly-roll motif. Structural comparison shows that this loop selectively competes with the unmethylated strand of the DNA duplex for binding to FTO, suggesting that it has an important role in FTO selection against double-stranded nucleic acids. The ability of FTO to distinguish 3-meT or 3-meU from other nucleotides is conferred by its hydrogen-bonding interaction with the two carbonyl oxygen atoms in 3-meT or 3-meU. Taken together, these results provide a structural basis for understanding FTO substrate-specificity, and serve as a foundation for the rational design of FTO inhibitors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, Zhifu -- Niu, Tianhui -- Chang, Junbiao -- Lei, Xiaoguang -- Zhao, Mingyan -- Wang, Qiang -- Cheng, Wei -- Wang, Jinjing -- Feng, Yi -- Chai, Jijie -- England -- Nature. 2010 Apr 22;464(7292):1205-9. doi: 10.1038/nature08921. Epub 2010 Apr 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute of Biological Sciences, No. 7 Science Park Road, Beijing 102206, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20376003" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; DNA, Single-Stranded/chemistry/metabolism ; Humans ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Proteins/*chemistry/genetics/*metabolism ; RNA/chemistry/metabolism ; Structure-Activity Relationship ; Substrate Specificity ; Thymidine/analogs & derivatives/chemistry/metabolism ; Uracil/analogs & derivatives/chemistry/metabolism
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  • 98
    Publication Date: 2010-06-11
    Description: Populations of cells are almost always heterogeneous in function and fate. To understand the plasticity of cells, it is vital to measure quantitatively and dynamically the molecular processes that underlie cell-fate decisions in single cells. Early events in cell signalling often occur within seconds of the stimulus, whereas intracellular signalling processes and transcriptional changes can take minutes or hours. By contrast, cell-fate decisions, such as whether a cell divides, differentiates or dies, can take many hours or days. Multiparameter experimental and computational methods that integrate quantitative measurement and mathematical simulation of these noisy and complex processes are required to understand the highly dynamic mechanisms that control cell plasticity and fate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spiller, David G -- Wood, Christopher D -- Rand, David A -- White, Michael R H -- 67252/Wellcome Trust/United Kingdom -- BB/D010748/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E004210/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E012965/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E013600/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F005814/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F005938/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H013725/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBD0107481/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBE0042101/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBE0129651/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBE0136001/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBF0052611/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBF0053181/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBF0058061/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBF0059381/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0500346/Medical Research Council/United Kingdom -- England -- Nature. 2010 Jun 10;465(7299):736-45. doi: 10.1038/nature09232.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Cell Imaging, School of Biological Sciences, Bioscience Research Building, Crown Street, Liverpool L69 7ZB, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20535203" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Differentiation ; *Cell Physiological Phenomena/genetics/physiology ; Cytological Techniques/*methods ; Microfluidics/methods ; Protein Binding ; Protein Transport ; Signal Transduction ; Transcription, Genetic
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  • 99
    Publication Date: 2011-06-15
    Description: Polyhydroxylated steroids are regulators of body shape and size in higher organisms. In metazoans, intracellular receptors recognize these molecules. Plants, however, perceive steroids at membranes, using the membrane-integral receptor kinase BRASSINOSTEROID INSENSITIVE 1 (BRI1). Here we report the structure of the Arabidopsis thaliana BRI1 ligand-binding domain, determined by X-ray diffraction at 2.5 A resolution. We find a superhelix of 25 twisted leucine-rich repeats (LRRs), an architecture that is strikingly different from the assembly of LRRs in animal Toll-like receptors. A 70-amino-acid island domain between LRRs 21 and 22 folds back into the interior of the superhelix to create a surface pocket for binding the plant hormone brassinolide. Known loss- and gain-of-function mutations map closely to the hormone-binding site. We propose that steroid binding to BRI1 generates a docking platform for a co-receptor that is required for receptor activation. Our findings provide insight into the activation mechanism of this highly expanded family of plant receptors that have essential roles in hormone, developmental and innate immunity signalling.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280218/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280218/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hothorn, Michael -- Belkhadir, Youssef -- Dreux, Marlene -- Dabi, Tsegaye -- Noel, Joseph P -- Wilson, Ian A -- Chory, Joanne -- AI042266/AI/NIAID NIH HHS/ -- R01 AI042266/AI/NIAID NIH HHS/ -- R01 AI042266-05/AI/NIAID NIH HHS/ -- R37 AI042266/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Jun 12;474(7352):467-71. doi: 10.1038/nature10153.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21666665" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/*chemistry/metabolism ; Arabidopsis Proteins/*chemistry/*metabolism ; Binding Sites ; Brassinosteroids ; Cholestanols/chemistry/*metabolism ; Crystallography, X-Ray ; Enzyme Activation ; Models, Molecular ; Molecular Sequence Data ; Plant Growth Regulators/chemistry/*metabolism ; Protein Binding ; Protein Kinases/*chemistry/*metabolism ; Protein Multimerization ; Protein Structure, Tertiary ; Steroids, Heterocyclic/chemistry/*metabolism ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 100
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    Nature Publishing Group (NPG)
    Publication Date: 2010-10-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cressey, Daniel -- England -- Nature. 2010 Oct 21;467(7318):895-6. doi: 10.1038/467895b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20962815" target="_blank"〉PubMed〈/a〉
    Keywords: Advisory Committees/*organization & administration ; *Federal Government ; Great Britain ; Politics ; Public Policy ; Science/*organization & administration/*standards
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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