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  • 2010-2014
  • 2005-2009  (207)
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  • 2009  (207)
  • 1
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    Structural insights into mechanisms of the small RNA methyltransferase HEN1 (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-10-09
    Description: RNA silencing is a conserved regulatory mechanism in fungi, plants and animals that regulates gene expression and defence against viruses and transgenes. Small silencing RNAs of approximately 20-30 nucleotides and their associated effector proteins, the Argonaute family proteins, are the central components in RNA silencing. A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2'-O-methylation on the 3' terminal nucleotide. A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification. Here we report the 3.1 A crystal structure of full-length HEN1 from Arabidopsis in complex with a 22-nucleotide small RNA duplex and cofactor product S-adenosyl-l-homocysteine. Highly cooperative recognition of the small RNA substrate by multiple RNA binding domains and the methyltransferase domain in HEN1 measures the length of the RNA duplex and determines the substrate specificity. Metal ion coordination by both 2' and 3' hydroxyls on the 3'-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel Mg(2+)-dependent 2'-O-methylation mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Ying -- Ji, Lijuan -- Huang, Qichen -- Vassylyev, Dmitry G -- Chen, Xuemei -- Ma, Jin-Biao -- GM074252/GM/NIGMS NIH HHS/ -- R01 GM074840/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Oct 8;461(7265):823-7. doi: 10.1038/nature08433.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812675" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Arabidopsis/*enzymology/genetics ; Arabidopsis Proteins/*chemistry/genetics/*metabolism ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Magnesium/metabolism ; Methylation ; Methyltransferases/*chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Protein Structure, Tertiary ; RNA/genetics/*metabolism ; RNA-Binding Proteins/chemistry/metabolism ; S-Adenosylhomocysteine/chemistry/metabolism ; Structure-Activity Relationship ; Substrate Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Direct activation of protein kinases by unanchored polyubiquitin chains (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-08-14
    Description: TRAF6 is a ubiquitin ligase that is essential for the activation of NF-kappaB and MAP kinases in several signalling pathways, including those emanating from the interleukin 1 and Toll-like receptors. TRAF6 functions together with a ubiquitin-conjugating enzyme complex consisting of UBC13 (also known as UBE2N) and UEV1A (UBE2V1) to catalyse Lys 63-linked polyubiquitination, which activates the TAK1 (also known as MAP3K7) kinase complex. TAK1 in turn phosphorylates and activates IkappaB kinase (IKK), leading to the activation of NF-kappaB. Although several proteins are known to be polyubiquitinated in the IL1R and Toll-like receptor pathways, it is not clear whether ubiquitination of any of these proteins is important for TAK1 or IKK activation. By reconstituting TAK1 activation in vitro using purified proteins, here we show that free Lys 63 polyubiquitin chains, which are not conjugated to any target protein, directly activate TAK1 by binding to the ubiquitin receptor TAB2 (also known as MAP3K7IP2). This binding leads to autophosphorylation and activation of TAK1. Furthermore, we found that unanchored polyubiquitin chains synthesized by TRAF6 and UBCH5C (also known as UBE2D3) activate the IKK complex. Disassembly of the polyubiquitin chains by deubiquitination enzymes prevented TAK1 and IKK activation. These results indicate that unanchored polyubiquitin chains directly activate TAK1 and IKK, suggesting a new mechanism of protein kinase regulation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747300/" 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/PMC2747300/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xia, Zong-Ping -- Sun, Lijun -- Chen, Xiang -- Pineda, Gabriel -- Jiang, Xiaomo -- Adhikari, Anirban -- Zeng, Wenwen -- Chen, Zhijian J -- R01 AI060919/AI/NIAID NIH HHS/ -- R01 AI060919-05/AI/NIAID NIH HHS/ -- R01 GM063692/GM/NIGMS NIH HHS/ -- R01 GM063692-08/GM/NIGMS NIH HHS/ -- R01-AI09919/AI/NIAID NIH HHS/ -- R01-GM63692/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Sep 3;461(7260):114-9. doi: 10.1038/nature08247. Epub 2009 Aug 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas, Southwestern Medical Center, Dallas, Texas 75390-9148, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19675569" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/metabolism ; Cell Line ; DEAD-box RNA Helicases/metabolism ; Enzyme Activation/drug effects ; HeLa Cells ; Humans ; I-kappa B Kinase/*metabolism ; Interleukin-1beta/pharmacology ; Lysine/metabolism ; MAP Kinase Kinase Kinases/*metabolism ; Phosphorylation ; Polyubiquitin/biosynthesis/*metabolism ; TNF Receptor-Associated Factor 6/metabolism ; Tumor Suppressor Proteins/metabolism ; Ubiquitin-Conjugating Enzymes ; Ubiquitination
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Increasing hyperpolarized spin lifetimes through true singlet eigenstates (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-03-28
    Description: The sensitivity limitations for magnetic resonance imaging of organic molecules have recently been addressed by hyperpolarization methods, which prepare excess nuclear spin polarization. This approach can increase sensitivity by orders of magnitude, but the enhanced signal relaxes away in tens of seconds, even in favorable cases. Here we show theoretically that singlet states between strongly coupled spins in molecules can be used to store and retrieve population in very-long-lived disconnected eigenstates, as long as the coupling between the spins substantially exceeds both the couplings to other spins and the resonance frequency difference between them. Experimentally, 2,3-carbon-13-labeled diacetyl has a disconnected eigenstate that can store population for minutes and is read out by hydration to make the two spins inequivalent.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080756/" 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/PMC3080756/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warren, Warren S -- Jenista, Elizabeth -- Branca, Rosa Tamara -- Chen, Xin -- EB02122/EB/NIBIB NIH HHS/ -- R01 EB002122/EB/NIBIB NIH HHS/ -- R01 EB002122-22A2/EB/NIBIB NIH HHS/ -- New York, N.Y. -- Science. 2009 Mar 27;323(5922):1711-4. doi: 10.1126/science.1167693.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Center for Molecular and Biomolecular Imaging, Duke University, Durham, NC 27708, USA. warren.warren@duke.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19325112" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Isotopes ; Chemical Phenomena ; Diacetyl/*analysis/chemistry ; Magnetic Resonance Imaging ; *Magnetic Resonance Spectroscopy ; Magnetics ; Molecular Structure ; *Nuclear Magnetic Resonance, Biomolecular ; Sensitivity and Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Diversity and complexity in DNA recognition by transcription factors (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-05-16
    Description: Sequence preferences of DNA binding proteins are a primary mechanism by which cells interpret the genome. Despite the central importance of these proteins in physiology, development, and evolution, comprehensive DNA binding specificities have been determined experimentally for only a few proteins. Here, we used microarrays containing all 10-base pair sequences to examine the binding specificities of 104 distinct mouse DNA binding proteins representing 22 structural classes. Our results reveal a complex landscape of binding, with virtually every protein analyzed possessing unique preferences. Roughly half of the proteins each recognized multiple distinctly different sequence motifs, challenging our molecular understanding of how proteins interact with their DNA binding sites. This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905877/" 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/PMC2905877/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Badis, Gwenael -- Berger, Michael F -- Philippakis, Anthony A -- Talukder, Shaheynoor -- Gehrke, Andrew R -- Jaeger, Savina A -- Chan, Esther T -- Metzler, Genita -- Vedenko, Anastasia -- Chen, Xiaoyu -- Kuznetsov, Hanna -- Wang, Chi-Fong -- Coburn, David -- Newburger, Daniel E -- Morris, Quaid -- Hughes, Timothy R -- Bulyk, Martha L -- R01 HG003985/HG/NHGRI NIH HHS/ -- R01 HG003985-01/HG/NHGRI NIH HHS/ -- R01 HG003985-02/HG/NHGRI NIH HHS/ -- R01 HG003985-03/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19443739" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; DNA/chemistry/*metabolism ; Electrophoretic Mobility Shift Assay ; Gene Expression Regulation ; Gene Regulatory Networks ; Humans ; Mice ; Protein Array Analysis ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Transcription Factors/*chemistry/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    A kinase-START gene confers temperature-dependent resistance to wheat stripe rust (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-02-21
    Description: Stripe rust is a devastating fungal disease that afflicts wheat in many regions of the world. New races of Puccinia striiformis, the pathogen responsible for this disease, have overcome most of the known race-specific resistance genes. We report the map-based cloning of the gene Yr36 (WKS1), which confers resistance to a broad spectrum of stripe rust races at relatively high temperatures (25 degrees to 35 degrees C). This gene includes a kinase and a putative START lipid-binding domain. Five independent mutations and transgenic complementation confirmed that both domains are necessary to confer resistance. Yr36 is present in wild wheat but is absent in modern pasta and bread wheat varieties, and therefore it can now be used to improve resistance to stripe rust in a broad set of varieties.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737487/" 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/PMC4737487/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fu, Daolin -- Uauy, Cristobal -- Distelfeld, Assaf -- Blechl, Ann -- Epstein, Lynn -- Chen, Xianming -- Sela, Hanan -- Fahima, Tzion -- Dubcovsky, Jorge -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Mar 6;323(5919):1357-60. doi: 10.1126/science.1166289. Epub 2009 Feb 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences, University of California, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19228999" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Basidiomycota/*pathogenicity ; Cloning, Molecular ; Crosses, Genetic ; Down-Regulation ; *Genes, Plant ; Hot Temperature ; Immunity, Innate ; Molecular Sequence Data ; Phosphotransferases/chemistry/*genetics/metabolism ; Physical Chromosome Mapping ; *Plant Diseases/immunology/microbiology ; Plant Proteins/chemistry/genetics/metabolism ; Plants, Genetically Modified ; Triticum/*genetics/*microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    The domestication process and domestication rate in rice: spikelet bases from the Lower Yangtze (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-03-21
    Description: The process of rice domestication occurred in the Lower Yangtze region of Zhejiang, China, between 6900 and 6600 years ago. Archaeobotanical evidence from the site of Tianluoshan shows that the proportion of nonshattering domesticated rice (Oryza sativa) spikelet bases increased over this period from 27% to 39%. Over the same period, rice remains increased from 8% to 24% of all plant remains, which suggests an increased consumption relative to wild gathered foods. In addition, an assemblage of annual grasses, sedges, and other herbaceous plants indicates the presence of arable weeds, typical of cultivated rice, that also increased over this period.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fuller, Dorian Q -- Qin, Ling -- Zheng, Yunfei -- Zhao, Zhijun -- Chen, Xugao -- Hosoya, Leo Aoi -- Sun, Guo-Ping -- New York, N.Y. -- Science. 2009 Mar 20;323(5921):1607-10. doi: 10.1126/science.1166605.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Archaeology, University College London, London WC1H 0PY, UK. d.fuller@ucl.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19299619" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*history ; Archaeology ; China ; Crops, Agricultural/*history ; History, Ancient ; *Oryza/anatomy & histology/growth & development ; Seeds/anatomy & histology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Revealing the maximum strength in nanotwinned copper (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-01-31
    Description: The strength of polycrystalline materials increases with decreasing grain size. Below a critical size, smaller grains might lead to softening, as suggested by atomistic simulations. The strongest size should arise at a transition in deformation mechanism from lattice dislocation activities to grain boundary-related processes. We investigated the maximum strength of nanotwinned copper samples with different twin thicknesses. We found that the strength increases with decreasing twin thickness, reaching a maximum at 15 nanometers, followed by a softening at smaller values that is accompanied by enhanced strain hardening and tensile ductility. The strongest twin thickness originates from a transition in the yielding mechanism from the slip transfer across twin boundaries to the activity of preexisting easy dislocation sources.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, L -- Chen, X -- Huang, X -- Lu, K -- New York, N.Y. -- Science. 2009 Jan 30;323(5914):607-10. doi: 10.1126/science.1167641.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016, P.R. China. llu@imr.ac.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19179523" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Time-dependent amplitude analysis ofB0→KS0π+π− (2009)
    American Physical Society
    Details
    Publication Date: 2009-12-02
    Print ISSN: 1550-7998
    Electronic ISSN: 1550-2368
    Topics: Physics
    Published by American Physical Society
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  • 9
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    Measurement of time-dependentCPasymmetry inB0→cc¯K(*)0decays (2009)
    American Physical Society
    Details
    Publication Date: 2009-04-29
    Print ISSN: 1550-7998
    Electronic ISSN: 1550-2368
    Topics: Physics
    Published by American Physical Society
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  • 10
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    Dalitz plot analysis ofDs+→π+π−π+ (2009)
    American Physical Society
    Details
    Publication Date: 2009-02-09
    Print ISSN: 1550-7998
    Electronic ISSN: 1550-2368
    Topics: Physics
    Published by American Physical Society
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