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  • 1
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    Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2 (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-05-28
    Description: MicroRNAs (miRNAs) mediate post-transcriptional gene regulation through association with Argonaute proteins (AGOs). Crystal structures of archaeal and bacterial homologues of AGOs have shown that the MID (middle) domain mediates the interaction with the phosphorylated 5' end of the miRNA guide strand and this interaction is thought to be independent of the identity of the 5' nucleotide in these systems. However, analysis of the known sequences of eukaryotic miRNAs and co-immunoprecipitation experiments indicate that there is a clear bias for U or A at the 5' position. Here we report the crystal structure of a MID domain from a eukaryotic AGO protein, human AGO2. The structure, in complex with nucleoside monophosphates (AMP, CMP, GMP, and UMP) mimicking the 5' end of miRNAs, shows that there are specific contacts made between the base of UMP or AMP and a rigid loop in the MID domain. Notably, the structure of the loop discriminates against CMP and GMP and dissociation constants calculated from NMR titration experiments confirm these results, showing that AMP (0.26 mM) and UMP (0.12 mM) bind with up to 30-fold higher affinity than either CMP (3.6 mM) or GMP (3.3 mM). This study provides structural evidence for nucleotide-specific interactions in the MID domain of eukaryotic AGO proteins and explains the observed preference for U or A at the 5' end of miRNAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frank, Filipp -- Sonenberg, Nahum -- Nagar, Bhushan -- MOP-82929/Canadian Institutes of Health Research/Canada -- England -- Nature. 2010 Jun 10;465(7299):818-22. doi: 10.1038/nature09039. Epub 2010 May 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20505670" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Argonaute Proteins ; Base Sequence ; Crystallography, X-Ray ; Cytidine Monophosphate/metabolism ; Eukaryotic Initiation Factor-2/*chemistry/*metabolism ; Guanosine Monophosphate/metabolism ; Humans ; Kinetics ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Protein Structure, Tertiary ; RNA, Guide/chemistry/*genetics/*metabolism ; Structure-Activity Relationship ; Substrate Specificity ; Thermodynamics ; Uridine Monophosphate/metabolism
    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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    X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2 (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-06-20
    Description: Activation and covalent attachment of complement component C3 to pathogens is the key step in complement-mediated host defense. Additionally, the antigen-bound C3d fragment interacts with complement receptor 2 (CR2; also known as CD21) on B cells and thereby contributes to the initiation of an acquired humoral response. The x-ray crystal structure of human C3d solved at 2.0 angstroms resolution reveals an alpha-alpha barrel with the residues responsible for thioester formation and covalent attachment at one end and an acidic pocket at the other. The structure supports a model whereby the transition of native C3 to its functionally active state involves the disruption of a complementary domain interface and provides insight into the basis for the interaction between C3d and CR2.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nagar, B -- Jones, R G -- Diefenbach, R J -- Isenman, D E -- Rini, J M -- New York, N.Y. -- Science. 1998 May 22;280(5367):1277-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9596584" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Complement C3d/*chemistry/metabolism ; Conserved Sequence ; Crystallography, X-Ray ; Humans ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Complement 3d/*metabolism ; Sequence Alignment
    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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  • 3
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    Structural basis for viral 5'-PPP-RNA recognition by human IFIT proteins (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-01-22
    Description: Interferon-induced proteins with tetratricopeptide repeats (IFITs) are innate immune effector molecules that are thought to confer antiviral defence through disruption of protein-protein interactions in the host translation-initiation machinery. However, it was recently discovered that IFITs can directly recognize viral RNA bearing a 5'-triphosphate group (PPP-RNA), which is a molecular signature that distinguishes it from host RNA. Here we report crystal structures of human IFIT5, its complex with PPP-RNAs, and an amino-terminal fragment of IFIT1. The structures reveal a new helical domain that houses a positively charged cavity designed to specifically engage only single-stranded PPP-RNA, thus distinguishing it from the canonical cytosolic sensor of double-stranded viral PPP-RNA, retinoic acid-inducible gene I (RIG-I, also known as DDX58). Mutational analysis, proteolysis and gel-shift assays reveal that PPP-RNA is bound in a non-sequence-specific manner and requires a 5'-overhang of approximately three nucleotides. Abrogation of PPP-RNA binding in IFIT1 and IFIT5 was found to cause a defect in the antiviral response by human embryonic kidney cells. These results demonstrate the mechanism by which IFIT proteins selectively recognize viral RNA, and lend insight into their downstream effector function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abbas, Yazan M -- Pichlmair, Andreas -- Gorna, Maria W -- Superti-Furga, Giulio -- Nagar, Bhushan -- MOP-82929/Canadian Institutes of Health Research/Canada -- England -- Nature. 2013 Feb 7;494(7435):60-4. doi: 10.1038/nature11783. Epub 2013 Jan 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Groupe de Recherche Axe sur la Structure des Proteines, McGill University, Montreal, Quebec H3G 0B1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23334420" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Binding Sites ; Carrier Proteins/*chemistry/*metabolism ; Humans ; Immunity, Innate/immunology ; Models, Molecular ; Neoplasm Proteins/*chemistry/*metabolism ; Phosphorylation ; Protein Conformation ; RNA, Viral/*chemistry/genetics/*metabolism ; Reproducibility of Results ; 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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  • 4
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    Structure of parkin reveals mechanisms for ubiquitin ligase activation (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-05-11
    Description: Mutations in the PARK2 (parkin) gene are responsible for an autosomal recessive form of Parkinson's disease. The parkin protein is a RING-in-between-RING E3 ubiquitin ligase that exhibits low basal activity. We describe the crystal structure of full-length rat parkin. The structure shows parkin in an autoinhibited state and provides insight into how it is activated. RING0 occludes the ubiquitin acceptor site Cys(431) in RING2, whereas a repressor element of parkin binds RING1 and blocks its E2-binding site. Mutations that disrupted these inhibitory interactions activated parkin both in vitro and in cells. Parkin is neuroprotective, and these findings may provide a structural and mechanistic framework for enhancing parkin activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Trempe, Jean-Francois -- Sauve, Veronique -- Grenier, Karl -- Seirafi, Marjan -- Tang, Matthew Y -- Menade, Marie -- Al-Abdul-Wahid, Sameer -- Krett, Jonathan -- Wong, Kathy -- Kozlov, Guennadi -- Nagar, Bhushan -- Fon, Edward A -- Gehring, Kalle -- MOP-14219/Canadian Institutes of Health Research/Canada -- MOP-62714/Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Jun 21;340(6139):1451-5. doi: 10.1126/science.1237908. Epub 2013 May 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McGill Parkinson Program, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23661642" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Parkinson Disease ; Parkinsonian Disorders ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Rats ; Ubiquitin-Protein Ligases/*chemistry/genetics/*metabolism ; Ubiquitination ; Zinc Fingers
    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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  • 5
    Electronic Resource
    Electronic Resource
    Examination of the Structure of Soil Humic Acids by Pyrolysis – Gas Chromatography (1963)
    [s.l.] : Nature Publishing Group
    Nature 199 (1963), S. 1213-1214 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Four samples of soil humic acids (extracted by sodium hydroxide by the technique suggested by Lynch11) obtained from widely different pedological, vegetational and climatic type soils, namely, a half-bog soil from southern Delaware (Pocomoke), a prairie soil from Illinois (Sable), a red yellow ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/1991213a0
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    Paper (German National Licenses)
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  • 6
    Electronic Resource
    Electronic Resource
    Free Monosaccharides in Soil Organic Matter (1962)
    [s.l.] : Nature Publishing Group
    Nature 194 (1962), S. 896-897 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Four widely different pedological, vegetational and climatic type soils, namely, a half-bog soil from southern Delaware (Pocomoke), a prairie soil from Illinois (Sable), a red-yellow podzol from North Carolina (Cecil), and a tropical latosol from Brazil (samples passing through 60 mesh sieve) were ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/194896a0
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  • 7
    Electronic Resource
    Electronic Resource
    Studies on the structure and origin of soil humic acids by curie point pyrolysis in direct combination with low-voltage mass spectrometry (1975)
    Springer
    Plant and soil 43 (1975), S. 681-685 
    Details
    ISSN: 1573-5036
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Curie point pyrolysis in combination with low voltage mass spectrometry has shown that humic acids extracted from three typical Indian soils have similar structures which resemble that of a fungal ‘humic acid’ rather than that of a lignin.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01928529
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  • 8
    Electronic Resource
    Electronic Resource
    Studies on the structure and origin of soil humic acids by curie point pyrolysis in direct combination with low-voltage mass spectrometry (1975)
    Springer
    Plant and soil 43 (1975), S. 681-685 
    Details
    ISSN: 1573-5036
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Curie point pyrolysis in combination with low voltage mass spectrometry has shown that humic acids extracted from three typical Indian soils have similar structures which resemble that of a fungal ‘humic acid’ rather than that of a lignin.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01928529
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  • 9
    Electronic Resource
    Electronic Resource
    Darstellung und Reaktionen von Enamiden (1967)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 79 (1967), S. 385-385 
    Details
    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/ange.19670790815
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  • 10
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    Einfluß von Spannung, Zeit und Faserrichtung auf die Dämpfungseigenschaften von Holz (1965)
    Springer
    Details
    Publication Date: 1965-01-01
    Print ISSN: 0018-3768
    Electronic ISSN: 1436-736X
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Springer
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