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  • 1
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    Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-&jnodot;oining [Biochemistry] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-08-03
    Description: Cernunnos/XLF is a core protein of the nonhomologous DNA end-joining (NHEJ) pathway that processes the majority of DNA double-strand breaks in mammals. Cernunnos stimulates the final ligation step catalyzed by the complex between DNA ligase IV and Xrcc4 (X4). Here we present the crystal structure of the X41–157-Cernunnos1–224 complex at 5.5-Å resolution and identify the relative positions of the two factors and their binding sites. The X-ray structure reveals a filament arrangement for X41–157 and Cernunnos1–224 homodimers mediated by repeated interactions through their N-terminal head domains. A filament arrangement of the X4–Cernunnos complex was confirmed by transmission electron microscopy analyses both with truncated and full-length proteins. We further modeled the interface and used structure-based site-directed mutagenesis and calorimetry to characterize the roles of various residues at the X4–Cernunnos interface. We identified four X4 residues (Glu55, Asp58, Met61, and Phe106) essential for the interaction with Cernunnos. These findings provide new insights into the molecular bases for stimulatory and bridging roles of Cernunnos in the final DNA ligation step.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Crystal structure of the 14-subunit RNA polymerase I (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-10-25
    Description: Protein biosynthesis depends on the availability of ribosomes, which in turn relies on ribosomal RNA production. In eukaryotes, this process is carried out by RNA polymerase I (Pol I), a 14-subunit enzyme, the activity of which is a major determinant of cell growth. Here we present the crystal structure of Pol I from Saccharomyces cerevisiae at 3.0 A resolution. The Pol I structure shows a compact core with a wide DNA-binding cleft and a tightly anchored stalk. An extended loop mimics the DNA backbone in the cleft and may be involved in regulating Pol I transcription. Subunit A12.2 extends from the A190 jaw to the active site and inserts a transcription elongation factor TFIIS-like zinc ribbon into the nucleotide triphosphate entry pore, providing insight into the role of A12.2 in RNA cleavage and Pol I insensitivity to alpha-amanitin. The A49-A34.5 heterodimer embraces subunit A135 through extended arms, thereby contacting and potentially regulating subunit A12.2.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fernandez-Tornero, Carlos -- Moreno-Morcillo, Maria -- Rashid, Umar J -- Taylor, Nicholas M I -- Ruiz, Federico M -- Gruene, Tim -- Legrand, Pierre -- Steuerwald, Ulrich -- Muller, Christoph W -- England -- Nature. 2013 Oct 31;502(7473):644-9. doi: 10.1038/nature12636. Epub 2013 Oct 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas, Ramiro de Maeztu 9, 28040 Madrid, Spain [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24153184" target="_blank"〉PubMed〈/a〉
    Keywords: Catalytic Domain ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; Models, Molecular ; Peptide Chain Elongation, Translational ; Protein Binding ; Protein Conformation ; Protein Multimerization ; Protein Subunits/*chemistry ; RNA Polymerase I/*chemistry ; RNA Polymerase II/chemistry ; RNA Polymerase III/chemistry ; Saccharomyces cerevisiae/*enzymology ; Transcription, Genetic
    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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    Structural insight into magnetochrome-mediated magnetite biomineralization (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-10-08
    Description: Magnetotactic bacteria align along the Earth's magnetic field using an organelle called the magnetosome, a biomineralized magnetite (Fe(II)Fe(III)2O4) or greigite (Fe(II)Fe(III)2S4) crystal embedded in a lipid vesicle. Although the need for both iron(II) and iron(III) is clear, little is known about the biological mechanisms controlling their ratio. Here we present the structure of the magnetosome-associated protein MamP and find that it is built on a unique arrangement of a self-plugged PDZ domain fused to two magnetochrome domains, defining a new class of c-type cytochrome exclusively found in magnetotactic bacteria. Mutational analysis, enzyme kinetics, co-crystallization with iron(II) and an in vitro MamP-assisted magnetite production assay establish MamP as an iron oxidase that contributes to the formation of iron(III) ferrihydrite eventually required for magnetite crystal growth in vivo. These results demonstrate the molecular mechanisms of iron management taking place inside the magnetosome and highlight the role of magnetochrome in iron biomineralization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siponen, Marina I -- Legrand, Pierre -- Widdrat, Marc -- Jones, Stephanie R -- Zhang, Wei-Jia -- Chang, Michelle C Y -- Faivre, Damien -- Arnoux, Pascal -- Pignol, David -- T32 GM066698/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Oct 31;502(7473):681-4. doi: 10.1038/nature12573. Epub 2013 Oct 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Commissariat a l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Biologie Environnementale et de Biotechnologies,, F-13108, France [2] Centre National de la Recherche Scientifique, Unite Mixte de Recherche Biologie Vegetale et Microbiologie Environnementales, Saint-Paul-lez-Durance, F-13108, France [3] Aix-Marseille Universite, Saint-Paul-lez-Durance, F-13108, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24097349" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*cytology/enzymology/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Conserved Sequence ; Ferric Compounds/metabolism ; Ferrosoferric Oxide/*metabolism ; Genes, Bacterial/genetics ; Iron/metabolism ; Magnetosomes/*metabolism ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/metabolism ; Protein Multimerization ; Protein Structure, Tertiary ; Static Electricity
    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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    Priming and polymerization of a bacterial contractile tail structure (2016)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2016-02-26
    Description: Contractile tails are composed of an inner tube wrapped by an outer sheath assembled in an extended, metastable conformation that stores mechanical energy necessary for its contraction. Contraction is used to propel the rigid inner tube towards target cells for DNA or toxin delivery. Although recent studies have revealed the structure of the contractile sheath of the type VI secretion system, the mechanisms by which its polymerization is controlled and coordinated with the assembly of the inner tube remain unknown. Here we show that the starfish-like TssA dodecameric complex interacts with tube and sheath components. Fluorescence microscopy experiments in enteroaggregative Escherichia coli reveal that TssA binds first to the type VI secretion system membrane core complex and then initiates tail polymerization. TssA remains at the tip of the growing structure and incorporates new tube and sheath blocks. On the basis of these results, we propose that TssA primes and coordinates tail tube and sheath biogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zoued, Abdelrahim -- Durand, Eric -- Brunet, Yannick R -- Spinelli, Silvia -- Douzi, Badreddine -- Guzzo, Mathilde -- Flaugnatti, Nicolas -- Legrand, Pierre -- Journet, Laure -- Fronzes, Remi -- Mignot, Tam -- Cambillau, Christian -- Cascales, Eric -- England -- Nature. 2016 Mar 3;531(7592):59-63. doi: 10.1038/nature17182. Epub 2016 Feb 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire d'Ingenierie des Systemes Macromoleculaires, Institut de Microbiologie de la Mediterranee, CNRS UMR7255, Aix-Marseille Universite, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. ; Architecture et Fonction des Macromolecules Biologiques, Centre National de la Recherche Scientifique, UMR 7257, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France. ; Architecture et Fonction des Macromolecules Biologiques, Aix-Marseille Universite, UMR 7257, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France. ; G5 Biologie structurale de la secretion bacterienne, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France. ; UMR 3528, CNRS, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France. ; Laboratoire de Chimie Bacterienne, Institut de Microbiologie de la Mediterranee, CNRS UMR7283, Aix-Marseille Universite, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. ; Synchrotron Soleil, L'Orme des merisiers, Saint-Aubin BP48, 91192 Gif-sur-Yvette Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26909579" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Escherichia coli/*chemistry/ultrastructure ; Escherichia coli Proteins/*chemistry/*metabolism/ultrastructure ; Microscopy, Electron ; Microscopy, Fluorescence ; Models, Molecular ; *Polymerization ; Protein Structure, Tertiary ; Type VI Secretion Systems/chemistry/metabolism/ultrastructure
    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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  • 5
    Electronic Resource
    Electronic Resource
    One-sided action of amphotericin B on cholesterol-containing membranes is determined by its self-association in the medium (1991)
    s.l. : American Chemical Society
    Biochemistry 30 (1991), S. 5707-5715 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00237a011
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  • 6
    Electronic Resource
    Electronic Resource
    Combining T/P altimetric data with hydrographic data to estimate the mean dynamic topography of the North Atlantic and improve the geoid (1998)
    Springer
    Annales geophysicae 16 (1998), S. 638-650 
    Details
    ISSN: 0992-7689
    Keywords: Oceanography: general (climate and interannual variability) ; Oceanography: physical (general circulation; remote sensing)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The mean dynamic topography of the surface of the North Atlantic is estimated using an inverse model of the ocean circulation constrained by hydro-graphic and altimetric observations. In the North Atlantic, altimetric observations have no significant impact on the topography estimate because of the limited precision of available geoid height models. They have a significant impact, however, when uncertainties in the density field are increased to simulate interpolation errors in regions where hydrographic data are scarce. This result, which moderates the conclusion drawn by Ganachaud and co-workers of no significant contribution of altimetric observations to the determination of the large-scale steady circulation, reflects the simple idea that altimetric data are most useful near the surface of the ocean and in areas where the hydrography is poorly determined. One application of the present inverse estimate of the mean dynamic topography is to compute a geoid height correction over the North Atlantic which reduces the uncertainty in the geoid height expanded to spherical harmonic 40 down to a level of about 5 cm.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s00585-998-0638-0
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  • 7
    Electronic Resource
    Electronic Resource
    In which Metals are High Electronic Excitations Able to Create Damage? (1992)
    s.l. ; Stafa-Zurich, Switzerland
    Materials science forum Vol. 97-99 (Jan. 1992), p. 587-592 
    Details
    ISSN: 1662-9752
    Source: Scientific.Net: Materials Science & Technology / Trans Tech Publications Archiv 1984-2008
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Type of Medium: Electronic Resource
    URL: http://www.tib-hannover.de/fulltexts/2011/0528/02/21/transtech_doi~10.4028%252Fwww.scientific.net%252FMSF.97-99.587.pdf
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  • 8
    Electronic Resource
    Electronic Resource
    Contribution of Electronic Energy Losses to Radiation Damage in Austenitic Alloys (1992)
    s.l. ; Stafa-Zurich, Switzerland
    Materials science forum Vol. 97-99 (Jan. 1992), p. 593-598 
    Details
    ISSN: 1662-9752
    Source: Scientific.Net: Materials Science & Technology / Trans Tech Publications Archiv 1984-2008
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Type of Medium: Electronic Resource
    URL: http://www.tib-hannover.de/fulltexts/2011/0528/02/21/transtech_doi~10.4028%252Fwww.scientific.net%252FMSF.97-99.593.pdf
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  • 9
    Electronic Resource
    Electronic Resource
    Crystallization and 2.2 Å resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 52-60 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: R-phycoerythrin, a light-harvesting component from the red algae Gracilaria chilensis, was crystallized by vapour diffusion using ammonium sulfate as precipitant agent. Red crystals grew after one week at 293 K and diffracted to 2.70 Å resolution. Three serial macroseeding assays were necessary to grow a second larger crystal to dimensions of 0.68 × 0.16 × 0.16 mm. This crystal diffracted to 2.24 Å resolution using synchrotron radiation at beamline BM14 of the European Synchrotron Radiation Facility (ESRF) at Grenoble, France and was used for structure determination. Data were collected at 100 K to a completeness of 98.6%. The crystal was trigonal, space group R3, with unit-cell parameters a = b = 187.3, c = 59.1 Å, α = β = 90, γ = 120°. Data treatment using the CCP4 suite of programs indicated that the crystal was twinned (〈I2〉/〈I〉2 = 1.41). Molecular replacement was performed with AMoRe using the R-phycoerythrin from Polysiphonia urceolata [Chang et al. (1996), J. Mol. Biol. 249, 424–440] as a search model. In order to overcome the twinning problem, SHELX97 was used for the crystallographic refinement. The twin fraction was 0.48, indicating a nearly perfect hemihedrally twinned crystal. The final Rwork and Rfree factors are 0.16 and 0.25, respectively. All the residues and chromophores of the α- and β-chains are well defined in the electron-density maps. Some residues belonging to the γ-linker are also recognizable.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900015274
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  • 10
    Electronic Resource
    Electronic Resource
    A vibrational molecular force field of model compounds with biological interest-III. Harmonic dynamics of α- and β-d-galactose in the crystalline state
    Amsterdam : Elsevier
    Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy Section 48 (1992), S. 959-973 
    Details
    ISSN: 0584-8539
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0584-8539(92)80172-S
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