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  • 1
    Publication Date: 2016-05-20
    Description: Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This macromolecular machine resembles a stretched, coiled spring (or sheath) wound around a rigid tube with a spike-shaped protein at its tip. A baseplate structure, which is arguably the most complex part of this assembly, relays the contraction signal to the sheath. Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. We establish the identity and function of a minimal set of components that is conserved in all contractile injection systems and show that the triggering mechanism is universally conserved.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taylor, Nicholas M I -- Prokhorov, Nikolai S -- Guerrero-Ferreira, Ricardo C -- Shneider, Mikhail M -- Browning, Christopher -- Goldie, Kenneth N -- Stahlberg, Henning -- Leiman, Petr G -- England -- Nature. 2016 May 18;533(7603):346-52. doi: 10.1038/nature17971.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ecole Polytechnique Federale de Lausanne (EPFL), BSP-415, 1015 Lausanne, Switzerland. ; Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, pr. 60-letiya Oktyabrya, 7 build. 2, 117312, Moscow, Russia. ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Bioengineering, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia. ; Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27193680" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    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
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  • 3
    Publication Date: 2016-04-28
    Description: Post mortem imaging is playing an increasingly important role in perinatal autopsy, and correct interpretation of imaging changes is paramount. This is particularly important following intra-uterine fetal deat...
    Electronic ISSN: 1471-2342
    Topics: Biology
    Published by BioMed Central
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  • 4
    Publication Date: 2014-12-15
    Description: For the first time a mesoscale-resolving whole atmosphere general circulation model (GCM) has been developed, using the NCAR Whole Atmosphere Community Climate Model (WACCM) with ~0.25° horizontal resolution and 0.1 scale height vertical resolution above the middle stratosphere (higher resolution below). This is made possible by the high accuracy and high scalability of the spectral element dynamical core from the High-Order Method Modeling Environment (HOMME). For the simulated January-February period, the latitude-height structure and the magnitudes of the temperature variance compare well with those deduced from SABER observations. The simulation reveals the increasing dominance of gravity waves (GWs) at higher altitudes through both the height dependence of the kinetic energy spectra, which display a steeper slope (~-3) in the stratosphere and an increasingly shallower slope above, and the increasing spatial extent of GWs (including a planetary-scale extent of a concentric GW excited by a tropical cyclone) at higher altitudes. GW impacts on the large-scale flow is evaluated in terms of zonal mean zonal wind and tides: with no GW drag parameterized in the simulations, forcing by resolved GWs does reverse the summer mesospheric wind, albeit at an altitude higher than climatology, and only slows down the winter mesospheric wind without closing it. The hemispheric structures and magnitudes of diurnal and semidiurnal migrating tides compare favorably with observations.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
    Publication Date: 2011-12-09
    Description: Regenerative vibration, or chatter, limits the performance of machining processes. Consequences of chatter include tool wear and poor machined surface finish. Process damping by tool-workpiece contact can reduce chatter effects and improve productivity. Process damping occurs when the flank (also known as the relief face) of the cutting tool makes contact with waves on the workpiece surface, created by chatter motion. Tool edge features can act to increase the damping effect. This paper examines how a tool's edge condition combines with the relief angle to affect process damping. An analytical model of cutting with chatter leads to a two-section curve describing how process damped vibration amplitude changes with surface speed for radiussed tools. The tool edge dominates the process damping effect at the lowest surface speeds, with the flank dominating at higher speeds. A similar curve is then proposed regarding tools with worn edges. Experimental data supports the notion of the...
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 6
    Publication Date: 2013-10-19
    Description: Transcription of tRNA-encoding genes by RNA polymerase (Pol) III requires the six-subunit general transcription factor IIIC that uses subcomplexes A and B to recognize two gene-internal promoter elements named A- and B-box. The Schizosaccharomyces pombe A subcomplex comprises subunits Sfc1, Sfc4 and Sfc7. The crystal structure of the Sfc1/Sfc7 heterodimer reveals similar domains and overall domain architecture to the Pol II-specific general transcription factor TFIIF Rap30/Rap74. The N-terminal Sfc1/Sfc7 dimerization module consists of a triple β-barrel similar to the N-terminal TFIIF Rap30/Rap74 dimerization module, whereas the C-terminal Sfc1 DNA-binding domain contains a winged-helix domain most similar to the TFIIF Rap30 C-terminal winged-helix domain. Sfc1 DNA-binding domain recognizes single and double-stranded DNA by an unknown mechanism. Several features observed for A-box recognition by A resemble the recognition of promoters by bacterial RNA polymerase, where factor unfolds double-stranded DNA and stabilizes the non-coding DNA strand in an open conformation. Such a function has also been proposed for TFIIF, suggesting that the observed structural similarity between Sfc1/Sfc7 and TFIIF Rap30/Rap74 might also reflect similar functions.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2019
    Description: 〈sec〉〈st〉Synopsis〈/st〉〈p〉〈textbox textbox-type="graphic"〉〈p〉〈inline-fig〉〈/inline-fig〉〈/p〉〈/textbox〉〈/p〉 〈p〉The attachment and host envelope penetration mechanism of bacteriophages that employ a rigid tube/contractile sheath complex for infection of Gram-positive bacteria is poorly understood. This study describes the structure of the 〈i〉Listeria〈/i〉 phage A511 contractile tail in the pre- and post-host attachment state.〈/p〉 〈p〉 〈l type="unord"〉〈li〉〈p〉The A511 baseplate-tail fiber complex undergoes a massive conformational change and switches from threefold to sixfold symmetry upon attachment to the host cell.〈/p〉〈/li〉 〈li〉〈p〉The distal tail fiber protein gp108 attaches to the host cell wall before the sheath contracts.〈/p〉〈/li〉 〈li〉〈p〉The proximal part of the tail fiber carries two pyramids that are formed by gp106 trimers.〈/p〉〈/li〉 〈li〉〈p〉The gp106 pyramids reorient to point toward the cell surface, change their conformation to protrude attachment domain, and bind to the cell wall.〈/p〉〈/li〉 〈li〉〈p〉Contraction of the phage tail sheath assembly starts at the baseplate and propagates through the sheath in a wave-like motion.〈/p〉〈/li〉〈/l〉 〈/p〉〈/sec〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
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  • 8
    Publication Date: 2019
    Description: 〈p〉Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteriophages that infect Gram-positive bacteria represent the least understood members. Here, we describe the structure of 〈i〉Listeria〈/i〉 bacteriophage A511 tail in its pre- and post-host attachment states (extended and contracted, respectively) using cryo-electron microscopy, cryo-electron tomography, and X-ray crystallography. We show that the structure of the tube-baseplate complex of A511 is similar to that of phage T4, but the A511 baseplate is decorated with different receptor-binding proteins, which undergo a large structural transformation upon host attachment and switch the symmetry of the baseplate-tail fiber assembly from threefold to sixfold. For the first time under native conditions, we show that contraction of the phage tail sheath assembly starts at the baseplate and propagates through the sheath in a domino-like motion.〈/p〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
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