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  • 1
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    Ribosome-dependent activation of stringent control (2016)
    Springer Nature
    In: Nature
    Details
    Publication Date: 2016-06-09
    Description: Ribosome-dependent activation of stringent control Nature 534, 7606 (2016). doi:10.1038/nature17675 Authors: Alan Brown, Israel S. Fernández, Yuliya Gordiyenko & V. Ramakrishnan In order to survive, bacteria continually sense, and respond to, environmental fluctuations. Stringent control represents a key bacterial stress response to nutrient starvation that leads to rapid and comprehensive reprogramming of metabolic and transcriptional patterns. In general, transcription of genes for growth and proliferation is downregulated, while those important for survival and virulence are upregulated. Amino acid starvation is sensed by depletion of the aminoacylated tRNA pools, and this results in accumulation of ribosomes stalled with non-aminoacylated (uncharged) tRNA in the ribosomal A site. RelA is recruited to stalled ribosomes and activated to synthesize a hyperphosphorylated guanosine analogue, (p)ppGpp, which acts as a pleiotropic secondary messenger. However, structural information about how RelA recognizes stalled ribosomes and discriminates against aminoacylated tRNAs is missing. Here we present the cryo-electron microscopy structure of RelA bound to the bacterial ribosome stalled with uncharged tRNA. The structure reveals that RelA utilizes a distinct binding site compared to the translational factors, with a multi-domain architecture that wraps around a highly distorted A-site tRNA. The TGS (ThrRS, GTPase and SpoT) domain of RelA binds the CCA tail to orient the free 3′ hydroxyl group of the terminal adenosine towards a β-strand, such that an aminoacylated tRNA at this position would be sterically precluded. The structure supports a model in which association of RelA with the ribosome suppresses auto-inhibition to activate synthesis of (p)ppGpp and initiate the stringent response. Since stringent control is responsible for the survival of pathogenic bacteria under stress conditions, and contributes to chronic infections and antibiotic tolerance, RelA represents a good target for the development of novel antibacterial therapeutics.
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 2
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    Nature of single-particle states in disordered graphene (2016)
    American Physical Society (APS)
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    Publication Date: 2016-06-16
    Description: Author(s): Sabyasachi Nag, Arti Garg, and T. V. Ramakrishnan We analyze the nature of the single-particle states, away from the Dirac point in the presence of long-range charge impurities in a tight-binding model for electrons on a two-dimensional honeycomb lattice which is of direct relevance for graphene. For a disorder potential V ( r ⃗ ) = V 0 exp ( − | r ⃗ − r ⃗ imp | 2 / ξ 2 … [Phys. Rev. B 93, 235426] Published Wed Jun 15, 2016
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    Raman Spectroscopic Studies on L-histidine, aniline Doped Triglycine Sulphate Single Crystals (2015)
    Institute of Physics (IOP)
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    Publication Date: 2015-02-18
    Description: Single crystals of triglycine sulphate (TGS) doped with L-histidine and aniline were studied by Raman Spectroscopy. The structure and symmetry of molecules, the nature of bonding and the effect of crystalline field on molecular vibrations were studied for pure and doped TGS. The characteristic group frequencies were identified and analysed for H 2 SO 4 and glycine. The skeletal motion, lattice vibrational peaks were observed in the low wavenumber region. The site symmetry effect and the correlation field effect were studied from the splitting of vibrational bands. The observed Raman shift towards higher wave number region reveals that the symmetry reduction in doped TGS crystals. The broadening of Raman spectral line showed that a decrease in the hardness value for the doped crystals. Comparative studies of the Raman Spectra of pure TGS and doped TGS were also carried out.
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 4
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    Effect of pairing fluctuations on low-energy electronic spectra in cuprate superconductors (2011)
    American Physical Society (APS)
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    Publication Date: 2011-11-01
    Description: Author(s): Sumilan Banerjee, T. V. Ramakrishnan, and Chandan Dasgupta [Phys. Rev. B 84, 144525] Published Mon Oct 31, 2011
    Keywords: Superfluidity and superconductivity
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    Phenomenological Ginzburg-Landau-like theory for superconductivity in the cuprates (2011)
    American Physical Society (APS)
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    Publication Date: 2011-02-01
    Description: Author(s): Sumilan Banerjee, T. V. Ramakrishnan, and Chandan Dasgupta We propose and develop here a phenomenological Ginzburg-Landau-like theory of cuprate high-temperature superconductivity. The free energy of a cuprate superconductor is expressed as a functional F of the complex spin-singlet pair amplitude ψ_{ij} ≡ψ_{m} =Δ_{m} exp(iϕ_{m} ), where i and j are n... [Phys. Rev. B 83, 024510] Published Mon Jan 31, 2011
    Keywords: Superfluidity and superconductivity
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    Royal Society president stands up for Chinese scientists in the United States (2019)
    Springer Nature
    In: Nature
    Details
    Publication Date: 2019
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    Optical conductivity of perovskite manganites (2011)
    American Physical Society (APS)
    Details
    Publication Date: 2011-08-23
    Description: Author(s): Nandan Pakhira, H. R. Krishnamurthy, and T. V. Ramakrishnan We calculate the optical conductivity σ ( ω ) for doped rare-earth manganites based on the recently proposed microscopic “two fluid” ℓ − b model. We study the temperature dependence of σ ( ω ) for La 0.825 Sr 0.175 MnO 3 , which has a metallic ground state. At low temperatures, the calculated σ ( ω ) shows a “two-pe... [Phys. Rev. B 84, 085115] Published Mon Aug 22, 2011
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 8
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    Crystal structure of an initiation factor bound to the 30S ribosomal subunit (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-03
    Description: Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit. Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, A P -- Clemons, W M Jr -- Brodersen, D E -- Morgan-Warren, R J -- Hartsch, T -- Wimberly, B T -- Ramakrishnan, V -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jan 19;291(5503):498-501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11228145" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Crystallography, X-Ray ; Eukaryotic Initiation Factor-1/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA, Ribosomal, 16S/*chemistry/metabolism ; RNA, Transfer/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism ; Thermus thermophilus/*chemistry
    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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  • 9
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    Recognition of cognate transfer RNA by the 30S ribosomal subunit (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-08
    Description: Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ogle, J M -- Brodersen, D E -- Clemons , W M Jr -- Tarry, M J -- Carter, A P -- Ramakrishnan, V -- F31 GM019384/GM/NIGMS NIH HHS/ -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 May 4;292(5518):897-902.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11340196" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/metabolism/pharmacology ; Anticodon/chemistry/metabolism ; Base Pairing ; Binding Sites ; Codon/chemistry/metabolism ; Crystallography, X-Ray ; Guanosine Triphosphate/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Paromomycin/metabolism/pharmacology ; Peptide Chain Elongation, Translational ; Peptide Elongation Factor Tu/metabolism ; Protein Biosynthesis ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA, Ribosomal, 16S/chemistry/*metabolism ; RNA, Transfer/chemistry/*metabolism ; RNA, Transfer, Amino Acid-Specific/chemistry/*metabolism ; RNA, Transfer, Phe/chemistry/metabolism ; Ribosomes/chemistry/*metabolism/ultrastructure ; Thermodynamics ; Thermus thermophilus/chemistry/metabolism/*ultrastructure
    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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  • 10
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    What recent ribosome structures have revealed about the mechanism of translation (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-10-20
    Description: The high-resolution structures of ribosomal subunits published in 2000 have revolutionized the field of protein translation. They facilitated the determination and interpretation of functional complexes of the ribosome by crystallography and electron microscopy. Knowledge of the precise positions of residues in the ribosome in various states has facilitated increasingly sophisticated biochemical and genetic experiments, as well as the use of new methods such as single-molecule kinetics. In this review, we discuss how the interaction between structural and functional studies over the last decade has led to a deeper understanding of the complex mechanisms underlying translation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmeing, T Martin -- Ramakrishnan, V -- MC_U105184332/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2009 Oct 29;461(7268):1234-42. doi: 10.1038/nature08403. Epub 2009 Oct 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. schmeing@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19838167" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Biocatalysis ; Protein Biosynthesis/*physiology ; Ribosomal Proteins/metabolism ; Ribosomes/*chemistry/*metabolism ; Structure-Activity Relationship
    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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