Mg 2+ Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction.

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  • Additional Information
    • Source:
      Publisher: Cell Press Country of Publication: United States NLM ID: 0370626 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1542-0086 (Electronic) Linking ISSN: 00063495 NLM ISO Abbreviation: Biophys J Subsets: MEDLINE
    • Publication Information:
      Publication: Cambridge, MA : Cell Press
      Original Publication: New York, Published by Rockefeller University Press [etc.] for the Biophysical Society.
    • Subject Terms:
      Nucleic Acid Conformation*; Endoribonucleases/*metabolism ; Magnesium/*metabolism ; RNA, Catalytic/*metabolism ; RNA, Fungal/*metabolism; Cations, Divalent/chemistry ; Cations, Divalent/metabolism ; Endoribonucleases/chemistry ; Hydrogen Bonding ; Magnesium/chemistry ; Models, Genetic ; Molecular Dynamics Simulation ; Neurospora ; RNA, Catalytic/chemistry ; RNA, Fungal/chemistry
    • Abstract:
      Though the structure of the substrate stem loop I (SLI)-stem loop V (SLV) kissing loop junction of the Varkud Satellite ribozyme has been experimentally characterized, the dynamics of this Mg 2+ -dependent loop-loop interaction have been elusive. Specifically, each hairpin loop contains a U-turn motif, but only SLV shows a conformational shift triggered by Mg 2+ ion association. Here, we use molecular dynamics simulations to analyze the binding and dynamics of this kissing loop junction. We show that SLV acts as a scaffold, providing stability to the junction. Mg 2+ ions associate with SLV when it is part of the junction in a manner similar to when it is unbound, but there is no specificity in Mg 2+ binding for the SLI loop. This suggests that the entropic penalty of ordering the larger SLI is too high, allowing SLV to act as a scaffold for multiple substrate loop sequences.
      (Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.)
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    • Grant Information:
      R01 GM098102 United States GM NIGMS NIH HHS
    • Accession Number:
      0 (Cations, Divalent)
      0 (RNA, Catalytic)
      0 (RNA, Fungal)
      EC 3.1.- (Endoribonucleases)
      EC 3.1.27.- (varkud satellite ribozyme)
      I38ZP9992A (Magnesium)
    • Publication Date:
      Date Created: 20170704 Date Completed: 20170821 Latest Revision: 20181113
    • Publication Date:
      20240829
    • Accession Number:
      PMC5529310
    • Accession Number:
      10.1016/j.bpj.2017.06.008
    • Accession Number:
      28669407