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      How do metal ions direct ribozyme folding?

      1 , 1 , 2
      Nature chemistry
      Springer Nature

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          Abstract

          Ribozymes, which carry out phosphoryl-transfer reactions, often require Mg(2+) ions for catalytic activity. The correct folding of the active site and ribozyme tertiary structure is also regulated by metal ions in a manner that is not fully understood. Here we employ coarse-grained molecular simulations to show that individual structural elements of the group I ribozyme from the bacterium Azoarcus form spontaneously in the unfolded ribozyme even at very low Mg(2+) concentrations, and are transiently stabilized by the coordination of Mg(2+) ions to specific nucleotides. However, competition for scarce Mg(2+) and topological constraints that arise from chain connectivity prevent the complete folding of the ribozyme. A much higher Mg(2+) concentration is required for complete folding of the ribozyme and stabilization of the active site. When Mg(2+) is replaced by Ca(2+) the ribozyme folds, but the active site remains unstable. Our results suggest that group I ribozymes utilize the same interactions with specific metal ligands for both structural stability and chemical activity.

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          Author and article information

          Journal
          Nat Chem
          Nature chemistry
          Springer Nature
          1755-4349
          1755-4330
          Oct 2015
          : 7
          : 10
          Affiliations
          [1 ] Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.
          [2 ] Department of Chemistry and Biochemistry and Biophysics Program, University of Maryland, College Park, Maryland 20742, USA.
          Article
          nchem.2330
          10.1038/nchem.2330
          26391078
          33d31542-c7fe-428a-a078-116bba7eb8f4
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