Model for the Functional Active State of the TS Ribozyme from Molecular Simulation

Colin S. Gaines, Darrin M. York

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


Recently, a crystal structure has been reported of a new catalytic RNA, the TS ribozyme, that has been identified through comparative genomics and is believed to be a metalloribozyme having novel mechanistic features. Although this data provides invaluable structural information, analysis suggests a conformational change is required to arrive at a catalytically relevant state. We report results of molecular simulations that predict a spontaneous local rearrangement of the active site, leading to solution structures consistent with available functional data and providing competing mechanistic hypotheses that can be experimentally tested. The two competing hypotheses differ in the proposed identity of the catalytic general acid: either a water molecule coordinating a Mg2+ ion bound at the Watson–Crick edge of residue C7, or the N3 position of residue C7 itself.

Original languageEnglish (US)
Pages (from-to)13392-13395
Number of pages4
JournalAngewandte Chemie - International Edition
Issue number43
StatePublished - Oct 16 2017

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)


  • RNA
  • biocatalysis
  • general acids
  • molecular dynamics
  • ribozymes


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