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Ribozyme catalysis via orbital steering.

W G Scott1

  • 1Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA. wgscott@chemistry.ucsc.edu

Journal of Molecular Biology
|September 5, 2001
PubMed
Summary
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Orbital steering prevents hammerhead ribozyme self-cleavage by misaligning electron orbitals. This mechanism, distinct from conformational changes, reveals a key factor in RNA catalysis, potentially explaining enzyme activity.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Hammerhead ribozymes are small self-cleaving RNAs that catalyze RNA hydrolysis.
  • The catalytic mechanism involves nucleophilic attack by the 2' oxygen of a ribose on a scissile phosphate.
  • Understanding the factors governing ribozyme catalysis is crucial for RNA biology and enzyme mechanisms.

Purpose of the Study:

  • To investigate the role of orbital steering in hammerhead ribozyme self-cleavage.
  • To differentiate the effects of orbital steering from conformational changes on catalysis.
  • To estimate the contribution of orbital steering to the catalytic power of ribozymes.

Main Methods:

  • Analysis of the three-dimensional structure of the hammerhead ribozyme.

Related Experiment Videos

  • Computational modeling to assess orbital alignment and overlap.
  • Comparison of catalytic mechanisms involving orbital steering versus conformational changes.

    • Main Results:

    • The 2' oxygen atom is positioned for in-line attack but orbital steering prevents catalysis.
    • Hydrogen bonds in the ribozyme core misdirect the nucleophile's orbitals away from the phosphate.
    • Conformational changes and subsequent orbital steering are required for cleavage, each potentially enhancing rates 1000-fold.

    Conclusions:

    • Orbital steering is a significant factor that can prevent or enable RNA autocatalysis.
    • This phenomenon, uncoupled from conformational effects, contributes substantially to ribozyme catalytic power.
    • Orbital steering may offer a unified explanation for catalysis in both ribozymes and protein enzymes.