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Productive folding to the native state by a group II intron ribozyme
Jennifer F Swisher1, Linhui J Su, Michael Brenowitz
1Integrated Program in Cellular, Molecular, and Biophysical Studies, Columbia University, New York, NY 10032, USA.
Journal of Molecular Biology
|January 12, 2002
Summary
Group II introns fold slowly and synchronously into a catalytically active structure. This slow folding, driven by early tertiary contacts, resembles protein folding with high contact order.
Area of Science:
- Biochemistry
- Molecular Biology
- RNA Biology
Background:
- Group II introns are large catalytic RNA molecules crucial for splicing and mobility.
- Their folded structure is essential for catalysis, but folding pathways and ionic requirements are poorly understood.
Purpose of the Study:
- To investigate the folding pathway and ionic requirements of a group II intron ribozyme.
- To elucidate the kinetics and mechanism of group II intron folding.
Main Methods:
- Folding isotherms were determined using hydroxyl radical footprinting.
- Time-resolved hydroxyl radical footprinting tracked folding kinetics.
- Catalytic activity assays in the presence of urea assessed kinetic traps.
Main Results:
- Folding isotherms showed similar Mg(2+) concentration ranges and cooperativity indices.
- All ribozyme regions folded slowly and synchronously into a single active structure.
- Folding rate constants matched catalytic activity recovery, with no evidence of kinetic traps.
Conclusions:
- The rate-limiting step for group II intron ai5gamma folding occurs early in the pathway.
- Slow folding is likely due to the formation of distant tertiary interactions, similar to high-contact-order protein folding.