Related Experiment Video
Updated: May 31, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized
Somdeb Mitra1, Alain Laederach, Barbara L Golden
1Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
RNA (New York, N.Y.)
|June 30, 2011
Summary
RNA folding balances function and kinetics. Different group I intron ribozymes use unique strategies to achieve a common core structure, guided by tertiary motif strength, not size.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Biopolymer folding requires balancing functional and kinetic constraints.
- Homologous RNA molecules often share conserved core structures despite variations in size and complexity.
Purpose of the Study:
- To investigate the folding mechanisms of phylogenetically divergent group I intron ribozymes.
- To understand how different RNA architectures achieve a common functional core structure.
Main Methods:
- Time-resolved hydroxyl radical probing of backbone solvent accessibility.
- Catalytic activity measurements.
- Integrated structural-kinetic modeling.
Main Results:
- Each ribozyme employs a distinct folding strategy to reach the conserved functional fold.
- Folding rates are determined by the strength of tertiary motifs, not overall size or complexity.
- Folding intermediates' stability and conformational freedom dictate folding flux and prevent kinetic trapping.
Conclusions:
- A universal RNA folding principle: flux proceeds through optimally structured kinetic intermediates that nucleate structure without kinetic trapping.
- Peripheral A-minor interactions may balance RNA structural stability and folding efficiency.
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