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Modeling active RNA structures using the intersection of conformational space: application to the lead-activated
S Lemieux1, P Chartrand, R Cedergren
1Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Québec, Canada.
RNA (New York, N.Y.)
|July 22, 1998
Summary
Researchers developed a 3D model for the leadzyme, a yeast tRNA(Phe) variant highly active in lead-assisted RNA catalysis. This model reveals the ribozyme's active conformation, suggesting an SN2 attack mechanism and two lead binding sites.
Area of Science:
- Structural Biology
- RNA Catalysis
- Computational Chemistry
Background:
- Lead (Pb2+)-assisted cleavage of yeast tRNA(Phe) is a model for metal-catalyzed RNA reactions.
- In vitro selection identified a highly active tRNA(Phe) variant, termed the leadzyme, for Pb2+ cleavage.
Purpose of the Study:
- To propose a three-dimensional structure for the highly active leadzyme ribozyme.
- To elucidate the mechanism of Pb2+-catalyzed RNA cleavage by the leadzyme.
Main Methods:
- Developed a 3D modeling protocol integrating sequence variants and chemical modification data.
- Employed computational modeling to identify compatible conformations with known leadzyme variants.
- Experimentally validated structural hypotheses using modified nucleotide analogues in the catalytic core.
Main Results:
- Generated a structural model for the leadzyme consistent with all available structural data.
- The proposed active conformation suggests an in-line SN2 attack mechanism for phosphodiester bond cleavage.
- The model predicts the presence of two essential Pb2+ binding sites within the ribozyme's active center.
Conclusions:
- The study presents a validated structural model for the leadzyme, advancing understanding of metal-assisted RNA catalysis.
- The findings elucidate the catalytic mechanism and identify key metal ion binding sites.
- The presented modeling protocol is broadly applicable to RNA structure-function studies involving activity data of analogues.