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Modeling active RNA structures using the intersection of conformational space: Application to the lead-activated ribozyme

Published online by Cambridge University Press:  01 July 1998

SÉBASTIEN LEMIEUX
Affiliation:
Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, Québec, Canada H3C 3J7
PASCAL CHARTRAND
Affiliation:
Département de Biochimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7
ROBERT CEDERGREN
Affiliation:
Département de Biochimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7
FRANÇOIS MAJOR
Affiliation:
Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, Québec, Canada H3C 3J7
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Abstract

The Pb2+ cleavage of a specific phosphodiester bond in yeast tRNAPhe is the classical model of metal-assisted RNA catalysis. In vitro selection experiments have identified a tRNAPhe variant, the leadzyme, that is very active in cleavage by Pb2+. We present here a three-dimensional modeling protocol that was used to propose a structure for this ribozyme, and is based on the computation of the intersection of conformational space of sequence variants and the use of chemical modification data. Sequence and secondary structure data were used in a first round of computer modeling that allowed identification of conformations compatible with all known leadzyme variants. Common conformations were then tested experimentally by evaluating the activity of analogues containing modified nucleotides in the catalytic core. These experiments led to a new structural hypothesis that was tested in a second round of computer modeling. The resulting proposal for the active conformation of the leadzyme is consistent with all known structural data. The final model suggests an in-line SN2 attack mechanism and predicts two Pb2+ binding sites. The protocol presented here is generally applicable in modeling RNAs whenever the catalytic or binding activity of structural analogues is known.

Type
Research Article
Copyright
© 1998 RNA Society

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