RNA


Research Article

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


SÉBASTIEN LEMIEUX a1 fn1 , PASCAL CHARTRAND a2 fn1 , ROBERT CEDERGREN a2 and FRANÇOIS MAJOR a1 c1
a1 Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, Québec, Canada H3C 3J7
a2 Département de Biochimie, Université de Montréal, Montréal, Québec, Canada H3C 3J7

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.

(Received August 12 1997)
(Revised October 2 1997)
(Accepted April 10 1998)

Key Words: base triple; catalytic RNA; internal loop; MC-SYM; metalo-nucleotide complex; molecular modeling; noncanonical base pairs.

Correspondence:

c1 Reprint requests to: François Major, Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, Québec, Canada H3C 3J7; e-mail: major@iro.umontreal.ca.

fn1 The first two authors contributed equally to the work.