Nucleic Acids Research Advance Access published online on June 6, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm394
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Nucleic Acid Enzymes |
‘In-line attack’ conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation study
1School of Computational Science, 2Institute of Molecular Biophysics and 3Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306
*To whom correspondence should be addressed. Tel: 01-850-645-6884; Fax: 01-850-644-7244; Email: yang{at}sb.fsu.edu
Received February 5, 2007. Revised April 10, 2007. Accepted May 1, 2007.
Since the proposal of ‘in-line attack’ conformation as a possibly important intermediate in RNA cleavage, its structure has been captured in various protein and RNA enzymes; these structures strengthen the belief that this conformation plays an essential role in the catalysis of RNA cleavage. As generally discussed, this intermediate structure can be involved in energy barrier reduction in two possible ways, e.g. through either conformational effect or electrostatic effect. In order to quantitatively elucidate the contribution of conformational effect in this type of enzyme catalysis, free energy simulations were performed on the RNA structures both in a splicing endonuclease complex and in the aqueous solution. Our free energy simulation results revealed that the ‘in-line attack’ conformational effect plays a modest role in facilitating the reaction rate enhancement (
12-fold) compared with the overall 1012-fold rate increase. The close agreement between the present computational estimation and an experimental measurement on the spontaneous RNA cleavage in an in vitro evolved ATP aptamer motives us to realize that the conformation distribution of an enzyme substrate prior to rather than after its binding determines the upper bound of the rate enhancement ability through the conformational strategy.
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