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'In-line attack' conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation study.

Min D, Xue S, Li H, Yang W - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: School of Computational Science, Florida State University, Tallahassee, FL 32306, USA.

ABSTRACT
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 (approximately 12-fold) compared with the overall 10(12)-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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The illustration of the ‘in-line attack’ conformation in RNA cleavage reaction (B) and its conformation effect in enzyme catalysis (A).
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Figure 1: The illustration of the ‘in-line attack’ conformation in RNA cleavage reaction (B) and its conformation effect in enzyme catalysis (A).

Mentions: Regardless of catalysis strategies in various biomolecular processes, many RNA cleavage reactions undergo an intra-molecular phosphoester transfer (1). This mechanism involves a nucleophilic attack by the 2′ oxygen on the adjacent phosphorus center, followed by the formation of a pentacovalent phosphate intermediate and the subsequent departure of the 5′-oxyanion group (Scheme 1B). Both protein enzymes, as typified by Ribonuclease A (RNase A) (2) and RNA enzymes, as represented by hammerhead ribozyme (3–5), can facilitate this RNA cleavage reaction. The mechanism on how these enzymes exert their catalytic powers is of intense interest (1–6).Scheme 1


'In-line attack' conformational effect plays a modest role in an enzyme-catalyzed RNA cleavage: a free energy simulation study.

Min D, Xue S, Li H, Yang W - Nucleic Acids Res. (2007)

The illustration of the ‘in-line attack’ conformation in RNA cleavage reaction (B) and its conformation effect in enzyme catalysis (A).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1919504&req=5

Figure 1: The illustration of the ‘in-line attack’ conformation in RNA cleavage reaction (B) and its conformation effect in enzyme catalysis (A).
Mentions: Regardless of catalysis strategies in various biomolecular processes, many RNA cleavage reactions undergo an intra-molecular phosphoester transfer (1). This mechanism involves a nucleophilic attack by the 2′ oxygen on the adjacent phosphorus center, followed by the formation of a pentacovalent phosphate intermediate and the subsequent departure of the 5′-oxyanion group (Scheme 1B). Both protein enzymes, as typified by Ribonuclease A (RNase A) (2) and RNA enzymes, as represented by hammerhead ribozyme (3–5), can facilitate this RNA cleavage reaction. The mechanism on how these enzymes exert their catalytic powers is of intense interest (1–6).Scheme 1

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: School of Computational Science, Florida State University, Tallahassee, FL 32306, USA.

ABSTRACT
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 (approximately 12-fold) compared with the overall 10(12)-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.

Show MeSH