ReviewCurrent opinion in chemical biology2008
Experimental analyses of the chemical dynamics of ribozyme catalysis.
Review in Current opinion in chemical biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution.Nucleic acids research · 2019Article
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
- Molecular simulations of RNA 2'-O-transesterification reaction models in solution.The journal of physical chemistry. B · 2013Article
- Biological phosphoryl-transfer reactions: understanding mechanism and catalysis.Annual review of biochemistry · 2011Review
- Kinetic isotope effects for RNA cleavage by 2'-O- transphosphorylation: nucleophilic activation by specific base.Journal of the American Chemical Society · 2010Article
- Model systems: how chemical biologists study RNA.Current opinion in chemical biology · 2009Review
- Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.Methods (San Diego, Calif.) · 2009Review
- Identification of catalytic metal ion ligands in ribozymes.Methods (San Diego, Calif.) · 2009Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Most ribozymes in Nature catalyze alcoholysis or hydrolysis of RNA phosphodiester bonds. Studies of the corresponding non-enzymatic reactions reveal a complex mechanistic landscape allowing for a variety of transition states and both concerted and stepwise mechanisms. High-resolution structures, incisive biochemical studies and computer simulations are providing glimpses into how ribozyme catalyzed reactions traverse this landscape. However, direct experimental tests of mechanistic detail at the chemical level are not easily achieved. Kinetic isotope effects (KIEs) probe directly the differences in the vibrational 'environment' of the atoms undergoing chemical transformation on going from the ground state to the transition state. Thus, KIEs can in principle provide direct information about transition state bonding and so may be instrumental in evaluating possible transition states for ribozyme catalyzed reactions. Understanding charge distribution in the transition state may help resolve how rate acceleration is accomplished and perhaps the similarities and differences in how RNA and protein active sites operate. Several barriers to successful application of KIE analysis to ribozymes have recently been overcome, and new chemical details are beginning to emerge.
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Registered trials
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