ArticleProceedings of the National Academy of Sciences of the United States of America1997
Use of intrinsic binding energy for catalysis by an RNA enzyme.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 54 citations in OpenAlex.
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- Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs.Molecular therapy. Nucleic acids · 2025Article
- A role for conformational changes in enzyme catalysis.Biophysical journal · 2024Article
- Investigation of the pThe journal of physical chemistry. B · 2021Article
- Small Molecule Catalysts with Therapeutic Potential.Molecules (Basel, Switzerland) · 2018Review
- Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes.Biochemistry · 2013Review
- Tightening of active site interactions en route to the transition state revealed by single-atom substitution in the guanosine-binding site of the Tetrahymena group I ribozyme.Journal of the American Chemical Society · 2011Article
- Variables and strategies in development of therapeutic post-transcriptional gene silencing agents.Journal of ophthalmology · 2011Article
- Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases.RNA (New York, N.Y.) · 2008Article
- Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis.RNA (New York, N.Y.) · 2008Article
- Ribozymes, riboswitches and beyond: regulation of gene expression without proteins.Nature reviews. Genetics · 2007Review
- Efficient ligation of the Schistosoma hammerhead ribozyme.Biochemistry · 2007Article
- Aptamers selected for higher-affinity binding are not more specific for the target ligand.Journal of the American Chemical Society · 2006Article
- Measurements of weak interactions between truncated substrates and a hammerhead ribozyme by competitive kinetic analyses: implications for the design of new and efficient ribozymes with high sequence specificity.Nucleic acids research · 2002Article
- The global structure of the VS ribozyme.The EMBO journal · 2002Article
- Energetic contribution of non-essential 5' sequence to catalysis in a hepatitis delta virus ribozyme.The EMBO journal · 2001Article
- The virtues of self-binding: high sequence specificity for RNA cleavage by self-processed hammerhead ribozymes.Nucleic acids research · 2000Article
- Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: the spandrels of RNA evolution.Proceedings of the National Academy of Sciences of the United States of America · 1999Article
- Hammerhead ribozyme kinetics.RNA (New York, N.Y.) · 1998Review
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The contribution of several individual ribozyme.substrate base pairs to binding and catalysis has been investigated using hammerhead ribozyme substrates that were truncated at their 3' or 5' ends. The base pairs at positions 1.1-2.1 and 15.2-16.2, which flank the conserved core, each contribute 10(4)-fold in the chemical step, without affecting substrate binding. In contrast, base pairs distal to the core contribute to substrate binding but have no effect on the chemical step. These results suggest a "fraying model" in which each ribozyme.substrate helix can exist in either an unpaired ("open") state or a helical ("closed") state, with the closed state required for catalysis. The base pairs directly adjacent to the conserved core contribute to catalysis by allowing the closed state to form. Once the number of base pairs is sufficient to ensure that the closed helical state predominates, additional residues provide stabilization of the helix, and therefore increase binding, but have no further effect on the chemical step. Remarkably, the >5 kcal/mol free energy contribution to catalysis from each of the internal base pairs is considerably greater than the free energy expected for formation of a base pair. It is suggested that this unusually large energetic contribution arises because free energy that is typically lost in constraining residues within a base pair is expressed in the transition state, where it is used for positioning. This extends the concept of "intrinsic binding energy" from protein to RNA enzymes, suggesting that intrinsic binding energy is a fundamental feature of biological catalysis.
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