The ribosome as an entropy trap
Open Access
- 12 May 2004
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 101 (21) , 7897-7901
- https://doi.org/10.1073/pnas.0402488101
Abstract
To determine the effectiveness of the ribosome as a catalyst, we compared the rate of uncatalyzed peptide bond formation, by the reaction of the ethylene glycol ester of N-formylglycine with Tris(hydroxymethyl)aminomethane, with the rate of peptidyl transfer by the ribosome. Activation parameters were also determined for both reactions, from the temperature dependence of their second-order rate constants. In contrast with most protein enzymes, the enthalpy of activation is slightly less favorable on the ribosome than in solution. The 2 × 107-fold rate enhancement produced by the ribosome is achieved entirely by lowering the entropy of activation. These results are consistent with the view that the ribosome enhances the rate of peptide bond formation mainly by positioning the substrates and/or water exclusion within the active site, rather than by conventional chemical catalysis.Keywords
This publication has 32 references indexed in Scilit:
- A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunitsNature Structural & Molecular Biology, 2002
- The Structural Basis of Ribosome Activity in Peptide Bond SynthesisScience, 2000
- The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å ResolutionScience, 2000
- The Temperature Dependence of Enzyme Rate EnhancementsJournal of the American Chemical Society, 1999
- Puromycin reaction for the A site‐bound peptidyl‐tRNAFEBS Letters, 1992
- The formation of dipeptides from amino acids and the 2′(3′)-glycyl ester of an adenylateJournal of Molecular Evolution, 1979
- Ester aminolysis. Structure-reactivity relationships and the rate-determining step in the aminolysis of substituted diphenyl carbonatesJournal of the American Chemical Society, 1977
- General Base Catalysis of the Aminolysis of Phenyl Acetate by Primary Alkylamines1Journal of the American Chemical Society, 1966
- The Compensation in ΔH[UNK] and ΔS[UNK] Accompanying the Conversion of Lower Order Nucleophilic Displacement Reactions to Higher Order Catalytic Processes. The Temperature Dependence of the Hydrazinolysis and Imidazole-Catalyzed Hydrolysis of Substituted Phenyl AcetatesJournal of the American Chemical Society, 1964
- Studies in the Physical Chemistry of Amino Acids, Peptides, and Related Substances. IX. The Dissociation Constants of Some Amino Acid DerivativesJournal of the American Chemical Society, 1937