The Ribosome as an Entropy Trap

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 we...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2004-05, Vol.101 (21), p.7897-7901
Main Authors: Sievers, Annette, Beringer, Malte, Rodnina, Marina V., Wolfenden, Richard
Format: Article
Language:English
Subjects:
Active sites
Amines
Binding Sites
Biochemistry
Biological Sciences
Catalysis
Chemical bonding
Entropy
Esters
Glycine - analogs & derivatives
Glycine - metabolism
Glycols
Kinetics
Magnetic Resonance Spectroscopy
Physical Sciences
Protein Biosynthesis
Protons
Ribonucleic acid
Ribosomes
Ribosomes - metabolism
RNA
Temperature
Transfer RNA
Tromethamine - metabolism
Viscosity
Water - metabolism
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Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0402488101