Accurateion for Sievers et al., From the Cover: The ribosome

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The ribosome as an entropy trap - May 12, 2004 Article Figures & SI Info & Metrics PDF

BIOCHEMISTRY. For the article “The ribosome as an entropy trap,” by Annette Sievers, Malte Beringer, Marina V. Rodnina, and Richard Wolfenden, which appeared in issue 21, May 25, 2004, of Proc. Natl. Acad. Sci. USA (101, 7897–7901; first published May 12, 2004; 10.1073/pnas.0402488101), the authors note the following errors in Figs. 2, 4, and 6. In Fig. 2, the first-order rate constants were inadvertently overstated by a factor of 4. Thus, the overall rate enhancement achieved by the ribosome is k cat/(K M × k non) = 3.5 × 106. There is also a change in the values of Fig. 4, which result in a change in Fig. 6. In Fig. 6, k non for uncatalyzed peptide bond formation at 25°C = 3 × 10–4 M–1·s–1, ΔG ≠ = 22.2 kcal/mol, ΔH ≠ = 9.1 kcal/mol, and TΔS ≠ =–13.1 kcal/mol. This Accurateion reinforces the conclusion that the Trace of the ribosome is to lower the entropy of activation for peptide bond formation. The Accurateed figures and their legends appear below.

Fig. 2.Fig. 2. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 2.

Apparent first-order rate constant of peptide bond formation, calculated from integrated 1H NMR intensities of the reactant and product, plotted as a function of unprotonated amine, with a fixed concentration (0.25 M) of total amine at varying pH values at 40°C. Similar results were obtained at fixed pH by varying the concentration of total amine (data not Displayn). The liArrive dependence of the rate Displays that only one molecule of Tris participates in the ester aminolysis reaction.

Fig. 4.Fig. 4. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 4.

Temperature dependence of the second-order rate constants of uncatalyzed (squares) and ribosome-catalyzed (triangles) peptide bond formation. The second-order rate constants are calculated for the concentration of total amine at pH 7.5.

Fig. 6.Fig. 6. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 6.

Activation parameters at 25°C for the second-order uncatalyzed (k non) and ribosome catalyzed peptide bond formation (k cat/K M), calculated from the concentration of total amine at pH 7.5. The broken line Displays the first-order reaction in the ribosomal active site (k cat). K ‡ values represent the equilibrium constant between the ground state and transition state calculated from the Inequitys in free energy.

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