Analysis of Predictions for the Catalytic Mechanism of Ribosomal Peptidyl Transfer

Abstract

The reaction mechanism of peptide bond formation on the ribosome is now becoming established by results from both experiments and computer simulations. Here, we analyze predictions from molecular dynamics simulations, as well as from new crystal structures, and examine their implications for the mechanisms of peptidyl transfer and peptidyl-tRNA hydrolysis. A number of computational predictions for the peptidyl transfer reaction, including quantitative energetics, stereochemistry, hydrogen bonding network, and role of solvent molecules, are found to be supported and confirmed by kinetic and structural data. The results show that this type of reaction calculations can provide important links between structure and function that cannot be obtained by experimental means.