Quantum Mechanical Study on the Mechanism of Peptide Release in the Ribosome

Abstract

A quantum mechanical study of different concerted mechanisms of peptide release in the ribosome has been carried out using the M06-2X density functional. Reoptimization with MP2 has also been carried out for the stationary points of some selected mechanisms. The uncatalyzed processes in solution have been treated with the SMD solvation model. We conclude that the 2'-OH plays an important catalytic role and that it takes place via a zwitterionic transition state, this TS being stabilized by the presence of oxyanion holes or by the solvent. The comparison with our previous study on the peptide bond formation shows that both processes proceed via two different mechanisms, in such a way that the TS of the aminolysis has an ion-pair instead of a zwitterionic character. So, despite the limitations of the model we have used, we can conclude that there is catalytic promiscuity at the peptidyl transferase center (PTC) of the ribosome.