Theoretical study of a proton wire mechanism for the peptide bond formation in the ribosome

© 2017, Springer-Verlag Berlin Heidelberg. A computational approach has allowed us to get an insight on a recently proposed mechanism for the peptide bond formation in the ribosome. This new mechanism suggests a proton transfer from the attacking amine to a water molecule through a short network of hydrogen bonds, leading to the formation of a negatively charged tetrahedral intermediate. Our results show that a first water molecule provokes the deprotonation of the 2′OH of A76 through the 2′OH of A2451, thus increasing the basicity of the O2′. Our study also confirms the presence of an anionic tetrahedral intermediate in which a proton of NH2 has been transferred to O2′, the negative charge being mainly located over the carbonyl oxygen atom (O1), and it is stabilized by a second water molecule. The decomposition of the intermediate takes place by the breaking of the C-O3′ bond and a proton transfer from O2′ to O3′ through the presence of a third water molecule. Finally, the loss of a proton by O2′ provokes the inverse transfer from A2451. A good agreement between theoretical and experimental results has been found. In particular, our theoretical study confirms the feasibility of the proton wire mechanism and helps to clarify the decomposition of the intermediate.