Stereochemical analysis of ribosomal transpeptidation conformation of nascent peptide

Transpeptidation performed by the ribosome is considered as a nucleophilic Sn2 substitution reaction, passing through a tetrahedral intermediate. A stereochemically universal mechanism of the reaction is assumed to exist for all 20 amino acid residues, both in the attacked (donor) and in the attacking (acceptor) substrates. The angles of internal rotation around the bonds of the attacked carbonyl carbon and around the neighbouring bonds in the tetrahedral intermediate, as well as the stereoconfiguration of the intermediate, have been varied. All 54 combinations of the sterically allowed rotational isomers determined by the five torsional angles have been analysed by using Corey-Pauling-Koltun models and by direct calculations permitting the “extreme limits” in interatomic distances and ±7° deviations in bond angles. Only one combination, i.e. one unique conformation of the tetrahedral intermediate, is found to be sterically compatible with all 400 possible pairs of the reacting amino acid residues and at the same time to be capable of cleaving into a planar trans-peptide group. The torsion anglesand ω of this universally allowed intermediate and the peptide product resulting from its cleavage are similar to those in an α-helix. It is suggested that the ribosome generates the α-helical conformation at the C-end of the nascent peptide.