Effect of the H38 helix conformation on stability of pre-reactional state of peptidyl transferase center of A ribosome: a molecular dynamics study

Abstract

Molecular dynamics simulations of the 70 E.coli ribosome complex in the canonical A/A, P/P-state, carrying ErmBL stalling peptide, enabled us to observe formation and destabilization of pre-reactional conformation of the peptidyl transferase center (PTC). In the absence of antibiotics in the nascent peptide exit tunnel (NPET), the peptidyl transferase reaction (PTR) substrates, specifi-cally, the Lys-aa-tRNA aminogroup and the Asp-P-tRNA ester, were found to be steadily close to each other at a distance of no more than 4.5 Å during 200 ns of simulation. In the presence of erythromycin in NPET that distance increased to 6 Å and more during the same time of simulation; moreover, the binding site of the CCA-end of A-tRNA became distorted. An important role in the A-tRNA positioning was played by H38 of 23S rRNA: its binding patterns with A-tRNA and the H84 neighboring helix, which participates in the P-tRNA positioning, altered significantly. In the trajectory, where the PTR substrates are the most converged, the H38 and H84 helices are linked to each other by stacking interaction of the U890 and G2308 residues, and the A896 residue formed a stacking contact with G19 of A-tRNA. The presence of erythromycin in NPET destructs the stack-ing contact between H38 and H84, while the A-tRNA position alters to such an extent, that it inter-acts with H38 by its another residue, C56. Such a distortion of the A-tRNA binding results in de-struction of the pre-reactional state of PTR, which could explain the antibiotic’s action. It is significant that the H38 position is worth to be additionally optimized for obtaining the pre-reactional ribosomal structures due to insufficiency of the structural data regarding this helix.