Speaker
Description
The ability of ribosomes to catalyze peptide bond formation is attributed to the peptidyl transferase center (PTC), a catalytic site composed solely of ribosomal RNA (rRNA). Within the ribosome, a structurally symmetric region envelops the PTC, and this feature has been observed consistently across diverse species. This intriguing symmetry hints at an ancient evolutionary origin, suggesting that over billions of years, the PTC has evolved through the accretion of rRNA and ribosomal proteins. However, the precise roles of ribosomal proteins (rProteins) and rRNA in conferring stability to the PTC remain elusive, with the prevailing assumption that the PTC has become less flexible over time. To explore this hypothesis, we conducted all-atom (AA) and Martini coarse-grained (CG) molecular dynamics simulations on two ancestral ribosomes, reconstructed from a modern ribosomal template. We focused on PTC constructs incorporating various rProtein fragments. The AA simulations reveal striking structural similarities between ancestral and modern PTCs. Furthermore, the interactions between rProteins and rRNA appear to play a crucial role in maintaining the conformational stability of the PTC, potentially enhancing the specificity of peptide bond formation. Comparing the results of CG and AA simulations, the transition between different conformational states is not observed during the CG simulations, as the ensemble is under the restrictive influence of the elastic network. Our findings provide valuable insights into the molecular mechanisms underpinning the evolutionary stability of the PTC within ribosomes.
