Speaker
Description
The ribosome is a ribonucleoprotein complex responsible for protein synthesis, with ribosomal proteins surrounding and interacting with the highly conserved RNA catalytic core. Some protein fragments located close to the peptidyl transferase center adopt characteristic backbone conformations in the ribosome. Our previous molecular dynamics simulations showed that isolated ribosomal protein fragments can sample similar conformations in aqueous solution (outside the ribosome), This suggests that part of their ribosome-associated conformational preference may be intrinsic to the peptide sequence.
We investigate whether these preferences are determined by the specific amino-acid order or arise primarily from peptide composition. Short fragments from ribosomal proteins uL2, uL3, uL13 and uL22 were simulated in explicit solvent together with shuffled variants. Multiple independent molecular dynamics simulations were performed for each peptide. Backbone conformational ensembles were characterized using residue-specific Ramachandran φ/ψ torsions and respective free-energy landscapes, allowing direct comparison between native and shuffled sequences.
We found that native and sequence-shuffled peptides showed broadly similar φ/ψ distributions despite differences in amino-acid order. Nevertheless, localized changes were observed at several residue positions, indicating that local sequence context can modulate backbone conformational preferences. These results suggest that the conformational behaviour of evolutionary old ribosomal protein fragments is relatively robust to sequence randomization. The conformations found in the ribosome were readily sampled in the aqueous solution, which implies that the conformational penalties associated with the fragment binding to the RNA were low.