Speaker
Description
Nascent peptides can regulate gene expression while they are still being synthesized, using interactions within the ribosomal exit tunnel to interrupt elongation. The Vibrio export-monitoring peptide (VemP) links protein export to translational control. Its compact C-terminal helix lies next to the peptidyl-transferase center (PTC), where peptide bonds are formed, and constrains conserved nucleotides implicated in aminoacyl-tRNA accommodation. Cryogenic-electron microscopy resolves two alternative conformations of nucleotide U2506, referred to as A and B, within the arrested complex. Previous studies suggested that these states support distinct peptide-ribosome interactions, but their relationship to peptide relaxation and PTC remodeling remains unresolved.
We ask which PTC rearrangements accompany reduced VemP helicity and how they differ between the two identified U2506 conformational states.
We used bias-exchange well-tempered metadynamics to sample the C-terminal 11-residue helical VemP segment in a ribosomal tunnel model initialized separately from A and B. The peptide remained linked to P-site tRNA. Analysis of unbiased replica configurations related peptide helicity, extension, and tunnel position to nucleotide fluctuations and structural changes of the PTC related to the release of translational arrest.
Reduced VemP helicity was associated with peptide extension in both systems, but substantially greater U2584/U2585 remodeling in A. These nucleotides also exhibited larger conformational fluctuations in A. Within this ensemble, lower helicity was associated with peptide displacement away from the PTC and U2584/U2585 conformations closer to the substrate-accommodated reference. U2506 nevertheless retained distinct conformations, and steric overlaps with the reference substrate persisted. Our findings suggest that VemP relaxation can accompany selective PTC remodeling without an A-site substrate, while complete restoration of substrate-compatible geometry requires additional rearrangements that likely happen before the VemP segment is fully synthesized.