Rearrangements of Nascent Peptide Inside the Ribosomal Exit Tunnel

Abstract

All proteins, from bacteria to man, are made in the ribosome and are elongated, one residue at a time, at the peptidyl transferase center (PTC). This growing peptide chain wends its way through the ribosomal tunnel to the exit port, ∼ 100 angstroms from the PTC. Regulation of the movement of the peptide within the tunnel and allosteric communication along the tunnel during translation are not well understood. Previously, we demonstrated that solvent-accessible volume surrounding a modifiable cysteine increases monotonically with increase in the van der Waal's volume of the adjacent side chain (Lu et al., J.Mol.Biol. 411: 499-510, 2011) and that the magnitude of this effect depends on location within the ribosomal tunnel. using a photocrosslinking approach, we confirm these results. We extend these studies to investigate whether mutations in the nascent peptide deep in the tunnel affect the accessibility of a modifiable reporter cysteine at the exit port and whether specific regions of the tunnel instigate these effects. Tryptophan vis-a-vis alanine, engineered into the nascent peptide at a distance of 17-19 residues from the PTC, alters the accessibility of residues at the exit port, a distance of 33 residues from the PTC, roughly 50 angstroms from the introduced point mutations. These findings are consistent with long-range rearrangements and may contribute to mechanisms governing sequence-specific signaling from different regions of the tunnel during translation. Supported by NIH grant R01GM52302.