Translocation of a β-hairpin-forming peptide through a cylindrical tunnel

We use Langevin dynamics simulations of a minimalist off-lattice model to study the translocation of a beta hairpin forming peptide through a tunnel that mimics the exit tunnel in a ribosome. We have computed the free energy of the peptide as a function of its position relative to the tunnel exit and also studied the properties of the conformational ensemble, when the peptide's position is restricted at different points along the tunnel. Confining the peptide within a sufficiently wide tunnel stabilizes the folded state. The protein then remains folded as it moves towards the tunnel exit. However, when the diameter D of the tunnel is below a certain critical value D-c, confinement destabilizes the folded state and forces the peptide to assume an extended configuration. In this case, as the peptide progresses towards the tunnel exit and eventually leaves the tunnel, it goes through a series of compact, misfolded conformations and eventually folds when it gets close to the exit. The critical tunnel diameter D-c is comparable to the width of ribosomal tunnels. Our results suggest that co-translational folding is probably not universal, but rather a protein-specific phenomenon. (C) 2004 American Institute of Physics.