Abstract
We study the post-translational escape of nascent proteins at the ribosomal exit tunnel by using the Go-like model for proteins and a real shape atomistic tunnel built on the protein data bank (PDB) structure of a ribosome of Haloarcula marismortui. The full translation and escape processes of the immunoglobulin binding B1 domain of protein G (GB1) at the tunnel were simulated by using Langevin dynamics. We show that at the simulation temperature corresponding to a physiological temperature, the escape time follows quite well the one-dimensional diffusion model proposed in our earlier works. The relationship between folding and escape obtained for the atomistic tunnel is similar to those obtained previously for the cylinder tunnel.
Published Version
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