Journal of Physics: Conference Series 1506, 012022 (2020)

ISSN: 1742-6596

Protein escape at an atomistic model of the ribosomal exit tunnel

Phuong Thuy Bui and Trinh Xuan Hoang

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.

DOI: 10.1088/1742-6596/1506/1/012022

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