Open AccessProtein escape at an atomistic model of the ribosomal exit tunnel
Author(s) -
Phuong Thuy Bui,
Trinh Xuan Hoang
Publication year - 2020
Publication title -
journal of physics. conference series
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.21
H-Index - 85
eISSN - 1742-6596
pISSN - 1742-6588
DOI - 10.1088/1742-6596/1506/1/012022
Subject(s) - ribosomal protein , ribosome , molecular dynamics , protein data bank (rcsb pdb) , physics , protein folding , folding (dsp implementation) , ribosomal rna , statistical physics , biology , gene , nuclear magnetic resonance , engineering , rna , genetics , quantum mechanics , electrical engineering
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.