Communications in Physics 23
, 219-225 (2013)
Effects of ribosomal exit tunnel on protein
Bui Phuong Thuy and Trinh Xuan Hoang
In vivo, folding of many proteins occurs during their synthesis in the ribosome and
continues after they have escaped from the ribosomal exit tunnel. In this research, we investigate
the confinement effects of the ribosome on the cotranslational folding of three proteins, of PDB
codes 1PGA, 1CRN and 2RJX, by using a coarse-grained model and molecular dynamics simula-
tion. The exit tunnel is modeled as a hollow cylinder attached to a flat wall, whereas a Go-like
model is adopted for the proteins. Our results show that the exit tunnel has a strong effect on the
folding mechanism by setting an order by which the secondary and tertiary structures are formed.
For protein 1PGA, the folding follows two different folding routes. The presence of the tunnel also
improves the foldability of protein.