Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome.

ABSTRACT: Molecular dynamics simulations were carried out on Thermus thermophilus 70S ribosome with and without a nascent polypeptide inside the exit tunnel. Modeling of the polypeptide in the tunnel revealed two possible paths: one over Arg92 of L22 and one under (from the viewpoint of 50S on top of 30S). A strong interaction between L4 and Arg92 was observed without the polypeptide and when it passed over Arg92. However, when the polypeptide passed under, Arg92 repositioned to interact with Ade2059 of 23S rRNA. Using steered molecular dynamics the polypeptide could be pulled through the L4-L22 constriction when situated under Arg92, but did not move when over. These results suggest that the tunnel is closed by the Arg92-L4 interaction before elongation of the polypeptide and the tunnel leads the e

SUBMITTER: Ishida H 

PROVIDER: S-EPMC2599861 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature