Simulating the pulling of stalled elongated peptide from the ribosome by the translocon.

ABSTRACT: The nature of the coupling between the stalling of the elongated nascent peptide chain in the ribosome and its insertion through the translocon is analyzed, focusing on the recently discovered biphasic force that overcomes the stalling barrier. The origin of this long-range coupling is explored by coarse-grained simulations that combine the translocon (TR) insertion profile and the effective chemical barrier for the extension of the nascent chain in the ribosome. Our simulation determined that the inserted H segment is unlikely to climb the TR barrier in parallel with the peptide synthesis chemical step and that the nascent chain should first overcome the chemical barriers and move into the ribosome-TR gap region before the insertion into the TR tunnel. Furthermore, the simulations indicat

SUBMITTER: Rychkova A 

PROVIDER: S-EPMC3690858 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature