Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel.

ABSTRACT: The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in so

SUBMITTER: Kolar MH 

PROVIDER: S-EPMC8887479 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature