Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel.

ABSTRACT: Nascent polypeptide chains (NCs) are extruded from the ribosome through an exit tunnel (ET) traversing the large ribosomal subunit. The ET's irregular and chemically complex wall allows for various NC-ET interactions. Translational arrest peptides (APs) bind in the ET to induce translational arrest, a property that can be exploited to study NC-ET interactions by Force Profile Analysis (FPA). We employed FPA and molecular dynamics (MD) simulations to investigate how individual residues placed in a glycine-serine repeat segment within an AP-stalled NC interact with the ET to exert a pulling force on the AP and release stalling. Our results indicate that large and hydrophobic residues generate a pulling force on the NC when placed ≳10 residues away from the peptidyl transfer center (PTC). Mor

SUBMITTER: Pardo-Avila F 

PROVIDER: S-EPMC11370347 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature