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

• Published in: Nucleic acids research 2022-02, Vol.50 (4), p.2258-2269
• Main Authors: Kolář, Michal H, Nagy, Gabor, Kunkel, John, Vaiana, Sara M, Bock, Lars V, Grubmüller, Helmut
• Format: Article
• Language: English
• Subjects: Peptides - metabolism; Peptidyl Transferases - metabolism; Protein Biosynthesis; Protein Folding; Protein Structure, Secondary; Proteins - metabolism; Ribosomes - metabolism; RNA and RNA-protein complexes; Water - metabolism
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkac038

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 solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest.