Leonardo G. Trabuco, Christopher B Harrison, Eduard Schreiner, and Klaus
Schulten.
Recognition of the regulatory nascent chain TnaC by the ribosome.
Structure, 18:627-637, 2010.
TRAB2010
Regulatory nascent chains interact with the ribosomal exit tunnel and modulate their own
translation. To characterize nascent chain recognition by the ribosome at the atomic level,
extensive molecular
dynamics simulations of TnaC, the leader peptide of the tryptophanase
operon, inside the exit tunnel were performed for an aggregate time of 2.1s. The
simulations, complemented by quantum chemistry calculations, suggest that the critical
TnaC residue W12 is recognized by the ribosome via a cation- interaction, whereas
TnaC's D16 forms salt bridges with ribosomal proteins. The simulations also show that
TnaC-mediated translational arrest does not involve a swinging of ribosomal protein L22,
as previously proposed. Furthermore, bioinformatic analyses and simulations suggest
nascent chain elements which may prevent translational arrest in various organisms.
Altogether, the current study unveils atomic-detail interactions that explain the role of
elements of TnaC and the ribosome essential for translational arrest.