Paper Citing NAMD - Abstract
Trabuco, Leonardo G.; Harrison, Christopher B.; Schreiner, Eduard; Schulten, Klaus
Recognition of the Regulatory Nascent Chain TnaC by the Ribosome
STRUCTURE, 18:627-637, MAY 12 2010
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 2.1 mu s. The simulations, complemented by quantum chemistry calculations, suggest that the critical TnaC residue W12 is recognized by the ribosome via a cation-pi 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 that 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.
