A vast majority of proteins in living organisms are synthesized by ribosomes. The ribosome is a biomolecular complex of ribosomal RNA and a few dozen proteins. The ribosome consists of two subunits, which have distinct roles. While the small 30S subunit reads the genetic information stored in messenger RNA, the large 50S subunit catalyzes peptide bond formation. The catalytic center is located deep in the 50S subunit, so the nascent peptide chain leaves the ribosome through a 10-nm long tunnel. A growing body of evidence has been gathered suggesting that the exit tunnel is not a passive environment but a functional part of the ribosome. For instance, certain nascent peptide sequences interact with the tunnel walls and cause ribosomal stalling. The translational arrest is also involved in the action of a large class of antibiotics.
Traditional biophysical techniques such as X-ray crystallography or cryo-electron microscopy have difficulties in resolving the tunnel content due to the high intrinsic flexibility of the nascent peptide. All-atom computer simulations can provide insights into the protein synthesis on ribosomes at molecular details and complement the structural information by dynamics and energetic data [1].
This contribution gives a brief overview of our results related to the ribosome exit tunnel. In particular, we describe a stalling peptide called VemP, which forms a compact secondary structure within the ribosome tunnel and causes translational arrest. We show that various amino acids of VemP play various roles in sequence sensitivity of translational stalling previously reported by biochemical experiments. While the amino acids near the tunnel constriction act as an anchor which likely slows down the translation, the C-terminal directly inhibits the ribosome catalytic center. Further through bioinformatic analyses, we explain how the tunnel walls are modulated by the presence of a nascent peptide or an antibiotic.
A part of the simulation results was obtained through Open Calls of IT4Innovations Ostrava in projects OPEN-12-9 and OPEN-15-49.