REU Project

Ribosomes are complex macromolecules that translate messenger RNA into proteins. Their large subunit contains an exit tunnel through which the growing peptide chain passes before leaving the ribosome. While most studies have focused on the proteins lining the tunnel, comparatively little is known about the highly conserved ribosomal RNA surrounding it. As a result, the three-dimensional organization of this ribosomal RNA is not fully understood. This project examined how RNA structural motifs are arranged near the exit tunnel and whether parts of this organization are conserved across species. Ribosome structures and motif annotations were obtained from the RCSB Protein Data Bank and DSSR, respectively, and the resulting data were analyzed and visualized using RiboVision 2.0, PyMOL, and Python. The main analysis focused on nucleotides within 20 Å of the exit-tunnel centerline in the Escherichia coli ribosome structure 5AFI. A Python program was also developed to superimpose ribosome structures from different species to better compare the exit tunnels. This work provides a computational and visual framework for studying RNA motif organization and future cross-species comparisons.