Constraining ribosomal RNA conformational space

Despite the potential for many possible secondary-structure conformations, the native sequence of ribosomal RNA (rRNA) is able to find the correct and universally conserved core fold. This study reports a computational analysis investigating two mechan-isms that appear to constrain rRNA secondary-structure conformational space: ribosomal proteins and rRNA sequence composition. The analysis was carried out by using rRNA–ribosomal protein inter-action data for the Escherichia coli 16S rRNA and free energy minimization software for secondary-structure prediction. The results indicate that selec-tion pressures on rRNA sequence composition and ribosomal protein–rRNA interaction play a key role in constraining the rRNA secondary structure to a single stable form