Constraining Ribosomal RNA Conformational Space
Date
2005-09-09
Authors
Favaretto, Paola
Bhutkar, Arjun
Smith, Temple F.
Version
OA Version
Citation
Favaretto, Paola, Arjun Bhutkar, Temple F. Smith. "Constraining ribosomal RNA conformational space" Nucleic Acids Research 33(16): 5106-5111. (2005)
Abstract
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 mechanisms 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 interaction data for the Escherichia coli 16S rRNA and free energy minimization software for secondary-structure prediction. The results indicate that selection 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.