title: Constraining ribosomal RNA conformational space.
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.
authors.affiliation: BioMolecular Engineering Research Center, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
authors.forename: Paola
authors.initials: P
authors.lastname: Favaretto
authors.forename: Arjun
authors.initials: A
authors.lastname: Bhutkar
authors.forename: Temple F
authors.initials: TF
authors.lastname: Smith
mesh_terms: D020029:Base Pairing; D019295:Computational Biology; D004926:Escherichia coli / Q000235:genetics; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry; D012336:RNA, Ribosomal, 16S / Q000737:chemistry*; D012269:Ribosomal Proteins / Q000737:chemistry; D017423:Sequence Analysis, RNA
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012269:Ribosomal Proteins