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Nucleic Acids Research 2005 33(16):5106-5111; doi:10.1093/nar/gki805
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Published online 9 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Computational Biology

Constraining ribosomal RNA conformational space

Paola Favaretto, Arjun Bhutkar and Temple F. Smith*

BioMolecular Engineering Research Center, Boston University 36 Cummington Street, Boston MA 02215, USA

*To whom correspondence should be addressed. Tel: +1 617 353 7123; Fax: +1 617 353 7020; Email: tsmith{at}darwin.bu.edu

Received January 24, 2005. Revised July 20, 2005. Accepted August 15, 2005.

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.


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