Published online 6 March 2006
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Structural and evolutionary classification of G/U wobble basepairs in the ribosome
Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University OH 43403, USA 1Institute of Biophysics, Academy of Sciences of the Czech Republic Kralovopolska 135, 612 65, Brno, Czech Republic
*To whom correspondence should be addressed. Tel: +1 419 372 2332; Fax: +1 419 372 2024; Email: Mali{at}bgnet.bgsu.edu
Received December 6, 2005. Revised February 16, 2006. Accepted February 16, 2006.
We present a comprehensive structural, evolutionary and molecular dynamics (MD) study of the G/U wobble basepairs in the ribosome based on high-resolution crystal structures, including the recent Escherichia coli structure. These basepairs are classified according to their tertiary interactions, and sequence conservation at their positions is determined. G/U basepairs participating in tertiary interactions are more conserved than those lacking any interactions. Specific interactions occurring in the G/U shallow groove pocket—like packing interactions (P-interactions) and some phosphate backbone interactions (phosphate-in-pocket interactions)—lead to higher G/U conservation than others. Two salient cases of unique phylogenetic compensation are discovered. First, a P-interaction is conserved through a series of compensatory mutations involving all four participating nucleotides to preserve or restore the G/U in the optimal orientation. Second, a G/U basepair forming a P-interaction and another one forming a phosphate-in-pocket interaction are replaced by GNRA loops that maintain similar tertiary contacts. MD simulations were carried out on eight P-interactions. The specific GU/CG signature of this interaction observed in structure and sequence analysis was rationalized, and can now be used for improving sequence alignments.
Correspondence may also be addressed to Neocles B. Leontis. Tel: +1 419 372 8663; Fax: +1 419 372 9809; Email: Leontis{at}bgnet.bgsu.edu
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