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Biophys. J. BioFAST: First Published February 18, 2005. doi:10.1529/biophysj.104.054916
© 2005 by the Biophysical Society.

A more recent version of this article appeared on May 1, 2005.
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NUCLEIC ACIDS

Hinge-like motions in RNA Kink-turns: The role of the second A-minor motif and nominally unpaired bases

Filip Razga 1, Jaroslav Koca 2, Jiri Sponer 1* and Neocles B. Leontis 3

1 Natl Cntr for Biomolecular Research, Kotlárska 2, 61137 Brno; Institute of Biophysics,Brno
2 Natl Cntr for Biomolecular Research, Kotlárska 2, 61137 Brno
3 Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University

* To whom correspondence should be addressed. E-mail: sponer{at}ncbr.chemi.muni.cz.

Submitted on October 21, 2004
Revised on December 7, 2004
Accepted on 26 January 2005


  Abstract
Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent Molecular Dynamics simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in Domain III and for K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. The simulated A-minor geometries fully agree with x-ray data. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused by conformational change of the adenosine from the nominally unpaired region. Despite the observed substantial dynamics of K-turns, key tertiary interactions are stable and no sign of unfolding is seen. We suggest that K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle.

Key Words: Molecular dynamics, RNA flexibility, RNA hydration, Ribosome function, non-Watson-Crick base pairs




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