Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Hinge-like Motions in RNA Kink-turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases

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 (MD) simulations were carried out for selected K-turns from 23S rRNA (Kt-38, Kt-42, Kt-58) and for K-turn of human U4 snRNA (Kt-U4). The MD simulations reveal hinge-like K-turn motions on the nanosecond time-scale and thus indicate that K-turns are dynamically flexible, and capable of regulating significant inter-segmental motions (1).

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. 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 (2).

The presence of K-turns at key functional sites in the ribosome suggests that they confer flexibility to RNA protuberances that regulate the traversal of tRNAs from one binding site to another across the interface between the small and large subunit during protein synthesis cycle.

References and Footnotes
  1. F. Razga, N. Spackova, K. Reblova, J. Koca, N. B. Leontis, and J. Sponer. J. Biomol. Struct. Dyn. 22, 183-194 (2004).
  2. F. Razga, J. Koca, J. Sponer, and N. B. Leontis. Biophys. J. In press (2005).

Filip Razga1,2,*
Jaroslav Koca1
Neocles B.Leontis3
Jiri Sponer1,4,*

1National Centre for Biomolecular Research
Kotlá_ska 2
61137 Brno, Czech Republic
2Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
61265 Brno, Czech Republic
3Chemistry Department and Center for Biomolecular Sciences
Bowling Green State University
Bowling Green, OH 43403
4Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic

*Email: sponer@ncbr.chemi.muni.cz