This Article Full Text Full Text (PDF) supplemental file Supplemental File All Versions of this Article: biophysj.104.054916v1 88/5/3466    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Rázga, F. Articles by Leontis, N. B. Search for Related Content PubMed PubMed Citation Articles by Rázga, F. Articles by Leontis, N. B.

Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-Minor Motif and Nominally Unpaired Bases

Filip Rázga ^* , Jaroslav Koa ^*, Jií poner   and Neocles B. Leontis 

^* National Centre for Biomolecular Research, Brno, Czech Republic; Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic; and Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio

Correspondence: Address reprint requests to Jií poner, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic. E-mail: sponer{at}ncbr.chemi.muni.cz; or to Neocles B. Leontis, Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403. E-mail: leontis{at}bgnet.bgsu.edu.

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 the 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 some K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle.

This article has been cited by other articles:

				D. Piekna-Przybylska, P. Przybylski, A. Baudin-Baillieu, J.-P. Rousset, and M. J. Fournier Ribosome Performance Is Enhanced by a Rich Cluster of Pseudouridines in the A-site Finger Region of the Large Subunit J. Biol. Chem., September 19, 2008; 283(38): 26026 - 26036. [Abstract] [Full Text] [PDF]

				K. Reblova, E. Fadrna, J. Sarzynska, T. Kulinski, P. Kulhanek, E. Ennifar, J. Koca, and J. Sponer Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics Biophys. J., December 1, 2007; 93(11): 3932 - 3949. [Abstract] [Full Text] [PDF]

				C. Musselman, H. M. Al-Hashimi, and I. Andricioaei iRED Analysis of TAR RNA Reveals Motional Coupling, Long-Range Correlations, and a Dynamical Hinge Biophys. J., July 15, 2007; 93(2): 411 - 422. [Abstract] [Full Text] [PDF]

				T. Komoda, N. S. Sato, S. S. Phelps, N. Namba, S. Joseph, and T. Suzuki The A-site Finger in 23 S rRNA Acts as a Functional Attenuator for Translocation J. Biol. Chem., October 27, 2006; 281(43): 32303 - 32309. [Abstract] [Full Text] [PDF]

				M. V. Krasovska, J. Sefcikova, K. Reblova, B. Schneider, N. G. Walter, and J. Sponer Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme Biophys. J., July 15, 2006; 91(2): 626 - 638. [Abstract] [Full Text] [PDF]

				A. Mokdad, M. V. Krasovska, J. Sponer, and N. B. Leontis Structural and evolutionary classification of G/U wobble basepairs in the ribosome Nucleic Acids Res., March 6, 2006; 34(5): 1326 - 1341. [Abstract] [Full Text] [PDF]

				N. Spackova and J. Sponer Molecular dynamics simulations of sarcin-ricin rRNA motif Nucleic Acids Res., February 2, 2006; 34(2): 697 - 708. [Abstract] [Full Text] [PDF]

				Y. Mu and G. Stock Conformational Dynamics of RNA-Peptide Binding: A Molecular Dynamics Simulation Study Biophys. J., January 15, 2006; 90(2): 391 - 399. [Abstract] [Full Text] [PDF]

				V. Cojocaru, R. Klement, and T. M. Jovin Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif Nucleic Acids Res., June 13, 2005; 33(10): 3435 - 3446. [Abstract] [Full Text] [PDF]