Publication details

Structure and Dynamics of RNA K-turn Motifs


RÁZGA Filip ŠPAČKOVÁ Naděžda RÉBLOVÁ Kamila KOČA Jaroslav ŠPONER Jiří LEONTIS Neocles, B.

Year of publication 2003
Type Article in Proceedings
Conference RNA klub
MU Faculty or unit

Faculty of Science

Field Physical chemistry and theoretical chemistry
Keywords Molecular Dynamics; non-Watson-Crick basepairs; RNA flexibility
Description Hinge-like RNA motifs occur at conserved positions in the 16S and 23S ribosomal RNAs, as revealed by x-ray crystallography of the 50S subunits of H. marismortui and D. radiodurans and the 30S subunit of T. thermophilus. The conformation of these asymmetric internal loops, called Kink-turns or K-turns, produces sharp, 120-degree bends in both phosphodiester backbones resulting in a V-shaped structure with an acute angle of ca.60 deg. between the RNA helices flanking the motif. In addition, some K-turns are specific binding sites for ribosomal proteins and others take part in RNA-RNA tertiary interactions. We have carried out a set of explicit-solvent Molecular Dynamics (MD) simulations for selected K-turn RNA motifs, including K-turn 38,K-turn 42 and K-turn 58 from the 23S ribosomal RNA of Haloarcula marismortui. The simulations reveal an unprecedented dynamical flexibility, suggesting that K-turn motifs may function as a very flexible internal loops linking rigid helix stems and thus capable of regulating significant inter-segmental motions. On a nano-second timescale, K-turns sample different isoenergetic conformational substates that are separated by virtually no free energy barriers and that are stabilized by specific long-residency hydration sites and monovalent counterions. The unique flexibility of K-turn RNA motifs contrasts sharply with the rigidity of other non-Watson-Crick RNA motifs, such as the 5S rRNA loop E and the sarcin-ricin motif. K-turn conformational changes may be modulated by protein-RNA or RNA-RNA interactions. Thus, K-turns can be utilized as hinges allowing flexible movements of selected parts of the ribosome during protein synthesis cycle.K-turns occur in the A-site finger domain, the factor-binding domain, and the L1-binding domain and even at the base of Domain VI includes the sarcin/ricin loop.
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