Structure and Dynamics of RNA K-turn Motifs
| Authors | |
|---|---|
| Year of publication | 2003 |
| Type | Article in Proceedings |
| Conference | RNA klub |
| MU Faculty or unit | |
| Citation | |
| 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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