RNA Kink-turns as Flexible Molecular Hinges of the Ribosomal "LEGO". The Role of Second A-minor Motif and Nominally Unpaired Bases
| Authors | |
|---|---|
| Year of publication | 2005 |
| Type | Article in Proceedings |
| Conference | 14th Conference on Current Trends in Computational Chemistry 2005 |
| MU Faculty or unit | |
| Citation | |
| Field | Physical chemistry and theoretical chemistry |
| Keywords | Kink-turn; RNA flexibility; A-minor; Ribosome dynamics |
| Description | 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 and 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. 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. 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. Specifically, Kt-42 is suggested to allow the large scale motions of the factor binding domain (seen in Cryo-EM) in all three kingdoms while Kt-38 (when present) may be essential for the dynamics of the A-finger regulating the access of tRNA from A-site to P-site. Thus, while the whole ribosomal assembly superficially resembles a sophisticated LEGO toy, the K-turns are well poised to act as major recurrent elbow-like dynamical ribosomal building blocks. |
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