RNA K-turns-Flexible Ribosomal Motifs:Dynamics, Hydration, Conformations and Biological Relevance
| Authors | |
|---|---|
| Year of publication | 2005 |
| Type | Article in Proceedings |
| Conference | Workshop on Modeling Interactions in Biomolecules II |
| MU Faculty or unit | |
| Citation | |
| Field | Physical chemistry and theoretical chemistry |
| Keywords | RNA flexibility; Kink turn motif; A-minor motif; Molecular dynamics |
| Description | High-resolution x-ray structures of large and small ribosomal subunits revealed that rRNAs form intricate shapes and architectures, comprising single stranded loops, double stranded helices, and non-canonical regions compactly folded in specific rRNA segments known as RNA motifs. RNA motifs are biologically important structural segments necessary for correct functioning of ribosome. They are characterized by specific 3D architectures (consisting of canonical and non-canonical regions) which are in most cases very well conserved, and by their unique intrinsic properties. Kink-turns (Kt) are RNA motifs with sharp bend of phosphodiester backbone (~120) leading to "V" - shaped 3D architecture. They are composed of three distinct structural elements: canonical Watson-Crick helix (C-stem), internal loop (Kink) with nominally unpaired bases, and non-canonical helix (NC-stem). The Kink thus forms a tip of a "V" with C- and NC-stems attached as arms. The interaction between stems is mediated by A-minor interactions Explicit-solvent Molecular Dynamics (MD) simulations were carried out for selected isolated K-turns from 23S rRNA (Kt-38, Kt-42, Kt-58), for K-turn of human U4 snRNA (Kt-U4) and for Kt-42 in complex with factor-binding site (i.g. GTPase-associated center). 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. Crucial role in K-turns dynamics is played by A-minor interaction. The presence of K-turns at key functional sites in the ribosome (A-site finger, factor-binding site, etc.), 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. |
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