1National Centre for Biomolecular Research, Kotlarska 2, 61137 Brno, Czech Republic
2Institute of Biophysics, Academy of Sciences of the Czech Republic and National Centre for
Biomolecular Research, Kralovopolska 135, 61265 Brno, Czech Republic
3Chemistry Department and Center for Biomolecular Sciences, Bowling Green State
University, Bowling Green, OH 43403
Keywords: Molecular dynamics, RNA Flexibility, non-Watson-Crick basepair,
modular building, long-residency hydration
Abstract: 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. These motifs, asymmetric internal loops, are called Kink-turns (K-turns), and are characterized by a sharp, ca. 120° bend in both phosphodiester backbones producing a V-shaped structure with an acute angle of ca. 60° between the flanking RNA helices. The bend is stabilized by non-Watson-Crick basepairs involving the minor (shallow) grooves of the helices.
We have carried out a set of explicit-solvent Molecular Dynamics (MD) simulations for selected K-turn motifs, including K-turn 38 (Kt-38) occurred in the A-site finger, Kt-42 occurred in the Factor-binding domain and Kt-58 occurred in the Domain III from the 23S ribosomal RNA of H. marismortui. The presence of K-turns at these key functional sites of the 50S subunit of the ribosome suggests that they confer flexibility to RNA protuberances that regulate the traversal of bound tRNAs from one binding site to another across the interface between the small and large subunit during the protein synthesis cycle. The simulations indicate that K-turns are dynamically very flexible internal loops linking geometrically rigid helical domains (modular building character of these motifs) and thus capable of regulating significant inter-segmental motions. The simulations reveal that on a nano-second timescale, K-turns sample at least two major isoenergetic conformational substates that are separated by very low energy barrier and that are stabilized by different specific long-residency hydration sites. The long-residency hydration sites stabilize non-Watson-Crick basepairs and sharp turns of the phosphodiester backbone, they mediate inter-segment contacts and may actually act as permanent waters inside these motifs. The unique flexibility of K-turn RNA motifs contrasts sharply with the rigidity of other non-Watson-Crick RNA motifs, such as the loop E (5S rRNA) and the sarcin-ricin motif (23S rRNA).