RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics

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Authors

RÁZGA Filip ZACHARIAS Martin RÉBLOVÁ Kamila KOČA Jaroslav ŠPONER Jiří

Year of publication 2006
Type Article in Periodical
Magazine / Source Structure
MU Faculty or unit

Faculty of Science

Citation
Field Physical chemistry and theoretical chemistry
Keywords Kink-turn; A-minor motif; RNA flexibility; Molecular Dynamics; Ribosome function
Description The presence of Kink-turns (Kt) at key functional sites in the ribosome (e.g., A-site finger and L7/L12 stalk) suggests that some Kink-turns can confer flexibility on RNA protuberances that regulate the traversal of tRNAs during translocation. Explicit solvent molecular dynamics demonstrates that Kink-turns can act as flexible molecular elbows. Kink-turns are associated with a unique network of long-residency static and dynamical hydration sites that is intimately involved in modulating their conformational dynamics. An implicit solvent conformational search confirms the flexibility of Kink-turns around their X-ray geometries and identifies a second low-energy region with open structures that could correspond to Kink-turn geometries seen in solution experiments. An extended simulation of Kt-42 with the factor binding site (helices 43 and 44) shows that the local Kt-42 elbow-like motion fully propagates beyond the Kink-turn, and that there is no other comparably flexible site in this rRNA region. Kink-turns could mediate large-scale adjustments of distant RNA segments.
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