RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function
| Authors | |
|---|---|
| Year of publication | 2005 |
| Type | Article in Proceedings |
| Conference | Strukturní biofyzika makromolekul |
| MU Faculty or unit | |
| Citation | |
| Field | Physical chemistry and theoretical chemistry |
| Keywords | Molecular Dynamics; RNA Kink Turn; Ribosome; RNA flexibility; |
| Description | Explicit-solvent Molecular Dynamics (MD) simulations were carried out for three K-turns (Kt) from 23S rRNA, i.e., Kt-38 located at the A-site finger base, Kt-42 located at the L7/L12 stalk base, and Kt-58 located in Domain III and for K-turn of human U4 snRNA. The presence of K-turns at key functional sites in the ribosome (e.g., A-site finger and L7/L12 stalk) suggests that some K-turns can confer flexibility on RNA protuberances that regulate the traversal of tRNAs during translocation. MD simulations demonstrated that the K-turns can act as flexible molecular elbows. The angle between the helical arms is regulated by local variations of the second A-minor (type I) interaction, which mediates the contact between the helical stems, and by conformational change of the single base from the nominally unpaired region. Moreover, K-turns are associated with a unique network of long-residency and dynamical hydration sites that are intimately involved in modulating their conformational dynamics. Variability of A-minor interaction ranges from closed geometries to open ones stabilized by insertion of long-residency waters between the interacting bases. Implicit solvent conformational search confirms the flexibility of K-turns around their x-ray geometries and identifies a second separate low-energy region with more open structures that could correspond to K-turn geometries seen in solution experiments. An extended simulation of Kt-42 with the factor-binding site shows that elbow-like motion fully propagates beyond the K-turn and could mediate large-scale adjustments of distant RNA regions. |
| Related projects: |