RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

Abstract

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.

The role of specific 2′-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA

“…The kinked conformation confers strongly retarded electrophoretic mobility to the RNA, whereas the extended structure migrates with a mobility typical of a simple 3-nt bulge (Goody et al 2003;Matsumura et al 2003). Fluorescence resonance energy transfer (FRET) measurements (Goody et al 2003) show that the RNA undergoes an ion-induced two-state transition between the two structures, consistent with molecular dynamics studies that have predicted structural bistability in K-turn RNA (Cojocaru et al 2005;Razga et al 2005Razga et al , 2006. Single-molecule FRET data indicate that transitions between the kinked and extended forms are fast (B. Turner, J.C. Penedo, and D.M.J.…”

“…The relatively weak effects arising from removal of the 29-OH of À1n suggest that these interactions are not critical to the formation of the kinked geometry, but form adventitiously. Moreover, molecular dynamics simulations have suggested a degree of hinge-like flexibility in the K-turn (Cojocaru et al 2005;Razga et al 2004Razga et al , 2005Razga et al , 2006, and it is possible that these interactions may be continually forming and rearranging.…”

Molecular dynamics simulations of RNA: An in silico single molecule approach

“…64 The calculations, however, were not sufficiently accurate to achieve conclusive results. Zacharias applied such calculations quite successfully to investigate the context dependence of the structure of G/A base pairs in internal RNA loops, though large error margins in the calculations were reported.69…”

“…Such dynamics of Kink-turns have been implicated in large scale motions in the ribosome during protein synthesis (see Figure 4). 50,64,102 Complex RNA folds are also associated with major cation binding sites that are not typically found around standard A-form RNA helices. For example, the loop E motif and RNA kissing complexes form unique ion binding pockets that are continuously occupied by 2-3 monovalent cations in simulations.54,57,104,105 Despite this high occupancy, the kissing complex ions are delocalized and smoothly exchange with bulk solvent (see Figure 5).…”

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

“…Several MD simulations of apo-sRNA or their complex have been made to reveal the recognition mechanism and the conformational change, [38][39][40] which also indicated that the flexibility of the V-shaped K-turn sRNA and the tertiary interactions between the sRNA and its chaperon protein play critical roles in the binding procedure. 38,39,[41][42][43] Among these previous observations, most attention was focused on the interactions between sRNA and its chaperon, while the internal folding kinetics of sRNA upon L7Ae-binding were poorly understood. In the current study, we compared the hinge motion and folding kinetics of L7Ae-bound and apo sRNA to further discover the mechanism of recognition between sRNA and L7Ae using MD simulations.…”