Ribosomal RNA Kink-turn motif – a flexible molecular hinge

Filip Razga¹, Nada Spackova², Kamila Reblova¹, Jaroslav Koca¹, Neocles B. Leontis³ and Jiri Sponer²

¹National Centre for Biomolecular Research, Kotlarska 2, 61137 Brno, Czech Republic,

²Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic,

³Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403 and

Ribosomal RNA K-turn motifs are asymmetric internal loops characterized by a sharp bend in the phosphodiester backbone resulting in “V” shaped structures, recurrently observed in ribosomes and showing high degree of sequence conservation. We have carried out extended explicit solvent molecular dynamics simulations of selected K-turns, in order to investigate their intrinsic structural and dynamical properties. The simulations reveal an unprecedented dynamical flexibility of the K-turns around their x-ray geometries. The K-turns sample, on the nanosecond timescale, different conformational substates. The overall behaviour of the simulations suggests that the sampled geometries are essentially isoenergetic and separated by minimal energy barriers. The nanosecond dynamics of isolated K-turns can be qualitatively considered as motion of two rigid helix stems controlled by a very flexible internal loop which then leads to substantial hinge-like motions between the two stems. This internal dynamics of K-turns is strikingly different for example from the bacterial 5S rRNA Loop E motif or BWYV frameshifting pseudoknot which appear to be rigid in the same type of simulations. Bistability and flexibility of K-turns was also suggested by several recent biochemical studies. Although the results of MD simulations should be considered as a qualitative picture of the K-turn dynamics due to force field and sampling limitations, the main advantage of the MD technique is it ability to investigate the region immediately around their ribosomal-like geometries. This part of the conformational space is not well characterised by the solution experiments due to large-scale conformational changes seen in the experiments. We suggest that K-turns are well suited to act as flexible structural elements of ribosomal RNA. They can for example be involved in mediation of large–scale motions or they can allow a smooth assembling of the other parts of the ribosome.