Publication details

 

Ribosomal RNA Kink-turn motif - a flexible molecular hinge

Basic information
Original title:Ribosomal RNA Kink-turn motif - a flexible molecular hinge
Authors:Filip Rázga, Naděžda Špačková, Kamila Réblová, Jaroslav Koča, Neocles B. Leontis, Jiří Šponer
Further information
Citation:RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Ribosomal RNA Kink-turn motif - a flexible molecular hinge. In Materials Structure in chemistry, biology, physics and technology. prve. Praha: Krystalograficka spolecnost, 2005. s. 38-38, 1 s. ISBN 1221-5894.Export BibTeX
@inproceedings{569019,
author = {Rázga, Filip and Špačková, Naděžda and Réblová, Kamila and Koča, Jaroslav and Leontis, Neocles B. and Šponer, Jiří},
address = {Praha},
booktitle = {Materials Structure in chemistry, biology, physics and technology},
edition = {prve},
keywords = {RNA; Kink-turn; non-Watson-Crick base pair;},
language = {cze},
location = {Praha},
isbn = {1221-5894},
pages = {38-38},
publisher = {Krystalograficka spolecnost},
title = {Ribosomal RNA Kink-turn motif - a flexible molecular hinge},
year = {2005}
}
Original language:Czech
Field:Physical chemistry and theoretical chemistry
Type:Article in Proceedings
Keywords:RNA; Kink-turn; non-Watson-Crick base pair;

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 largescale motions or they can allow a smooth assembling of the other parts of the ribosome.

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 largescale motions or they can allow a smooth assembling of the other parts of the ribosome.

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