D 2005

Ribosomal RNA Kink-turn motif - a flexible molecular hinge

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS et. al.

Basic information

Original name

Ribosomal RNA Kink-turn motif - a flexible molecular hinge

Name in Czech

Ribozomalny RNA Kink-turn motiv - flexibilny molekularny pant

Name (in English)

Ribosomal RNA Kink-turn motif - a flexible molecular hinge

Authors

RÁZGA, Filip (703 Slovakia), Naděžda ŠPAČKOVÁ (203 Czech Republic), Kamila RÉBLOVÁ (203 Czech Republic), Jaroslav KOČA (203 Czech Republic), Neocles B. LEONTIS (840 United States of America) and Jiří ŠPONER (203 Czech Republic, guarantor)

Edition

prve. Praha, Materials Structure in chemistry, biology, physics and technology, p. 38-38, 1 pp. 2005

Publisher

Krystalograficka spolecnost

Other information

Language

Czech

Type of outcome

Stať ve sborníku

Field of Study

10403 Physical chemistry

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14310/05:00013642

Organization unit

Faculty of Science

ISBN

1221-5894

UT WoS

000223795600007

Keywords in English

RNA; Kink-turn; non-Watson-Crick base pair;

Tags

Kink-turn, non-Watson-Crick base pair, RNA
Změněno: 3/6/2005 17:09, prof. RNDr. Jaroslav Koča, DrSc.

Abstract

ORIG EN

V originále

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.

In English

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.

Links

MSM0021622413, plan (intention)
Name: Proteiny v metabolismu a při interakci organismů s prostředím
Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment
Displayed: 2/11/2024 13:13