Ribosomal RNA Kink-turn Motif - A Flexible Molecular Hinge

RÁZGA, Filip, Naďa ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Ribosomal RNA Kink-turn Motif - A Flexible Molecular Hinge. Online. Journal of Biomolecular Structure & Dynamics. Adenine Press, 2004, roč. 22, č. 2, s. 183-193. ISSN 0739-1102. [citováno 2024-04-24]

Základní údaje

• Originální název: Ribosomal RNA Kink-turn Motif - A Flexible Molecular Hinge
• Název česky: Ribozomalny RNA Kink-turn motiv - flexibilny molekulovy pant
• Autoři: RÁZGA, Filip (703 Slovensko), Naďa ŠPAČKOVÁ (203 Česká republika), Kamila RÉBLOVÁ (203 Česká republika), Jaroslav KOČA (203 Česká republika), Neocles B. LEONTIS (840 Spojené státy) a Jiří ŠPONER (203 Česká republika, garant)
• Vydání: Journal of Biomolecular Structure & Dynamics, Adenine Press, 2004, 0739-1102.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Článek v odborném periodiku
• Obor: 10403 Physical chemistry
• Stát vydavatele: Spojené státy
• Utajení: není předmětem státního či obchodního tajemství
• Impakt faktor: Impact factor: 1.113
• Kód RIV: RIV/00216224:14310/04:00010224
• Organizační jednotka: Přírodovědecká fakulta
• UT WoS: 000223795600007
• Klíčová slova anglicky: Ribosomal RNA Kink-turn Motif; molecular dynamics
• Štítky: molecular dynamics, Ribosomal RNA Kink-turn Motif

Anotace

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 a 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 behavior 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 its ability to investigate the region close to K-turn ribosomal-like geometries. This part of the conformational space is not well characterized 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.

Anotace česky

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 a 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 behavior 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 its ability to investigate the region close to K-turn ribosomal-like geometries. This part of the conformational space is not well characterized 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.

Návaznosti

• LN00A016, projekt VaV: Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum