Dynamics of RNA Kink-turns: Role of water molecules

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F04%3A00010007" target="_blank" >RIV/00216224:14310/04:00010007 - isvavai.cz</a>

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Dynamics of RNA Kink-turns: Role of water molecules

Original language description

Hinge-like RNA motifs called kink-turns occur at conserved positions in the 16S and 23S ribosomal RNAs.The presence of K-turns at key functional sites in the ribosome suggests that they confer flexibility to RNA protuberances that regulate the traversalof tRNAs from one binding site to another across the interface between the small and large subunit during protein synthesis cycle. We have carried out a set of explicit-solvent Molecular Dynamics (MD) simulations for selected K-turn motifs. The simulations indicate that K-turns are dynamically flexible, and thus capable of regulating significant inter-segmental motions. The simulations reveal specific long-residency hydration sites and monovalent counterions that stabilize non-Watson-Crick basepairs, sharp turns of the phosphodiester backbone and even mediate inter-segmental contacts. The implications for ribosome function will be discussed.

Czech name

Dynamika RNA Kink-turnov: uloha molekul vody

Czech description

Hinge-like RNA motifs called kink-turns occur at conserved positions in the 16S and 23S ribosomal RNAs.The presence of K-turns at key functional sites in the ribosome suggests that they confer flexibility to RNA protuberances that regulate the traversalof tRNAs from one binding site to another across the interface between the small and large subunit during protein synthesis cycle. We have carried out a set of explicit-solvent Molecular Dynamics (MD) simulations for selected K-turn motifs. The simulations indicate that K-turns are dynamically flexible, and thus capable of regulating significant inter-segmental motions. The simulations reveal specific long-residency hydration sites and monovalent counterions that stabilize non-Watson-Crick basepairs, sharp turns of the phosphodiester backbone and even mediate inter-segmental contacts. The implications for ribosome function will be discussed.

Type

D - Article in proceedings

CEP classification

CF - Physical chemistry and theoretical chemistry

OECD FORD branch

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Project

<a href="/en/project/LN00A016" target="_blank" >LN00A016: BIOMOLECULAR CENTER</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2004

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Article name in the collection

American Chemical Society Division of Computers in Chemistry - Abstracts

ISBN

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ISSN

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e-ISSN

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Number of pages

1

Pages from-to

10

Publisher name

American Chemical Society

Place of publication

Washington

Event location

Anaheim, California, USA

Event date

Mar 28, 2004

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

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