Hinge-like motions in RNA kink-turn motifs

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F04%3A00010307" target="_blank" >RIV/00216224:14310/04:00010307 - 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

Hinge-like motions in RNA kink-turn motifs

Original language description

Molecular dynamics (MD) simulations of Kink-turn (K-turn) RNA motifs reveal hinge-like motions on the nano-second (ns) timescale. K-turn motifs are asymmetric internal loops found at conserved positions in the 16S and 23S ribosomal RNAs, and characterized by sharp bends in both phosphodiester backbones producing V-shaped structures. The bend is stabilized by non-Watson-Crick basepairs involving the minor (shallow) grooves of the helices. We have carried out a set of explicit-solvent MD simulations for selected K-turn motifs from 23S ribosomal RNA, Kt-38 (located at the base of the A-site finger), Kt-42 (located at the base of the L7/L12 stalk in the factor-binding site) and Kt-58 (located in Domain III). On a nano-second timescale, K-turns sample isoenergetic conformational substates. The simulations reveal the presence of long-residency sites for water, one of which is located close to the sharp turn of the phosphodiester backbones and, when occupied, mediates minor-groove interaction

Czech name

Pantove pohyby RNA Kink-turn motivov

Czech description

Molecular dynamics (MD) simulations of Kink-turn (K-turn) RNA motifs reveal hinge-like motions on the nano-second (ns) timescale. K-turn motifs are asymmetric internal loops found at conserved positions in the 16S and 23S ribosomal RNAs, and characterized by sharp bends in both phosphodiester backbones producing V-shaped structures. The bend is stabilized by non-Watson-Crick basepairs involving the minor (shallow) grooves of the helices. We have carried out a set of explicit-solvent MD simulations for selected K-turn motifs from 23S ribosomal RNA, Kt-38 (located at the base of the A-site finger), Kt-42 (located at the base of the L7/L12 stalk in the factor-binding site) and Kt-58 (located in Domain III). On a nano-second timescale, K-turns sample isoenergetic conformational substates. The simulations reveal the presence of long-residency sites for water, one of which is located close to the sharp turn of the phosphodiester backbones and, when occupied, mediates minor-groove interaction

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

Modelling and Design of Molecular Materials, Program-Book of Abstract

ISBN

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ISSN

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e-ISSN

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Number of pages

1

Pages from-to

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Publisher name

University of Wroclav

Place of publication

Wroclaw

Event location

Wroclaw

Event date

Jan 1, 2004

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

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