Elbow-like motions in Ribosomal Kink-turns: The role of the second A-minor motif and Nominally unpaired bases

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F05%3A00013831" target="_blank" >RIV/00216224:14310/05:00013831 - 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

Elbow-like motions in Ribosomal Kink-turns: The role of the second A-minor motif and Nominally unpaired bases

Original language description

Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing "V"-shaped structures. Explicit-solvent Molecular Dynamics (MD) simulations were carried out forselected K-turns from 23S rRNA (Kt-38, Kt-42, Kt-58) and for K-turn of human U4 snRNA (Kt-U4). The MD simulations reveal hinge-like K-turn motions on the nanosecond time-scale and thus indicate that K-turns are dynamically flexible, and capable of regulating significant inter-segmental motions. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor(type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused b

Czech name

Klbove pohyby Ribosomalnych Kink turnov: Uloha druhej A-minor interakcie a nesparenych nukleotidov

Czech description

Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing "V"-shaped structures. Explicit-solvent Molecular Dynamics (MD) simulations were carried out forselected K-turns from 23S rRNA (Kt-38, Kt-42, Kt-58) and for K-turn of human U4 snRNA (Kt-U4). The MD simulations reveal hinge-like K-turn motions on the nanosecond time-scale and thus indicate that K-turns are dynamically flexible, and capable of regulating significant inter-segmental motions. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor(type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused b

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

2005

Confidentiality

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

Article name in the collection

Journal Of Biomolecular Structure and Dynamics

ISBN

1533-0346

ISSN

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e-ISSN

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Number of pages

2

Pages from-to

800-801

Publisher name

Adenine Press

Place of publication

New York, USA

Event location

Albany, NY, USA

Event date

Jan 1, 2005

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

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