RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F06%3A00015722" target="_blank" >RIV/00216224:14310/06:00015722 - isvavai.cz</a>

Alternative codes found

RIV/68081707:_____/06:00039256

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics

Original language description

The presence of Kink-turns (Kt) at key functional sites in the ribosome (e.g., A-site finger and L7/L12 stalk) suggests that some Kink-turns can confer flexibility on RNA protuberances that regulate the traversal of tRNAs during translocation. Explicit solvent molecular dynamics demonstrates that Kink-turns can act as flexible molecular elbows. Kink-turns are associated with a unique network of long-residency static and dynamical hydration sites that is intimately involved in modulating their conformational dynamics. An implicit solvent conformational search confirms the flexibility of Kink-turns around their X-ray geometries and identifies a second low-energy region with open structures that could correspond to Kink-turn geometries seen in solution experiments. An extended simulation of Kt-42 with the factor binding site (helices 43 and 44) shows that the local Kt-42 elbow-like motion fully propagates beyond the Kink-turn, and that there is no other comparably flexible site in this rR

Czech name

RNA kink-turn jako molekulové lokty: Hydratace, vazba iontů a dynamika

Czech description

K-turn motivy jsou funkční klíčové RNA elementy (např:A-site finger and L7/L12 stalk), které regulují flexibilitu ribosomální RNA během procesu translokace. Explicit solvent MD simulace ukazují, že tyto struktury jsou asociovány se sití molekul vod, které významně ovlivňují jejich konformace.

Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CF - Physical chemistry and theoretical chemistry

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year

2006

Confidentiality

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

Name of the periodical

Structure

ISSN

0969-2126

e-ISSN

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Volume of the periodical

14

Issue of the periodical within the volume

5

Country of publishing house

US - UNITED STATES

Number of pages

10

Pages from-to

825-835

UT code for WoS article

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EID of the result in the Scopus database

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