Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F11%3A10224797" target="_blank" >RIV/61989592:15310/11:10224797 - isvavai.cz</a>
Alternative codes found
RIV/68081707:_____/11:00370399 RIV/61388963:_____/11:00370399
Result on the web
<a href="http://dx.doi.org/10.1021/ct200204t" target="_blank" >http://dx.doi.org/10.1021/ct200204t</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/ct200204t" target="_blank" >10.1021/ct200204t</a>

Result language
angličtina
Original language name
Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs
Original language description
We report unrestrained, explicit solvent molecular dynamics simulations of ribosomal and intron reverse kink-turns (54 simulations in total) with different variants (ff94, ff99, ff99bsc0, ff99chiOL, and ff99bsc0chiOL) of the Cornell et al. force field. The simulations characterize the directional intrinsic flexibility of reverse kink-turns pertinent to their folded functional geometries. The reverse kink-turns are the most flexible RNA motifs studied so far by explicit solvent simulations which are capable at the present simulation time scale to spontaneously and reversibly sample a wide range of geometries from tightly kinked ones through flexible intermediates up to extended, unkinked structures. Among the tested force fields, the latest chiOL variant is essential to obtaining stable trajectories while all force field versions lacking the chi correction are prone to a swift degradation toward senseless ladder-like structures of stems, characterized by high-anti glycosidic torsions.
Czech name
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Czech description
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Type
J<sub>x</sub> - 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
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>Z - Vyzkumny zamer (s odkazem do CEZ)<br>S - Specificky vyzkum na vysokych skolach

Publication year
2011
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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