| RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA and Jiří ŠPONER. RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics. Structure. USA: CELL PRESS, 1100 MASSACHUSETTS AVE, CAMB, 2006, vol. 14, No 5, p. 825-835, 10 pp. ISSN 0969-2126. |
Other formats:
BibTeX
LaTeX
RIS
@article{637330,
author = {Rázga, Filip and Zacharias, Martin and Réblová, Kamila and Koča, Jaroslav and Šponer, Jiří},
article_location = {USA},
article_number = {5},
keywords = {Kink-turn; A-minor motif; RNA flexibility; Molecular Dynamics; Ribosome function},
language = {eng},
issn = {0969-2126},
journal = {Structure},
title = {RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics},
volume = {14},
year = {2006}
}
TY - JOUR
ID - 637330
AU - Rázga, Filip - Zacharias, Martin - Réblová, Kamila - Koča, Jaroslav - Šponer, Jiří
PY - 2006
TI - RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics
JF - Structure
VL - 14
IS - 5
SP - 825-835
EP - 825-835
PB - CELL PRESS, 1100 MASSACHUSETTS AVE, CAMB
SN - 09692126
KW - Kink-turn
KW - A-minor motif
KW - RNA flexibility
KW - Molecular Dynamics
KW - Ribosome function
N2 - 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 rRNA region. Kink-turns could mediate large-scale adjustments of distant RNA segments.
ER -
RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA and Jiří ŠPONER. RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics. \textit{Structure}. USA: CELL PRESS, 1100 MASSACHUSETTS AVE, CAMB, 2006, vol.~14, No~5, p.~825-835, 10 pp. ISSN~0969-2126.
|
