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@article{634034,
author = {Mokdad, Ali and Krasovska, Maryna and Šponer, Jiří and Leontis, Neocles B.},
article_number = {5},
keywords = {molecular dynamics; G/U wobble basepairs; RNA},
language = {eng},
issn = {0006-3465},
journal = {Nucleic Acids Research},
title = {Structural and evolutionary classification of G/U wobble basepairs in the ribosome},
url = {www.oxfordjournals.org},
volume = {34},
year = {2006}
}
TY - JOUR
ID - 634034
AU - Mokdad, Ali - Krasovska, Maryna - Šponer, Jiří - Leontis, Neocles B.
PY - 2006
TI - Structural and evolutionary classification of G/U wobble basepairs in the ribosome
JF - Nucleic Acids Research
VL - 34
IS - 5
SP - 1326-1341
EP - 1326-1341
PB - Oxford University Press
SN - 00063465
KW - molecular dynamics
KW - G/U wobble basepairs
KW - RNA
UR - www.oxfordjournals.org
N2 - We present a comprehensive structural, evolutionary and molecular dynamics (MD) study of the G/U wobble basepairs in the ribosome based on highresolution crystal structures, including the recent Escherichia coli structure. These basepairs are classified according to their tertiary interactions, and sequence conservation at their positions is determined. G/U basepairs participating in tertiary interactions are more conserved than those lacking any interactions. Specific interactions occurring in the G/Ushallowgroove pocketlike packinginteractions (P-interactions) and some phosphate backbone interactions (phosphate-in-pocket interactions) lead to higher G/U conservation than others. Two salient cases of unique phylogenetic compensation are discovered. First, a P-interaction is conserved through a series of compensatory mutations involving all four participating nucleotides to preserve or restore the G/U in the optimal orientation. Second, a G/U basepair forming a P-interaction and another one forming a phosphate-in-pocket interaction are replaced by GNRA loops that maintain similar tertiary contacts. MD simulations were carried out on eight P-interactions. The specific GU/CG signature of this interaction observed in structure and sequence analysis was rationalized, and can now be used for improving sequence alignments.
ER -
MOKDAD, Ali, Maryna KRASOVSKA, Jiří ŠPONER and Neocles B. LEONTIS. Structural and evolutionary classification of G/U wobble basepairs in the ribosome. \textit{Nucleic Acids Research}. Oxford University Press, 2006, vol.~34, No~5, p.~1326-1341. ISSN~0006-3465.
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