2006
Structural and evolutionary classification of G/U wobble basepairs in the ribosome
MOKDAD, Ali; Maryna KRASOVSKA; Jiří ŠPONER a Neocles B. LEONTISZákladní údaje
Originální název
Structural and evolutionary classification of G/U wobble basepairs in the ribosome
Název česky
Structural and evolutionary classification of G/U wobble basepairs in the ribosome
Autoři
MOKDAD, Ali; Maryna KRASOVSKA; Jiří ŠPONER a Neocles B. LEONTIS
Vydání
Nucleic Acids Research, Oxford University Press, 2006, 0006-3465
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10403 Physical chemistry
Stát vydavatele
Česká republika
Utajení
není předmětem státního či obchodního tajemství
Odkazy
Kód RIV
RIV/00216224:14310/06:00016780
Organizační jednotka
Přírodovědecká fakulta
UT WoS
000236432900013
Klíčová slova anglicky
molecular dynamics; G/U wobble basepairs; RNA
Štítky
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 29. 6. 2007 00:16, Olga Křížová
V originále
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.
Česky
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.
Návaznosti
| MSM0021622413, záměr |
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