Detailed Information on Publication Record
2006
Structural and evolutionary classification of G/U wobble basepairs in the ribosome
MOKDAD, Ali, Maryna KRASOVSKA, Jiří ŠPONER and Neocles B. LEONTISBasic information
Original name
Structural and evolutionary classification of G/U wobble basepairs in the ribosome
Name in Czech
Structural and evolutionary classification of G/U wobble basepairs in the ribosome
Authors
MOKDAD, Ali (840 United States of America), Maryna KRASOVSKA (804 Ukraine), Jiří ŠPONER (203 Czech Republic, guarantor) and Neocles B. LEONTIS (840 United States of America)
Edition
Nucleic Acids Research, Oxford University Press, 2006, 0006-3465
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10403 Physical chemistry
Country of publisher
Czech Republic
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
RIV identification code
RIV/00216224:14310/06:00016780
Organization unit
Faculty of Science
UT WoS
000236432900013
Keywords in English
molecular dynamics; G/U wobble basepairs; RNA
Tags
International impact, Reviewed
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.
In Czech
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.
Links
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