Structural and evolutionary classification of G/U wobble basepairs in the ribosome

Nucleic Acids Research
Ali MokdadNeocles Leontis

Abstract

We present a comprehensive structural, evolutionary and molecular dynamics (MD) study of the G/U wobble basepairs in the ribosome based on high-resolution 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/U shallow groove pocket--like packing interactions (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 struct...Continue Reading

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Citations

Feb 20, 2008·Journal of Biomolecular Structure & Dynamics·Ali Mokdad, Alan D Frankel
Nov 28, 2008·Nucleic Acids Research·Luc JaegerCody Geary
Jun 17, 2009·Nucleic Acids Research·Craig L ZirbelNeocles B Leontis
Feb 9, 2010·Nucleic Acids Research·Matthieu G GagnonSergey V Steinberg
Dec 30, 2009·RNA·Matthieu G Gagnon, Sergey V Steinberg
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Feb 11, 2015·Wiley Interdisciplinary Reviews. RNA·Blake A SweeneyNeocles B Leontis
Sep 25, 2012·Journal of Molecular Biology·Wade W GrabowLuc Jaeger
Jun 7, 2015·Nucleic Acids Research·Jamie J CannoneNeocles Leontis
Aug 8, 2009·Journal of Molecular Biology·Christian LaingTamar Schlick
Jan 30, 2015·Physical Chemistry Chemical Physics : PCCP·Kamali N SripathiNils G Walter
Oct 25, 2006·The Journal of Biological Chemistry·Matthieu G GagnonSergey V Steinberg
Sep 15, 2018·Nucleic Acids Research·Maryam HosseiniNeocles Leontis
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Nov 10, 2011·Journal of Biomolecular Structure & Dynamics·Swati PanigrahiDhananjay Bhattacharyya
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Jan 20, 2009·The Journal of Physical Chemistry. B·Arnost MládekJudit E Sponer
Jan 4, 2018·Chemical Reviews·Jiří ŠponerMichal Otyepka

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Methods Mentioned

BETA
X-ray

Software Mentioned

ribostral
AMBER7
MATLAB
InsightII
DeepView
VMD
FR3D

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