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PDBsum entry 3rkf
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References listed in PDB file
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Key reference
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Title
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Influence of ground-State structure and mg2+ binding on folding kinetics of the guanine-Sensing riboswitch aptamer domain.
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Authors
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J.Buck,
A.Wacker,
E.Warkentin,
J.Wöhnert,
J.Wirmer-Bartoschek,
H.Schwalbe.
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Ref.
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Nucleic Acids Res, 2011,
39,
9768-9778.
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PubMed id
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Abstract
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Riboswitch RNAs fold into complex tertiary structures upon binding to their
cognate ligand. Ligand recognition is accomplished by key residues in the
binding pocket. In addition, it often crucially depends on the stability of
peripheral structural elements. The ligand-bound complex of the guanine-sensing
riboswitch from Bacillus subtilis, for example, is stabilized by extensive
interactions between apical loop regions of the aptamer domain. Previously, we
have shown that destabilization of this tertiary loop-loop interaction abrogates
ligand binding of the G37A/C61U-mutant aptamer domain (Gsw(loop)) in the absence
of Mg(2+). However, if Mg(2+) is available, ligand-binding capability is
restored by a population shift of the ground-state RNA ensemble toward RNA
conformations with pre-formed loop-loop interactions. Here, we characterize the
striking influence of long-range tertiary structure on RNA folding kinetics and
on ligand-bound complex structure, both by X-ray crystallography and
time-resolved NMR. The X-ray structure of the ligand-bound complex reveals that
the global architecture is almost identical to the wild-type aptamer domain. The
population of ligand-binding competent conformations in the ground-state
ensemble of Gsw(loop) is tunable through variation of the Mg(2+) concentration.
We quantitatively describe the influence of distinct Mg(2+) concentrations on
ligand-induced folding trajectories both by equilibrium and time-resolved NMR
spectroscopy at single-residue resolution.
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Headers
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