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PDBsum entry 4xic
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Transcription regulator/DNA
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PDB id
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4xic
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References listed in PDB file
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Key reference
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Title
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Entropic enhancement of protein-Dna affinity by oxygen-To-Sulfur substitution in DNA phosphate.
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Authors
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L.Zandarashvili,
D.Nguyen,
K.M.Anderson,
M.A.White,
D.G.Gorenstein,
J.Iwahara.
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Ref.
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Biophys J, 2015,
109,
1026-1037.
[DOI no: ]
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PubMed id
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Abstract
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Dithioation of DNA phosphate is known to enhance binding affinities, at least
for some proteins. We mechanistically characterized this phenomenon for the
Antennapedia homeodomain-DNA complex by integrated use of fluorescence,
isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography.
By fluorescence and isothermal titration calorimetry, we found that this
affinity enhancement is entropy driven. By NMR, we investigated the ionic
hydrogen bonds and internal motions of lysine side-chain NH3(+) groups involved
in ion pairs with DNA. By x-ray crystallography, we compared the structures of
the complexes with and without dithioation of the phosphate. Our NMR and x-ray
data show that the lysine side chain in contact with the DNA phosphate becomes
more dynamic upon dithioation. Our thermodynamic, structural, and dynamic
investigations collectively suggest that the affinity enhancement by the
oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic
gain arising from mobilization of the intermolecular ion pair at the protein-DNA
interface.
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Secondary reference #1
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Title
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Wilms tumor protein recognizes 5-Carboxylcytosine within a specific DNA sequence.
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Authors
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H.Hashimoto,
Y.O.Olanrewaju,
Y.Zheng,
G.G.Wilson,
X.Zhang,
X.Cheng.
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Ref.
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Genes Dev, 2014,
28,
2304-2313.
[DOI no: ]
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PubMed id
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