Abstract
A binding ensemble profiling with (f)photoaffinity labeling (BEProFL) approach that utilizes photolabeling of HDAC8 with a probe containing a UV-activated aromatic azide, mapping of the covalent modifications by liquid chromatography-tandem mass spectrometry, and a computational method to characterize the multiple binding poses of the probe is described. By use of the BEProFL approach, two distinct binding poses of the HDAC8 probe were identified. The data also suggest that an "upside-down" pose with the surface binding group of the probe bound in an alternative pocket near the catalytic site may contribute to the binding.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Amino Acid Sequence
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Azides / chemistry
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Azides / metabolism
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Azides / pharmacology
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Chromatography, Liquid
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Histone Deacetylase Inhibitors / chemistry
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Histone Deacetylase Inhibitors / metabolism*
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Histone Deacetylase Inhibitors / pharmacology*
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Histone Deacetylases / chemistry
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Histone Deacetylases / metabolism*
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Molecular Dynamics Simulation
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Molecular Sequence Data
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Peptide Fragments / chemistry
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Peptide Fragments / metabolism
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Photoaffinity Labels / metabolism*
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Protein Binding
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Protein Conformation
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Repressor Proteins / antagonists & inhibitors*
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Repressor Proteins / chemistry
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Repressor Proteins / metabolism*
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Tandem Mass Spectrometry
Substances
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Azides
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Histone Deacetylase Inhibitors
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Peptide Fragments
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Photoaffinity Labels
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Repressor Proteins
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HDAC8 protein, human
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Histone Deacetylases