Photoreactive “Nanorulers” Detect a Novel Conformation of Full Length HDAC3-SMRT Complex in Solution

Histone
deacetylase 3 (HDAC3) is a promising epigenetic drug target
for multiple therapeutic applications. Direct interaction between
the Deacetylase Activating Domain of the silencing mediator for retinoid or thyroid-hormone receptors (SMRT-DAD) is required for
activation of enzymatic activity of HDAC3. The structure of this complex
and the nature of interactions with HDAC inhibitors in solution are
unknown. Using novel photoreactive HDAC probes, “nanorulers”,
we determined the distance between the catalytic site of the full-length
HDAC3 and SMRT-DAD in solution at physiologically relevant conditions
and found it to be substantially different from that predicted by
the X-ray model with a Δ379–428 aa truncated HDAC3. Further
experiments indicated that in solution this distance might change
in response to chemical stimuli, while the enzymatic activity remained
unaffected. These observations were further validated by Saturation Transfer Difference (STD) NMR experiments. We propose that the
observed changes in the distance are an important part of the histone
code that remains to be explored. Mapping direct interactions and
distances between macromolecules with such “nanorulers”
as a function of cellular events facilitates better understanding
of basic biology and ways for its manipulation in a cell- and tissue-specific
manner.