Photoaffinity Labeling of the Ligand-Interacting Helix of the Retinoic Acid Receptor Alpha

Abstract

Two photoaffinity-labeling probes for retinoic acid receptor (RAR) α, 4-[(3-(3-(trifluoromethyl)-3H-diazirin-3-yl)phenyl)carboxamido]benzoic acid (3DIAM) and its para-isomer (4DIAM), were designed and synthesized. Both compounds possess high affinity for recombinant RARα (MBP-RARα/E) and bind covalently to its cognate ligand-binding site. The labeled site of MBP-RARα/E with 3DIAM was determined, by the endoproteinase combination method, to be located in helix 11 of the ligand-binding domain of RARα, which is the position at which the ligand is considered to bind, on the basis of the reported crystal structure of the retinoic acid/RARγ complex.