RAR antagonists diminish the level of DNA binding by the RAR/RXR heterodimer

A purified RAR/RXR-DeltaAB heterodimer was obtained by production of His-tagged RAR and untagged RXR in Escherichia coli, followed by combined purification on a Ni2+ affinity column using excess RXR extract, and finally a gel filtration chromatography step to isolate a pure heterodimer. The purified heterodimer preparation bound 9-cisRA at a level of 0.85-0.95 mol of binding sites per mole of protein monomer. Titration of a 26 kDa fluorescent labeled fragment of the SRC-1 coactivator protein with the purified heterodimer in the presence of the agonist 9-cisRA yielded a binding affinity near 300 nM, whereas no binding was observed in the absence of agonist. Binding of the purified heterodimer to a DR5 target was identical in the absence of ligand and in the presence of 9-cisRA. Competition by unlabeled specific and nonspecific DNA allowed us to demonstrate that the binding curve was bimodal. The first phase of binding was highly specific and of high affinity. This phase also exhibited a high degree of cooperativity in the binding profile. Nonspecific DNA efficiently competes for the second phase. Thus, the first phase of binding likely corresponds to the formation of the specific heterodimer complex in which heterodimerization is energetically coupled to DNA binding. While agonist binding had no effect on the apparent affinity of the heterodimer for DR5, a series of antagonists significantly destabilized the heterodimer-DR5 complex, either through a direct decrease in the affinity of the protein for the DNA or through destabilization of the heterodimer itself. Impeding the interaction between the heterodimer and DNA appears as an additional mechanism of antagonist action of varying efficiency, depending upon the chemical structure of the antagonist.