The nuclear receptors are a superfamily of transcription factors which use conserved, modular DNA binding domains (DBDs) to recognize their DNA response elements. These receptors control diverse genes in mammalian development and homeostasis. The response elements are composed of similar hexameric sequences but can be arranged with different types of geometry. The DNA configurations include a) direct-repeats with alternate inter-half-site spacings, b) a single copy extended by unique trinucleotide sequences, c) inverted repeats, and d) everted repeats. On bipartite response elements, pairs of receptors are able to cooperate as homo- and heterodimers in a manner that allow them to detect the correct half-site sequences, and also the orientation and the spacing relating these half-sites. In the previous period, we focused on direct-repeat arrangements and used crystallographic studies to visualize a series of pairwise receptor assemblies that were strictly dependent on the size of inter-half-site spacings. We now propose to continue our crystallographic studies to see how two distinct receptor heterodimers can assemble on the same type of direct-repeat element. We will also expand our crystallographic studies to receptor complexes that target monomeric sites, inverted repeat elements, and everted repeat element. These alternate DNA configurations are expected to foster new modes of subunit assemblies which can be contrasted to each other and to the direct-repeat complexes. Finally, to learn how some receptor DBDs reconfigure themselves to cooperate with their dimeric partners on DNA sites, we will use NMR spectroscopy to characterize the backbone structures of free DBDs, so that we may better describe the process by which molecular interactions are enhanced in these ternary complexes.
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