title: Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors.
abstract: Nuclear receptors are ubiquitous eukaryotic ligand-activated transcription factors that modulate gene expression through varied interactions. However, the highly conserved functional sites known today seem insufficient to explain receptor specific recruitment of different coactivator and corepressor proteins and regulation of transcription. To search for new receptor-subtype specific functional sites, we applied difference evolutionary trace (difference ET) analysis to the ligand binding domain of steroid receptors, a subgroup of the nuclear receptor (NR) family. This computational approach identified a new functional site located on a surface opposite to currently known protein-protein interaction sites and distinct from the ligand binding pocket. Strikingly, the literature shows that in vivo variations at residues in the new site are linked to androgen resistance and leukemia, and our own targeted mutations to this site lower but do not eradicate transcriptional activation by estrogen receptor alpha (ERalpha), with reduced ligand binding affinity and SRC-1 interaction. Thus, these data demonstrate that this evolutionary important surface can function as an allosteric site that modulates some but not all receptor binding interactions. Evolutionary analysis further shows that this allosteric regulatory site is shared among all NRs from groups 2 (HNF4-like) and 4 (NGFIB-like), suggesting a role among many nuclear receptors. Its concave structure, hydrophobic composition, and residue variability among nuclear receptors further suggest that it would be amenable for specific drug design. This highlights the power of evolutionary information for the identification of new functional sites even in a protein family as well studied as NRs.
authors.affiliation: W. M. Keck Center for Computational and Structural Biology, Baylor College of Medicine, Houston Texas 77030, USA.
authors.forename: Michele
authors.initials: M
authors.lastname: Raviscioni
authors.forename: Qiang
authors.initials: Q
authors.lastname: He
authors.forename: Eleni M
authors.initials: EM
authors.lastname: Salicru
authors.forename: Carolyn L
authors.initials: CL
authors.lastname: Smith
authors.forename: Olivier
authors.initials: O
authors.lastname: Lichtarge
mesh_terms: D000495:Allosteric Site / Q000235:genetics*; D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D019143:Evolution, Molecular; D006367:HeLa Cells; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009154:Mutation; D011960:Receptors, Estrogen / Q000235:genetics*
chemical_list: D008024:Ligands; D011960:Receptors, Estrogen