Ligand Specificity in Progesterone Receptor

Abstract

Progesterone receptor, nuclear receptor subfamily 3, group C, member 3 (PR, NR3C3) is a member of the steroid receptor subfamily of nuclear receptors (NR3), i.e. ligand‐regulated transcription factors. PR regulates multiple biological processes in response to binding of steroid‐derived hormones. PR is promiscuously activated by various steroid hormones, including estrogens, androgens, and corticosteroids. Currently, it is not understood how steroid hormones differentially modulate the ligand binding domain (LBD) of PR to achieve various transcriptional outcomes. Here, we use a computational approach to investigate how dynamics of PR are altered by ligand binding to achieve distinct transcriptional properties. Previous studies on the PR LBD revealed that residues in helices 3, 5 and 12 are functionally conserved in nuclear receptors and play important roles in stabilizing agonistic conformations. To probe the roles of these residues in discriminating between steroid hormones, we performed long MD simulations, using a library of 34 steroidal ligands with EC50 values ranging from inactive to 1E‐02 nM. To investigate ligand‐specific allosteric signaling, we investigated communication pathways between the ligand binding pocket and key regulatory surfaces on the PR LBD surface to determine the specificity with which ligands modulate allosteric coupling between two sites. Our weighted dynamic network analysis revealed that the active and inactive steroids modulated key regions of PR distinctly. Additional analysis of communication paths allowed us to further categorize agonists into three groups, consistent with their potency of activation. We used in silico mutagenesis to investigate roles for specific residues in achieving ligand‐selective PR signaling. Combined, the results of the study provide structural and dynamic insight into how PR achieves ligand specificity. Further, these studies can illuminate strategies for the design of novel PR ligands for therapeutical uses.