Structural Determinants of Allosteric Ligand Activation in RXR Heterodimers

Abstract

Allosteric communication underlies ligand-dependent transcriptional responses mediated by nuclear receptors. While studies have elucidated many of the components involved in this process, the energetic architecture within the receptor protein that mediates allostery remains unknown. Using a sequence-based method designed to detect coevolution of amino acids in a protein, termed the statistical coupling analysis (SCA), we identify a network of energetically coupled residues that link the functional surfaces of nuclear receptor ligand binding domains. Functional analysis of these predicted residues demonstrates their participation in an allosteric network that governs the ability of heterodimeric receptors to activate transcription in response to ligand binding by either partner. Interestingly, mutation of a single network residue can discriminate between receptor activation by endocrine, dietary, and synthetic agonists. These results reveal a structural network required for RXR heterodimer allosteric communication and suggest that the specificity of ligand response and permissivity coevolved to enable signal discrimination.

Retinoid X receptors: common heterodimerization partners with distinct functions

“…In contrast, low affinity-binding, lipid-activated nuclear receptors such as peroxisome proliferator-activated receptors (PPARs), the bile acid/farnesoid receptor (FXR) or oxysterol receptors (LXRs) are considered as permissive entities, suggesting that the functional control of RXR partners evolved to couple differentially endocrine and metabolic regulations 80 . The mechanism by which this molecular crosstalk takes place is still poorly defined, and is very certainly specific for each heterodimer: indeed, while the C-terminal activating function 2 (AF2, required for coactivator recruitment) of RXR is dispensable for PPARγ synergistic activation, it is required for PPAR and T3R activation 81,82 .…”

Mechanistic insight into the allosteric activation of a ubiquitin-conjugating enzyme by RING-type ubiquitin ligases

“…In this study, we sought to identify residues within E2s that mediate their allosteric activation by E3s using SCA (22)(23)(24)(25). The key premise of SCA is that functionally or structurally coupled residues within a protein should coevolve and show covariation in a large, diverse multiple sequence alignment (MSA) of members of a given protein family (22)(23)(24)(25)28). If allostery is a conserved feature of E2s, residues of the E3-binding site and residues at or near the active site of E2s are expected to show covariation during evolution.…”

“…Using an algorithm that detects coevolving residues within a protein, called statistical coupling analysis (SCA) (22)(23)(24)(25), we have identified clusters of coevolving and possibly energetically coupled residues within E2s that physically link their E3-binding and active sites. Mutations of a subset of these residues disrupt the allosteric communication between the E3-binding and active sites of E2s.…”

New insight into long‐range nonadditivity within protein double‐mutant cycles

“…Consequently, poor predictability for site-pairs that are structurally well separated generally persists in spite of the high-profile example to the contrary found in the PDZ binding domain by Lockless and Ranganathan (14). Furthermore, Fodor and Aldrich go on to argue that thermodynamic coupling is insensitive to protein sequence, based on their observation that nonadditivity is not limited to the subset of highly covarying residue positions, which goes against the premise of evolutionarily conserved energetic pathways championed by Ranganathan et al (14,(16)(17)(18). Rather, they conclude that the success of coevolutionary metrics to predict nonadditivity is fortuitously well correlated with reliable predictions of structurally proximal pairs.…”