Conformational Diversity of the Helix 12 of the Ligand Binding Domain of PPARγ and Functional Implications

Abstract

Nuclear hormone receptors (NR) are transcription factors that activate gene expression in response to ligands. Structural and functional studies of the ligand binding domains (LBD) of NRs revealed that the dynamics of their C-terminal helix (H12) is fundamental for NR activity. H12 is rigid and facilitates binding of coactivator proteins in the agonist-bound LBD. In the absence of ligand, H12 exhibits increased flexibility. To provide a comprehensive picture of the H12 conformational equilibrium, extensive molecular dynamics simulations of the LBD of the PPARγ receptor in the presence or absence of ligand, and of coactivators and corepressor peptides, were performed. Free-energy profiles of the conformational variability of the H12 were obtained from more than four microseconds of simulations using adaptive biasing-force calculations. Our results demonstrate that, without ligand, multiple conformations of the H12 are accessible, including agonist-like conformations. We also confirm that extended H12 conformations are not accessible at ordinary temperatures. Ligand binding stabilizes the agonist H12 conformation relative to other structures, promoting a conformational selection. Similar effects are observed with coactivator association. The presence of corepressor peptides stabilizes conformations not allowed in the ligand-free, Rosiglitazone-bound or coactivator-bound LBDs. Corepressor binding, therefore, induces a conformational transition in the protein. Nevertheless, initial stages of corepressor dissociation could be induced by the ligand as it stabilizes the H12 in agonist form. Therefore, the present results provide a comprehensive picture of the H12 motions and their functional implications, with molecular resolution.

The conformational dynamics of H2-H3n and S2-H6 in gating ligand entry into the buried binding cavity of vitamin D receptor

“…In contrast, H12 was positioned closer to the empty binding cavity from our atomistic and CG MD simulations, compared to the initial structure. Furthermore, this observation is in agreement with a previous study on H12 of PPARγ which showed H12 is limited to local movements at ordinary temperatures39.…”

Structural review of PPARγ in complex with ligands: Cartesian- and dihedral angle principal component analyses of X-ray crystallographic data

“…Both the larger conformational freedom of helix 12 in apo‐PPARγ, as well as helix 12 conformations similar to those observed by X‐ray crystallography in the type A and type B chains [Fig. (C,D)] have recently been reproduced in MD simulations …”

“…Interestingly, in these structures, helix 12 of the type B chains is positioned roughly in the coactivator groove of the type A chains. Recently, a role for conformations similar to the type B chains in the binding of transcriptional corepressors has been suggested by MD simulations of PPARα . In summary, a more complete understanding of the role of PPARγ conformers similar to the type B chains requires further study.…”

“…More specifically, a collective classification of these complexes could aid the development of new PPARγ ligands that do not stabilize helix 12, neither through direct nor allosteric mechanisms, by indicating suitable starting structures for in silico , structure‐based ligand design. While in a dynamical sense, these ligands may be envisioned to contribute to populational shifts between PPARγ conformational ensembles, possibly already present in the apo‐state, the extent to which this influence is represented in the crystal phase is less well understood. Aiming to shed light on these questions, we evaluated the distributions of the structures projected onto principal component axes and the relation of these distributions to PPARγ structural parameters or ligand functional attributes ( vide infra ).…”

An alternative conformation of ERβ bound to estradiol reveals H12 in a stable antagonist position

“…Part of this peptide corresponds to the region that changes more its position between the studied ERβ LBD conformations. The use of reaction coordinates based on the RMSD of the region of the protein known to be important for the conformational change provides a more accurate description of the process pathways 11, 62 . Each RMSD coordinate covered a range of 1 to 10 Å.…”