Molecular dynamics simulation of the ligand binding domain of farnesoid X receptor. Insights into helix-12 stability and coactivator peptide stabilization in response to agonist binding

The dynamic changes which take place in the ligand binding domain (LBD) of farneosid X receptor (FXR) in response to agonist binding and in the presence of coactivator peptides were studied with nanosecond time-scale molecular dynamics. Four different systems were analyzed, including the holo-LBD complexed with 6ECDCA, the holo-LBD in the presence of two coactivator peptides, and two artificial apo forms, with and without coactivator peptides. Our results revealed a detailed picture of the differential micro- and macromodifications occurring in the LBD in the presence or not of the agonist molecule and the coactivator peptides. In the apo simulation a major conformational change took place in the crucial helix 12, while the holo-LBD was globally stabilized by the ligand. When the coactivator peptides were included in the simulation, a clear agonist-induced stabilization was observed for the canonical peptide. Interestingly, the second peptide was released from the holo-LBD while it was kept bound in the apo simulation. The present results provide a molecular basis for the understanding the role played by the bile acid agonist in receptor stabilization and enhanced cofactor recruitments.