Year of Award


Document Type


Degree Type

Master of Science (MS)

Degree Name

Biochemistry & Biophysics

Department or School/College

Chemistry and Biochemistry

Committee Chair

Bruce Bowler

Committee Co-chair

Travis Hughes

Commitee Members

Steve Sprang, J.B. Alexander (Sandy) Ross, Jesse Hay.


FXR-LBD, Nuclear Receptor, Ligand, Coactivator peptide affinity, Tropifexor, H-12 conformational change


University of Montana

Subject Categories

Biochemistry | Biophysics | Molecular Biology


The nuclear receptor ligand-binding domain (LBD) is a highly dynamic entity. The FXR LBD shows multiple low-energy conformational states of the activation function-2 (AF-2) coregulator binding surface upon ligand binding, indicating the complexity of FXR activation. However, it is unknown how ligand binding leads to different conformational states within the AF-2 region centered on helix 12 (H-12) of the LBD. Here we observe the conformation of the coregulator binding surface (H-12 specifically) of FXR upon ligand binding in solution using fluorine-19 (19F) nuclear magnetic resonance (NMR) and simulations of this surface using molecular dynamics. Fluorescence anisotropy of fluorescein-labeled coregulator peptides reveals a correlation between structural conformations of the coregulator binding surface and the function of FXR. While the coregulator surface of apo FXR and partial-agonist bound FXR exchanges between multiple low energy conformations, full-agonist bound FXR is restricted to few conformations, which favor coactivator binding. Furthermore, we find that two ligands that induce similar affinities for a coactivator peptide have distinct coregulator binding surface structures.



© Copyright 2021 Vikash Kumar