On the Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors

Abstract

The ligand binding domain (LBD) of nuclear hormone receptors adopts a very compact, mostly R-helical structure that binds specific ligands with very high affinity. We use circular dichroism spectroscopy and high-temperature molecular dynamics simulations to investigate unfolding of the LBDs of thyroid hormone receptors (TRs). A molecular description of the denaturation mechanisms is obtained by molecular dynamics simulations of the TRR and TR LBDs in the absence and in the presence of the natural ligand Triac. The simulations show that the thermal unfolding of the LBD starts with the loss of native contacts and secondary structure elements, while the structure remains essentially compact, resembling a molten globule state. This differs from most protein denaturation simulations reported to date and suggests that the folding mechanism may start with the hydrophobic collapse of the TR LBDs. Our results reveal that the stabilities of the LBDs of the TRR and TR subtypes are affected to different degrees by the binding of the isoform selective ligand Triac and that ligand binding confers protection against thermal denaturation and unfolding in a subtype specific manner. Our simulations indicate two mechanisms by which the ligand stabilizes the LBD: (1) by enhancing the interactions between H8 and H11, and the interaction of the region between H1 and the Ω-loop with the core of the LBD, and (2) by shielding the hydrophobic H6 from hydration.

Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis

“…3E , the lower part of the structure, which diverges structurally, contains the ligand binding pocket. As we reported previously [ 19 ], the ligand protects the structure from denaturation by linking the secondary structural elements that, in the example shown here without ligand, diverge the most from the crystallographic model.…”

“…3JZC) [ 18 ] in a high-temperature (498K) simulation used for the study of its denaturation mechanisms. All details of these simulations were published previously [ 19 ].…”

Dynamics of Nuclear Receptor Helix-12 Switch of Transcription Activation by Modeling Time-Resolved Fluorescence Anisotropy Decays

“…Additionally, it was suggested that the lower subdomain of ER LBD can adopt a loosely folded globular state, which facilitates ligand binding and release (30). Structural models for denaturation intermediates were suggested for TRs by our group and, in accordance with experiment, were shown to be globular (32). It is natural that modeling studies follow experimental observations, as the molecular basis for the macroscopic experimental observations can only be inferred from indirect evidence.…”

Helix 12 Dynamics and Thyroid Hormone Receptor Activity: Experimental and Molecular Dynamics Studies of Ile280 Mutants

“…The chosen structural properties were as follows: RMSDs of the Cα atoms, RMSD; radius of gyration R g ; percentage of native contacts, % N cont ; percentage of secondary structure, % N sec (for more details, see Martínez et al 70 ). The initial structure of the simulations was used as reference in these calculations.…”