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

Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains

Native states of folded proteins are characterized by a large ensemble of conformations whose relative populations and interconversion dynamics determine the functional output. This is more apparent in transcription factors that have evolved to be inherently sensitive to small perturbations, thus fine-tuning gene expression. To explore the extent to which such functional features are imprinted on the folding landscape of transcription factor ligand-binding domains (LBDs), we characterize paralogous LBDs of the nuclear receptor (NR) family employing an energetically detailed and ensemble-based Ising-like statistical mechanical model. We find that the native ensembles of the LBDs from glucocorticoid receptor, PPAγ, and thyroid hormone receptor display a remarkable diversity in the width of the native wells, the number and nature of partially structured states, and hence the degree of conformational order. Monte Carlo simulations employing the full state representation of the ensemble highlight that many of the functional conformations coexist in equilibrium, whose relative populations are sensitive to both temperature and the strength of ligand binding. Allosteric modulation of the degree of structure at a coregulator binding site on ligand binding is shown to arise via a redistribution of populations in the native ensembles of glucocorticoid and PPAγ LBDs. Our results illustrate how functional requirements can drive the evolution of conformationally diverse native ensembles in paralogs.

Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.

Dynamics of nuclear receptor Helix-12 switch of transcription activation by modeling time-resolved fluorescence anisotropy decays

Nuclear hormone receptors (NRs) are major targets for pharmaceutical development. Many experiments demonstrate that their C-terminal Helix (H12) is more flexible in the ligand-binding domains (LBDs) without ligand, this increased mobility being correlated with transcription repression and human diseases. Crystal structures have been obtained in which the H12 is extended, suggesting the possibility of large amplitude H12 motions in solution. However, these structures were interpreted as possible crystallographic artifacts, and thus the microscopic nature of H12 movements is not well known. To bridge the gap between experiments and molecular models and provide a definitive picture of H12 motions in solution, extensive molecular dynamics simulations of the peroxisome proliferator-activated receptor-γ LBD, in which the H12 was bound to a fluorescent probe, were performed. A direct comparison of the modeled anisotropy decays to time-resolved fluorescence anisotropy experiments was obtained. It is shown that the decay rates are dependent on the interactions of the probe with the surface of the protein, and display little correlation with the flexibility of the H12. Nevertheless, for the probe to interact with the surface of the LBD, the H12 must be folded over the body of the LBD. Therefore, the molecular mobility of the H12 should preserve the globularity of the LBD, so that ligand binding and dissociation occur by diffusion through the surface of a compact receptor. These results advance the comprehension of both ligand-bound and ligand-free receptor structures in solution, and also guide the interpretation of time-resolved anisotropy decays from a molecular perspective, particularly by the use of simulations.

Molecular modeling revealed that ligand dissociation from thyroid hormone receptors is affected by receptor heterodimerization

Numerous ligands bind tightly to thyroid hormone receptors (TRs), and exploring the binding and dissociation of these ligands from TRs will increase our understanding of their mechanisms of action. TRs form transcriptionally active heterodimers with retinoid X receptor (RXR); whether this heterodimerization affects ligand dissociation is poorly understood. To investigate the effects of heterodimerization, classical molecular dynamics (MD) simulations and random acceleration molecular dynamics (RAMD) simulations were performed to probe the dissociation of triiodothyronine (T3) from a TRα-RXR ligand binding domain (LBD) heterodimer and the TRα and TRβ LBDs at the atomic level. Seven (I-VII) dissociation pathways were identified for T3. Heterodimerization inhibited pathway I in the TRα-RXR LBD heterodimer, which may block the proper orientation of the helix 12 (H12), therefore affecting the biological functions of TRs. Upon TR heterodimerization, the second most dominant dissociation pathway switched from pathway IV for TRα LBD to pathway II for TRα-RXR LBD. No significant effects of TR heterodimerization were observed on the dominant dissociation pathway III that was located between H3, the H1-H2 loop and the β-sheet. Our study revealed that TR heterodimerization significantly affects T3 dissociation, which provides important information for the study of other TR ligands.

Helix 12 dynamics and thyroid hormone receptor activity: experimental and molecular dynamics studies of Ile280 mutants

Nuclear hormone receptors (NRs) form a family of transcription factors that mediate cellular responses initiated by hormone binding. It is generally recognized that the structure and dynamics of the C-terminal helix 12 (H12) of NRs' ligand binding domain (LBD) are fundamental to the recognition of coactivators and corepressors that modulate receptor function. Here we study the role of three mutations in the I280 residue of H12 of thyroid hormone receptors using site-directed mutagenesis, functional assays, and molecular dynamics simulations. Although residues at position 280 do not interact with coactivators or with the ligand, we show that its mutations can selectively block coactivator and corepressor binding, and affect hormone binding affinity differently. Molecular dynamics simulations suggest that ligand affinity is reduced by indirectly displacing the ligand in the binding pocket, facilitating water penetration and ligand destabilization. Mutations I280R and I280K link H12 to the LBD by forming salt bridges with E457 in H12, stabilizing H12 in a conformation that blocks both corepressor and coactivator recruitment. The I280M mutation, in turn, blocks corepressor binding, but appears to enhance coactivator affinity, suggesting stabilization of H12 in agonist conformation.

Analysis of agonist and antagonist effects on thyroid hormone receptor conformation by hydrogen/deuterium exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T(3)) or antagonist (NH3). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, C-terminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T(3), but not NH3, increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T(3) but not NH3. We present data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes.