Allosteric Pathways in the Multi-Domain Thyroid Hormone Receptor

Abstract

Allostery is an important regulatory mechanism in biology. Such mechanisms fine-tune the response of the nuclear hormone receptors (NRs) to extracellular stimuli. The structural topology of NRs consists of a mostly unstructured N-terminal (NTD)/activation function-1 domain (AF-1), a DNA binding domain (DBD) that recognizes and binds specific DNA sequences and a C-terminal ligand binding domain (LBD). Besides DNA, these domains also interact with specific factors that are subunits of the basal transcriptional machinery. Through multiple sources of data, we have observed that NRs are not simply docking sites for cellular molecules. Instead, we have characterized multiple allosteric pathways that link ligand, DNA and coactivator-binding sites. Here, we will present data from biophysical and cell-based studies on the thyroid-hormone receptor (TR). TR is a type II NR and functions as a heterodimer with the retinoid X receptor (RXR). Thyroid hormone (T3) is essential for development, differentiation, and metabolic balance in higher organisms and humans. Improper functioning of TR has been associated with pathophysiological conditions such as prostate cancer, colon cancer and hypothyroidism. Yet, the mechanism of transcriptional regulation by TR is not completely understood. Here, we present data that describes specific allosteric communication between the multiple TR domains. Specifically, we show how the AF1 influences DNA binding by the DBD and that the DNA-DBD interactions influence AF1 structural conformations. Furthermore, we show that there are direct interactions between the DBD and LBD and these are dependent on the DNA-bound state of the DBD. Our study on TR allostery also links the DNA and coactivator. Finally, propose a novel ‘frustrated-fit’ model to explain the negative cooperativity between TR and RXR ligands in the TR:RXR heterodimeric complex. For our studies, we utilize a combination of crystallography, experimental and theoretical biophysics and cell-based reporter gene assays.