Intrinsic disorder in nuclear hormone receptors

Abstract

Many proteins possess intrinsic disorder (ID) and lack a rigid three-dimensional structure in at least part of their sequence. ID has been hypothesized to influence protein-protein and protein-ligand interactions. We calculated ID for nearly 400 vertebrate and invertebrate members of the biomedically important nuclear hormone receptor (NHR) superfamily, including all 48 known human NHRs. The predictions correctly identified regions in 20 of the 23 NHRs suggested as disordered based on published X-ray and NMR structures. Of the four major NHR domains (N-terminal domain, DNA-binding domain, D-domain, and ligand-binding domain), we found ID to be highest in the D-domain, a region of NHRs critical in DNA recognition and heterodimerization, coactivator/corepressor interactions and protein-protein interactions. ID in the D-domain and LBD was significantly higher in "hub" human NHRs that have 10 or more downstream proteins in their interaction networks compared to "non-hub" NHRs that interact with fewer than 10 downstream proteins. ID in the D-domain and LBD was also higher in classic, ligand-activated NHRs than in orphan, ligand-independent NHRs in human. The correlation between ID in human and mouse NHRs was high. Less correlation was found for ID between mammalian and non-mammalian vertebrate NHRs. For some invertebrate species, particularly sea squirts ( Ciona), marked differences were observed in ID between invertebrate NHRs and their vertebrate orthologs. Our results indicate that variability of ID within NHRs, particularly in the D-domain and LBD, is likely an important evolutionary force in shaping protein-protein interactions and NHR function. This information enables further understanding of these therapeutic targets.

Figure 1

A. Downstream and B. Upstream direct interaction networks for human FXR (NR1H4) showing connected genes using Ingenuity Pathways Analysis 5.0 (Ingenuity Systems). Human receptors (rectangles), transporters (trapezoid) and enzymes (diamonds) are shown connected to FXR.

Figure 2

Patterns of predicted ID in human NHRs. In the bar graphs, stretches of 30 or more consecutive amino acids that each had a disorder probability of 0.5 or higher (“predicted disorder blocks”) are colored grey. Black bars indicate “ordered” sequence. The NHRs are aligned to the beginning of the DBD to allow for easier comparison between domains. The DBD and LBD domains are annotated. The NTD and D-domain regions are to the left of the DBD and LBD, respectively.

Figure 3

Cross-species comparisons of predicted ID for the FXRs. See Figure 2 for details on the color coding and annotation of the plots. The NTD of the sea squirt FXR, which has a predicted ID pattern different from vertebrate FXRs, is indicated by *.

Figure 4

Cross-species comparisons of predicted ID for the LXRs. See Figure 2 for details on the color coding and annotation of the plots. A segment of LBD predicted as disordered in some LXRs is indicated by **.

Figure 5

Cross-species comparisons of predicted ID for the USPs and RXRs. See Figure 2 for details on the color coding and annotation of the plots.

Figure 6

Cross-species comparisons of predicted ID for the ecdysone receptors (EcRs). See Figure 2 for details on the color coding and annotation of the plots.

Figure 7

Cross-species comparisons of predicted ID for the NR1I (VDR, PXR, and CAR) receptors. (A) Cross-species comparisons of predicted ID for the NR1I receptors. See Figure 2 for details on the color coding and annotation of the plots. Disordered sequence in the H1–H3 interhelical domain is indicated by *. (B) Comparison of the longest predicted disorder block in the H1–H3 interhelical domain of VDRs and PXRs. For the mouse, rat, African clawed frog, and Western clawed frog PXRs, no stretch of 10 or more amino acid residues were identified in the H1–H3 interhelical domain that had disorder probabilities of 0.5 or more.

Figure 8

Cross-species comparisons of predicted ID for the NR3C (GR, MR, PR, and AR) receptors. See Figure 2 for details on the color coding and annotation of the plots.

Figure 9

Cross-species comparisons of predicted ID for the ERs. See Figure 2 for details on the color coding and annotation of the plots.

Figure 10

Cross-species comparisons of predicted ID for the GCNFs. See Figure 2 for details on the color coding and annotation of the plots. Differences in the predicted ID for the sea squirt NTD and LBD compared to vertebrate GCNFs are indicated by *.