Structural Basis for the Accommodation of Bis- and Tris-Aromatic Derivatives in Vitamin D Nuclear Receptor

Actual use of the active form of vitamin D (calcitriol or 1α,25-dihydroxyvitamin D₃) to treat hyperproliferative disorders is hampered by calcemic effects, hence the continuous development of chemically modified analogues with dissociated profiles. Structurally distinct nonsecosteroidal analogues have been developed to mimic calcitriol activity profiles with low calcium serum levels. Here, we report the crystallographic study of vitamin D nuclear receptor (VDR) ligand binding domain in complexes with six nonsecosteroidal analogues harboring two or three phenyl rings. These compounds induce a stimulated transcription in the nanomolar range, similar to calcitriol. Examination of the protein–ligand interactions reveals the mode of binding of these nonsecosteroidal compounds and highlights the role of the various chemical modifications of the ligands to VDR binding and activity, notably (de)­solvation effects. The structures with the tris-aromatic ligands exhibit a rearrangement of a novel region of the VDR ligand binding pocket, helix H6

Protein Structural Statistics with PSS

Characterizing the variability within an ensemble of protein structures is a common requirement in structural biology and bioinformatics. With the increasing number of protein structures becoming available, there is a need for new tools capable of automating the structural comparison of large ensemble of structures. We present Protein Structural Statistics (PSS), a command-line program written in Perl for Unix-like environments, dedicated to the calculation of structural statistics for a set of proteins. PSS can perform multiple sequence alignments, structure superpositions, calculate Cartesian and dihedral coordinate statistics, and execute cluster analyses. An HTML report that contains a convenient summary of results with figures, tables, and hyperlinks can also be produced. PSS is a new tool providing an automated way to compare multiple structures. It integrates various types of structural analyses through an user-friendly and flexible interface, facilitating the access to powerful but more specialized programs. PSS is easy to modify and extend and is distributed under a free and open source license. The relevance of PSS is illustrated by examples of application to pertinent biological problems

Phosphorylation of the Retinoic Acid Receptor Alpha Induces a Mechanical Allosteric Regulation and Changes in Internal Dynamics

<div><p>Nuclear receptor proteins constitute a superfamily of proteins that function as ligand dependent transcription factors. They are implicated in the transcriptional cascades underlying many physiological phenomena, such as embryogenesis, cell growth and differentiation, and apoptosis, making them one of the major signal transduction paradigms in metazoans. Regulation of these receptors occurs through the binding of hormones, and in the case of the retinoic acid receptor (RAR), through the binding of retinoic acid (RA). In addition to this canonical scenario of RAR activity, recent discoveries have shown that RAR regulation also occurs as a result of phosphorylation. In fact, RA induces non-genomic effects, such as the activation of kinase signaling pathways, resulting in the phosphorylation of several targets including RARs themselves. In the case of RARα, phosphorylation of Ser369 located in loop L9–10 of the ligand-binding domain leads to an increase in the affinity for the protein cyclin H, which is part of the Cdk-activating kinase complex of the general transcription factor TFIIH. The cyclin H binding site in RARα is situated more than 40 Å from the phosphorylated serine. Using molecular dynamics simulations of the unphosphorylated and phosphorylated forms of the receptor RARα, we analyzed the structural implications of receptor phosphorylation, which led to the identification of a structural mechanism for the allosteric coupling between the two remote sites of interest. The results show that phosphorylation leads to a reorganization of a local salt bridge network, which induces changes in helix extension and orientation that affects the cyclin H binding site. This results in changes in conformation and flexibility of the latter. The high conservation of the residues implicated in this signal transduction suggests a mechanism that could be applied to other nuclear receptor proteins.</p></div

Histograms of the following four distances: S369-R367 (A), E325-R367 (B), D323-R192 (C), E320-R367 (D), and R347-D256 (E), for the unphosphorylated RARα (in black) and the phosphorylated RARα (in grey).

<p>Histograms of the following four distances: S369-R367 (A), E325-R367 (B), D323-R192 (C), E320-R367 (D), and R347-D256 (E), for the unphosphorylated RARα (in black) and the phosphorylated RARα (in grey).</p

Distribution of the angle values in the unphosphorylated (in black) and the phosphorylated (in grey) simulations of RARα between H9–H10 (A) and H4–H9 (B).

<p>Distribution of the angle values in the unphosphorylated (in black) and the phosphorylated (in grey) simulations of RARα between H9–H10 (A) and H4–H9 (B).</p

Backbone RMS fluctuations as a function of residue number calculated from the last 40 ns of the molecular dynamics simulations (A) and from the ten lowest frequency modes of the quasi-harmonic analysis (B).

<p>Black lines correspond to the average over the three unphosphorylated RARα, dashed lines to the three phosphorylated RARα. In <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003012#pcbi-1003012-g007" target="_blank">Figure 7.A</a>, dotted lines correspond to the experimental B-factor values. Similar behavior is observed for the fluctuations calculated from simulations and the experimental values. The RMS fluctuations are averaged and displayed by residue. Fluctuations of loop L8–9 are highlighted in purple color.</p

Distribution of the radius of the circle fitted to the α-carbons (Å) of helix H9 in the unphosphorylated (in black) and the phosphorylated (in grey) simulations of RARα.

<p>A decrease in the radius of the circle corresponds to an increase in the bend of the helix.</p

Cross-correlation networks in the unphosphorylated (A) and phosphorylated (B) forms of RARα.

<p>The figures show cross-correlations between loops L9–10 and L8–9 and the other structural elements of the LBD by drawing a specific line between two residues if their motion is correlated. The color code corresponds to the value of the cross-correlation coefficient (ccc, see also <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003012#pcbi.1003012.s005" target="_blank">Figure S5</a>). Marine blue is used for anti-correlated motions (ccc between −0.2 to −0.1), whereas orange (ccc 0.2 to 0.3), salmon (ccc 0.3 to 0.4), light red (ccc 0.4 to 0.7) and red (ccc 0.7 to 1) are used for correlated motions. The changes in the dynamics upon phosphorylation are reflected by the loss of anti-correlated motions connecting loop L8–9 with H11 and the increased anti-correlations of loop L9–10.</p

Conservation profile of the residues implicated in identified salt bridges in sequence alignments from heterodimeric nuclear receptors sequences.

<p>The alignment is represented using the WebLogo 3 program <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003012#pcbi.1003012-Crooks1" target="_blank">[70]</a> with the degree of sequence conservation being represented by the height of the amino-acid letter, i.e. the more conserved is the amino acid, the greater is the relative height. Heterodimeric sequences are extracted from the alignment performed by Brelivet et al <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003012#pcbi.1003012-Brelivet1" target="_blank">[29]</a>.</p

Structural representation of the ligand-binding domain of RARα illustrating the cyclin H docking site (CDS) and the phosphorylation site (S369).

<p>Structural representation of the ligand-binding domain of RARα illustrating the cyclin H docking site (CDS) and the phosphorylation site (S369).</p