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

Abstract

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.

Genes involved in cell adhesion and signaling: A new repertoire of Retinoic Acid Receptors target genes in mouse embryonic fibroblasts

“…According to our recent studies, phosphorylation controls the association-dissociation of coregulators involved in transcription, through allosteric control (Chebaro et al, 2013;Samarut et al, 2011). Moreover, we have shown that phosphorylation of the Nterminal serine residue, which is located in the vicinity of the DBD, controls the association-dissociation of coregulators (Lalevée et al, 2010) and therefore the recruitment of RARs to some promoters (Bruck et al, 2009;Lalevée et al, 2010).…”

“…These two sites are rapidly phosphorylated in response to RA (Bruck et al, 2009) subsequent to extranuclear and non-genomic effects of RA that lead to the activation of the p38MAPK-MSK1 pathway (Piskunov and Rochette-Egly, 2012). RA-activated MSK1 phosphorylates RARs at the serine residue located in the LBD and phosphorylation of this residue allows the recruitment of the cyclin-H-cdk7 subcomplex of TFIIH, which then can phosphorylate the second site located in the NTD (Chebaro et al, 2013;Samarut et al, 2011). This final phosphorylation step is crucial for the binding of the receptor to DR5 RAREs and the transcription of canonical RA target genes (Bruck et al, 2009).…”

Singular value decomposition for the correlation of atomic fluctuations with arbitrary angle

“…The analysis reveals that significant inter‐residue and inter‐domain couplings as well as the allosteric response can be inferred from correlated atomic fluctuations. Conventionally, the cross‐correlations of atoms or residues are measured by the DP form of the correlation coefficient, defined as where Δ r i and Δ r j are the displacements of residues (atoms) i and j from their average positions, respectively. Here, the superscript “DP” distinguishes the DP correlation coefficient from the proposed correlation coefficient (defined below).…”

“…The analysis reveals that significant inter-residue and inter-domain couplings [32][33][34] as well as the allosteric response [35][36][37] can be inferred from correlated atomic fluctuations. Conventionally, the cross-correlations of atoms or residues are measured by the DP form of the correlation coefficient, 35,[38][39][40][41][42][43][44][45][46][47][48][49][50] defined as…”

Subtype-Specific Modulation of Estrogen Receptor–Coactivator Interaction by Phosphorylation

“…Molecular Dynamics highlight stabilizing effect phosphorylation. MD has proven to be a useful tool in the analysis of NR dynamics 43,44. To further elucidate the atomistic mechanism of the phosphorylation mediated modulation of the ER, MD simulations were performed in different molecular contexts: the ER/coactivator peptide complex in absence (1) and presence of E2 (2), the phosphorylated ER/coactivator peptide complex in absence (3) and presence of E2 (4), in all the aforementioned cases with the starting coordinates of H12 in a 'closed' conformation; and the ER/coactivator peptide complex in absence of E2 for the non-…”