Willis Scooter, Griffin Patrick R
Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL, USA.
Nucl Recept Signal. 2011 Feb 25;9:e001. doi: 10.1621/nrs.09001.
Members of the nuclear receptor superfamily differentiate in terms of specificity for DNA recognition and binding, oligomeric state, and ligand binding. The wide range of specificities are impressive given the high degree of sequence conservation in the DNA binding domain (DBD) and moderate sequence conservation with high structural similarity within the ligand binding domains (LBDs). Determining sequence positions that are conserved within nuclear receptor subfamilies can provide important indicators into the structural dynamics that translate to oligomeric state of the active receptor, DNA binding specificity and ligand affinity and selectivity. Here we present a method to analyze sequence data from all nuclear receptors that facilitates detection of co-evolving pairs using Mutual Information (MI). Using this method we demonstrate that MI can reveal functionally important sequence positions within the superfamily and the approach identified three sequence positions that have conserved sequence patterns across all nuclear receptors and subfamilies. Interestingly, two of the sequence positions identified are located within the DBD CII and the third was within Helix c of the DBD. These sequences are located within the heterodimer interface of PPARγ (CII) and RXRα (Helix c) based on PDB:3DZU. Helix c of PPARγ, which is not involved in the DBD dimer interface, binds the minor groove in the 5' flanking region in a consensus PPARγ response element (PPRE) and the corresponding RXRα (CII) is found in the 3' flanking region of RXRE (3DZU). As these three sequence positions represent unique identifiers for all nuclear receptors and they are located within the dimer interface of PPARγ-RXRα DBD (3DZU) interfacing with the flanking regions of the NRRE, we conclude they are critical sequence positions perhaps dictating nuclear receptor (NR) DNA binding specificity.
核受体超家族的成员在DNA识别与结合的特异性、寡聚状态以及配体结合方面存在差异。鉴于DNA结合结构域（DBD）中高度的序列保守性以及配体结合结构域（LBD）内具有高结构相似性的适度序列保守性，其广泛的特异性令人印象深刻。确定核受体亚家族内保守的序列位置可为转化为活性受体寡聚状态、DNA结合特异性以及配体亲和力和选择性的结构动力学提供重要指标。在此，我们提出一种分析所有核受体序列数据的方法，该方法利用互信息（MI）促进共进化对的检测。使用此方法，我们证明MI可揭示超家族内功能上重要的序列位置，并且该方法确定了三个在所有核受体和亚家族中具有保守序列模式的序列位置。有趣的是，所确定的两个序列位置位于DBD CII内，第三个位于DBD的螺旋c内。基于PDB:3DZU，这些序列位于PPARγ（CII）和RXRα（螺旋c）的异二聚体界面内。PPARγ的螺旋c不参与DBD二聚体界面，它在共有PPARγ反应元件（PPRE）的5'侧翼区域结合小沟，而相应的RXRα（CII）则位于RXRE（3DZU）的3'侧翼区域。由于这三个序列位置代表所有核受体的独特标识符，并且它们位于与NRRE侧翼区域相连的PPARγ - RXRα DBD（3DZU）二聚体界面内，我们得出结论，它们是可能决定核受体（NR）DNA结合特异性的关键序列位置。
