The use of in vitro peptide binding profiles and in silico ligand-receptor interaction profiles to describe ligand-induced conformations of the retinoid X receptor α ligand-binding domain
The use of in vitro peptide binding profiles and in silico ligand-receptor interaction profiles to describe ligand-induced conformations of the retinoid X receptor α ligand-binding domain
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DOI：
10.1210/me.2006-0072
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发表时间：
2007-01-01
影响因子：
--
通讯作者：
de Vlieg, Jacob
中科院分区：
文献类型：
--
作者：
Folkertsma, Simon;van Noort, Paula I.;de Vlieg, Jacob
据推测，不同的配体诱导的构象变化可以解释核受体与调节蛋白的不同相互作用，从而产生特定的生物活性。了解配体如何调节辅因子相互作用的机制有助于药物设计。为了研究这些配体诱导的蛋白质表面构象变化，我们使用 52 种不同的辅因子肽进行了时间分辨荧光共振能量转移测定，测量了在 11 种化合物存在的情况下配体诱导的辅因子募集到类维生素A X 受体-α (RXR α) 的情况。同时我们通过分子对接分析了这些化合物的结合模式。一种自动化方法将配体-蛋白质相互作用的复杂三维数据转换为二维指纹，即所谓的配体-受体相互作用谱。对于一部分化合物，通过肽募集测量的表面构象变化与计算的结合模式密切相关，这表明配体-受体相互作用谱的聚类是区分可能在细胞环境中诱导不同构象和可能不同效应的化合物的非常有用的工具。此外，我们成功地将配体-受体相互作用谱和肽招募数据结合起来，揭示了可能参与配体诱导构象的结构元件。有趣的是，我们可以预测 LG100754 的可能结合模式，LG100754 是一种同型二聚体拮抗剂，对肽募集没有影响。最后，对肽招募谱的广泛分析为该化合物的潜在细胞效应提供了新的见解；我们首次表明，除了诱导共激活肽结合外，所有众所周知的 RXR α 激动剂还诱导辅阻遏肽与 RXR α 结合。
It is hypothesized that different ligand-induced conformational changes can explain the different interactions of nuclear receptors with regulatory proteins, resulting in specific biological activities. Understanding the mechanism of how ligands regulate cofactor interaction facilitates drug design. To investigate these ligand-induced conformational changes at the surface of proteins, we performed a time-resolved fluorescence resonance energy transfer assay with 52 different cofactor peptides measuring the ligand-induced cofactor recruitment to the retinoid X receptor-alpha (RXR alpha) in the presence of 11 compounds. Simultaneously we analyzed the binding modes of these compounds by molecular docking. An automated method converted the complex three-dimensional data of ligand-protein interactions into two-dimensional fingerprints, the so-called ligand-receptor interaction profiles. For a subset of compounds the conformational changes at the surface, as measured by peptide recruitment, correlate well with the calculated binding modes, suggesting that clustering of ligand-receptor interaction profiles is a very useful tool to discriminate compounds that may induce different conformations and possibly different effects in a cellular environment. In addition, we successfully combined ligand-receptor interaction profiles and peptide recruitment data to reveal structural elements that are possibly involved in the ligand-induced conformations. Interestingly, we could predict a possible binding mode of LG100754, a homodimer antagonist that showed no effect on peptide recruitment. Finally, the extensive analysis of the peptide recruitment profiles provided novel insight in the potential cellular effect of the compound; for the first time, we showed that in addition to the induction of coactivator peptide binding, all well-known RXR alpha agonists also induce binding of corepressor peptides to RXR alpha.