Departamento de Química Orgánica and UMYMFOR, CONICET-UBA, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina.
Proteins. 2012 Jul;80(7):1798-809. doi: 10.1002/prot.24076. Epub 2012 May 10.
A structure for the ligand binding domain (LBD) of the DAF-12 receptor from Caenorhabditis elegans was obtained from the X-ray crystal structure of the receptor LBD from Strongyloides stercoralis bound to (25R)-Δ(7)-dafachronic acid (DA) (pdb:3GYU). The model was constructed in the presence of the ligand using a combination of Modeller, Autodock, and molecular dynamics (MD) programs, and then its dynamical behavior was studied by MD. A strong ligand binding mode (LBM) was found, with the three arginines in the ligand binding pocket (LBP) contacting the C-26 carboxylate group of the DA. The quality of the ceDAF-12 model was then evaluated by constructing several ligand systems for which the experimental activity is known. Thus, the dynamical behavior of the ceDAF-12 complex with the more active (25S)-Δ(7)-DA showed two distinct binding modes, one of them being energetically more favorable compared with the 25R isomer. Then the effect of the Arg564Cys and Arg598Met mutations on the (25R)-Δ(7)-DA binding was analyzed. The MD simulations showed that in the first case the complex was unstable, consistent with the lack of transactivation activity of (25R)-Δ(7)-DA in this mutant. Instead, in the case of the Arg598Met mutant, known to produce a partial loss of activity, our model predicted smaller effects on the LBM with a more stable MD trajectory. The model also showed that removal of the C-25 methyl does not impede the simultaneous strong interaction of the carboxylate with the three arginines, predicting that 27-nor-DAs are putative ceDAF-12 ligands.
从秀丽隐杆线虫 DAF-12 受体的 X 射线晶体结构获得了该受体配体结合域 (LBD) 的结构，该结构来自与（25R）-Δ(7)-dafachronic 酸 (DA)（pdb:3GYU）结合的 Strongyloides stercoralis 受体 LBD。该模型是在配体存在的情况下使用 Modeller、Autodock 和分子动力学 (MD) 程序构建的，然后通过 MD 研究其动力学行为。发现了一种强烈的配体结合模式 (LBM)，配体结合口袋 (LBP) 中的三个精氨酸与 DA 的 C-26 羧酸盐基团接触。然后，通过构建几个已知实验活性的配体系统来评估 ceDAF-12 模型的质量。因此，对于更具活性的（25S）-Δ(7)-DA，构建了几种配体系统来研究 ceDAF-12 复合物的动力学行为，结果表明存在两种不同的结合模式，其中一种模式的能量更有利与 25R 异构体相比。然后分析了 Arg564Cys 和 Arg598Met 突变对（25R）-Δ(7)-DA 结合的影响。MD 模拟表明，在第一种情况下，该复合物不稳定，这与该突变体中（25R）-Δ(7)-DA 缺乏反式激活活性一致。相反，在 Arg598Met 突变体的情况下，已知其产生部分活性丧失，我们的模型预测 LBM 的影响较小，具有更稳定的 MD 轨迹。该模型还表明，去除 C-25 甲基不会阻碍羧酸盐与三个精氨酸的同时强烈相互作用，预测 27-去甲基-DAs 是潜在的 ceDAF-12 配体。
