Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach.
Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach.
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DOI：
10.1016/j.jmgm.2008.12.005
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发表时间：
2009-04
影响因子：
2.9
通讯作者：
Zou, Xiaoqin
中科院分区：
文献类型：
--
作者：
Huang, Sheng-You;Bolser, Diana;Liu, Hao-Yang;Hwang, Tzyh-Chang;Zou, Xiaoqin
我们提出了一种新的蛋白质-蛋白质对接方法来模拟基于单体单位构象的异二聚体结构。传统的建模方法依赖于将两个单体结构叠加到同源蛋白二聚体的晶体结构上。所得到的结构可能在二聚体界面上表现出严重的主链冲突，这取决于靶蛋白和模板蛋白之间的主链不相似。我们的方法克服了主链冲突问题，并且不需要同源蛋白二聚体结构的先验知识。在这里，我们使用人类囊性纤维化跨膜电导调节剂（CFTR）作为例子，这是一种氯离子通道，其功能障碍导致囊性纤维化。CFTR的两个胞内核苷酸结合结构域（nbd）控制通道的打开和关闭。然而，CFTR的NBD1-NBD2复合物的结构尚未被实验确定。因此，这种异二聚体结构的正确建模对于理解CFTR功能是有价值的，并且在囊性纤维化治疗的药物设计中具有潜在的应用。基于人CFTR的NBD1晶体结构，构建了NBD1 - nbd2复合物模型。所构建的模型与其他ABC转运蛋白晶体结构中观察到的二聚体模式一致。为了验证我们的结构模型，ATP底物被停靠在核苷酸结合位点。预测的结合模式与相关的晶体学发现和CFTR功能研究一致。最后，染料木黄酮，一种增强CFTR活性的药物，尽管这种增强的机制尚不清楚，被对接到模型中。我们的预测与染料木黄酮的钟形剂量-反应关系一致。为了进一步了解染料木素的增强机制，并为针对CFTR的药物设计提供有意义的信息，提出了潜在的诱变实验。本研究中使用的方法可以应用于其他二聚体蛋白质结构的建模研究。
We have presented a new protein–protein docking approach to model heterodimeric structures based on the conformations of the monomeric units. The conventional modeling method relies on superimposing two monomeric structures onto the crystal structure of a homologous protein dimer. The resulting structure may exhibit severe backbone clashes at the dimeric interface depending on the backbone dissimilarity between the target and template proteins. Our method overcomes the backbone clashing problem and requires no a priori knowledge of the dimeric structure of a homologous protein. Here we used human Cystic Fibrosis Transmembrane conductance Regulator (CFTR), a chloride channel whose dysfunction causes cystic fibrosis, for illustration. The two intracellular nucleotide-binding domains (NBDs) of CFTR control the opening and closing of the channel. Yet, the structure of the CFTR’s NBD1–NBD2 complex has not been experimentally determined. Thus, correct modeling of this heterodimeric structure is valuable for understanding CFTR functions and would have potential applications for drug design for cystic fibrosis treatment. Based on the crystal structure of human CFTR’s NBD1, we constructed a model of the NBD1–NBD2 complex. The constructed model is consistent with the dimeric mode observed in the crystal structures of other ABC transporters. To verify our structural model, an ATP substrate was docked into the nucleotide-binding site. The predicted binding mode shows consistency with related crystallographic findings and CFTR functional studies. Finally, genistein, an agent that enhances CFTR activity, though the mechanism for such enhancement is unclear, was docked to the model. Our predictions agreed with genistein’s bell-shaped dose-response relationship. Potential mutagenesis experiments were proposed for understanding the potentiation mechanism of genistein and for providing insightful information for drug design targeting at CFTR. The method used in this study can be applied to modeling studies of other dimeric protein structures.
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影响因子：
64.8
作者：
Hollenstein, Kaspar;Frei, Dominik C.;Locher, Kaspar P.
通讯作者：
Locher, Kaspar P.
影响因子：
2.9
作者：
Huang, Sheng-You;Zou, Xiaoqin
通讯作者：
Zou, Xiaoqin
DOI：
10.1085/jgp.200308798
发表时间：
2003-09
期刊：
The Journal of general physiology
影响因子：
--
作者：
Basso C;Vergani P;Nairn AC;Gadsby DC
通讯作者：
Gadsby DC
影响因子：
64.8
作者：
Dawson, Roger J. P.;Locher, Kaspar P.
通讯作者：
Locher, Kaspar P.
影响因子：
3
作者：
Huang, Sheng-You;Zou, Xiaoqin
通讯作者：
Zou, Xiaoqin