Multiscale Simulations Suggest a Mechanism for the Association of the Dok7 PH Domain with PIP-Containing Membranes.
Multiscale Simulations Suggest a Mechanism for the Association of the Dok7 PH Domain with PIP-Containing Membranes.
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DOI：
10.1371/journal.pcbi.1005028
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发表时间：
2016-07
影响因子：
4.3
通讯作者：
Sansom MS
中科院分区：
文献类型：
--
作者：
Buyan A;Kalli AC;Sansom MS
Dok 7是与MuSK受体酪氨酸激酶相关的外周膜蛋白。Dok 7/MuSK/膜复合物的形成是MuSK激活所必需的。这是神经元和肌肉之间复杂信号交换的关键步骤，导致神经肌肉接头形成，其功能障碍与先天性肌无力综合征有关。Dok 7结构由Pleckstrin同源（PH）结构域和磷酸酪氨酸结合（PTB）结构域组成。Dok 7与膜结合的机制在很大程度上仍然未知。使用多尺度分子动力学模拟，我们探索了Dok 7 PH/膜复合物的形成。我们的模拟表明，Dok 7的PH结构域通过β1/β2、β3/β4和β5/β6环的相互作用与含有磷脂酰肌醇磷酸（PIP）的膜缔合，这些环一起在PH结构域上形成带正电荷的表面，并与PIP分子的带负电荷的头基相互作用。Dok 7 PH结构域的最初遭遇之后是与脂质双层，特别是与PIP分子形成额外的相互作用，这稳定了Dok 7 PH/膜复合物。我们已经量化的PH结构域的模型双层的结合，通过计算蛋白质/膜相互作用的密度景观。PH/PIP相互作用的详细分析揭示了阴离子脂质所占据的典型和非典型位点。PH结构域结合导致PIP分子在双层中局部聚集。因此，Dok 7 PH结构域与PIP脂质的结合被视为Dok 7定位于膜并与MuSK形成复合物的关键步骤。神经肌肉接头的形成和维持是一个重要的生物学过程，其破坏会导致先天性肌无力综合征和过早死亡。Dok 7是神经肌肉接头形成、维持和信号传导的关键成员。Dok 7是一种外周膜蛋白，其对于受体酪氨酸激酶MuSK（一种位于突触后膜中的受体酪氨酸激酶）的完全激活是必需的。Dok 7的结构由PH结构域和PTB结构域组成。Dok 7与细胞膜的相互作用还不清楚。在这里，我们使用分子模拟来显示Dok 7 PH结构域在与膜结合时优先结合PIP脂质分子。Dok 7以典型结合模式和替代结合模式与双分子层相互作用。我们的模拟还表明，存在一个典型的和一个非典型的结合位点的PIP协议与最近的晶体学研究的ASAP 1 PH结构域。Dok 7 PH结构域与含PIP的脂质双层的相互作用的密度景观的分析也能够识别典型的和替代的结合模式。我们对Dok 7如何与膜相互作用的理解是研究Dok 7/MuSK信号传导的关键。
Dok7 is a peripheral membrane protein that is associated with the MuSK receptor tyrosine kinase. Formation of the Dok7/MuSK/membrane complex is required for the activation of MuSK. This is a key step in the complex exchange of signals between neuron and muscle, which lead to neuromuscular junction formation, dysfunction of which is associated with congenital myasthenic syndromes. The Dok7 structure consists of a Pleckstrin Homology (PH) domain and a Phosphotyrosine Binding (PTB) domain. The mechanism of the Dok7 association with the membrane remains largely unknown. Using multi-scale molecular dynamics simulations we have explored the formation of the Dok7 PH/membrane complex. Our simulations indicate that the PH domain of Dok7 associates with membranes containing phosphatidylinositol phosphates (PIPs) via interactions of the β1/β2, β3/β4, and β5/β6 loops, which together form a positively charged surface on the PH domain and interact with the negatively charged headgroups of PIP molecules. The initial encounter of the Dok7 PH domain is followed by formation of additional interactions with the lipid bilayer, and especially with PIP molecules, which stabilizes the Dok7 PH/membrane complex. We have quantified the binding of the PH domain to the model bilayers by calculating a density landscape for protein/membrane interactions. Detailed analysis of the PH/PIP interactions reveal both a canonical and an atypical site to be occupied by the anionic lipid. PH domain binding leads to local clustering of PIP molecules in the bilayer. Association of the Dok7 PH domain with PIP lipids is therefore seen as a key step in localization of Dok7 to the membrane and formation of a complex with MuSK. Neuromuscular junction formation and maintenance is an essential biological process, the disruption of which leads to congenital myasthenic syndromes and premature death. Dok7 is a key member in formation, maintenance and signaling in neuromuscular junctions. Dok7 is a peripheral membrane protein that is necessary for full activation of the receptor tyrosine kinase MuSK, a receptor tyrosine kinase residing in the postsynaptic membrane. The structure of Dok7 consists of both a PH domain and a PTB domain. The interaction of Dok7 with cell membranes is not well understood. Here, we use molecular simulations to show that the Dok7 PH domain preferentially binds to PIP lipid molecules when associating with a membrane. Dok7 interacts with the bilayer in both a canonical binding mode and an alternative binding mode. Our simulations also demonstrate the presence of both a canonical and an atypical binding site for PIPs in agreement with recent crystallographic studies of the ASAP1 PH domain. Analysis of density landscapes for the interaction of the Dok7 PH domain with PIP-containing lipid bilayers is also able to identify both canonical and alternative binding modes. Our improved understanding of how Dok7 interacts with a membrane is key to examining Dok7/MuSK signaling.