Activation loop plasticity and active site coupling in the MAP kinase, ERK2.
Activation loop plasticity and active site coupling in the MAP kinase, ERK2.
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MAP 激酶 ERK2 中的激活环可塑性和活性位点耦合。
DOI：
10.1101/2023.04.15.537040
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Ahn,Natalie
中科院分区：
文献类型：
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作者：
Pegram,Laurel;Riccardi,Demian;Ahn,Natalie
以前的研究蛋白激酶，ERK 2，使用NMR和氢交换测量已经显示了动力学的变化，伴随着其激活磷酸化。然而，有关构象运动的知识是不完整的。在这里，我们研究了ERK 2使用长的传统分子动力学（MD）模拟从磷酸化（2 P）和非磷酸化（0 P）形式的晶体结构。单个轨迹运行（5至25）μ s，总计727 μ s。结果显示A环具有意想不到的灵活性，在2 P-ERK 2和0 P-ERK 2中都具有多个长寿命（> 5 μ s）构象状态。差分接触网络和主成分分析揭示了A环折叠和活性位点动力学之间的耦合，有证据表明2 P-ERK 2而不是0 P-ERK 2的激酶核心中存在构象选择。2 P-ERK 2的模拟显示A环状态对应于N叶内的受约束动力学，包括催化残基周围的区域。一个A环构象异构体与L16片段形成持久的相互作用，导致RMSF降低和活性位点的更大压缩。相比之下，OP-ERK 2的模拟揭示了A环残基远离C端半叶的偏移，导致更大的活性位点移动性。因此，ERK 2中的A环在不同的构象之间切换，这些构象反映了与活性位点的偶联，可能是通过L16片段。晶体堆积相互作用表明，晶格接触的A-环可能会抑制其结构变化的ERK 2的X射线结构。MD确定的新构象状态扩展了我们对ERK 2调节的理解，将激酶的活化状态与催化位点周围的动力学降低和更大的压实联系起来。
Previous studies of the protein kinase, ERK2, using NMR and hydrogen-exchange measurements have shown changes in dynamics accompanying its activation by phosphorylation. However, knowledge about the conformational motions involved is incomplete. Here, we examined ERK2 using long conventional molecular dynamics (MD) simulations starting from crystal structures of phosphorylated (2P) and unphosphorylated (0P) forms. Individual trajectories were run for (5 to 25) μ s, totaling 727 μ s. The results show unexpected flexibility of the A-loop, with multiple long-lived (> 5 μ s) conformational states in both 2P-and 0P-ERK2. Differential contact network and principal component analyses reveal coupling between the A-loop fold and active site dynamics, with evidence for conformational selection in the kinase core of 2P-ERK2 but not 0P-ERK2. Simulations of 2P-ERK2 show A-loop states corresponding to restrained dynamics within the N-lobe, including regions around catalytic residues. One A-loop conformer forms lasting interactions with the L16 segment, leading to reduced RMSF and greater compaction in the active site. By contrast, simulations of 0P-ERK2 reveal excursions of A-loop residues away from the C-lobe, leading to greater active site mobility. Thus, the A-loop in ERK2 switches between distinct conformations that reflect coupling with the active site, possibly via the L16 segment. Crystal packing interactions suggest that lattice contacts with the A-loop may restrain its structural variation in X-ray structures of ERK2. The novel conformational states identified by MD expand our understanding of ERK2 regulation, by linking the activated state of the kinase to reduced dynamics and greater compaction surrounding the catalytic site.