Computational Models for Activated Human MEK1: Identification of Key Active Site Residues and Interactions

MEK1 is a protein
kinase in the MAPK cellular signaling pathway
that is notable for its dual specificity and its potential as a drug
target for a variety of cancer therapies. While much is known about
the key role of MEK1 in signaling events, understanding of the structural
features that sustain MEK1 function remains limited because of the
absence of crystal or NMR structural insights into the phosphorylated
and activated form of MEK1. In this work, homology modeling was used
to overcome this limitation and generate computational models of the
doubly phosphorylated active MEK1 conformation. A variety of models
were generated using crystal structures of active protein kinases
as homology model templates. These models were equilibrated using
molecular dynamics simulations, and each model was validated against
several known structural characteristics of activated kinases. The
best model structures were used in docking studies with ATP and a
small peptide sequence that represents the activation loop of ERK2
to identify the most important residues in stabilizing protein docking
and phosphorylation. These results provide insights for the pursuit
of structure-guided mutagenesis and drug design.

丝裂原活化蛋白激酶激酶1（MEK1）是丝裂原活化蛋白激酶（Mitogen-Activated Protein Kinase，MAPK）细胞信号通路中的一类蛋白激酶，其以双重底物特异性以及可作为多种癌症治疗潜在药物靶点的特性而广受关注。尽管学界对MEK1在信号转导事件中的关键作用已有较多认知，但由于缺乏针对磷酸化活化态MEK1的晶体学或核磁共振（Nuclear Magnetic Resonance，NMR）结构解析数据，学界对维持MEK1功能的结构特征的理解仍较为有限。本研究借助同源建模技术突破了这一局限，构建了双磷酸化活化态MEK1构象的计算模型。研究以多种活化态蛋白激酶的晶体结构作为同源建模模板，生成了多组候选模型；随后通过分子动力学模拟对各模型进行平衡优化，并基于活化态激酶的多项已知结构特征对所有模型进行验证。选取最优的模型结构开展三磷酸腺苷（Adenosine Triphosphate，ATP）以及代表细胞外调节蛋白激酶2（Extracellular Signal-Regulated Kinase 2，ERK2）激活环的小肽序列的分子对接研究，以明确在稳定蛋白对接与磷酸化过程中发挥关键作用的氨基酸残基。本研究结果可为结构导向诱变及药物设计相关研究提供理论参考。