A computational study of the phosphorylation mechanism of the insulin receptor tyrosine kinase.
A computational study of the phosphorylation mechanism of the insulin receptor tyrosine kinase.
复制标题
胰岛素受体酪氨酸激酶的磷酸化机制的计算研究。
DOI：
10.1021/jp810827w
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发表时间：
2009-04-30
期刊：
影响因子：
--
通讯作者：
Wong CF
中科院分区：
文献类型：
--
作者：
Zhou B;Wong CF
虽然不同的研究小组对胰岛素受体酪氨酸激酶（IRK）的磷酸化机制进行了研究，但尚未形成一致的观点。在这项工作中，我们进行了计算研究以获得进一步的见解。我们首先以几种晶体结构和先前对环amp依赖性蛋白激酶的计算研究为指导，建立了反应物复合物的结构模型。然后，我们通过使用包含近300个原子的量子力学模型进行几何优化来优化结构。然后使用多坐标驱动方法跟踪反应物和产物之间的反应路径。计算绘制出了一系列结构变化，描绘了反应物向产物的转化。对结构变化的分析揭示了解离过渡态的形成以及质子从肽底物的酪氨酸残基的羟基转移到酶活性部位的保守天冬氨酸。质子转移早在过渡态达到之前就开始了，在产物完全形成前不久才结束。此外，Arg1136、Asp1132、ATP的γ-磷酸和底物的酪氨酸残基之间形成了一个氢键网络，使后者处于接近攻击的位置进行反应。模型估计反应势垒为14 kcal/mol，与实验结果半定量吻合。
Although various groups have studied the phosphorylation mechanism of the insulin receptor tyrosine kinase (IRK), an unanimous picture has not yet emerged. In this work, we performed a computational study to gain further insights. We first built a structural model of the reactant complex with the guide of several crystal structures and previous computational studies of the cyclic AMP-dependent protein kinase. We then optimized the structure by performing geometry optimization using a quantum mechanical model containing nearly 300 atoms. A reaction path was then traced between the reactant and the product using a multiple coordinate-driven method. The calculations mapped out a sequence of structural changes depicting the conversion of the reactant to the product. Analysis of the structural changes revealed the formation of a dissociative transition state and the the involvement of a proton transfer from the hydroxyl group of the tyrosyl residue of the peptide substrate to a conserved aspartate in the active site of the enzyme. The proton transfer began well before the transition state was reached and finished only shortly before the product was completely formed. In addition, the formation of a hydrogen bonding network among Arg1136, Asp1132, the γ-phosphate of ATP, and the tyrosine residue of the substrate appeared to hold the latter two in a near-attack position for reaction. The model estimated a reaction barrier of 14 kcal/mol, semi-quantitatively in accord with experiment.
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