Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.
Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.
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DOI：
10.1371/journal.pcbi.1000487
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发表时间：
2009-08
影响因子：
4.3
通讯作者：
Verkhivker GM
中科院分区：
文献类型：
--
作者：
Dixit A;Verkhivker GM
ABL和EGFR激酶结构域的结构与功能研究近期表明，致癌突变激活存在一种共同机制。然而，致癌突变激活激酶过程中刺激构象转变以及组成性激活激酶形式的热力学稳定性的动力学和机制方面仍然难以捉摸。我们对一组具有临床重要性的癌症突变体ABL - T315I、ABL - L387M、EGFR - T790M和EGFR - L858R在ABL和EGFR激酶结构域中的激活机制进行了大规模的计算研究。我们还模拟了守门员突变对ABL - SH2 - SH3调节复合物功能状态下构象动力学和变构相互作用的激活作用。使用一系列计算方法进行了综合分析，包括同源建模、分子动力学模拟、蛋白质稳定性分析、靶向分子动力学和分子对接。总体而言，这项研究的结果揭示了ABL和EGFR激酶结构域中主要致癌突变激活激酶的热力学和机制催化剂。通过使用ABL和EGFR的多种晶体状态，计算机模拟使人们能够绘制正常（野生型）和致癌激酶形式的构象波动和转变的动态图。一个提出的多阶段激活机制模型涉及不同构象状态之间的一系列协同转变，包括疏水脊的组装、Src样中间结构的形成以及特征性盐桥的协同断裂和形成，这些都标志着向活性激酶形式的转变。我们认为，癌症突变激活的分子机制可能模拟正常激酶的激活过程，但利用保守的结构催化剂来加速构象转变和增强活性激酶形式的稳定性。这项研究的结果将当前的实验数据与理论方法的见解相协调，指出了蛋白激酶激活转变的一般机制方面。
蛋白激酶中的突变与许多癌症有关，癌症研究的一个重要目标是阐明突变的激酶基因对肿瘤发生有贡献的分子效应。我们对致癌突变激活激酶的分子机制进行了全面的计算研究。使用一系列计算方法，我们系统地研究了具有临床重要性的癌症突变体对ABL和EGFR激酶结构域以及调节性多蛋白复合物动力学的影响。这项研究的结果阐明了ABL和EGFR正常形式和致癌形式激活机制的共同和特定特征。我们发现，具有较高致癌活性的突变体可能导致非活性结构的部分不稳定，同时促进激活转变和活性构象的增强稳定性。我们的结果为激活机制的热力学和机制方面提供了有用的见解，并强调了结构上不同的构象状态在激酶调节中的作用。最终，正常和致癌状态下激活机制的分子特征可能有助于将突变效应与临床结果相关联，并促进开发治疗策略以对抗依赖激酶突变的肿瘤发生。
Structural and functional studies of the ABL and EGFR kinase domains have recently suggested a common mechanism of activation by cancer-causing mutations. However, dynamics and mechanistic aspects of kinase activation by cancer mutations that stimulate conformational transitions and thermodynamic stabilization of the constitutively active kinase form remain elusive. We present a large-scale computational investigation of activation mechanisms in the ABL and EGFR kinase domains by a panel of clinically important cancer mutants ABL-T315I, ABL-L387M, EGFR-T790M, and EGFR-L858R. We have also simulated the activating effect of the gatekeeper mutation on conformational dynamics and allosteric interactions in functional states of the ABL-SH2-SH3 regulatory complexes. A comprehensive analysis was conducted using a hierarchy of computational approaches that included homology modeling, molecular dynamics simulations, protein stability analysis, targeted molecular dynamics, and molecular docking. Collectively, the results of this study have revealed thermodynamic and mechanistic catalysts of kinase activation by major cancer-causing mutations in the ABL and EGFR kinase domains. By using multiple crystallographic states of ABL and EGFR, computer simulations have allowed one to map dynamics of conformational fluctuations and transitions in the normal (wild-type) and oncogenic kinase forms. A proposed multi-stage mechanistic model of activation involves a series of cooperative transitions between different conformational states, including assembly of the hydrophobic spine, the formation of the Src-like intermediate structure, and a cooperative breakage and formation of characteristic salt bridges, which signify transition to the active kinase form. We suggest that molecular mechanisms of activation by cancer mutations could mimic the activation process of the normal kinase, yet exploiting conserved structural catalysts to accelerate a conformational transition and the enhanced stabilization of the active kinase form. The results of this study reconcile current experimental data with insights from theoretical approaches, pointing to general mechanistic aspects of activating transitions in protein kinases. Mutations in protein kinases are implicated in many cancers, and an important goal of cancer research is to elucidate molecular effects of mutated kinase genes that contribute to tumorigenesis. We present a comprehensive computational study of molecular mechanisms of kinase activation by cancer-causing mutations. Using a battery of computational approaches, we have systematically investigated the effects of clinically important cancer mutants on dynamics of the ABL and EGFR kinase domains and regulatory multi-protein complexes. The results of this study have illuminated common and specific features of the activation mechanism in the normal and oncogenic forms of ABL and EGFR. We have found that mutants with the higher oncogenic activity may cause a partial destabilization of the inactive structure, while simultaneously facilitating activating transitions and the enhanced stabilization of the active conformation. Our results provided useful insights into thermodynamic and mechanistic aspects of the activation mechanism and highlighted the role of structurally distinct conformational states in kinase regulation. Ultimately, molecular signatures of activation mechanisms in the normal and oncogenic states may aid in the correlation of mutational effects with clinical outcomes and facilitate the development of therapeutic strategies to combat kinase mutation-dependent tumorigenesis.
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