Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck
Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck
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DOI：
10.1002/prot.21334
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发表时间：
2007-06-01
影响因子：
2.9
通讯作者：
Roux, Benoit
中科院分区：
文献类型：
--
作者：
Banavali, Nilesh K.;Roux, Benoit
Src激酶活性与细胞生长过程中涉及的下游信号转导通路的调节有关。晶体学研究表明，造血细胞激酶（Hck）作为Src激酶家族的一员，其激活在结构上伴随着其催化结构域两个特定部分的大构象变化：α - C螺旋和激活环。在本研究中，分子动力学（MD）模拟被用于表征从失活状态到激活状态的转变途径。考虑了四种不同的条件：激活环中Tyr416磷酸化的存在与否，以及活性位点中底物ATP - 2Mg(+2)的存在与否。通过将受限分子动力学模拟与均方根距离（RMSD）偏置势相结合来确定局部残基的有效自由能面，以强制实现变化，随后进行自由分子动力学模拟，以便从人为强制的中间态松弛。将激酶催化结构域概念性地细分为四个运动部分：灵活的激活环片段、埋藏的激活环片段、α - C螺旋和N末端连接子，这引出了一个简洁的假设，即每个运动部分仅需与其最近邻耦合，以确保蛋白酪氨酸激酶调节中的双向变构作用。Tyr416磷酸化和ATP - 2Mg(+2)都会影响伴随结构转变的局部主链扭转自由能面。当这两个因素同时存在时，观察到ATP - 2Mg(+2)和磷酸化的Tyr416处于亚稳态的协同状态，这为由于Mg+2离子浓度增加导致的蛋白激酶活性抑制提供了一种可能的解释。《蛋白质》2007年；67卷：1096 - 1112页。（C）2007年威利 - 利斯公司
Src kinase activity is implicated in the regulation of downstream signal transduction pathways involved in cell growth processes. Crystallographic studies indicate that activation of Hematopoietic cell kinase (Hck), a member of the Src kinase family, is accompanied structurally by a large conformational. change in two specific parts of its catalytic domain: the a-C helix and the activation loop. In the present study, molecular dynamics (MD) simulations are used to characterize the transformation pathway from the inactive to the active state. Four different conditions are considered: the presence or absence of Tyr416 phosphorylation in the activation loop, and the presence or absence of substrate ATP-2Mg(+2) in the active site. Effective free energy landscapes for local residues are determined using a combination of restrained MD simulations with a Root Mean Square Distance (RMSD) biasing potential to enforce the change followed by free MD simulations to allow relaxation from artificially enforced intermediates. A conceptual subdivision of the kinase catalytic domain into four moving parts: the flexible activation loop segment, the buried activation loop segment, the a-C helix, and the N-terminal end linker, leads to a concise hypothesis in which each of the moving parts are only required to be coupled to their nearest neighbor to ensure bidirectional allostery in the regulation of protein tyrosine kinases. Both Tyr416 phosphorylation and ATP-2Mg(+2) affect the local backbone torsional free energy landscapes accompanying the structural transition. When these two factors are present together, a metastable coordinated state of ATP-2Mg(+2) and the phosphorylated Tyr416 is observed that offers a possible explanation for the inhibition of protein kinase activity due to increase in Mg+2 ion concentration. Proteins 2007;67:1096-1112. (C) 2007 Wiley-Liss, Inc.