Zou Jun, Wang Yi-Dong, Ma Fan-Xin, Xiang Ming-Li, Shi Bing, Wei Yu-Quan, Yang Sheng-Yong
State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, People's Republic of China.
Proteins. 2008 Jul;72(1):323-32. doi: 10.1002/prot.21928.
The stem cell factor receptor (c-Kit) plays critical roles in initiating cell growth and proliferation. Its kinase functional abnormality has been thought to associate with several human cancers. The regulation of c-Kit kinase activity is achieved by phosphorylation on the residues Tyr568 and Tyr570 within juxtamembrane region (JMR) and subsequent structural transition of JMR and activation loop (A-loop). However, the detailed conformational dynamics of JMR and A-loop are far from clear, especially whether their conformational changes are coupled or not during the kinase activation transition. In this investigation, the complete conformational transition pathway was determined using a series of nanosecond conventional molecular dynamics (MD) and targeted molecular dynamics (TMD) simulations in explicit water systems. The results of the MD simulations show that the phosphorylation of residues Tyr568 and Tyr570 within JMR induces the detachment of JMR from the kinase C-lobe and increases the fluctuation in the structure of JMR, thus appearing to initiate the kinase activation process. During the course of the TMD simulation, which characterizes the conformational transition of c-Kit from autoinhibitory to activated state, the JMR undergoes a rapid departure from the allosteric binding site and drifts into solvent, followed by the conformational flip of A-loop from inactive (fold) state to active (extended) state. A change in the orientation of helix alphaC in response to the motion of JMR and A-loop has also been observed. The computational results presented here indicate that the dissociation of JMR from the kinase domain is prerequisite to c-Kit activation, which is consistent with previous experiments.
干细胞因子受体（c-Kit）在启动细胞生长和增殖过程中发挥着关键作用。其激酶功能异常被认为与多种人类癌症相关。c-Kit激酶活性的调节是通过近膜区（JMR）内酪氨酸568和酪氨酸570残基的磷酸化以及随后JMR和激活环（A-loop）的结构转变来实现的。然而，JMR和A-loop的详细构象动力学仍远未明确，尤其是在激酶激活转变过程中它们的构象变化是否耦合。在本研究中，使用一系列纳秒级常规分子动力学（MD）和靶向分子动力学（TMD）模拟在明确的水体系中确定了完整的构象转变途径。MD模拟结果表明，JMR内酪氨酸568和酪氨酸570残基的磷酸化诱导JMR从激酶C叶脱离，并增加了JMR结构的波动，从而似乎启动了激酶激活过程。在表征c-Kit从自抑制状态到激活状态构象转变的TMD模拟过程中，JMR迅速从变构结合位点脱离并漂移到溶剂中，随后A-loop从无活性（折叠）状态构象翻转到活性（伸展）状态。还观察到αC螺旋的取向响应JMR和A-loop的运动而发生变化。此处呈现的计算结果表明，JMR从激酶结构域的解离是c-Kit激活的先决条件，这与先前的实验一致。
