Department of Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 60637, United States.
J Phys Chem B. 2017 Apr 20;121(15):3352-3363. doi: 10.1021/acs.jpcb.6b08409. Epub 2016 Oct 28.
Tyrosine kinases are important cellular signaling allosteric enzymes that regulate cell growth, proliferation, metabolism, differentiation, and migration. Their activity must be tightly controlled, and malfunction can lead to a variety of diseases, particularly cancer. The nonreceptor tyrosine kinase c-Src, a prototypical model system and a representative member of the Src-family, functions as complex multidomain allosteric molecular switches comprising SH2 and SH3 domains modulating the activity of the catalytic domain. The broad picture of self-inhibition of c-Src via the SH2 and SH3 regulatory domains is well characterized from a structural point of view, but a detailed molecular mechanism understanding is nonetheless still lacking. Here, we use advanced computational methods based on all-atom molecular dynamics simulations with explicit solvent to advance our understanding of kinase activation. To elucidate the mechanism of regulation and self-inhibition, we have computed the pathway and the free energy landscapes for the "inactive-to-active" conformational transition of c-Src for different configurations of the SH2 and SH3 domains. Using the isolated c-Src catalytic domain as a baseline for comparison, it is observed that the SH2 and SH3 domains, depending upon their bound orientation, promote either the inactive or active state of the catalytic domain. The regulatory structural information from the SH2-SH3 tandem is allosterically transmitted via the N-terminal linker of the catalytic domain. Analysis of the conformational transition pathways also illustrates the importance of the conserved tryptophan 260 in activating c-Src, and reveals a series of concerted events during the activation process.
酪氨酸激酶是重要的细胞信号变构酶，可调节细胞生长、增殖、代谢、分化和迁移。其活性必须受到严格控制，功能失调可导致多种疾病，尤其是癌症。非受体酪氨酸激酶 c-Src 是一个典型的模型系统，也是 Src 家族的代表性成员，作为复杂的多结构域变构分子开关起作用，由调节催化结构域活性的 SH2 和 SH3 结构域组成。从结构角度来看，c-Src 通过 SH2 和 SH3 调节结构域的自我抑制的整体情况已经得到很好的描述，但仍缺乏对其详细分子机制的理解。在这里，我们使用基于含溶剂的全原子分子动力学模拟的先进计算方法来深入了解激酶的激活机制。为了阐明调节和自我抑制的机制，我们计算了不同 SH2 和 SH3 结构域构象下 c-Src 的“非活性-活性”构象转变的途径和自由能图谱。将孤立的 c-Src 催化结构域作为比较的基准，观察到 SH2 和 SH3 结构域根据其结合的取向，促进催化结构域的非活性或活性状态。来自 SH2-SH3 串联的调节结构信息通过催化结构域的 N 端接头进行变构传递。构象转变途径的分析还说明了保守色氨酸 260 在激活 c-Src 中的重要性，并揭示了激活过程中的一系列协同事件。
