Meng Yilin, Shukla Diwakar, Pande Vijay S, Roux Benoît
Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637;
Department of Chemistry, Stanford University, Stanford, CA 94305; Simulation of Biological Structures NIH Center for Biomedical Computation, Stanford University, Stanford, CA 94305.
Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9193-8. doi: 10.1073/pnas.1602790113. Epub 2016 Aug 1.
Nonreceptor tyrosine kinases of the Src family are large multidomain allosteric proteins that are crucial to cellular signaling pathways. In a previous study, we generated a Markov state model (MSM) to simulate the activation of c-Src catalytic domain, used as a prototypical tyrosine kinase. The long-time kinetics of transition predicted by the MSM was in agreement with experimental observations. In the present study, we apply the framework of transition path theory (TPT) to the previously constructed MSM to characterize the main features of the activation pathway. The analysis indicates that the activating transition, in which the activation loop first opens up followed by an inward rotation of the αC-helix, takes place via a dense set of intermediate microstates distributed within a fairly broad "transition tube" in a multidimensional conformational subspace connecting the two end-point conformations. Multiple microstates with negligible equilibrium probabilities carry a large transition flux associated with the activating transition, which explains why extensive conformational sampling is necessary to accurately determine the kinetics of activation. Our results suggest that the combination of MSM with TPT provides an effective framework to represent conformational transitions in complex biomolecular systems.
Src家族的非受体酪氨酸激酶是大型多结构域变构蛋白，对细胞信号通路至关重要。在先前的一项研究中，我们生成了一个马尔可夫状态模型（MSM）来模拟作为典型酪氨酸激酶的c-Src催化结构域的激活。MSM预测的长时间跃迁动力学与实验观察结果一致。在本研究中，我们将跃迁路径理论（TPT）框架应用于先前构建的MSM，以表征激活途径的主要特征。分析表明，激活跃迁过程中，激活环首先打开，随后αC螺旋向内旋转，这一过程通过分布在连接两个端点构象的多维构象子空间中相当宽的“跃迁管”内的一组密集中间微状态发生。具有可忽略平衡概率的多个微状态携带与激活跃迁相关的大量跃迁通量，这解释了为什么需要进行广泛的构象采样才能准确确定激活动力学。我们的结果表明，MSM与TPT的结合为表示复杂生物分子系统中的构象转变提供了一个有效的框架。
