Ma Liang, Cui Qiang
Graduate program in Biophysics and Department of Chemistry and Theoretical Chemical Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA.
J Am Chem Soc. 2007 Aug 22;129(33):10261-8. doi: 10.1021/ja073059f. Epub 2007 Jul 26.
Advanced computational techniques including transition path sampling and free energy calculations are combined synergistically to reveal the activation mechanism at unprecedented resolution for a small signaling protein, chemotaxis protein Y. In the conventional "Y-T coupling" model for response regulators, phosphorylation induces the displacement of the conserved Thr87 residue through hydrogen-bond formation, which in turn makes it sterically possible for Tyr106 to isomerize from a solvent exposed configuration to a buried rotameric state. More than 160 unbiased activation trajectories show, however, that the rotation of Tyr106 does not rely on the displacement of Thr87 per se. Free energy calculations reveal that the Tyr106 rotation is a low-barrier process in the absence of the Thr87-phosphate hydrogen bond, although the rotation is stabilized by the formation of this interaction. The simulations also find that structural change in the beta4-alpha4 loop does not gate the Tyr106 rotation as suggested previously; rather, the rotation of Tyr106 stabilizes the activated configuration of this loop. The computational strategy used and mechanistic insights obtained have an impact on the study of signaling proteins and allosteric systems in general.
包括过渡路径采样和自由能计算在内的先进计算技术被协同结合起来，以前所未有的分辨率揭示了一种小信号蛋白——趋化蛋白Y的激活机制。在传统的响应调节因子“Y-T偶联”模型中，磷酸化通过氢键形成诱导保守的苏氨酸87残基发生位移，这反过来又使得酪氨酸106从溶剂暴露构型异构化为埋藏的旋转异构体状态在空间上成为可能。然而，超过160条无偏激活轨迹表明，酪氨酸106的旋转本身并不依赖于苏氨酸87的位移。自由能计算表明，在没有苏氨酸87-磷酸氢键的情况下，酪氨酸106的旋转是一个低势垒过程，尽管这种相互作用的形成会使旋转更加稳定。模拟还发现，β4-α4环的结构变化并不像之前所认为的那样控制酪氨酸106的旋转；相反，酪氨酸106的旋转稳定了该环的激活构型。所采用的计算策略和获得的机制见解总体上对信号蛋白和变构系统的研究产生了影响。
