Transient dynamics of genetic regulatory networks
Transient dynamics of genetic regulatory networks
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DOI：
10.1529/biophysj.106.095638
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发表时间：
2007-05-10
影响因子：
3.4
通讯作者：
Hasty, Jeff
中科院分区：
文献类型：
--
作者：
Bennett, Matthew R.;Volfson, Dmitri;Hasty, Jeff
我们提出了一种近似方案来推导遗传调控网络的反应速率方程。该方案通过在控制蛋白质浓度动态的ODE中引入预因子，比标准准稳态分析更准确地预测此类网络的暂态动态的时间尺度。这些前置因素使得常微分方程系统比准稳态近似系统慢。我们通过检验一个正反馈的基因调控网络来介绍该方法，并展示了当包含前置因子时如何更准确地模拟该网络的暂态动态。接下来，我们研究了抑制器，一种遗传振荡器，并证明了周期，振幅和分叉图。用预因子法较好地估计了振荡的开始时间。最后，我们考察了该方法对噬菌体波长开关简化模型动力学的影响，并表明由于蛋白质多聚化和DNA结合所产生的前因子的存在，两种状态之间的切换时间被减缓。
We present an approximation scheme for deriving reaction rate equations of genetic regulatory networks. This scheme predicts the timescales of transient dynamics of such networks more accurately than does standard quasi-steady state analysis by introducing prefactors to the ODEs that govern the dynamics of the protein concentrations. These prefactors render the ODE systems slower than their quasi-steady state approximation counterparts. We introduce the method by examining a positive feedback gene regulatory network, and show how the transient dynamics of this network are more accurately modeled when the prefactor is included. Next, we examine the repressilator, a genetic oscillator, and show that the period, amplitude, and bifurcation diagram de. ning the onset of the oscillations are better estimated by the prefactor method. Finally, we examine the consequences of the method to the dynamics of reduced models of the phage lambda switch, and show that the switching times between the two states is slowed by the presence of the prefactor that arises from protein multimerization and DNA binding.