Coarse-Grained Modeling of Genetic Circuits as a Function of the Inherent Time Scales
Coarse-Grained Modeling of Genetic Circuits as a Function of the Inherent Time Scales
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作为固有时间尺度函数的遗传电路的粗粒度建模
DOI：
10.1103/physreve.87.062706
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发表时间：
2013
期刊：
影响因子：
--
通讯作者：
H. Meyer-Ortmanns
中科院分区：
文献类型：
--
作者：
D. Labavić;H. Nagel;W. Janke;H. Meyer-Ortmanns
从粗粒度的角度来看，自激活物种的基序，激活作为其自身阻遏物的第二物种，广泛存在于生物系统中，特别是在具有固有振荡行为的遗传系统中。在这里，我们考虑这个基序的一个具体实现，作为一个遗传电路，被称为基因受挫单元，其中基因被描述为直接产生蛋白质。在改进的时间分辨率后，我们专注于基础尺度上的固有时间尺度对粗尺度上的分叉模式的影响。时间尺度由转录因子与基因的启动子区域的结合和解结合速率设定。根据这些比率的衰减时间的两种蛋白质，适当的平均程序，以获得一个粗粒度的描述的变化，并导致组的确定性方程，这大大不同的分歧结构。特别是，当基因的结合速率与蛋白质的衰变时间相比不快时，所需的中间范围的规则极限环逐渐消失。我们的分析表明，共同的拓扑结构的广泛发现的主题本身并不意味着普遍的功能，在动态。
From a coarse-grained perspective, the motif of a self-activating species, activating a second species that acts as its own repressor, is widely found in biological systems, in particular in genetic systems with inherent oscillatory behavior. Here we consider a specific realization of this motif as a genetic circuit, termed the bistable frustrated unit, in which genes are described as directly producing proteins. Upon an improved resolution in time, we focus on the effect that inherent time scales on the underlying scale can have on the bifurcation patterns on a coarser scale. Time scales are set by the binding and unbinding rates of the transcription factors to the promoter regions of the genes. Depending on the ratio of these rates to the decay times of both proteins, the appropriate averaging procedure for obtaining a coarse-grained description changes and leads to sets of deterministic equations, which considerably differ in their bifurcation structure. In particular, the desired intermediate range of regular limit cycles fades away when the binding rates of genes are not fast as compared to the decay time of the proteins. Our analysis illustrates that the common topology of the widely found motif alone does not imply universal features in the dynamics.
DOI：
10.1007/b98848
发表时间：
2023
期刊：
Applied Mathematical Sciences
影响因子：
--
作者：
Y. Kuznetsov
通讯作者：
Y. Kuznetsov
(±)-Scandine的合成研究
DOI：
--
发表时间：
2011
期刊：
影响因子：
--
作者：
林佑次郎
通讯作者：
林佑次郎