酵母中高渗透压甘油途径的形式表示。

Clemens Kühn, K V S Prasad, Edda Klipp, Peter Gennemark
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引用次数: 0

摘要

酵母中的高渗透压甘油(HOG)信号系统属于丝裂原活化蛋白激酶(MAPK)途径,在所有真核生物中都有发现。它包括至少三种形成复合物的支架蛋白,并涉及严格依赖于与特定复合物结合的物种集的反应。支架蛋白导致可能状态数量的组合增加。迄今为止,HOG途径的表示已经使用简化的假设来避免这种组合问题。这样的假设很难做出,可能会模糊或删除系统的基本属性。本文给出了没有这些假设的HOG系统的详细的一般形式表示,显示了从文献中已知的分子相互作用。该模型考虑了复杂性,并以明确和详细的表示总结了现有知识。因此,它可以用来锚定关于HOG系统的讨论。在常用的系统生物学标记语言(SBML)中,这样的模型需要显式地枚举所有状态变量。我们使用的Kappa建模语言支持没有这种枚举的复合体的表示。最后,我们将Kappa与其他一些建模语言和软件工具进行了比较,这些语言和软件工具也可用于表示和建模HOG系统。
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Formal representation of the high osmolarity glycerol pathway in yeast.

The high osmolarity glycerol (HOG) signalling system in yeast belongs to the class of Mitogen Activated Protein Kinase (MAPK) pathways that are found in all eukaryotic organisms. It includes at least three scaffold proteins that form complexes, and involves reactions that are strictly dependent on the set of species bound to a certain complex. The scaffold proteins lead to a combinatorial increase in the number of possible states. To date, representations of the HOG pathway have used simplifying assumptions to avoid this combinatorial problem. Such assumptions are hard to make and may obscure or remove essential properties of the system. This paper presents a detailed generic formal representation of the HOG system without such assumptions, showing the molecular interactions known from the literature. The model takes complexes into account, and summarises existing knowledge in an unambiguous and detailed representation. It can thus be used to anchor discussions about the HOG system. In the commonly used Systems Biology Markup Language (SBML), such a model would need to explicitly enumerate all state variables. The Kappa modelling language which we use supports representation of complexes without such enumeration. To conclude, we compare Kappa with a few other modelling languages and software tools that could also be used to represent and model the HOG system.

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