The partition representation of enzymatic reaction networks and its application for searching bi-stable reaction systems
| Autor: | Takashi Naka |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2022 |
| Předmět: |
Cell biology
Cell signaling Computer and Information Sciences MAPK signaling cascades Science Reaction Systems Signal transduction Research and Analysis Methods Biochemistry Systems Science Differential Equations Computer Simulation Post-Translational Modification Multidisciplinary Applied Mathematics Simulation and Modeling Biology and Life Sciences Proteins Signaling cascades Enzymes Chemistry Models Chemical Physical Sciences Enzymology Medicine Protein Processing Post-Translational Algorithms Mathematics Research Article Chemical Elements |
| Zdroj: | PLoS ONE, Vol 17, Iss 1 (2022) PLoS ONE PLoS ONE, Vol 17, Iss 1, p e0263111 (2022) |
| ISSN: | 1932-6203 |
| Popis: | The signal transduction system, which is known as a regulatory mechanism for biochemical reaction systems in the cell, has been the subject of intensive research in recent years, and its design methods have become necessary from the viewpoint of synthetic biology. We proposed the partition representation of enzymatic reaction networks consisting of post-translational modification reactions such as phosphorylation, which is an important basic component of signal transduction systems, and attempted to find enzymatic reaction networks with bistability to demonstrate the effectiveness of the proposed representation method. The partition modifiers can be naturally introduced into the partition representation of enzymatic reaction networks when applied to search. By randomly applying the partition modifiers as appropriate, we searched for bistable and resettable enzymatic reaction networks consisting of four post-translational modification reactions. The proposed search algorithm worked well and we were able to find various bistable enzymatic reaction networks, including a typical bistable enzymatic reaction network with positive auto-feedbacks and mutually negative regulations. Since the search algorithm is divided into an evaluation function specific to the characteristics of the enzymatic reaction network to be searched and an independent algorithm part, it may be applied to search for dynamic properties such as biochemical adaptation, the ability to reset the biochemical state after responding to a stimulus, by replacing the evaluation function with one for other characteristics. |
| Databáze: | OpenAIRE |
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