定向和加权代谢超图的稳定性和复杂性
Pietro Traversa1,2,3, Guilherme Ferraz de Arruda3, Alexei Vazquez4
1Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain.
Entropy (Basel, Switzerland)
|November 24, 2023
概括
我们介绍了一种新的定向超图框架来建模代谢网络,捕捉复杂的相互作用. 这种方法揭示了高结构强度与抗生素耐药性相关,复杂性区分了生物类型.
科学领域:
- 系统生物学 系统生物学
- 生物信息学是一种生物信息学.
- 网络科学 网络科学
背景情况:
- 代谢网络对于理解生物体的功能和弹性至关重要.
- 现有的模型往往难以捕捉高阶相互作用和反应方向性.
研究的目的:
- 开发一种新的框架来使用指向超图来表示代谢网络.
- 引入用于量化网络稳定性和复杂性的指标.
- 分析网络结构与生物特性之间的关系.
主要方法:
- 代表代谢网络作为以边缘依赖的顶点权重为导向的超图.
- 定义和应用可传播性和搜索信息指标.
- 分析一个小规模的大肠杆菌核心模型.
- 将30种不同的代谢模型进行比较.
主要成果:
- 定向超图框架有效地保留了重要的代谢网络信息,包括更高层次的相互作用和定向性.
- 网络定向性影响了稳定性和复杂性指标.
- 代谢网络的高结构强度与抗生素耐药性有关.
- 网络复杂性可以区分真核生物和原核生物.
结论:
- 定向超图为代谢网络提供了一个强大的新表示方式.
- 网络结构,特别是强度和复杂性,为生物体的特征提供了洞察力,例如抗生素耐药性和进化分类.
相关概念视频
Protein Networks
4.0K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.0K
What is Metabolism?
114.4K
Overview
114.4K
Regulation of Metabolism
9.5K
Cellular needs and conditions vary from cell to cell and change within individual cells over time. For example, the required enzymes and energetic demands of stomach cells are different from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so do the amounts and...
9.5K
The Supercomplexes in the Crista Membrane
2.5K
The mitochondrial cristae membrane is the primary site for the oxidative phosphorylation (OXPHOS) process of energy conversion mediated through respiratory complexes I to V. These complexes have been widely studied for decades, and it has been proven that they form supramolecular structures called respiratory supercomplexes (SC). These higher-order complexes may be crucial in maintaining the biochemical structure and improving the physiological activity of the individual complexes while...
2.5K
Overview of Carbohydrate Metabolism
1.1K
Carbohydrate metabolism is a fundamental biochemical process that ensures a constant supply of energy to living cells. The most important carbohydrate is glucose, which can be broken down via glycolysis to enter into the Krebs cycle and eventually lead to the production of ATP through oxidative phosphorylation.
Glucose transport into cells is facilitated by a family of transport proteins called GLUT (Glucose Transporters). GLUT4 is the primary glucose transporter for insulin-stimulated glucose...
Glucose transport into cells is facilitated by a family of transport proteins called GLUT (Glucose Transporters). GLUT4 is the primary glucose transporter for insulin-stimulated glucose...
1.1K
Overview of Metabolism
30.4K
Living cells constantly carry out various chemical reactions which are necessary for their proper functioning. These reactions are interlinked to one another via multiple pathways. The collection of these chemical reactions is known as metabolism.
Plant Metabolism
Sunlight, the primary source of energy in plants, is first absorbed by the chlorophyll pigments present in their leaves. Plants then use this energy to carry out photosynthesis, where water is oxidized into oxygen and carbon dioxide...
Plant Metabolism
Sunlight, the primary source of energy in plants, is first absorbed by the chlorophyll pigments present in their leaves. Plants then use this energy to carry out photosynthesis, where water is oxidized into oxygen and carbon dioxide...
30.4K


