Optimality Principles in the Regulation of Metabolic Networks
One of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and whether universal design principles apply to molecular networks. To achieve this, the biophysical, evolutionary and physiological constraints that act on those networks nee...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2012-08-01
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| Series: | Metabolites |
| Subjects: | |
| Online Access: | http://www.mdpi.com/2218-1989/2/3/529 |
| _version_ | 1818198433242021888 |
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| author | Jan Berkhout Frank J. Bruggeman Bas Teusink |
| author_facet | Jan Berkhout Frank J. Bruggeman Bas Teusink |
| author_sort | Jan Berkhout |
| collection | DOAJ |
| description | One of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and whether universal design principles apply to molecular networks. To achieve this, the biophysical, evolutionary and physiological constraints that act on those networks need to be identified in addition to the characterisation of the molecular components and interactions. Then, the cellular “task” of the network—its function—should be identified. A network contributes to organismal fitness through its function. The premise is that the same functions are often implemented in different organisms by the same type of network; hence, the concept of design principles. In biology, due to the strong forces of selective pressure and natural selection, network functions can often be understood as the outcome of fitness optimisation. The hypothesis of fitness optimisation to understand the design of a network has proven to be a powerful strategy. Here, we outline the use of several optimisation principles applied to biological networks, with an emphasis on metabolic regulatory networks. We discuss the different objective functions and constraints that are considered and the kind of understanding that they provide. |
| first_indexed | 2024-12-12T02:05:47Z |
| format | Article |
| id | doaj.art-0666fec990be440fa2b9af96ef22394c |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-12-12T02:05:47Z |
| publishDate | 2012-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-0666fec990be440fa2b9af96ef22394c2022-12-22T00:42:03ZengMDPI AGMetabolites2218-19892012-08-012352955210.3390/metabo2030529Optimality Principles in the Regulation of Metabolic NetworksJan BerkhoutFrank J. BruggemanBas TeusinkOne of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and whether universal design principles apply to molecular networks. To achieve this, the biophysical, evolutionary and physiological constraints that act on those networks need to be identified in addition to the characterisation of the molecular components and interactions. Then, the cellular “task” of the network—its function—should be identified. A network contributes to organismal fitness through its function. The premise is that the same functions are often implemented in different organisms by the same type of network; hence, the concept of design principles. In biology, due to the strong forces of selective pressure and natural selection, network functions can often be understood as the outcome of fitness optimisation. The hypothesis of fitness optimisation to understand the design of a network has proven to be a powerful strategy. Here, we outline the use of several optimisation principles applied to biological networks, with an emphasis on metabolic regulatory networks. We discuss the different objective functions and constraints that are considered and the kind of understanding that they provide.http://www.mdpi.com/2218-1989/2/3/529metabolic regulatory networksoptimal regulationsystems biologydesign principles |
| spellingShingle | Jan Berkhout Frank J. Bruggeman Bas Teusink Optimality Principles in the Regulation of Metabolic Networks Metabolites metabolic regulatory networks optimal regulation systems biology design principles |
| title | Optimality Principles in the Regulation of Metabolic Networks |
| title_full | Optimality Principles in the Regulation of Metabolic Networks |
| title_fullStr | Optimality Principles in the Regulation of Metabolic Networks |
| title_full_unstemmed | Optimality Principles in the Regulation of Metabolic Networks |
| title_short | Optimality Principles in the Regulation of Metabolic Networks |
| title_sort | optimality principles in the regulation of metabolic networks |
| topic | metabolic regulatory networks optimal regulation systems biology design principles |
| url | http://www.mdpi.com/2218-1989/2/3/529 |
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