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Chemical Basis of Metabolic Network Organization
Although the metabolic networks of the three domains of life consist of different constituents and metabolic pathways, they exhibit the same scale-free organization. This phenomenon has been hypothetically explained by preferential attachment principle that the new-recruited metabolites attach prefe...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192814/ https://www.ncbi.nlm.nih.gov/pubmed/22022254 http://dx.doi.org/10.1371/journal.pcbi.1002214 |
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author | Zhu, Qiang Qin, Tao Jiang, Ying-Ying Ji, Cong Kong, De-Xin Ma, Bin-Guang Zhang, Hong-Yu |
author_facet | Zhu, Qiang Qin, Tao Jiang, Ying-Ying Ji, Cong Kong, De-Xin Ma, Bin-Guang Zhang, Hong-Yu |
author_sort | Zhu, Qiang |
collection | PubMed |
description | Although the metabolic networks of the three domains of life consist of different constituents and metabolic pathways, they exhibit the same scale-free organization. This phenomenon has been hypothetically explained by preferential attachment principle that the new-recruited metabolites attach preferentially to those that are already well connected. However, since metabolites are usually small molecules and metabolic processes are basically chemical reactions, we speculate that the metabolic network organization may have a chemical basis. In this paper, chemoinformatic analyses on metabolic networks of Kyoto Encyclopedia of Genes and Genomes (KEGG), Escherichia coli and Saccharomyces cerevisiae were performed. It was found that there exist qualitative and quantitative correlations between network topology and chemical properties of metabolites. The metabolites with larger degrees of connectivity (hubs) are of relatively stronger polarity. This suggests that metabolic networks are chemically organized to a certain extent, which was further elucidated in terms of high concentrations required by metabolic hubs to drive a variety of reactions. This finding not only provides a chemical explanation to the preferential attachment principle for metabolic network expansion, but also has important implications for metabolic network design and metabolite concentration prediction. |
format | Online Article Text |
id | pubmed-3192814 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-31928142011-10-21 Chemical Basis of Metabolic Network Organization Zhu, Qiang Qin, Tao Jiang, Ying-Ying Ji, Cong Kong, De-Xin Ma, Bin-Guang Zhang, Hong-Yu PLoS Comput Biol Research Article Although the metabolic networks of the three domains of life consist of different constituents and metabolic pathways, they exhibit the same scale-free organization. This phenomenon has been hypothetically explained by preferential attachment principle that the new-recruited metabolites attach preferentially to those that are already well connected. However, since metabolites are usually small molecules and metabolic processes are basically chemical reactions, we speculate that the metabolic network organization may have a chemical basis. In this paper, chemoinformatic analyses on metabolic networks of Kyoto Encyclopedia of Genes and Genomes (KEGG), Escherichia coli and Saccharomyces cerevisiae were performed. It was found that there exist qualitative and quantitative correlations between network topology and chemical properties of metabolites. The metabolites with larger degrees of connectivity (hubs) are of relatively stronger polarity. This suggests that metabolic networks are chemically organized to a certain extent, which was further elucidated in terms of high concentrations required by metabolic hubs to drive a variety of reactions. This finding not only provides a chemical explanation to the preferential attachment principle for metabolic network expansion, but also has important implications for metabolic network design and metabolite concentration prediction. Public Library of Science 2011-10-13 /pmc/articles/PMC3192814/ /pubmed/22022254 http://dx.doi.org/10.1371/journal.pcbi.1002214 Text en Zhu et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Zhu, Qiang Qin, Tao Jiang, Ying-Ying Ji, Cong Kong, De-Xin Ma, Bin-Guang Zhang, Hong-Yu Chemical Basis of Metabolic Network Organization |
title | Chemical Basis of Metabolic Network Organization |
title_full | Chemical Basis of Metabolic Network Organization |
title_fullStr | Chemical Basis of Metabolic Network Organization |
title_full_unstemmed | Chemical Basis of Metabolic Network Organization |
title_short | Chemical Basis of Metabolic Network Organization |
title_sort | chemical basis of metabolic network organization |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192814/ https://www.ncbi.nlm.nih.gov/pubmed/22022254 http://dx.doi.org/10.1371/journal.pcbi.1002214 |
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