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Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis

The understanding of the effective functionality that governs the enzymatic self-organized processes in cellular conditions is a crucial topic in the post-genomic era. In recent studies, Transfer Entropy has been proposed as a rigorous, robust and self-consistent method for the causal quantification...

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Detalles Bibliográficos
Autores principales: De la Fuente, Ildefonso M., Cortes, Jesus M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3290614/
https://www.ncbi.nlm.nih.gov/pubmed/22393350
http://dx.doi.org/10.1371/journal.pone.0030162
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author De la Fuente, Ildefonso M.
Cortes, Jesus M.
author_facet De la Fuente, Ildefonso M.
Cortes, Jesus M.
author_sort De la Fuente, Ildefonso M.
collection PubMed
description The understanding of the effective functionality that governs the enzymatic self-organized processes in cellular conditions is a crucial topic in the post-genomic era. In recent studies, Transfer Entropy has been proposed as a rigorous, robust and self-consistent method for the causal quantification of the functional information flow among nonlinear processes. Here, in order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the technique of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic rate equations of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. The results show the emergence of a new kind of dynamical functional structure, characterized by changing connectivity flows and a metabolic invariant that constrains the activity of the irreversible enzymes. In addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback-regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. The dynamical structure also exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis.
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spelling pubmed-32906142012-03-05 Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis De la Fuente, Ildefonso M. Cortes, Jesus M. PLoS One Research Article The understanding of the effective functionality that governs the enzymatic self-organized processes in cellular conditions is a crucial topic in the post-genomic era. In recent studies, Transfer Entropy has been proposed as a rigorous, robust and self-consistent method for the causal quantification of the functional information flow among nonlinear processes. Here, in order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the technique of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic rate equations of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. The results show the emergence of a new kind of dynamical functional structure, characterized by changing connectivity flows and a metabolic invariant that constrains the activity of the irreversible enzymes. In addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback-regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. The dynamical structure also exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis. Public Library of Science 2012-02-29 /pmc/articles/PMC3290614/ /pubmed/22393350 http://dx.doi.org/10.1371/journal.pone.0030162 Text en De la Fuente, Cortes. 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
De la Fuente, Ildefonso M.
Cortes, Jesus M.
Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis
title Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis
title_full Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis
title_fullStr Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis
title_full_unstemmed Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis
title_short Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis
title_sort quantitative analysis of the effective functional structure in yeast glycolysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3290614/
https://www.ncbi.nlm.nih.gov/pubmed/22393350
http://dx.doi.org/10.1371/journal.pone.0030162
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