ArticleBiophysical journal2010
Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Thermo-flux: generation and analysis of thermodynamic-stoichiometric metabolic network models.Molecular systems biology · 2026Article
- Mathematical Modelling of the Mitochondrial Dicarboxylate Carrier (SLC25A10).Bulletin of mathematical biology · 2026Article
- Inferring mitochondrial and cytosolic metabolism by coupling isotope tracing and deconvolution.Nature communications · 2023Article
- Redox-informed models of global biogeochemical cycles.Nature communications · 2020Review
- Redox controls metabolic robustness in the gas-fermenting acetogenProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Anaplerotic Pathways inFrontiers in microbiology · 2020Article
- Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks.PLoS computational biology · 2017Article
- Quantification of Microbial Phenotypes.Metabolites · 2016Review
- The Influence of Crowding Conditions on the Thermodynamic Feasibility of Metabolic Pathways.Biophysical journal · 2015Article
- Metabolomics integrated elementary flux mode analysis in large metabolic networks.Scientific reports · 2015Article
- Network thermodynamic curation of human and yeast genome-scale metabolic models.Biophysical journal · 2014Article
- Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.Biophysical journal · 2012Article
- System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes.PLoS computational biology · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the calculation of the change in Gibbs energy of biochemical reactions have long been established. However, a concept for incorporation of cross-membrane transport in these calculations is still missing, although the theory for calculating thermodynamic properties of transport processes is long known. Here, we have developed two equivalent equations to calculate the change in Gibbs energy of combined transport and reaction processes based on two different ways of treating biochemical thermodynamics. We illustrate the need for these equations by showing that in some cases there is a significant difference between the proposed correct calculation and using an approximative method. With the developed equations, thermodynamic analysis of metabolic networks spanning over multiple physical compartments can now be correctly described.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.