ArticleBiotechnology and bioengineering2009
Thermodynamic analysis of biodegradation pathways.
Article in Biotechnology and bioengineering, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed.
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- Moving persistence assessments into the 21st century: A role for weight-of-evidence and overall persistence.Integrated environmental assessment and management · 2022Review
- Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions.ACS omega · 2021Article
- Thermodynamic Limits and Optimality of Microbial Growth.Entropy (Basel, Switzerland) · 2020Review
- Integrated Framework for Identifying Toxic Transformation Products in Complex Environmental Mixtures.Environmental science & technology letters · 2017Article
- Quantification of Microbial Phenotypes.Metabolites · 2016Review
- Dynamics of benzoate metabolism inMetabolic engineering communications · 2016Article
- Production of 3-Hydroxypropionic Acid via the Propionyl-CoA Pathway Using Recombinant Escherichia coli Strains.PloS one · 2016Article
- Computational evaluation of factors governing catalytic 2-keto acid decarboxylation.Journal of molecular modeling · 2014Article
- Pathway thermodynamics highlights kinetic obstacles in central metabolism.PLoS computational biology · 2014Article
- Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.Biophysical journal · 2013Article
- Systematic applications of metabolomics in metabolic engineering.Metabolites · 2012Article
- Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.Biophysical journal · 2012Article
- Synthetic biology: mapping the scientific landscape.PloS one · 2012Article
- Brønsted-Evans-Polanyi relationships for C-C bond forming and C-C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory.Journal of molecular modeling · 2012Article
- IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities.Biophysical journal · 2010Article
- In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene.BMC systems biology · 2010Article
- Computational framework for predictive biodegradation.Biotechnology and bioengineering · 2009Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Microorganisms provide a wealth of biodegradative potential in the reduction and elimination of xenobiotic compounds in the environment. One useful metric to evaluate potential biodegradation pathways is thermodynamic feasibility. However, experimental data for the thermodynamic properties of xenobiotics is scarce. The present work uses a group contribution method to study the thermodynamic properties of the University of Minnesota Biocatalysis/Biodegradation Database. The Gibbs free energies of formation and reaction are estimated for 914 compounds (81%) and 902 reactions (75%), respectively, in the database. The reactions are classified based on the minimum and maximum Gibbs free energy values, which accounts for uncertainty in the free energy estimates and a feasible concentration range relevant to biodegradation. Using the free energy estimates, the cumulative free energy change of 89 biodegradation pathways (51%) in the database could be estimated. A comparison of the likelihood of the biotransformation rules in the Pathway Prediction System and their thermodynamic feasibility was then carried out. This analysis revealed that when evaluating the feasibility of biodegradation pathways, it is important to consider the thermodynamic topology of the reactions in the context of the complete pathway. Group contribution is shown to be a viable tool for estimating, a priori, the thermodynamic feasibility and the relative likelihood of alternative biodegradation reactions. This work offers a useful tool to a broad range of researchers interested in estimating the feasibility of the reactions in existing or novel biodegradation pathways.
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Registered trials
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