Consistent Estimation of Gibbs Energy Using Component Contributions
Publication Date
July 11, 2013
Journal
PLOS Computational Biology
Authors
Elad Noor, Hulda S. Haraldsdóttir, Ron Milo & Ronan M. T. Fleming
Volume
9
Issue
7
Pages
e1003098
DOI
https://dx.plos.org/10.1371/journal.pcbi.1003098
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003098
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23874165
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708888
Europe PMC
http://europepmc.org/abstract/MED/23874165
Web of Science
000322320200001
Scopus
84880781653
Mendeley
http://www.mendeley.com/research/consistent-estimation-gibbs-energy-using-component-contributions
Events
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Mendeley | Further Information

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CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1117633"], "description"=>"<div><p>Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the reactions in metabolism. Group contribution methods greatly increase coverage, albeit at the price of decreased precision. We present here a way to combine the estimations of group contribution with the more accurate reactant contributions by decomposing each reaction into two parts and applying one of the methods on each of them. This method gives priority to the reactant contributions over group contributions while guaranteeing that all estimations will be consistent, i.e. will not violate the first law of thermodynamics. We show that there is a significant increase in the accuracy of our estimations compared to standard group contribution. Specifically, our cross-validation results show an 80% reduction in the median absolute residual for reactions that can be derived by reactant contributions only. We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism.</p></div>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Physical chemistry", "thermodynamics", "estimation", "gibbs"], "article_id"=>744512, "categories"=>["Chemistry", "Biological Sciences"], "users"=>["Elad Noor", "Hulda S. Haraldsdóttir", "Ron Milo", "Ronan M. T. Fleming"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003098", "stats"=>{"downloads"=>34, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Consistent_Estimation_of_Gibbs_Energy_Using_Component_Contributions_/744512", "title"=>"Consistent Estimation of Gibbs Energy Using Component Contributions", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-11 03:43:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1117621"], "description"=>"<p>The coverage is calculated as the percent of the relevant reactions in the KEGG database (i.e. reactions that have full chemical descriptions and are chemically balanced). The median residual (in absolute values) is calculated using leave-one-out cross-validation over the set of reactions that are within the scope of each method. Note that the reason component contribution has a higher median absolute residual than RC is only due to its higher coverage of reactions (for reactions covered by RC, the component contribution method gives the exact same predictions). *The residual value for Alberty's method is not based on cross-validation since it is a result of manual curation of multiple data sources – a process that we cannot readily repeat.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Physical chemistry", "thermodynamics", "gibbs", "estimation"], "article_id"=>744500, "categories"=>["Chemistry", "Biological Sciences"], "users"=>["Elad Noor", "Hulda S. Haraldsdóttir", "Ron Milo", "Ronan M. T. Fleming"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003098.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_development_of_Gibbs_energy_estimation_frameworks_/744500", "title"=>"The development of Gibbs energy estimation frameworks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-11 03:43:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1117622"], "description"=>"<p>The combined stoichiometry of (1) threonine aldolase, (2) acetaldehyde dehydrogenase (acetylating), (3) glycine C-acetyltransferase, and (4) threonine:NAD oxidoreductase creates a futile cycle where all the inputs and outputs are balanced. Using RC we are able to derive the of reactions 1 and 2 (green), but since 2-amino-3-oxobutanoate does not appear in formation energy tables – we must use GC for reactions 3 and 4 (magenta). The sum of all in this case is −6.0 kJ/mol which is a violation of the first law of thermodynamics.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Physical chemistry", "thermodynamics", "futile", "gibbs", "energies", "derived", "rc"], "article_id"=>744501, "categories"=>["Chemistry", "Biological Sciences"], "users"=>["Elad Noor", "Hulda S. Haraldsdóttir", "Ron Milo", "Ronan M. T. Fleming"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003098.g002", "stats"=>{"downloads"=>9, "page_views"=>235, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_example_of_a_futile_cycle_where_Gibbs_energies_are_derived_using_RC_and_GC_/744501", "title"=>"An example of a futile cycle where Gibbs energies are derived using RC and GC.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-11 03:43:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1117624"], "description"=>"<p>(A) The reaction vector is decomposed into the two components and , where the reactant contribution and group contribution methods are used for the relevant components. Later, is decomposed into and . The same projection is shown graphically in (B) where the green plane represents the range of and the normal to that plane represents the null space of . (C) An example for a reaction which decomposes into two non-zero components. In this case, the component is equal to , which means that the reaction is covered by the component contribution method.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Physical chemistry", "thermodynamics", "diagram", "illustrating", "projects", "stoichiometric", "vector"], "article_id"=>744503, "categories"=>["Chemistry", "Biological Sciences"], "users"=>["Elad Noor", "Hulda S. Haraldsdóttir", "Ron Milo", "Ronan M. T. Fleming"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003098.g003", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_diagram_illustrating_how_the_component_contribution_method_projects_the_stoichiometric_vector_onto_the_different_spaces_/744503", "title"=>"A diagram illustrating how the component contribution method projects the stoichiometric vector onto the different spaces.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-11 03:43:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1117625"], "description"=>"<p>The CDF of the absolute-value residuals for both group contribution (, pink) and component contribution (, purple). The reactions were separated to ones which are (A) linearly-dependent on the set of all other reactions ( is in the range of , the stoichiometric matrix of all reactions except ), and (B) to ones which are linearly-independent (and thus component contribution uses group decompositions for at least part of the reaction). We found an 80% reduction in the median for the former set and no significant change for the latter (p-value = ).</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Physical chemistry", "thermodynamics", "distributions", "cross-validation"], "article_id"=>744504, "categories"=>["Chemistry", "Biological Sciences"], "users"=>["Elad Noor", "Hulda S. Haraldsdóttir", "Ron Milo", "Ronan M. T. Fleming"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003098.g004", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cumulative_distributions_for_the_cross_validation_results_/744504", "title"=>"Cumulative distributions for the cross-validation results.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-11 03:43:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1117626"], "description"=>"<p>in iAF1260 (<i>E. coli</i>) and Recon 1 (human), that were in the range of , and were thus evaluated with reactant contribution (RC). For a reaction , this fraction was calculated as . Passive and facilitated diffusion reactions, where the reactants undergo no chemical changes, are not included in the figure. 9.4% of all evaluated reactions in iAF1260 were fully evaluated using only reactant contributions. These reactions carried approximately half of the total flux (red) in 312 predicted flux distributions. The 8.3% of evaluated reactions in Recon 1 that were fully evaluated with reactant contributions, carried close to a third of the total flux in 97 predicted flux distributions.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Physical chemistry", "thermodynamics", "fractions", "vectors"], "article_id"=>744505, "categories"=>["Chemistry", "Biological Sciences"], "users"=>["Elad Noor", "Hulda S. Haraldsdóttir", "Ron Milo", "Ronan M. T. Fleming"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003098.g005", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_fractions_of_reaction_vectors_black_/744505", "title"=>"Distribution of the fractions of reaction vectors (black)", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-11 03:43:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1117628"], "description"=>"<p>Electrical potential in each compartment is relative to electrical potential in the cytosol. Temperature was set to 310.15 K (37°C), and ionic strength was assumed to be 0.25 M <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003098#pcbi.1003098-Alberty1\" target=\"_blank\">[14]</a> in all compartments. Taken from <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003098#pcbi.1003098-Fleming2\" target=\"_blank\">[8]</a>.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Physical chemistry", "thermodynamics", "compartment", "reconstruction"], "article_id"=>744507, "categories"=>["Chemistry", "Biological Sciences"], "users"=>["Elad Noor", "Hulda S. Haraldsdóttir", "Ron Milo", "Ronan M. T. Fleming"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003098.t001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_pH_and_electrical_potential_in_each_compartment_of_the_E_coli_reconstruction_iAF1260_/744507", "title"=>"pH and electrical potential in each compartment of the <i>E. coli</i> reconstruction iAF1260.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-11 03:43:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1117629"], "description"=>"<p>Comparison of standard transformed reaction Gibbs energy estimates based on component contributions, to estimates based on previously available data.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Physical chemistry", "thermodynamics", "transformed", "gibbs", "estimates"], "article_id"=>744508, "categories"=>["Chemistry", "Biological Sciences"], "users"=>["Elad Noor", "Hulda S. Haraldsdóttir", "Ron Milo", "Ronan M. T. Fleming"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003098.t003", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_standard_transformed_reaction_Gibbs_energy_estimates_based_on_component_contributions_to_estimates_based_on_previously_available_data_/744508", "title"=>"Comparison of standard transformed reaction Gibbs energy estimates based on component contributions, to estimates based on previously available data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-11 03:43:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1117630"], "description"=>"<p>Electrical potential in each compartment is relative to electrical potential in the cytosol. Temperature was set to 310.15 K (37°C), and ionic strength was assumed to be 0.15 M <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003098#pcbi.1003098-Alberty1\" target=\"_blank\">[14]</a> in all compartments. Taken from <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003098#pcbi.1003098-Haraldsdttir1\" target=\"_blank\">[10]</a>.</p>", "links"=>[], "tags"=>["Biochemistry", "metabolism", "Physical chemistry", "thermodynamics", "compartment", "reconstruction", "recon"], "article_id"=>744509, "categories"=>["Chemistry", "Biological Sciences"], "users"=>["Elad Noor", "Hulda S. Haraldsdóttir", "Ron Milo", "Ronan M. T. Fleming"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003098.t002", "stats"=>{"downloads"=>5, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_pH_and_electrical_potential_in_each_compartment_of_the_human_reconstruction_Recon_1_/744509", "title"=>"pH and electrical potential in each compartment of the human reconstruction Recon 1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-11 03:43:43"}

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Relative Metric

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