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PMID: 20513391 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities.

Biophysical journal ·Vol. 98 ·No. 11 ·2010-06-02 ·Pages 2478-86

Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhütter HG

Abstract

Mathematical analysis and modeling of biochemical reaction networks requires knowledge of the permitted directionality of reactions and membrane transport processes. This information can be gathered from the standard Gibbs energy changes (DeltaG(0)) of reactions and the concentration ranges of their reactants. Currently, experimental DeltaG(0) values are not available for the vast majority of cellular biochemical processes. We propose what we believe to be a novel computational method to infer the unknown DeltaG(0) value of a reaction from the known DeltaG(0) value of the chemically most similar reaction. The chemical similarity of two arbitrary reactions is measured by the relative number (T) of co-occurring changes in the chemical attributes of their reactants. Testing our method across a validated reference set of 173 biochemical reactions with experimentally determined DeltaG(0) values, we found that a minimum reaction similarity of T = 0.6 is required to infer DeltaG(0) values with an error of <10 kJ/mol. Applying this criterion, our method allows us to assign DeltaG(0) values to 458 additional reactions of the BioPath database. We believe our approach permits us to minimize the number of DeltaG(0) measurements required for a full coverage of a given reaction network with reliable DeltaG(0) values.

MeSH Terms
Computer Simulation Databases, Factual Energy Metabolism Models, Chemical Software Software Design
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Rother Kristian
International Institute of Molecular and Cell Biology-Warsaw, Warsaw, Poland.
Hoffmann Sabrina
Bulik Sascha
Hoppe Andreas
Gasteiger Johann
Holzhütter Herrmann-Georg
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Article Info
Journal
Biophysical journal
Abbr.
Biophys J
ISSN
1542-0086
DOI
10.1016/j.bpj.2010.02.052
Published
2010-06-02
Pages
2478-86
Language
English
Region
United States
NLM ID
0370626
PMCID
PMC2877342
Subset
IM
External Links
PubMed source DOI: 10.1016/j.bpj.2010.02.052 PMC Full Text View journal details
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