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2009 ; 103
(3
): 532-41
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Thermodynamic analysis of biodegradation pathways
#MMPMID19288443
Finley SD
; Broadbelt LJ
; Hatzimanikatis V
Biotechnol Bioeng
2009[Jun]; 103
(3
): 532-41
PMID19288443
show ga
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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