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The thermodynamic landscape of carbon redox biochemistry

Adrian Jinich, Benjamin Sanchez-Lengeling, Haniu Ren, Joshua E. Goldford, Elad Noor, Jacob N. Sanders, Daniel Segre, Alan Aspuru-Guzik
doi: https://doi.org/10.1101/245811
Adrian Jinich
Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA;
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Benjamin Sanchez-Lengeling
Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA;
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Haniu Ren
Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA;
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Joshua E. Goldford
Bioinformatics Program and Biological Design Center, Boston University, Boston, MA;
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Elad Noor
Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland;
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Jacob N. Sanders
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA;
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Daniel Segre
Boston University
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Alan Aspuru-Guzik
Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA;
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  • For correspondence: alan@aspuru.com
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Abstract

Redox biochemistry plays a key role in the transduction of chemical energy in all living systems. Observed redox reactions in metabolic networks represent only a minuscule fraction of the space of all possible redox reactions. Here we ask what distinguishes observed, natural redox biochemistry from the space of all possible redox reactions between natural and non-natural compounds. We generate the set of all possible biochemical redox reactions involving linear chain molecules with a fixed numbers of carbon atoms. Using cheminformatics and quantum chemistry tools we analyze the physicochemical and thermodynamic properties of natural and non-natural compounds and reactions. We find that among all compounds, aldose sugars are the ones with the highest possible number of connections (reductions and oxidations) to other molecules. Natural metabolites are significantly enriched in carboxylic acid functional groups and depleted in carbonyls and have significantly higher solubilities than non-natural compounds. Upon constructing a thermodynamic landscape for the full set of reactions as a function of pH and of steady-state redox cofactor potential, we find that, over this whole range of conditions, natural metabolites have significantly lower energies than the non-natural compounds. For the set of 4-carbon compounds, we generate a Pourbaix phase diagram to determine which metabolites are local energetic minima in the landscape as a function of pH and redox potential. Our results suggest that, across a set of conditions, succinate and butyrate are local minima and would thus tend to accumulate at equilibrium. Our work suggests that metabolic compounds could have been selected for thermodynamic stability, and yields insight into thermodynamic and design principles governing nature's metabolic redox reactions.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 10, 2018.
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The thermodynamic landscape of carbon redox biochemistry
Adrian Jinich, Benjamin Sanchez-Lengeling, Haniu Ren, Joshua E. Goldford, Elad Noor, Jacob N. Sanders, Daniel Segre, Alan Aspuru-Guzik
bioRxiv 245811; doi: https://doi.org/10.1101/245811
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The thermodynamic landscape of carbon redox biochemistry
Adrian Jinich, Benjamin Sanchez-Lengeling, Haniu Ren, Joshua E. Goldford, Elad Noor, Jacob N. Sanders, Daniel Segre, Alan Aspuru-Guzik
bioRxiv 245811; doi: https://doi.org/10.1101/245811

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