The thermodynamic landscape of carbon redox biochemistry
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Jinich, Adrian
Sanchez-Lengeling, Benjamin
Ren, Haniu
Goldford, Joshua
Noor, Elad
Sanders, Jacob
Segre, Daniel
Aspuru-Guzik, Alán
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OA Version
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Adrian Jinich, Benjamin Sanchez-Lengeling, Haniu Ren, Joshua Goldford, Elad Noor, Jacob Sanders, Daniel Segre, Alán Aspuru-Guzik. "The thermodynamic landscape of carbon redox biochemistry." BioRxiv, https://doi.org/10.1101/245811
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.