Using chemical thermodynamics on networks to understand the universality of biological sugar-phosphate metabolism

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We demonstrated a partly-automated computational model that converts five simple reaction mechanisms for sugar-phosphate molecules into a list of all possible chemical solutions to the conversion problem of the Pentose Phosphate Pathway. We coupled the automatically-generated list of compounds to extraction of thermochemical data using the SMILES molecules representation as input to the eQuilibrator 3.0 Application Programming Interface. The output data are group-contribution estimates for molecular free energy, and are also automated and can be arbitrarily large. Only our transfer of SMILES representation from the output of the graph-chemistry language MOD to eQuilibrator has been done manually.We analyzed the topology of the chemical reaction network and proved that all possible pathways for the same transformation are constructed from a finite basis of circulations that can be constructed from symmetry rules. We used the thermochemical data on this network to study the transduction of chemical work, and to define an evolutionary cost function for any pathway. Results were reported by the PI in two invited presentations: "Combinatorics in evolution: From rule-based systems to the thermodynamics of selectivities" at the American Physical Society March meeting in Chicago (https://meetings.aps.org/Meeting/MAR22/Session/K04.1 ), and "Combinatorial Chemistry with Rule-Based Systems and its Associated Information Theory" in Sofia Bulgaria (http://physicsoflivingsystems.org/events/workshop-life-in-the-universe/ ), partly sponsored by the U.S. National Science Foundation.