Fig 1.
Our study is based on predicting biochemical standard redox potentials using a calibrated quantum chemistry strategy.
(A) The four different redox reaction categories considered here are reduction of a carboxylic acid to a carbonyl—G1, reduction of a carbonyl to a hydroxycarbon—G2, or an amine—G3, and reduction of a hydroxycarbon to a hydrocarbon—G4. (B) For each redox reaction of interest, such as reduction of pyruvate to lactate, we select the most abundant protonation state at acidic pH (pH = 0) for quantum chemical simulation. (C) We estimate the chemical redox potential as the difference between Boltzmann-averaged electronic energies of geometric conformers of products and substrates. (D) In order to convert chemical redox potentials to biochemical potentials at pH = 7, we use cheminformatic pKa estimates and the Alberty-Legendre Transform (Supplementary Information). (E) Finally, we use a set of 105 experimental values obtained from the NIST Thermodynamics of Enzyme-Catalyzed Reactions database (TECRDB) [30] and a set of Gibbs formation energies compiled by Robert Alberty [31] (Supplementary Information) to calibrate redox potentials using linear regression.
Fig 2.
Quantum chemistry model predicts experimentally measured reduction potential with high accuracy.
Data shown corresponds to reactions where carbonyls are reduced to hydroxycarbons (group G2). (A) Quantum chemical predictions after calibration (linear regression with 2-parameters); S2 Fig shows how the calibration improves accuracy. (B) Prediction using group contribution method as implemented in eQuilibrator [36,37] (see Methods) (10 parameters for the G2 category) (C) Scatter plot of normalized prediction errors (z-scores) of G2 reactions for molecular fingerprints and quantum chemistry. The indolelactate dehydrogenase (EC 1.1.1.110) and the succinate semialdehyde reductase (EC 1.1.1.61) reactions (red points) have potentially erroneous experimental values.
Table 1.
Prediction accuracy of the quantum chemistry and group contribution method modeling approaches.
Fig 3.
Distributions of predicted standard transformed redox potentials at pH = 7 and I = 0.25 for a dataset of 650 natural and non-natural reactions.
The average reduction potentials for each reaction category are (values rounded to nearest multiple of 5): un-activated carboxylic acid to carbonyl (G1: <E′m> = −550 mV), activated carboxylic acid to carbonyl (activated G1: <E′m> = −300 mV), carbonyl to hydroxycarbon (G2: <E′m> = −225 mV), carbonyl to amine (G3: <E′m> = −225 mV), and hydroxycarbon to hydrocarbon (G4: <E′m> = −15 mV) Both histograms and cumulative distributions (bold lines, right y-axis) are shown. The distributions for unactivated and activated carboxylic acid to carbonyl reductions (red and purple) are the same, but shifted by +250 mV. Dashed colored lines show the median redox potential for each reaction category. Grey shaded regions corresponds to the range of NAD(P) redox potential, while light grey wavy lines delimit the region of reversible oxidation/reduction by NAD(P)/NAD(P)H. Ranges of reduction potentials for different alternative cofactors are shown as grey rectangles underneath graph (S1 Table).
Fig 4.
Comparison between the redox potentials of sub-groups for reactions in the G2 category (carbonyl to hydroxycarbon reductions).
(A) Aldehydes vs. ketones (non-statistically significant Δ <E′m>); (B) nearest-neighbor functional group (all subgroups have statistically significant Δ <E′m>, p<0.005, except hydroxyl/amine and hydrocarbon) (C) closed-ring sugar reduction to open-chain vs. open-chain sugar reduction to open-chain (statistically significant Δ <E′m>, p<10–5), (D) natural reactions appearing in KEGG vs. non-natural reactions (statistically significant Δ <E′m>, p<0.005) (E) natural reactions that only use NAD(P) as redox cofactor vs. those that use alternative cofactors (cytochromes, FAD, O2, or quinones) (non-statistically significant Δ <E′m>, p = 0.03).
Fig 5.
A schematic showing the location of different types of oxidoreductase reactions (oxidoreductase groups 1 to 4) within the extended central metabolic network.
We highlight reactions (purple) where a hydrocarbon is oxidized to a hydroxycarbon (G4 reactions, in the direction of oxidation) which generally cannot be sustained by NAD(P) as redox cofactor. See Supplementary Dataset 2 for full set of redox reactions in extended central metabolic network. G6P, Glucose-6-phosphate; F6P, Fructose-6-phosphate; DHAP, Dihydroxyacetone phosphate; GAP, Glyceraldehyde 3-phosphate; Gly1P; Glycerol 1-phosphate; 6PG, 6-Phosphogluconolactone; R5P, Ribulose 5-phosphate; E4P, Erythrose 4-phosphate; 3PG, 3-Phosphoglycerate; PEP, Phosphoenolpyruvate; PYR, Pyruvate; AcCoA, Acetyl coenzyme A; 2KG, 2-Ketoglutaric acid; OA, Oxaloacetate.