Kinetics and thermodynamics of enzymatic decarboxylation of α,β-unsaturated acid: a theoretical study

Abstract

The kinetically controlled path for enzymatic decarboxylation of α,β-unsaturated acid is proposed based on DFT and TST methods. The mechanism involves fluctuation of the local dielectric environment in the active site of the FDC1 enzyme.

Mechanisms of photoisomerization of the prenylated flavin mononucleotide cofactor: a theoretical study

“…For example, , and . Because our previous study 7 also revealed that the residue-to-residue distances (active site volume) do not change significantly during the enzymatic reaction, the lock-and-key model could explain the substrate specificity of the Fdc1 enzyme, and the catalytic efficiency of this enzymatic decarboxylation reaction is partly connected to the efficiency of the proton exchange between the substrate and Glu282, which is a part of the conserved Glu277–Arg173–Glu282 residue network. These results further suggested that the model active site clusters without the Fdc1 backbone are reasonable and can be used for further studies.…”

“…Because the analysis of the equilibrium structures and PESs in our previous study 7 showed that the Fdc1 backbone ( Fig. 2a ) does not play an important role in the decarboxylation reaction, the active site was modeled in this work by substituting the carbon atoms of the Fdc1 backbone that connect the residues with CH 3 groups ( Fig.…”

“…In our previous study, 7 the elementary reactions proposed in ref. 4 were examined in low and high local dielectric environments ( ε = 1 and 78) using the density functional theory (DFT) method with the Becke, 3-parameter, and Lee–Yang–Parr hybrid functionals and DZP basis set (DFT/B3LYP/DZP) and the transition state theory (TST) method.…”

“…[1][2][3] This enzymatic reaction can be effectively accomplished through 1,3dipolar cycloaddition between substrates and enzyme cofactors, 4 among which the prenylated avin mononucleotide (prFMN) has been proven to be effective for the biosynthesis of styrene. 1,[3][4][5]7 Payne et al 4 proposed a mechanism for the enzymatic decarboxylation of a,b-unsaturated acids using the prFMN cofactor. The mechanism comprising four consecutive elementary reactions has been widely accepted and further studied using various theoretical and experimental methods.…”

An Enzyme Catalyzing the Oxidative Maturation of Reduced Prenylated-FMN to Form the Active Coenzyme

“…MS analysis of this compound showed it to have a mass consistent with the formation of the C4a hydroxide (m/z = 543. 19). There was no evidence for the formation of the prFMN-like ylide form, pointing to the general unfavorability of eliminating water from N5-alkyl flavins.…”