Catalytic Reaction Mechanism of Lipoxygenase. A Density Functional Theory Study

Abstract

The mechanism of the full catalytic cycle for unsaturated fatty acids peroxidation by lipoxygenase has been studied by means of hybrid density functional theory (DFT-B3LYP). The model of the active site in lipoxygenase comprises iron ion coordinated by six-molecule model of the native protein and aqua ligands. Formic anion and formamide are employed to model isoleucine and asparagine, respectively. Histidine ligands are modeled by ammonia molecules. In regards to the substrate, a 2,5-heptadiene molecule is used to model the unsaturated hydrocarbon chain of fatty acids. Our results indicate that the first catalytic step consists of a hydrogen atom transfer from the hydrocarbon to the hydroxide group bound to ferric ion. This process proceeds through an early transition state with the activation energy amounting to 12.1 kcal/mol and the reaction energy being -12.6 kcal/mol. In the next step, the activated substrate, in the form of the diene radical, reacts with a triplet oxygen molecule in an exoergic (-7.8 kcal/mol) process characterized by small activation energy (2.0 kcal/mol). The possibility of an organo-iron intermediate formation has been ruled out by the fact that such a complex is unstable irrespective of the spin state assumed. Similarly, the reduced form of the active site seems not to bind molecular oxygen to any perceptible extent, which in turn remains at variance with the mechanism assuming molecular oxygen activation. The last step of the catalytic reaction involves the peroxy radical reduction by the ferrous form of the active site in lipoxygenase. This process is almost isoenergetic (0.3 kcal/mol) and completes the catalytic cycle. Two possible mechanisms of this last step are discussed with particular attention on the possible catalytic relevance of the so-called purple form.

Quantum Chemical Studies of Intermediates and Reaction Pathways in Selected Enzymes and Catalytic Synthetic Systems

“…247 In a recent density functional study, the full catalytic cycle for peroxidation of polyunsaturated fatty acids by sLO-1 was investigated using the B3LYP method. 252 A simplified active site model was adopted in which the histidine side-chain ligands were replaced by ammonia molecules and a 2,5-heptadiene was used as substrate. The geometries of reaction intermediates and transition states of all steps were optimized, and all transition states were confirmed by frequency calculations.…”

Theoretical studies of proton-coupled electron transfer: Models and concepts relevant to bioenergetics

“…The SLO reaction has been studied with a variety of theoretical approaches. [34,35,47,48,[61][62][63][64][65][66][67][68][69][70] Our calculations of this reaction were based on the vibronically nonadiabatic formulation for PCET reactions that includes the quantum mechanical effects of the active electrons and the transferring proton, as well as the motions of all atoms in the complete solvated enzyme system. [27,39] As described above, the rate is represented by the time integral of a probability flux correlation function that depends on the vibronic coupling, the average of the energy gap and R coordinate, and the time correlation functions of the energy gap and R coordinate.…”

Hydrogen Abstraction by Soybean Lipoxygenase-1. Density Functional Theory Study on Active Site Models in Terms of Gibbs Free Energies

“…The B3LYP/6-311+G(d,p)//B3LYP/LanL2DZ calculations allows for a comparison with the results of Borowski and Broclawik. 19 The potential energies, entropies, and free energies were obtained using the B3LYP/LanL2DZ geometries and frequencies (see Table 1). The classical potential energy barrier, the adiabatic energy barrier, and the free energy barrier are 15, 11.5, and 11.1 kcal/mol, respectively, with respect to RC a .…”