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Computational Modeling of the Catalytic Cycle of Glutathione Peroxidase Nanomimic
journal contribution
posted on 2016-12-07, 00:00 authored by Ramesh Kheirabadi, Mohammad IzadyarTo
elucidate the role of a derivative of ebselen as a mimic of the antioxidant
selenoenzyme glutathione peroxidase, density functional theory and
solvent-assisted proton exchange (SAPE) were applied to model the
reaction mechanism in a catalytic cycle. This mimic plays the role
of glutathione peroxidase through a four-step catalytic cycle. The
first step is described as the oxidation of 1 in the
presence of hydrogen peroxide, while selenoxide is reduced by methanthiol
at the second step. In the third step of the reaction, the reduction
of selenenylsulfide occurs by methanthiol, and the selenenic acid
is dehydrated at the final step. Based on the kinetic parameters,
step 4 is the rate-determining step (RDS) of the reaction. The bond
strength of the atoms involved in the RDS is discussed with the quantum
theory of atoms in molecules (QTAIM). Low value of electron density,
ρ(r), and positive Laplacian values are the evidence for the
covalent nature of the hydrogen bonds rupture (O30–H31, O33–H34). A change in the
sign of the Laplacian, L(r), from
the positive value in the reactant to a negative character at the
transition state indicates the depletion of the charge density, confirming
the N5–H10 and O11–Se1 bond breaking. The analysis of electron location function
(ELF) and localized orbital locator (LOL) of the Se1–N5 and Se1–O11 bonds have been
done by multi-WFN program. High values of ELF and LOL at the transition
state regions between the Se, N, and O atoms display the bond formation.
Finally, the main donor–acceptor interaction energies were
analyzed using the natural bond orbital analysis for investigation
of their stabilization effects on the critical bonds at the RDS.
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Keywords
hydrogen peroxideelectron location functionelectron densityglutathione peroxidasesolvent-assisted proton exchangecovalent natureselenenic acidO atoms displayGlutathione Peroxidase Nanomimichydrogen bonds rupturebond formationtransition stateLaplacian valuesstep 4Computational ModelingHigh valuesSAPEreaction mechanismrate-determining stepCatalytic Cyclecharge densityRDSELFSemulti-WFN programantioxidant selenoenzyme glutathione peroxidaseLOLstabilization effectsquantum theoryLow valuetransition state regionsQTAIMbond strength
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