The nature of tryptophan radicals involved in the long‐range electron transfer of lignin peroxidase and lignin peroxidase‐like systems: Insights from quantum mechanical/molecular mechanics simulations

Abstract

A catalytically active tryptophan radical has been demonstrated to be involved in the long-range electron transfer to the heme cofactor of lignin peroxidase (LiP) from Phanerochaete chrysosporium although no direct detection by EPR spectroscopy of the tryptophan radical intermediate has been reported to date. An engineering-based approach has been used to manipulate the microenvironment of the redox-active tryptophan site in LiP and Coprinus cinereus Peroxidase (CiP), allowing the direct evidence of the tryptophan radical species. In light of the newly available EPR experimental data, we performed a quantum mechanical/molecular mechanics computational study to characterize the tryptophan radicals in the above protein matrices as well as in pristine LiP. The nature of the tryptophan radicals is discussed together with the analysis of their environment with the aim of understanding the different behavior of pristine LiP in comparison with that of LiP and CiP variants.

Redox-Active Sites in Auricularia auricula-judae Dye-Decolorizing Peroxidase and Several Directed Variants: A Multifrequency EPR Study

“…It has been shown that methionine residues play a role in the electrostatic stabilization of Trp protein radicals 47,25,62,[66][67][68] .…”

Computational Modeling Methods for Understanding the Interaction of Lignin and Its Derivatives with Oxidoreductases as Biocatalysts

“…QM calculations at a DFT level (mainly B3LYP functional) have been used together with experimental data from multifrequency electronic paramagnetic resonance (EPR) and pulse electron nuclear double resonance (ENDOR) experiments to study the nature of the tryptophan radical (Trp164) of VP from Pleurotus eryngii [59]. Here, Pogni et al through the calculations of g-tensors, hyperfine (hf) couplings and spin densities identified that the radical form of Trp164 most likely corresponds to a neutral radical and not a cationic radical as it was thought to be for Trp171 from LiP [60]. However, it is very likely that the tryptophan cationic radical is indeed an intermediate which then becomes deprotonated at the indole nitrogen by Glu243, which is forming a hydrogen bond at this position, to form the more stable neutral radical [59].…”

“…Smith et al also studied different LiP variants (E168Q, E250Q and E250Q/E168Q) to compare the results obtained with the new-engineered CiP. Thus, in the theoretical work of Bernini et al [60] three systems were studied namely pristine LiP, the LiP variant E250Q/E168Q and the CiP variant D178W/R257E/R271D to allow direct comparison with the experimental data available for the last two systems. The values for g-tensors and hf coupling constants were calculated for the corresponding neutral and cationic radicals.…”

“…•+ might exist in pristine LiP due to the highly negative electrostatic potential around it [60]. QM and QM/MM calculations have also been carried out to understand the binding and the electron transfer mechanisms of VA at Tyr181 (redox-active amino acid) in Trametopsis cervina LiP [67].…”

“…Similar to versatile peroxidase, QM/MM calculations at the level B3LYP/CHARMM have been carried out to elucidate the nature of the tryptophan radical (Trp171) present in LiP from P. chrysosporium [60]. These calculations were based on the experimental work performed by Smith et al [66], where catalytic activity toward veratryl alcohol (VA) was engineered in Coprinus cinereus peroxidase (CiP).…”