Redox properties of the Fe3+/Fe2+ couple in Arthromyces ramosus class II peroxidase and its cyanide adduct

Efficient, fast and robust degradation of chlortetracycline in wastewater catalyzed by recombinant Arthromyces ramosus peroxidase

Chlortetracycline (CTC), a widely used antibiotic, is recalcitrant and ubiquitous in the environment. Enzymatic degradation of CTC is an economical and efficient bioremediation method. In this work, recombinant Arthromyces ramosus peroxidase (rARP) at a concentration of 3.13 × 10^-9 M was used to catalyze rapid degradation of CTC in water. The second-order rate constants of rARP showed up to 62-fold catalytic efficiency of horseradish peroxidase (HRP) toward CTC. The degradation half-life of CTC at the concentrations of 2 and 40 mg L^-1 in wastewater under the rARP catalysis was, respectively, 5.3 and 5.7 min at 25 °C, and 2.7 and 3.1 min at 40 °C, which were up to 15-fold and 111-fold faster than HRP and laccase, respectively, but use of 3 % the amount of rARP as HRP. rARP catalyzed degradation of CTC at 2-40 mg L^-1 in wastewater completed in 20-24 min, and its catalytic efficiency varied within only 2-fold at 25-40 °C. rARP showed only 2-3-fold discrepancy of catalytic efficiency among pH 5.0, 7.5 and 9.0. CTC under rARP catalysis underwent demethylation and oxidation to form nontoxic N-dedimethyl-9-hydroxy-CTC. The high catalytic efficiency of rARP agreed with a short distance between rARP's δN-His⁵⁶ and CTC's dimethylamine N as indicated by docking simulation. rARP is a useful enzyme for CTC bioremediation.

Recombinant Arthromyces ramosus Peroxidase Has Similar Substrate Specificity Profiles as, but a Catalytic Efficiency up to 11-Fold Higher than, Horseradish Peroxidase

Fungal peroxidases are valuable enzymes. Arthromyces ramosus peroxidase (ARP) and horseradish peroxidase (HRP) share a conserved catalytic site. Both native ARP and recombinant ARP (rARP) were not commercially available. The substrate specificity and kinetic parameters of rARP and HRP were not well compared, particularly relevent to structure-activity relationship. In this work, rARP expressed by Komagataella phaffii had a production yield of 6.2 mg/L, up to 155-fold higher than ARP and other recombinant peroxidases, and a specific activity of 3240 units/mg toward 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), up to 29-fold higher than HRP and other peroxidases. The Michaelis constant (K_m) and first-order rate constant (k_cat) of rARP showed 10-fold substrate affinity and consequently 6-fold catalytic efficiency of HRP toward ABTS. Under optimal conditions, rARP shared similar substrate specificity profiles as commercial HRP; the second-order rate constants (k_app) of rARP showed 2-11-fold catalytic efficiency of HRP toward well-known peroxidase substrates. rARP's higher catalytic efficiency was also in agreement with the shorter binding distance of H/N-His⁵⁶ in rARP/substrate in comparison to that of HRP/substrate, as illustrated by docking simulation. The rARP had similar substrate specificity profiles as, but higher specific activity and catalytic efficiency than, HRP, which merits its further structure-functional characterization and applications.

Met80 and Tyr67 affect the chemical unfolding of yeast cytochromec: comparing the solutionvs.immobilized state

The motional regime affects the unfolding propensity and axial heme coordination of the Met80Ala and Met80Ala/Tyr67Ala variants of yeast iso-1 cytochromec.

Redox thermodynamics of B-class dye-decolorizing peroxidases

With >5000 annotated genes dye-decolorizing peroxidases (DyPs) represent a heme b peroxidase family of broad functional diversity. Bacterial B-class DyPs are poor peroxidases of unknown physiological function. Hydrogen peroxide efficiently mediates the rapid formation of Compound I in B-class DyPs, which, however, is stable and shows modest reactivity towards organic and inorganic electron donors. To understand these characteristics, we have investigated the redox thermodynamics of the one-electron reduction of the ferric high-spin form of wild-type B-class DyP from the pathogenic bacterium Klebsiella pneumoniae (KpDyP) and the variants D143A, R232A and D143A/R232A. These distal amino acids are fully conserved in all DyPs and play important roles in Compound I formation and maintenance of the heme cavity architecture and substrate access route(s). The E°' values of the respective redox couples Fe(III)/Fe(II) varied from -350 mV (wild-type KpDyP) to -299 mV (D143A/R232A) at pH 7.0. Variable-temperature spectroelectrochemical experiments revealed that the reduction reaction of B-class DyPs is enthalpically unfavored but entropically favored with significant differences in enthalpic and entropic contributions to E°' between the four proteins. Molecular dynamics simulations demonstrated the impact of solvent reorganization on the entropy change during reduction reaction and revealed the dynamics and restriction of substrate access channels. Obtained data are discussed with respect to the poor peroxidase activities of B-class DyPs and compared with heme peroxidases from other (super)families as well as with chlorite dismutases, which do not react with hydrogen peroxide but share a similar fold and heme cavity architecture.

Increase of Redox Potential during the Evolution of Enzymes Degrading Recalcitrant Lignin

To investigate how ligninolytic peroxidases acquired the uniquely high redox potential they show today, their ancestors were resurrected and characterized. Unfortunately, the transient Compounds I (CI) and II (CII) from peroxide activation of the enzyme resting state (RS) are unstable. Therefore, the reduction potentials (E°') of the three redox couples (CI/RS, CI/CII and CII/RS) were estimated (for the first time in a ligninolytic peroxidase) from equilibrium concentrations analyzed by stopped-flow UV/Vis spectroscopy. Interestingly, the E°' of rate-limiting CII reduction to RS increased 70 mV from the common peroxidase ancestor to extant lignin peroxidase (LiP), and the same boost was observed for CI/RS and CI/CII, albeit with higher E°' values. A straightforward correlation was found between the E°' value and the progressive displacement of the proximal histidine Hϵ1 chemical shift in the NMR spectra, due to the higher paramagnetic effect of the heme Fe3+ . More interestingly, the E°' and NMR data also correlated with the evolutionary time, revealing that ancestral peroxidases increased their reduction potential in the evolution to LiP thanks to molecular rearrangements in their heme pocket during the last 400 million years.

Investigation of ion binding in chlorite dismutases by means of molecular dynamics simulations

Chlorite dismutases are prokaryotic heme b oxidoreductases that convert chlorite to chloride and dioxygen. It has been postulated that during turnover hypochlorite is formed transiently, which might be responsible for the observed irreversible inactivation of these iron proteins. The only charged distal residue in the heme cavity is a conserved and mobile arginine, but its role in catalysis and inactivation is not fully understood. In the present study, the pentameric chlorite dismutase (Cld) from the bacterium Candidatus Nitrospira defluvii was probed for binding of the low spin ligand cyanide, the substrate chlorite, and the intermediate hypochlorite. Simulations were performed with the enzyme in the ferrous, ferric, and compound I state. Additionally, the variant R173A was studied. We report the parametrization for the GROMOS force field of the anions ClO^–, ClO₂^–, ClO₃^–, and ClO₄^– and describe spontaneous binding, unbinding, and rebinding events of chlorite and hypochlorite, as well as the dynamics of the conformations of Arg173 during simulations. The findings suggest that (i) chlorite binding to ferric NdCld occurs spontaneously and (ii) that Arg173 is important for recognition and to impair hypochlorite leakage from the reaction sphere. The simulation data is discussed in comparison with experimental data on catalysis and inhibition of chlorite dismutase.

Redox thermodynamics of high-spin and low-spin forms of chlorite dismutases with diverse subunit and oligomeric structures

Chlorite dismutases (Clds) are heme b-containing oxidoreductases that convert chlorite to chloride and dioxygen. In this work, the thermodynamics of the one-electron reduction of the ferric high-spin forms and of the six-coordinate low-spin cyanide adducts of the enzymes from Nitrobacter winogradskyi (NwCld) and Candidatus “Nitrospira defluvii” (NdCld) were determined through spectroelectrochemical experiments. These proteins belong to two phylogenetically separated lineages that differ in subunit (21.5 and 26 kDa, respectively) and oligomeric (dimeric and pentameric, respectively) structure but exhibit similar chlorite degradation activity. The E°′ values for free and cyanide-bound proteins were determined to be −119 and −397 mV for NwCld and −113 and −404 mV for NdCld, respectively (pH 7.0, 25 °C). Variable-temperature spectroelectrochemical experiments revealed that the oxidized state of both proteins is enthalpically stabilized. Molecular dynamics simulations suggest that changes in the protein structure are negligible, whereas solvent reorganization is mainly responsible for the increase in entropy during the redox reaction. Obtained data are discussed with respect to the known structures of the two Clds and the proposed reaction mechanism.

Redox properties of heme peroxidases

Peroxidases are heme enzymes found in bacteria, fungi, plants and animals, which exploit the reduction of hydrogen peroxide to catalyze a number of oxidative reactions, involving a wide variety of organic and inorganic substrates. The catalytic cycle of heme peroxidases is based on three consecutive redox steps, involving two high-valent intermediates (Compound I and Compound II), which perform the oxidation of the substrates. Therefore, the thermodynamics and the kinetics of the catalytic cycle are influenced by the reduction potentials of three redox couples, namely Compound I/Fe3+, Compound I/Compound II and Compound II/Fe3+. In particular, the oxidative power of heme peroxidases is controlled by the (high) reduction potential of the latter two couples. Moreover, the rapid H2O2-mediated two-electron oxidation of peroxidases to Compound I requires a stable ferric state in physiological conditions, which depends on the reduction potential of the Fe3+/Fe2+ couple. The understanding of the molecular determinants of the reduction potentials of the above redox couples is crucial for the comprehension of the molecular determinants of the catalytic properties of heme peroxidases. This review provides an overview of the data available on the redox properties of Fe3+/Fe2+, Compound I/Fe3+, Compound I/Compound II and Compound II/Fe3+ couples in native and mutated heme peroxidases. The influence of the electron donor properties of the axial histidine and of the polarity of the heme environment is analyzed and the correlation between the redox properties of the heme group with the catalytic activity of this important class of metallo-enzymes is discussed.

Redox thermodynamics of lactoperoxidase and eosinophil peroxidase

Eosinophil peroxidase (EPO) and lactoperoxidase (LPO) are important constituents of the innate immune system of mammals. These heme enzymes belong to the peroxidase-cyclooxygenase superfamily and catalyze the oxidation of thiocyanate, bromide and nitrite to hypothiocyanate, hypobromous acid and nitrogen dioxide that are toxic for invading pathogens. In order to gain a better understanding of the observed differences in substrate specificity and oxidation capacity in relation to heme and protein structure, a comprehensive spectro-electrochemical investigation was performed. The reduction potential (E degrees ') of the Fe(III)/Fe(II) couple of EPO and LPO was determined to be -126mV and -176mV, respectively (25 degrees C, pH 7.0). Variable temperature experiments show that EPO and LPO feature different reduction thermodynamics. In particular, reduction of ferric EPO is enthalpically and entropically disfavored, whereas in LPO the entropic term, which selectively stabilizes the oxidized form, prevails on the enthalpic term that favors reduction of Fe(III). The data are discussed with respect to the architecture of the heme cavity and the substrate channel. Comparison with published data for myeloperoxidase demonstrates the effect of heme to protein linkages and heme distortion on the redox chemistry of mammalian peroxidases and in consequence on the enzymatic properties of these physiologically important oxidoreductases.

The redox properties of ascorbate peroxidase

Reduction potentials for the catalytic compound I/compound II and compound II/Fe3+ redox couples, and for the two-electron compound I/Fe3+ redox couple, have been determined for ascorbate peroxidase (APX) and for a number of site-directed variants. For the wild type enzyme, the values are E degrees '(compound I/compound II) = 1156 mV, E degrees '(compound II/Fe3+) = 752 mV, and E degrees '(compound I/Fe3+) = 954 mV. For the variants, the analysis also includes determination of Fe3+/Fe2+ potentials which were used to calculate (experimentally inaccessible) E degrees '(compound II/Fe3+) potentials. The data provide a number of new insights into APX catalysis. The measured values for E degrees '(compound I/compound II) and E degrees '(compound II/Fe3+) for the wild type protein account for the much higher oxidative reactivity of compound I compared to compound II, and this correlation holds for a number of other active site and substrate binding variants of APX. The high reduction potential for compound I also accounts for the known thermodynamic instability of this intermediate, and it is proposed that this instability can account for the deviations from standard Michaelis kinetics observed for most APX enzymes during steady-state oxidation of ascorbate. This study provides the first systematic evaluation of the redox properties of any ascorbate peroxidase using a number of methods, and the data provide an experimental and theoretical framework for accurate determination of the redox properties of Fe3+, compound I, and compound II species in related enzymes.

Redox reactivity of the heme Fe3+/Fe2+ couple in native myoglobins and mutants with peroxidase-like activity

The reaction enthalpy and entropy for the one-electron reduction of the ferric heme in horse heart and sperm whale aquometmyoglobins (Mb) have been determined exploiting a spectroelectrochemical approach. Also investigated were the T67R, T67K, T67R/S92D and T67R/S92D Mb-H variants (the latter containing a protoheme-L: -histidine methyl ester) of sperm whale Mb, which feature peroxidase-like activity. The reduction potential (E degrees ') in all species consists of an enthalpic term which disfavors Fe(3+) reduction and a larger entropic contribution which instead selectively stabilizes the reduced form. This behavior differs from that of the heme redox enzymes and electron transport proteins investigated so far. The reduction thermodynamics in the series of sperm whale Mb variants show an almost perfect enthalpy-entropy compensation, indicating that the mutation-induced changes in DeltaH(o')(rc) and DeltaS(o')(rc) are dominated by reduction-induced solvent reorganization effects. The modest changes in E degrees ' originate from the enthalpic effects of the electrostatic interactions of the heme with the engineered charged residues. The small influence that the mutations exert on the reduction potential of myoglobin suggests that the increased peroxidase activity of the variants is not related to changes in the redox reactivity of the heme iron, but are likely related to a more favored substrate orientation within the distal heme cavity.

Arthromyces ramosus peroxidase produces two chlorinating species

We previously reported that the hemes of horseradish peroxidase (HRP) and Arthromyces ramosus peroxidase (ARP) undergo vinyl and meso-carbon modifications when the enzymes oxidize chloride ion. Here we demonstrate for ARP that, although both modifications exhibit the same pH profile with an optimum at approximately pH 4.0, monochlorodimedone suppresses the vinyl but not meso-carbon modifications. Furthermore, meso-chlorination occurs when ARP reacts with exogenous HOCl, implicating an Fe(III)-O-Cl intermediate in the reaction. These results establish that (a) the chloro species involved in meso-modification differs from that which reacts with the vinyl groups, (b) equilibration of the vinyl modifying species (HOCl) into the medium occurs more rapidly than vinyl group modification, and (c) the oxidation of chloride by ARP produces two reactive species: HOCl, which adds to the heme vinyl but not meso-positions, and a distinct second species that adds to the meso-carbon.

Redox thermodynamics of the Fe(III)/Fe(II) couple of human myeloperoxidase in its high-spin and low-spin forms

Myeloperoxidase (MPO) (donor, hydrogen peroxide oxidoreductase, EC 1.11.1.7) is the most abundant neutrophil enzyme and catalyzes predominantly the two-electron oxidation of ubiquitous chloride (Cl-), to generate the potent bleaching oxidant hypochlorous acid (HOCl), thus contributing to bacterial killing and inflammatory reactions of neutrophils. Here, the thermodynamics of the one-electron reduction of the ferric heme in its ferric high-spin and cyanide-bound low-spin forms were determined through spectroelectrochemical experiments. The E(o)' values for free and cyanide-bound MPO (5 and -37 mV, respectively, at 25 degrees C and pH 7.0) are significantly higher than those of other heme peroxidases. Variable-temperature experiments revealed that the enthalpic stabilization of ferric high-spin MPO is much weaker than in other heme peroxidases and is exactly compensated by the entropic change upon reduction. In contrast to those of other heme peroxidases, the stabilization of the ferric cyanide-bound MPO is also very weak and fully entropic. This peculiar behavior is discussed with respect to the MPO-typical covalent heme to protein linkages as well as to the published structures of ferric MPO and its cyanide complex and the recently published structure of lactoperoxidase as well as the physiological role of MPO in bacterial killing.