Distinct Enzyme–Substrate Interactions Revealed by Two Dimensional Kinetic Comparison between Dehaloperoxidase-Hemoglobin and Horseradish Peroxidase

Dye-decolorizing peroxidase of Thermobifida halotolerance displays complex kinetics with both substrate inhibition and apparent positive cooperativity

Dye-decolorizing peroxidases (DyPs) have been intensively investigated for the purpose of industrial dye decolourization and lignin degradation. Unfortunately, the characterization of these peroxidases is hampered by their non-Michaelis-Menten kinetics, exemplified by substrate inhibition and/or positive cooperativity. Although often observed, the underlying mechanisms behind the unusual kinetics of DyPs are poorly understood. Here we studied the kinetics of the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), hydroquinones, and anthraquinone dyes by DyP from the bacterium Thermobifida halotolerans (ThDyP) and solved its crystal structure. We also provide rate equations for different kinetic mechanisms explaining the complex kinetics of heme peroxidases. Kinetic studies along with the analysis of the structure of ThDyP suggest that the substrate inhibition is caused by the non-productive binding of ABTS to the enzyme resting state. Strong irreversible inactivation of ThDyP by H2O2 in the absence of ABTS suggests that the substrate inhibition by H2O2 may be caused by the non-productive binding of H2O2 to compound I. Positive cooperativity was observed only with the oxidation of ABTS but not with the two electron-donating substrates. Although the conventional mechanism of cooperativity cannot be excluded, we propose that the oxidation of ABTS assumes the simultaneous binding of two ABTS molecules to reduce compound I to the enzyme resting state, and this causes the apparent positive cooperativity.

Deciphering the Kinetics of Spontaneous Generation of H2O2 in Individual Water Microdroplets

Spontaneous generation of H2O2 in sub-10 μm-sized water microdroplets has received increasing interest since its first discovery in 2019. On the other hand, due to the short lifetime of these microdroplets (rapid evaporation) and lack of suitable tools to real-time monitor the generation of H2O2 in individual microdroplets, such a seemingly thermodynamically unfavorable process has also raised vigorous debates on the origin of H2O2 and the underlying mechanism. Herein, we prepared water microdroplets with a long lifetime (>1 h) by virtue of microwell confinement and dynamically monitored the spontaneous generation of H2O2 in individual microdroplets via time-lapsed fluorescence imaging. It was unveiled that H2O2 was continuously generated in the as-prepared water microdroplets and an apparent equilibrium concentration of ∼3 μM of H2O2 in the presence of a H2O2-consuming reaction can be obtained. Through engineering the geometry of these microdroplets, we further revealed that the generation rates of H2O2 in individual microdroplets were positively proportional to their surface-to-volume ratios. This also allowed us to extract a maximal H2O2 generation rate of 7.7 nmol m-2 min-1 in the presence of a H2O2-consuming reaction and derive the corresponding probability of spontaneous conversion of interfacial H2O into H2O2 for the first time, that is, ∼1 of 65,000 water molecules in 1 s. These findings delivered strong evidence that the spontaneous generation of H2O2 indeed occurs at the surface of microdroplets and provided us with an important starting point to further enhance the yield of H2O2 in water microdroplets for future applications.

The divergent pH dependence of substrate turnover in dehaloperoxidases A and B

The pH-dependent peroxidase activity in both dehaloperoxidases A and B was studied by a kinetic assay, stopped flow spectroscopy, resonance Raman spectroscopy, and high-performance liquid chromatography at pH 5.0, 6.0, and 7.0. At pH 7.0, both isozymes follow the peroxidase ping-pong kinetic model derived from the three-step reaction scheme using the steady-state approximation. However, deviation from standard saturation behavior is observed at pH < 6.0 and [TCP] > 0.7 mM, owing to multiple processes: a) self-inhibition of TCP by internal binding; b) oxidation of the product by a pH- and concentration-dependent secondary reaction; and c) formation of an inactive species known as compound RH in the absence of oxidizable substrate. Although DHP-A and DHP-B differ by only 5 amino acids, they show a complete trend reversal in their observed peroxidase kinetics and product yields. Although at pH 7.0 DHP-B had higher TCP oxidation activity than DHP-A as reported previously, as pH was lowered, DHP-A appeared to have a higher peroxidase activity than DHP-B. This is an unprecedented result. However, the fact that there are multiple processes contributing to both kinetics and yield of TCP oxidation complicates interpretation of these data. Deactivation via compound RH and self-inhibition are pH dependent reactions that compete with substrate oxidation. Compound RH formation was observed to be rapid at low pH. A complete set of control experiments were conducted to differentiate the various contributions to the observed enzyme kinetics.

Oxidative dehalogenation of trichlorophenol catalyzed by a promiscuous artificial heme-enzyme

The miniaturized metalloenzyme Fe(iii)-mimochrome VI*a (Fe(iii)-MC6*a) acts as an excellent biocatalyst in the H₂O₂-mediated oxidative dehalogenation of the well-known pesticide and biocide 2,4,6-trichlorophenol (TCP). The artificial enzyme can oxidize TCP with a catalytic efficiency (k_cat/K^TCP_m = 150 000 mM⁻¹ s⁻¹) up to 1500-fold higher than the most active natural metalloenzyme horseradish peroxidase (HRP). UV-visible and EPR spectroscopies were used to provide indications of the catalytic mechanism. One equivalent of H₂O₂ fully converts Fe(iii)-MC6*a into the oxoferryl-porphyrin radical cation intermediate [(Fe(iv) Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O)por˙⁺], similarly to peroxidase compound I (Cpd I). Addition of TCP to Cpd I rapidly leads to the formation of the corresponding quinone, while Cpd I decays back to the ferric resting state in the absence of substrate. EPR data suggest a catalytic mechanism involving two consecutive one-electron reactions. All results highlight the value of the miniaturization strategy for the development of chemically stable, highly efficient artificial metalloenzymes as powerful catalysts for the oxidative degradation of toxic pollutants.

The artificial metalloenzyme FeMC6*a is able to perform the H₂O₂-mediated dechlorination of 2,4,6-trichlorophenol with unrivalled catalytic efficiency, highlighting its potential application for the removal of toxic pollutants.

Conversion of Human Neuroglobin into a Multifunctional Peroxidase by Rational Design

Protein design has received much attention in the last decades. With an additional disulfide bond to enhance the protein stability, human A15C neuroglobin (Ngb) is an ideal protein scaffold for heme enzyme design. In this study, we rationally converted A15C Ngb into a multifunctional peroxidase by replacing the heme axial His64 with an Asp residue, where Asp64 and the native Lys67 at the heme distal site were proposed to act as an acid-base catalytic couple for H₂O₂ activation. Kinetic studies showed that the catalytic efficiency of A15C/H64D Ngb was much higher (∼50-80-fold) than that of native dehaloperoxidase, which even exceeds (∼3-fold) that of the most efficient native horseradish peroxidase. Moreover, the dye-decolorizing peroxidase activity was also comparable to that of some native enzymes. Electron paramagnetic resonance, molecular docking, and isothermal titration calorimetry studies provided valuable information for the substrate-protein interactions. Therefore, this study presents the rational design of an efficient multifunctional peroxidase based on Ngb with potential applications such as in bioremediation for environmental sustainability.

Kinetic insights into the peroxygenase activity of cellulose-active lytic polysaccharide monooxygenases (LPMOs)

Lytic polysaccharide monooxygenases (LPMOs) are widely distributed in Nature, where they catalyze the hydroxylation of glycosidic bonds in polysaccharides. Despite the importance of LPMOs in the global carbon cycle and in industrial biomass conversion, the catalytic properties of these monocopper enzymes remain enigmatic. Strikingly, there is a remarkable lack of kinetic data, likely due to a multitude of experimental challenges related to the insoluble nature of LPMO substrates, like cellulose and chitin, and to the occurrence of multiple side reactions. Here, we employed competition between well characterized reference enzymes and LPMOs for the H₂O₂ co-substrate to kinetically characterize LPMO-catalyzed cellulose oxidation. LPMOs of both bacterial and fungal origin showed high peroxygenase efficiencies, with k_cat/K_mH2O2 values in the order of 10⁵-10⁶ M^-1 s^-1. Besides providing crucial insight into the cellulolytic peroxygenase reaction, these results show that LPMOs belonging to multiple families and active on multiple substrates are true peroxygenases.

Hydrogen-producing hyperthermophilic bacteria synthesized size-controllable fine gold nanoparticles with excellence for eradicating biofilm and antibacterial applications

An environment-friendly strategy for the controllable preparation of AuNPs is presented, which exhibited high peroxidase activity over a broad pH range.

Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin

The V21C/V66C/F46S myoglobin mutant, with a de novo designed intramolecular disulfide bond resembling that in cytoglobin without structural evidence, exhibits a dehalogenation activity exceeding that of a native dehaloperoxidase.

Bindings of NO, CO, and O2 to multifunctional globin type dehaloperoxidase follow the 'sliding scale rule'

Dehaloperoxidase-hemoglobin (DHP), a multifunctional globin protein, not only functions as an oxygen carrier as typical globins such as myoglobin and hemoglobin, but also as a peroxidase, a mono- and dioxygenase, peroxygenase, and an oxidase. Kinetics of DHP binding to NO, CO, and O₂ were characterized for wild-type DHP A and B and the H55D and H55V DHP A mutants using stopped-flow methods. All three gaseous ligands bind to DHP significantly more weakly than sperm whale myoglobin (SWMb). Both CO and NO bind to DHP in a one-step process to form a stable six-coordinate complex. Multiple-step NO binding is not observed in DHP, which is similar to observations in SWMb, but in contrast with many heme sensor proteins. The weak affinity of DHP for O₂ is mainly due to a fast O₂ dissociation rate, in accordance with a longer ^εN-Fe distance between the heme iron and distal histidine in DHP than that in Mb, and an open-distal pocket that permits ligand escape. Binding affinities in DHP show the same 3-4 orders separation between the pairs NO/CO and CO/O₂, consistent with the 'sliding scale rule' hypothesis. Strong gaseous ligand discrimination by DHP is very different from that observed in typical peroxidases, which show poor gaseous ligand selectivity, correlating with a neutral proximal imidazole ligand rather than an imidazolate. The present study provides useful insights into the rationale for DHP to function both as mono-oxygenase and oxidase, and is the first example of a globin peroxidase shown to follow the 'sliding scale rule' hypothesis in gaseous ligand discrimination.

Heme binding and peroxidase activity of a secreted minicatalase

Microbial pathogens often require efficient and robust H₂ O₂ scavenger activities to survive in the presence of reactive oxygen species generated by inflammatory responses. In addition to catalases and peroxidases, enzymes known to scavenge H₂ O₂ , a novel class of secreted minicatalases is found in diderm bacteria. Here, we characterize the Helicobacter pylori (Hp) minicatalase: a monomeric hemoprotein with catalase core homology. Overexpression of Hp minicatalase rescued a catalase/peroxidase-deficient Escherichia coli phenotype under aerobic conditions and limited H₂ O₂ stress. The purified enzyme lacks catalase activity, but has strong (k_cat > 100 s^-1 ) H₂ O₂ -dependent peroxidase activity toward a variety of organic substrates. Our investigations into heme binding revealed that the heme cofactor is assembled in the periplasm to form the functional holoprotein. Furthermore, we observed the presence of a disulfide bond near the heme cavity of Hp minicatalase, which is conserved in secreted minicatalases and, therefore, may play a role in heme binding.

Immobilization of soybean peroxidase on silica-coated magnetic particles: a magnetically recoverable biocatalyst for pollutant removal

Development of a recyclable biocatalystviaimmobilization of soybean peroxidase onto magnetic nanoparticles.