Oscillatory oxidations of reduced pyridine nucleotide by peroxidase

Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems

The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.

Complexity in subnetworks of a peroxidase-oxidase reaction model

The peroxidase-oxidase (PO) reaction is a paradigmatic (bio)chemical system well suited to study the organization and stability of self-sustained oscillatory phases typically present in nonlinear systems. The PO reaction can be simulated by the state-of-the-art Bronnikova-Fedkina-Schaffer-Olsen model involving ten coupled ordinary differential equations. The complex and dynamically rich distribution of self-sustained oscillatory stability phases of this model was recently investigated in detail. However, would it be possible to understand aspects of such a complex model using much simpler models? Here, we investigate stability phases predicted by three simple four-variable subnetworks derived from the complete model. While stability diagrams for such subnetworks are found to be distorted compared to those of the complete model, we find them to surprisingly preserve significant features of the original model as well as from the experimental system, e.g., period-doubling and period-adding scenarios. In addition, return maps obtained from the subnetworks look very similar to maps obtained in the experimental system under different conditions. Finally, two of the three subnetwork models are found to exhibit quint points, i.e., recently reported singular points where five distinct stability phases coalesce. We also provide experimental evidence that such quint points are present in the PO reaction.

Complexity of a peroxidase-oxidase reaction model

The peroxidase-oxidase oscillating reaction was the first (bio)chemical reaction to show chaotic behaviour. The reaction is rich in bifurcation scenarios, from period-doubling to peak-adding mixed mode oscillations. Here, we study a state-of-the-art model of the peroxidase-oxidase reaction. Using the model, we report systematic numerical experiments exploring the impact of changing the enzyme concentration on the dynamics of the reaction. Specifically, we report high-resolution phase diagrams predicting and describing how the reaction unfolds over a quite extended range of enzyme concentrations. Surprisingly, such diagrams reveal that the enzyme concentration has a huge impact on the reaction evolution. The highly intricate dynamical behaviours predicted here are difficult to establish theoretically due to the total absence of an adequate framework to solve nonlinearly coupled differential equations. But such behaviours may be validated experimentally.

Chaos in the peroxidase-oxidase oscillator

The peroxidase-oxidase (PO) reaction involves the oxidation of reduced nicotinamide adenine dinucleotide by molecular oxygen. When both reactants are supplied continuously to a reaction mixture containing the enzyme and a phenolic compound, the reaction will exhibit oscillatory behavior. In fact, the reaction exhibits a zoo of dynamical behaviors ranging from simple periodic oscillations to period-doubled and mixed mode oscillations to quasiperiodicity and chaos. The routes to chaos involve period-doubling, period-adding, and torus bifurcations. The dynamic behaviors in the experimental system can be simulated by detailed semiquantitative models. Previous models of the reaction have omitted the phenolic compound from the reaction scheme. In the current paper, we present new experimental results with the oscillating PO reaction that add to our understanding of its rich dynamics, and we describe a new variant of a previous model, which includes the chemistry of the phenol in the reaction mechanism. This new model can simulate most of the experimental behaviors of the experimental system including the new observations presented here. For example, the model reproduces the two main routes to chaos observed in experiments: (i) a period-doubling scenario, which takes place at low pH, and a period-adding scenario involving mixed mode oscillations (MMOs), which occurs at high pH. Our simulations suggest alternative explanations for the pH-sensitivity of the dynamics. We show that the MMO domains are separated by narrow parameter regions of chaotic behavior or quasiperiodicity. These regions start as tongues of secondary quasiperiodicity and develop into strange attractors through torus breakdown.

Chemical clocks, oscillations, and other temporal effects in analytical chemistry: oddity or viable approach?

Most analytical methods are based on "analogue" inputs from sensors of light, electric potentials, or currents. The signals obtained by such sensors are processed using certain calibration functions to determine concentrations of the target analytes. The signal readouts are normally done after an optimised and fixed time period, during which an assay mixture is incubated. This minireview covers another-and somewhat unusual-analytical strategy, which relies on the measurement of time interval between the occurrences of two distinguishable states in the assay reaction. These states manifest themselves via abrupt changes in the properties of the assay mixture (e.g. change of colour, appearance or disappearance of luminescence, change in pH, variations in optical activity or mechanical properties). In some cases, a correlation between the time of appearance/disappearance of a given property and the analyte concentration can be also observed. An example of an assay based on time measurement is an oscillating reaction, in which the period of oscillations is linked to the concentration of the target analyte. A number of chemo-chronometric assays, relying on the existing (bio)transformations or artificially designed reactions, were disclosed in the past few years. They are very attractive from the fundamental point of view but-so far-only few of them have be validated and used to address real-world problems. Then, can chemo-chronometric assays become a practical tool for chemical analysis? Is there a need for further development of such assays? We are aiming to answer these questions.

Changes in the abundance of sugars and sugar-like compounds in tall fescue (Festuca arundinacea) due to growth in naphthalene-treated sand

The hydrophilic metabolome of tall fescue (Festuca arundinacea) adapted to grow in naphthalene-treated sand (0.8 g kg(-1) sand dw) was analysed using gas chromatography-mass spectrometry, and peaks corresponding to the more abundant compounds were tentatively identified from analysis of their mass spectral features and reference to the NIST Mass Spectral Database. Particular attention was paid to sugars as they are known to play important roles as stress regulators in plants. The results showed that the abundance of sugars was greater in the roots but lesser in the shoots of treated plants when compared to their control counterparts. The results for indole acetic acid (IAA) were notable: IAA was prominently less in the treated roots compared to shoots, and in treated shoots, IAA was particularly subdued compared to untreated shoots consistent with IAA degradation in treated plant tissues. The differences in the molecular phenotype between control and treated plants were expressed in root structural differences. The treated roots were modified to have greater suberisation, enhanced thickening in the endodermis and distortions in the cortical zone as demonstrated through scanning electron and epi-fluorescence microscopy.

Effects of tyramine and 4-aminophenol on the oscillating peroxidase-oxidase reaction

The peroxidase-oxidase oscillator, a model of biological oscillations, is usually studied in conjunction with the effector molecule, 2,4-dichlorophenol. In this account, we present evidence of the effects of a naturally occurring phenol, tyramine, on the reaction, and also those of the structurally similar 4-aminophenol. Whereas 2,4-dichlorophenol gives rise to sustained oscillations at 40 μM, it was discovered that tyramine promotes damped oscillations at a concentration of 120 μM. Oxidation of NADH was completely inhibited by 4-aminophenol and ascorbate. In separate experiments, the peroxidase-catalyzed ring coupling of tyramine and 4-aminophenol was observed, which in the case of tyramine, may provide an explanation for the damping of oscillations.

Catalase in peroxidase clothing: Interdependent cooperation of two cofactors in the catalytic versatility of KatG

Catalase-peroxidase (KatG) is found in eubacteria, archaea, and lower eukaryotae. The enzyme from Mycobacterium tuberculosis has received the greatest attention because of its role in activation of the antitubercular pro-drug isoniazid, and the high frequency with which drug resistance stems from mutations to the katG gene. Generally, the catalase activity of KatGs is striking. It rivals that of typical catalases, enzymes with which KatGs share no structural similarity. Instead, catalatic turnover is accomplished with an active site that bears a strong resemblance to a typical peroxidase (e.g., cytochrome c peroxidase). Yet, KatG is the only member of its superfamily with such capability. It does so using two mutually dependent cofactors: a heme and an entirely unique Met-Tyr-Trp (MYW) covalent adduct. Heme is required to generate the MYW cofactor. The MYW cofactor allows KatG to leverage heme intermediates toward a unique mechanism for H2O2 oxidation. This review evaluates the range of intermediates identified and their connection to the diverse catalytic processes KatG facilitates, including mechanisms of isoniazid activation.

Biofilm effects on the peroxidase-oxidase reaction

In experiments on the kinetics of the peroxidase-oxidase oscillatory reaction in pH 5.l acetate buffer, biofilms form in less than 48 h on the quartz reactor surface. The nominally homogeneous peroxidase system shows dynamical changes in response to this biofilm growth, partially explaining subtle differences among dynamics observed over time and between laboratories. Kinetics data and model computations are correlated with micrographs of biofilm formation. It is evident that bare quartz also interacts with reaction species, so that the surface area-to-volume ratio is an important parameter on which observed dynamics depend.

Oscillations in peroxidase-catalyzed reactions and their potential function in vivo

The peroxidase-oxidase reaction has become a model system for the study of oscillations and complex dynamics in biochemical systems. In the present paper we give an overview of previous experimental and theoretical studies of the peroxidase-oxidase reaction. Recent in vitro experiments have raised the question whether the reaction also exhibits oscillations and complex dynamics in vivo. To investigate this possibility further we have undertaken new experimental studies of the reaction, using horseradish extracts and phenols which are widely distributed in plants. The results are discussed in light of the occurrence and a possible functional role of oscillations and complex dynamics of the peroxidase-oxidase reaction in vivo.

Principal component analysis of dynamical features in the peroxidase-oxidase reaction

Inherent variance due to oscillations in the peroxidase-oxidase (PO) reaction was studied using principal component analysis (PCA). The substrates were oxygen and reduced nicotinamide adenine dinucleotide (NADH). Horseradish peroxidase (HRP) catalyzed the reaction. The concentration of a cofactor, methylene blue (MB), was varied, and 2,4-dichlorophenol was kept constant. Increase in the NADH influx was used to change the reaction dynamics from periodic to chaotic. The reaction space was abstracted to the most significant, mutually independent, pairs of absorption and kinetic basis vectors (principal components). Typically, two significant principal components were extracted from the periodic time series and three from the chaotic data. The PCA models accounted for 70-97% of experimental variance. The greatest fraction of the total variance was accounted for in experiments exhibiting periodic dynamics and less than 25 nM MB. More MB induced an increased contribution of NADH to the PO oscillator variance, as did increased NADH influx. A simulated absorption time series, computed from a mass-action model of the chemistry, was analyzed by PCA as well. The comparison of simulation with experiment indicates that the chemical model renders the time series for HRP oxidation forms with fidelity, but incompletely represents NADH chemistry and other salient processes underlying the observed dynamics.

Heme Peroxidases: Structure, Function, Mechanism and Involvement in Activation of Carcinogens. A Review

Peroxidases are enzymes playing an important role in large and diverse numbers of physiological processes in organisms including human. We have attempted in this article to summarize and review the important structural and catalytic properties of principal classes of heme peroxidases as well as their biological functions. Major reactions catalyzed by these enzymes (a conventional peroxidase cycle, reactions using O2and halogenations) and their mechanism are reviewed, too. Moreover, the reaction mechanisms by which peroxidases are implicated in bioactivation of xenobiotic chemicals are presented. Numerous chemicals including protoxicants and procarcinogens are metabolized by equally numerous chemical reactions catalyzed by peroxidases. The unifying theme is the radical nature of the oxidations. The direct conventional peroxidase reaction forming reactive species is generally responsible for the activation of procarcinogenic substrates of peroxidases. The subsequent formation of a superoxide anion radical and peroxy radicals is necessary for activation of chemicals that are poor substrates for peroxidases. The significance of studies concerning the reactions catalyzed by peroxidases is underlined in the present review article. A review with 166 references.

Computer simulation of damped oscillations during peroxidase-catalyzed oxidation of indole-3-acetic acid

Oscillation patterns in horseradish peroxidase (HRP)-catalyzed oxidation of indole-3-acetic acid (IAA) at neutral pH were studied using computer simulation. Under certain conditions, such as the presence of a reaction promoter and continuous intake of oxygen from the gaseous phase, the simulated system exhibits damped oscillations of the concentrations of oxygen in the aqueous phase, [O(2)](aq), and of all the reaction intermediates. The critical concentration of oxygen in aqueous phase, [O(2)](cr)(aq), was used to describe the nature of the oscillations. The critical concentration is the concentration at which the system abruptly changes its properties. If [O(2)](aq) is higher than [O(2)](cr)(aq) then the reaction develops as an avalanche, otherwise, the reaction stops. The nature of oscillations is accounted for by the interaction of two processes: the consumption/accumulation of oxygen and the accumulation/consumption of reaction intermediates. Oscillations are always damped. Neither HRP or umbelliferone (Umb) deactivation nor IAA consumption can account for the damping. The nature of the damping is determined by the termination reactions of free radical intermediates and ROOH. The three major parameters of oscillations: period of oscillations, initial amplitude of oscillations and the rate of damping were studied as functions of: (i) oxygen concentration in the gaseous phase, (ii) initial oxygen concentration in aqueous phase, (iii) the concentration of IAA and (iv) the initial concentration of HRP.

Chaos via mixed-mode oscillations

The route by which chaos arises from mixed-mode periodic states in a model of the peroxidase enzyme catalysed oxidation of NADH is described. The specific model studied displays a rich variety of exotic dynamical behaviour including simple oscillations, quasiperiodicity, bistability between periodic states, complex periodic oscillations (including the mixed-mode type) and chaos. The route to chaos in this system involves a torus attractor which becomes destabilized and breaks up into a fractal object, a strange attractor. The mixed-mode states correspond to phase-locking on this fractal attractor and are arranged in staircases according to the complexity of the state. In this paper, we investigate the sequence leading from a mixed-mode periodic state to a chaotic one in the staircase region and find a familiar cascade of period-doubling bifurcations, which finally culminate in chaos.

Kinetic studies of the oscillatory dynamics in the peroxidase-oxidase reaction catalyzed by four different peroxidases

Oscillatory kinetics in the peroxidase-oxidase reaction catalyzed by structurally different peroxidases were investigated using NADH as a substrate. For horseradish peroxidase, lactoperoxidase, and soybean peroxidase the oscillatory waveforms of their dominating enzyme intermediates, ferric peroxidase and compound III, are similar. Coprinus peroxidase, on the other hand, has ferrous peroxidase and compound III as the dominating intermediates. The oscillatory waveform of its compound III differs from the waveforms of compound III of the three other peroxidases. Also, the phase plot of the signal for compound III versus the oxygen concentration for Coprinus peroxidase differs from the corresponding phase plots obtained using other peroxidases. A detailed model of the reaction mechanism is proposed, which is able to simulate these different kinds of behaviour. Substituting NADH with dihydroxyfumaric acid as a substrate, oscillations in the oxygen concentration were observed for about 1.5 h when a concentrated solution of this substrate was continuously fed to a solution containing horseradish peroxidase. This is the first demonstration of sustained oscillations with this substrate.

Oscillations in the peroxidase-oxidase reaction: a comparison of different peroxidases

The nonlinear behavior of the peroxidase-oxidase reaction was studied using structurally different peroxidases. For the first time sustained oscillations with peroxidases other than horseradish peroxidase in a single-enzyme system were observed. All peroxidases that showed significant oxidase activity were able to generate sustained oscillations. When adjusting the overall reaction rate, either of the two modifiers 2,4-dichlorophenol or Methylene blue could be omitted from the reaction. Due to the observation of different enzyme intermediates when using different peroxidases, we conclude that the mechanisms responsible for oscillatory kinetics may vary from one peroxidase to the other.

A hydrogen peroxide assay based on the peroxidase-oxidase reaction. Numerical simulation of the reaction mechanism

In order to explain an assay method for H2O2, based on the horseradish peroxidase/NADH/H2O2 system, we performed a numerical simulation of this complex reaction mechanism. For this purpose, we applied a simplified version of a model designed by Yokota and Yamazaki to our experimental conditions [Yokota, K. & Yamazaki, I. (1977) Biochemistry 16, 1913-1918]. This modification leads to a kinetic behaviour of the system very similar to our experimental results when the presence of superoxide dismutase is simulated. These simulations confirm that hydrogen peroxide concentrations are proportional to the total amount of NADH oxidized. We also showed that superoxide dismutase activity can be determined by this assay method. Moreover, in samples containing superoxide dismutase and hydrogen peroxide, the simulations showed that both superoxide dismutase and hydrogen peroxide can be determined using our assay method.

Periodicity and chaos in a photosynthetic system

In this paper experimental results of investigation of the oscillations in a photosynthetic system are presented and a model for their interpretation is suggested. Periodicities in photosynthetic systems detected in earlier studies by physical chemical methods can be also detected by means of recording the potential difference between two point electrodes. The observed dependences demonstrate a wide range of various types of behaviour of the system, working, e.g. in periodic, quasiperiodic, chaotic or 'pulse' regimes. Since the until-now-used 2-dimensional theoretical model, based on the existence of two dominant autocatalytical processes, appeared not to be sufficient for explaining such types of the regimes, a generalized 3-dimensional autocatalytical model is suggested, which is able to explain all the above mentioned photosynthetic regimes.

Hydrogen/deuterium isotope effect in the oscillating peroxidase-oxidase reaction

The oscillatory peroxidase-oxidase reaction has been investigated by using NADH deuterated in the nicotinamide 4-A position. A considerable kinetic hydrogen/deuterium isotope effect on the oscillatory behavior was revealed, which may provide an additional valuable tool for mechanistic studies and for discriminating between various mechanistic models of the peroxidase-oxidase reaction. Particularly, this effect manifests in different oscillation frequencies. A sequence of simple and aperiodic oscillations was found between two stable steady states.

Chaos in biological systems

Chaos is a widespread and easily recognizable phenomenon that hardly anybody took notice of until recently. The reason may be that chaos has something profoundly counterintuitive about it. It will not fit easily into any familiar cause–effect frame. The best introduction to chaos is by the way of an example. Consider a leaking faucet (Shaw, 1984). When the weight of the accumulating drop exceeds the surface tension the drop falls and a new drop begins to form. If the leak is small and the pressure in the faucet is constant, the time taken for the drop to reach the critical weight is constant. The dripping is perfectly periodic, the period depending on the leak rate. If the leak is slightly increased, the period of dripping will decrease slightly and vice versa. However, somewhere beyond this point the leaking faucet becomes a nuisance. When the leak is increased beyond a certain point the dripping looses its regularity. The time interval between the drops will first alternate periodically between a short and a long time interval. After a further increase of the leak this double periodic pattern will become unstable and change into a new pattern where four different time intervals between the drops alternate periodically. As the leak is further increased the period will double again and again and finally the dripping becomes completely irregular without any repeating pattern. When this occurs we are observing chaos. At the same time we are posed with the problem of understanding how such a ridiculously simple system can show random behaviour.

Computer simulation of sustained oscillations in peroxidase-oxidase reaction

A system of differential equations of second order exhibiting transitional behaviour and sustained oscillations has been obtained for a complete scheme of the peroxidase-oxidase reaction. The concentrations of hydrogen peroxide and of hydrogen donor radicals are slow variables of the system. The most essential reactions responsible for oscillations have been selected. Analysis of the system in phase plane and in parameter space has been carried out. The dependence of oscillation period and amplitude on the parameter values has been investigated.