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In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects. Moreover, it should be implemented by efficient algorithms requiring the shortest possible execution time, to avoid enlarging excessively the time elapsing between data analysis and any subsequent experiment. Besides the features of their topological structure, the complexity of biological networks also refers to their dynamics, that is often non-linear and stiff. The stiffness is due to the presence of molecular species whose abundance fluctuates by many orders of magnitude. A fully stochastic simulation of a stiff system is computationally time-expensive. On the other hand, continuous models are less costly, but they fail to capture the stochastic behaviour of small populations of molecular species. We introduce a new efficient hybrid stochastic-deterministic computational model and the software tool MoBioS (MOlecular Biology Simulator) implementing it. The mathematical model of MoBioS uses continuous differential equations to describe the deterministic reactions and a Gillespie-like algorithm to describe the stochastic ones. Unlike the majority of current hybrid methods, the MoBioS algorithm divides the reactions' set into fast reactions, moderate reactions, and slow reactions and implements a hysteresis switching between the stochastic model and the deterministic model. Fast reactions are approximated as continuous-deterministic processes and modelled by deterministic rate equations. Moderate reactions are those whose reaction waiting time is greater than the fast reaction waiting time but smaller than the slow reaction waiting time. A moderate reaction is approximated as a stochastic (deterministic) process if it was classified as a stochastic (deterministic) process at the time at which it crosses the threshold of low (high) waiting time. A Gillespie First Reaction Method is implemented to select and execute the slow reactions. The performances of MoBios were tested on a typical example of hybrid dynamics: that is the DNA transcription regulation. The simulated dynamic profile of the reagents' abundance and the estimate of the error introduced by the fully deterministic approach were used to evaluate the consistency of the computational model and that of the software tool.

The structures of copper amine oxidases from various sources show good similarity, suggesting similar catalytic mechanisms for all members of this enzyme family. However, the optimal substrates for each member differ, depending on the source of the enzyme and its location. The structural factors underlying substrate selectivity still remain to be discovered. With this in view, we examined the kinetic behaviour of pea seedling amine oxidase with cadaverine and hexylamine, the first bearing two, and the second only one, positively charged amino group. The dependence of Km and catalytic constant (kc) values on pH, ionic strength and temperature indicates that binding of the monoamine is driven by hydrophobic interactions. Instead, binding of the diamine is strongly facilitated by electrostatic factors, controlled by polar side-chains and two titratable residues present in the active site. The position of the docked substrate is also essential for the participation of titratable amino acid residues in the following catalytic steps. A new mechanistic model explaining the substrate-dependent kinetics of the reaction is discussed.

In this paper, we report on a method to evaluate the activity of water soluble and H-atom donor antioxidants as peroxyl radical scavengers in a micelle system reproducing the conditions occurring in the upper small intestine in humans, during digestion and absorption of lipids. This method, which overcomes some of the problems of the total radical trapping antioxidant parameter (TRAP) assays, measures the peroxyl radical trapping capacity (n) and the peroxyl radical trapping efficiency IC 50 − 1 of antioxidants, that is the number “n” of peroxyl radicals trapped by one molecule of the studied antioxidant and the reciprocal of the antioxidant concentration that halves the steady-state concentration of peroxyl radicals, respectively. These two fundamental parameters characterizing the radical chain breaking of many water soluble antioxidants, among which dietary polyphenols, can be obtained with relatively good precision from a single experiment, on the basis of a rigorous treatment of the kinetic data.

TPP+ (tetraphenylphosphonium ion) and its analogues were found to act as powerful competitive inhibitors of BSAO (bovine serum amine oxidase). The binding of this new class of inhibitors to BSAO was characterized by kinetic measurements. TPP+ can bind to the BSAO active site by hydrophobic and by coulombian interactions. The binding probably occurs in the region of the ‘cation-binding site’[Di Paolo, Scarpa, Corazza, Stevanato and Rigo (2002) Biophys. J. 83, 2231–2239]. Under physiological conditions, the association constant of TPP+ for this site is higher than 106 M−1, the change of enthalpy being the main free-energy term controlling binding. Analysis of the relationships between substrate structure and extent of inhibition by TPP+ reveals some new molecular features of the BSAO active site.

A steady-state kinetic study of bovine serum amine oxidase activity was performed, over a wide range of pH values (5.4-10.2) and ionic strength (10-200 mM), using various (physiological and analogue) substrates as specific probes of the active-site binding region. Relatively small changes in k (cat) values (approx. one order of magnitude) accompanied by marked changes in K(m) and k(cat)/K(m) values (approx. six orders of magnitude) were observed. This behaviour was correlated with the presence of positively charged groups or apolar chains in the substrates. In particular, it was found that the docking of the physiological polyamines, i.e. spermidine and spermine, appears to be modulated by three amino acid residues of the active site, which we have named L(-)H(+), G(-)H(+) and IH(+), characterized by p K (a) values of 6.2+/-0.2 [Di Paolo, Scarpa, Corazza, Stevanato and Rigo (2002) Biophys. J. 83, 2231-2239], 8.2+/-0.3 and 7.8+/-0.4 respectively. The electrostatic interaction between the protonated substrates and the enzyme containing the residues L(-)H(+), G(-)H(+) and IH(+) in the deprotonated form, the on/off role of the IH(+) residue and the role of hydrophobic interactions with substrates characterized by apolar chains are discussed.

The inhibitory effect of anthocyanins has been investigated in the peroxidation of linoleic acid in micelles in the presence and in the absence of (+)-catechin. The peroxidation was initiated by thermal decomposition of 2,2(')-azobis[2-(2-imidazolin-2-yl)propane], and the kinetics of peroxidation were followed by measuring the rate of oxygen consumption and the rate of disappearance of the antioxidant. The analysis of the antioxidant effect of various anthocyanins, alone or in the presence of catechin, demonstrates that catechin, which is relatively inefficient at inhibiting linoleic acid oxidation, regenerates the highly efficient antioxidant malvidin 3-glucoside and, at a lower extent, peonidin 3-glucoside. The malvidin 3-glucoside recycling by catechin strongly increases the antioxidant efficiency of these two antioxidants. This protective mechanism appears specific for malvidin and peonidin 3-glucosides. The high unpaired spin density of the phenolic O atoms in the radicals generated by these anthocyanins, calculated by the semiempirical quantum chemical AM1 method, may explain the observed behavior.

Dopaminochrome formation is catalyzed by commercially available purified peroxidases (EC 1.11.1.7) such as horseradish, lacto- and myelo-peroxidase using dopamine, hydrogen peroxide or promethazine sulfoxide as substrates. A rat brain fraction (RBF) catalyzes a similar reaction and its catalytic power increases after preincubation with hydrogen peroxide/ascorbic acid. The activity of both the purified enzymes and the RBF preparation is inhibited by carnosine and characterized by excess substrate inhibition. The enzymes recognize different substrates but show the highest affinity for dopamine. The RBF fraction is strongly buffered against oxidation by compounds such as glutathione and by bioreductive enzymes such as DT-diaphorase (EC 1.6.99.2) which can use as a substrate menadione or dopaminochrome. The rat brain dopamine peroxidizing activity appeared to be mostly bound to the synaptosomal fraction. The reaction catalyzed by the purified peroxidases was followed by electron spin resonance spectroscopy and, unlike that catalyzed by RBF, was shown to produce the signal of a transient dopamine-o-semiquinone radical.

The ionic-strength-dependence of steady-state kinetic parameters (kc and Km') for non-biogenic (benzylamine, butylamine) and biogenic (spermine, spermidine) amines has been measured in the bovine serum amine oxidase reaction. The catalytic rate constant (kc) values are similar (0.9-2.5 s-1) for all the substrates studied and are almost constant over the experimental ionic strength range (24-155 mM). In contrast, Km' values are in the range 6-2300 microM and undergo a 4-12-fold increase with increasing ionic strength, parallelled by a decrease in catalytic efficiency. From an analysis of the kc and Km' values and their dependence on ionic strength, we conclude that more than one negative site is involved in the binding of these amines and that the relative dielectric constant of the binding site is lower than that of aqueous solutions.

Kinetic and spectroscopic studies were carried out to study the role of hydrophobic effect on the activity of bovine serum amine oxidase (BSAO). Increasing the chain length of the substrates (linear aliphatic primary monoamines), the affinity for the active site increases while the catalytic constant decreases in accordance with a relative low value of dielectric constant (about 10) estimated for the microenvironment of BSAO active site using a fluorescent probe sensitive to solvent polarity. The aliphatic chain of 1-aminononane induces a shift in the p K a of the product Schiff base, the hydrolysis of which appears to be a rate-determining step of the reaction. Furthermore, circular dichroism studies highlighted the “flexibility” of BSAO secondary structure that can explain the wide substrate specificity of this enzyme. These results should be useful to elucidate the substrate/inhibitor preferences of CuAOs, in particular of the human enzyme.

Copper-containing amine oxidase extracted from bovine serum (BSAO) was crystallized and its three-dimensional structure at 2.37 A resolution is described. The biological unit of BSAO is a homodimer, formed by two monomers related to each other by a non-crystallographic 2-fold axis. Each monomer is composed of three domains, similar to those of other amine oxidases from lower species. The two monomers are structurally equivalent, despite some minor differences at the two active sites. A large funnel allows access of substrates to the active-site; another cavity, accessible to the solvent, is also present between the two monomers; this second cavity could allow the entrance of molecular oxygen necessary for the oxidative reaction. Some sugar residues, bound to Asn, were still present and visible in the electron density map, in spite of the exhaustive deglycosylation necessary to grow the crystals. The comparison of the BSAO structure with those of other resolved AO structures shows strong dissimilarities in the architecture and charge distribution of the cavities leading to the active-site, possibly explaining the differences in substrate specificity.

2H-NMR spectroscopy has been used to study the distribution of2H atoms in brain lactate, after intraperitoneal injection of2H2O. Information on brain metabolism was obtained from the ratio [(3-2H)lactate]/[(2-2H)lactate] which was found very sensitive to the PO2in the breathing air. The dependence of this ratio on the rates of metabolic pathways is an example of the possibility to use the distribution of2H atoms in a molecule to probe metabolic flow through different pathways.

The interaction between polyphosphates and polyamines was investigated by 31P-NMR spectroscopy and by amine oxidase activity measurements. An apparent competition between negatively charged polyphosphates (ATP, ADP, AMP, tripolyphosphate and pyrophosphate) and positively charged polyamine, for the active site of bovine serum and soybean seedling amine oxidases, was observed by activity measurements. This behavior was explained by formation of polyamine-polyphosphate complexes and the stability constants of these complexes were calculated by 31P NMR. However, at a given concentration of polyphosphate, the amine oxidase activity was found higher than that expected on the basis of the free amine concentration calculated according to the NMR stability constant. This fact, and the different extent of inhibition of the spermidine oxidase activity of soybean seedling and of bovine serum amine oxidases observed in the presence of a given polyphosphate, suggest that amine oxidases may be active also on the polyamine-polyphosphate complexes. This hypothesis was supported by the strong dependence of the k cal K m of bovine serum amine oxidase on ionic strength, indicating an electrostatic interaction between the charged amine and the active site, while no effect of ionic strength on k cat K m was observed in the presence of ATP. A kinetic model of this behavior was found to fit the experimental data.

The system bovine plasma amine oxidase-polyamine-phosphate ion was investigated by activity measurements and 31 P NMR spectroscopy. Lineweaver-Burk plots showed that phosphate ion, under physiological conditions, is an apparent competitive inhibitor of bovine plasma amine oxidase. While NMR measurements of the T1 of 31 P do not suggest the binding of phosphate to/or near the paramagnetic Cu(II) sites of bovine plasma amine oxidase, the chemical shift dependence of 31 P on spermidine concentration indicates the formation of a spermidine-phosphate complex. The value of the dissociation constant of this complex was found 18.5 ± 1.4 mM, at pH 7.2, by NMR, in good agreement with the value 17.0 ± 0.8 mM calculated from activity measurements, assuming the enzyme activity is proportional to the free amine concentration, under second order conditions. Our data suggest that the decrease of the free spermidine, due to the binding of phosphate ion, is responsible of the observed inhibition of bovine plasma amine oxidase.

F − added to an erythrocyte suspension shows two separated resonances arisen from intra and extracellular compartments. Cu, Zn superoxide dismutase dominates the longitudinal relaxation rate of the intracellular F − resonance, while diamagnetic interactions with hemoglobin contribute mainly to the transversal relaxation rate.

N.m.r. and e.p.r. were used to measure the oxidation state of copper in Cu, Zn superoxide dismutase treated with reducing agents such as NaBH4, K4Fe(CN)6, Na2S2O4 and H2O2. The activity and the electrophoretic pattern of the treated enzyme were also studied. On the basis of the reducing ability and of the absence of inactivating effects, NaBH4 was the most suitable reducer of those tested. Some characteristics of the reduction of superoxide dismutase by NaBH4 were further investigated. The results obtained indicate that NaBH4 can be used to prepare, in a few minutes, solutions of completely reduced enzyme without any apparent change of the activity and of the structure.

The events accompanying the inhibitory effect of alpha-tocopherol and/or ascorbate on the peroxidation of soybean L-alpha-phosphatidylcholine liposomes, which are an accepted model of biological membranes, were investigated by electron paramagnetic resonance, optical and polarographic methods. The presence of alpha-tocopherol radical in the concentration range 10(-8)-10(-7) M was detected from its EPR spectrum during the peroxidation of liposomes, catalysed by the Fe3+-triethylenetatramine complex. The alpha-tocopherol radical, generated in the phosphatidylcholine bilayer, is accessible to ascorbic acid, present in the aqueous phase at physiological concentrations. Ascorbic acid regenerates from it the alpha-tocopherol itself. A kinetic rate constant of about 2 X 10(5) M-1 X s-1 was estimated from the reaction as it occurs under the adopted experimental conditions. The scavenging effect of alpha-tocopherol on lipid peroxidation is maintained as long a ascorbic acid is present.

The amount of Mn superoxide dismutase (MnSOD) and the activity of Cu,Zn-superoxide dismutase (CuZnSOD) have been studied in human fibroblasts of five subjects with trisomy 21 and five subjects with normal karyotype, using nuclear magnetic relaxation and polarographic methods. In the trisomic fibroblasts we have found a mean molar amount of MnSOD 25.4% lower than in the control, and an amount of CuZnSOD 54.7% higher. A positive significant correlation between the activities of both enzymes has been observed indicating that the two enzymes dismute the O2- cooperatively. However, the increase of MnSOD per unit of CuZnSOD appears significantly lower in the trisomic fibroblasts, an effect that is not due to a diminished inducibility of MnSOD. These findings suggest that the MnSOD and CuZnSOD genes interact to preserve the normal level of total SOD activity.

H2O2 was shown to reduce the copper ion of native bovine Cu,Zn superoxide dismutase (superoxide:superoxide oxidoreductase, EC 1.15.1.1) (ECu2+) and to oxidize the reduced enzyme (ECu+). The time-course of these processes was monitored by NMR measurement of the longitudinal relaxation rate of the water protons. A steady-state characterized by the same ratio [ECu2+]/[( EC2+] + [ECu+]) was obtained either by starting from the oxidized or the reduced enzyme. The kinetics of these processes appear to be quite complex, since different reactions between H2O2, or its reaction products, and the enzyme-bound copper control the reaction rate. The solution of the differential equations describing the kinetic processes showed that the oxidation and the reduction of the copper ion by H2O2 are first-order with respect to the copper ion itself only when these processes approach the steady-state. The rate constants of the reduction and oxidation reactions were calculated according to these equations and were found to have comparable values which are in the range 5-80 and 5-45 M-1.min-1, respectively, changing the pH from 5.6 to 7 at 0.21 M ionic strength. This result, together with the dependence of the reaction rates on pH and ionic strength, points to HO2- as the reactive species in both processes, and indicates that the electrostatic control of the access of the peroxide to the active site is the rate-determining step of the two redox reactions.

The oxidation of ascorbic acid by molecular oxygen was investigated by optical and magnetic resonance methods in the presence and in the absence of copper and iron complexes. The results show that one superoxide ion is generated for each oxidized molecule of ascorbate. The effect of addition of Cu,Zn superoxide dismutase, which at concentrations higher than 10(-7) M halves the oxidation rate, is discussed and a reaction mechanism is proposed. An upper limit for the kinetic rate constant of the reaction between the ascorbate radical and the superoxide ion is reported.

The rate of oxidation of reduced bovine Cu,Zn superoxide dismutase [ECu(I)] by molecular O2 was studied by magnetic-resonance techniques and was found to be low under physiological conditions. The analysis of the kinetic data and of the experiments carried out in the presence of tetranitromethane confirms that O2.- is a product of the oxidation process. At [ECu(I)]/([ECu(I)] + [ECu(II)]) greater than 0.5 the O2.- produced reacts mainly with ECu(I), increasing the oxidation rate of the enzyme, whereas at [ECu(I)]/([ECu(I)] + [ECu(II)]) less than 0.5 it reacts mainly with ECu(II), decreasing the oxidation rate, the kinetics, at constant O2 concentration, being an apparent second-order process. The oxidation rate increased linearly with both O2 and OH- concentration, indicating that only a deprotonated form of the ECu(I) reacts with O2.-.

The oxidation state of Cu,Zn superoxide dismutase was investigated by 19F-NMR spectroscopy in intact red blood cells and in their lysates. The superoxide dismutase concentration was determined in the red cells both by activity and by F− nuclear relaxation rate measurements and the results obtained showed that the high relaxation rate of F− in erythrocytes is mainly due to the presence of superoxide dismutase. The relaxation rate of F− was unaffected or slightly increased by the addition of a superoxide ion generating system to the cells or to their lysates so indicating that superoxide dismutase is fundamentally in steady state. The results are discussed in terms of the possible reactions of the enzyme in erythrocytes.

The rate of generation of superoxide ion, the concentration of Cu, Zn superoxide dismutase and the hematalogical parameters were measured in red blood cells obtained from Fanconi anemia patients and from healthy individuals. No significative difference in the superoxide dismutase concentration was found, while the rate of generation of the superoxide ion doubled in Fanconi anemia patients. The steady-state concentration of the superoxide ion was calculated from these data and was found to be 2.3 times higher in Fanconi anemia erythrocytes than in controls. The possible consequences with respect to the alterations in FA are discussed.

The generation of superoxide ion in human red blood cell lysates was investigated by an experimental method employing Cu,Zn superoxide dismutase as O2- scavenger and EPR to probe the oxidation state of the enzyme. The average value of the O2- flux in the erythrocytes of 8 normal individuals was (2.02 +/- 0.97) X 10(-8) M S-1. A progressive saturation of the rate of O2- production was found increasing PO2, KM = 1.04 X 10(-4) M, while the autoxidation of oxyhemoglobin did not contribute significantly to the measured O2- production.