Biomedical subjects

R Varón

Publications and source records attributed to R Varón.

At least 19 recordsLinked to original sources

PubMed2006

An approximate analytical solution to the lag period of monophenolase activity of tyrosinase.

Tyrosinase shows a lag period in its action on monophenols (l-tyrosine). We propose an approximate analytical solution for the lag period, which fulfils the dependences with regard to initial enzyme concentration, and initial monophenol concentration. Furthermore, from a study of the dependences of the lag period on these variables, we can determine experimentally the o-diphenol concentration in the steady state. The Michaelis constant of the o-diphenol in the presence of the monophenol can be determined from the relationship between the o-diphenol concentration in the steady state and the initial monophenol concentration, taking into consideration the experimentally calculated Michaelis constant for the monophenol substrate. Although this Michaelis constant is much lower than the Michaelis constant for diphenol in the absence of monophenol, the binding site is the same. A kinetic analysis of the action mechanism of tyrosinase explains this difference in the values of the Michaelis constants.

Agaricales↗

PubMed2006

Expressions for the fractional modification in different monocyclic enzyme cascade systems: analysis of their validity tested by numerical integration.

This paper presents the derivation, under a minimal set of assumptions, of a general expression for the steady-state fractional modification of an interconvertible protein involved in four different schemes of monocyclic enzyme cascade systems. From this general expression we derive, as particular cases, other, simpler expressions by applying additional assumptions and which have, therefore, a smaller range of validity. Some of these particular expressions coincide with those already obtained in previous contributions on individualised analyses. We discuss the relationships between the kinetic parameters and the concentrations needed for the fulfilment of the additional assumptions. The goodness of the analysis was tested by reference to the shape in the steady-state of the simulated time progress curves obtained by numerical integration.

Algorithms↗

PubMed2006

Kinetic analysis of a general model of activation of aspartic proteinase zymogens.

Starting from a simple general reaction mechanism of activation of aspartic proteinase zymogens involving an uni- and a bimolecular simultaneous route, the time course equation of the concentration of the zymogen and of the activated enzyme have been derived. From these equations, an analysis quantifying the relative contribution to the global process of the two routes has been carried out for the first time. This analysis suggests a way to predict the time course of the relative contribution as well as the effect of the initial zymogen and activating enzyme concentrations, on the relative weight. An experimental design and kinetic data analysis is suggested to estimate the kinetic parameters involved in the reaction mechanism proposed. Finally, we apply some of our results to experimental data obtained by other authors in experimental studies of the activation of some aspartic proteinase zymogens.

Animals↗

PubMed2006

Calculating molar absorptivities for quinones: application to the measurement of tyrosinase activity.

The molar absorptivities of the quinones produced from different o-diphenols, triphenols, and flavonoids were calculated by generating the respective quinones through oxidation with an excess of periodate. Oxidation of these substrates by this reagent was analogous to oxidation by tyrosinase with molecular oxygen, although the procedure showed several advantages over the enzymatic method in that oxidation took place almost immediately and quinone stability was favored because no substrate remained. The o-diphenols studied were pyrocatechol, 4-methylcatechol, 4-tert-butylcatechol, 3,4-dihydroxyphenylalanine, 3,4-dihydroxyphenylethylamine, 3,4-dihydroxyphenylacetic acid, 3,4-dihydroxyphenylpropionic acid, and caffeic acid; the triphenols studied were pyrogallol, 1,2,4-benzenetriol, 6-hydroxydopa, and 6-hydroxydopamine; and the flavonoids studied were (+)catechin, (-)epicatechin, and quercetin. In addition, the stability of the quinones generated by oxidation of the compounds by [periodate]0/[substrate]0 << 1 was studied. Taking the findings into account, tyrosinase could be measured by following o-quinone formation in rapid kinetic studies using the stopped-flow method. However, measuring o-quinone formation could not be useful for steady-state studies. Therefore, several methods for following tyrosinase activity are proposed, and a kinetic characterization of the enzyme's action on these substrates is made.

Benzoquinones↗

PubMed2005

The influence of product instability on slow-binding inhibition.

We present a kinetic study of an enzyme reaction that takes place with slow-binding inhibition where the immediate product undergoes a spontaneous or induced process of decomposition. A kinetic study of an enzyme process, in which a slow-binding inhibition process and a decomposition of the immediate product of the reaction take place simultaneously is performed. The corresponding explicit concentration-time equations were obtained. Using the analytical solutions obtained, which were tested numerically, we suggest a procedure that allows the discrimination between the particular cases considered and the evaluation of the principal kinetic parameters of the reaction.

Enzyme Inhibitors↗

PubMed2004

Tyrosinase kinetics: discrimination between two models to explain the oxidation mechanism of monophenol and diphenol substrates.

The kinetic behaviour of tyrosinase is very complex because the enzymatic oxidation of monophenol and o-diphenol to o-quinones occurs simultaneously with the coupled non-enzymatic reactions of the latter. Both reaction types are included in the kinetic mechanism proposed for tyrosinase (Mechanism I [J. Biol. Chem. 267 (1992) 3801-3810]). We previously confirmed the validity of the rate equations by the oxidation of numerous monophenols and o-diphenols catalysed by tyrosinase from different fruits and vegetables. Other authors have proposed a simplified reaction mechanism for tyrosinase (Mechanism II [Theor. Biol. 203 (2000) 1-12]), although without deducing the rate equations. In this paper, we report new experimental work that provides the lag period value, the steady-state rate, o-diphenol concentration released to the reaction medium. The contrast between these experimental data and the respective numerical simulations of both mechanisms demonstrates the feasibility of Mechanism I. The need for the steps omitted from Mechanism II to interpret the experimental data for tyrosinase, based on the rate equations previously deduced for Mechanism I is explained.

Agaricales↗

PubMed2003

Mean residence times in linear compartmental systems. Symbolic formulae for their direct evaluation.

A complete analysis has been performed of the mean residence times in linear compartmental systems, closed or open, with or without traps and with zero input. This analysis allows the derivation of explicit and simple general symbolic formulae to obtain the mean residence time in any compartment of any linear compartmental system, closed or open, with or without traps, as well as formulae to evaluate the mean residence time in the entire system like the above situations. The formulae are given as functions of the fractional transfer coefficients between the compartments and, in the case of open systems, they also include the excretion coefficients to the environment from the different compartments. The relationship between the formulae derived and the particular connection properties of the compartments is discussed. Finally, some examples have been solved.

Algorithms↗

PubMed2002

Kinetic analysis of the general modifier mechanism of Botts and Morales involving a suicide substrate.

Suicide substrates are widely used in enzymology for studying enzyme mechanisms and designing potential drugs. The presence of a reversible modifier decreases or increases the rate of substrate-induced inactivation, with evident physiological and experimental consequences. To date, only the action of a competitive or uncompetitive inhibitor of an enzyme system involving suicide substrate has been reported. In this paper, we analyse the kinetics of enzyme-catalysed reactions which evolve in accordance with the general modifier mechanisms of Botts and Morales in which enzyme inactivation is induced by suicide substrate. Rapid equilibrium of all of the reversible reaction steps involved is assumed and the time course equations for the residual enzyme activity, the inactive enzyme forms and the reaction product are derived. Partition ratios giving the relative weight of the product and inactive enzyme concentrations, and the relative contribution to the product formation of each of the unmodified and modified catalytic routes, are studied. New indices pointing to the conditions under which the modifier acts as inhibitor or as activator are suggested. The goodness of the analytical solutions is tested by comparison with the simulated curves obtained by numerical integration. An experimental design and kinetic data analysis to evaluate the kinetic parameters from the time progress curves of the product are proposed. From these results, those corresponding to several reaction mechanisms involving both a suicide substrate and a modifier, and which can be regarded as particular cases of the general case analysed here, can be directly and easily derived.

Animals↗

PubMed2002

Linear mixed irreversible inhibition of the autocatalytic activation of zymogens. Kinetic analysis checked by simulated progress curves.

Autocatalytic zymogen activation is a phenomenon of great importance for understanding some fundamental physiological processes involved in the enzyme regulation of gastrointestinal-tract enzymes, blood coagulation, fibrinolysis and the complement system. Examples of such processes are the activation of prekallikrein, trypsinogen and pepsinogen, all of which are controlled by natural proteinase inhibitors. This work studies the kinetics of a general autocatalytic zymogen activation process overlapped by two two-step irreversible inhibitions, i.e. a linear mixed irreversible inhibition. The kinetic equations for the whole course of the reaction are derived for this mechanism. In addition, we determine the corresponding kinetics for a number of particular cases of the general model analyzed, i.e. for reversible and irreversible non-competitive, competitive and uncompetitive inhibition systems which are considered particular cases of the general mechanism studied. The kinetic behavior of the system is related to a parameter, a dimensionless quantity, which shows whether the inhibition or the activation route prevails, in a similar way to that which we have previously carried out for other mechanisms. Finally, based on the kinetic equations obtained, a procedure for discriminating between the different mechanisms considered is suggested. The results of this contribution can be directly applied to most physiological autocatalytic zymogen activations in the presence of an inhibitor, allowing their complete kinetic characterization and suggesting procedures for varying the relative weight of the catalytic and inhibition routes or for changing the predominant route.

Algorithms↗

PubMed2001

Tyrosinase action on monophenols: evidence for direct enzymatic release of o-diphenol.

Using gas chromatography-mass spectrometry, the direct enzymatic release of o-diphenol (4-tert-butylcatechol) during the action of tyrosinase on a monophenol (4-tert-butylphenol) has been demonstrated for the first time in the literature. The findings confirm the previously proposed mechanism to explain the action of tyrosinase on monophenols (J.N. Rodríguez-López, J. Tudela, R. Varón, F. García-Carmona, F. García-Cánovas, J. Biol. Chem. 267 (1992)). Oxytyrosinase, the oxidized form of the enzyme with a peroxide group, is the only form capable of catalysing the transformation of monophenols into diphenols, giving rise to an enzyme-substrate complex in the process. The o-diphenol formed is then released from the enzyme-substrate complex or oxidized to the corresponding o-quinone. In order to detect the enzymatic release of o-diphenol, the non-enzymatic evolution of the o-quinone to generate o-diphenol by weak nucleophilic attack reactions and subsequent oxidation-reduction was blocked by the nucleophilic attack of an excess of cysteine. Furthermore, the addition of catalytic quantities of an auxiliary o-diphenol (e.g. catechol) considerably increases the accumulation of 4-tert-butylcatechol. The enzyme acting on 4-tert-butylphenol generates the enzyme-4-tert-butylcatechol complex and 4-tert-butylcatechol is then released (with k(-2)) generating mettyrosinase. The auxiliary o-diphenol added (catechol) and the 4-tert-butylcatechol generated by the enzyme then enter into competition. When [catechol] >> [4-tert-butylcatechol], the enzyme preferentially binds with the catechol to close the catalytic cycle, while 4-tert-butylcatechol is accumulated in the medium. In conclusion, we demonstrate that the enzyme produces 4-tert-butylcatechol from 4-tert-butylphenol, the concentration of which increases considerably in the presence of an auxiliary o-diphenol such as catechol.

Agaricales↗

PubMed2001

Analysis and interpretation of the action mechanism of mushroom tyrosinase on monophenols and diphenols generating highly unstable o-quinones.

Tyrosinase can act on monophenols because of the mixture of met- (E(m)) and oxy-tyrosinase (E(ox)) which exists in the native form of the enzyme. The latter form is active on monophenols, while the former is not. However, the kinetics are complicated because monophenols can bind to both enzyme forms. This situation becomes even more complex since the products of the enzymatic reaction, the o-quinones, are unstable and continue evolving to generate o-diphenols in the medium. In the case of substrates such as L-tyrosine, tyrosinase generates very unstable o-quinones, in which a process of cyclation and subsequent oxidation-reduction generates o-diphenol through non-enzymatic reactions. However, the release of o-diphenol through the action of the enzyme on the monophenol contributes to the concentration of o-diphenol in the first pseudo-steady-state [D(0)](ss). Hence, the system reaches an initial pseudo-steady state when t-->0 and undergoes a transition phase (lag period) until a final steady state is reached when the concentration of o-diphenol in the medium reaches the concentration of the final steady state [D(f)](ss). These results can be explained by taking into account the kinetic and structural mechanism of the enzyme. In this, tyrosinase hydroxylates the monophenols to o-diphenols, generating an intermediate, E(m)D, which may oxidise the o-diphenol or release it directly to the medium. We surmise that the intermediate generated during the action of E(ox) on monophenols, E(m)D, has axial and equatorial bonds between the o-diphenol and copper atoms of the active site. Since the orbitals are not coplanar, the concerted oxidation-reduction reaction cannot occur. Instead, a bond, probably that of C-4, is broken to achieve coplanarity, producing a more labile intermediate that will then release the o-diphenol to the medium or reunite it diaxially, involving oxidation to o-quinone. The non-enzymatic evolution of the o-quinone would generate the o-diphenol ([D(f)](ss)) necessary for the final steady state to be reached after the lag period.

Agaricales↗

PubMed2001

The inactivation of horseradish peroxidase isoenzyme A2 by hydrogen peroxide: an example of partial resistance due to the formation of a stable enzyme intermediate.

The inactivation of horseradish peroxidase A2 (HRP-A2) with H2O2 as the sole substrate has been studied. In incubation experiments it was found that the fall in HRP-A2 activity was non-linearly dependent on H2O2 concentrations and that a maximum level of inactivation of approximately 80% (i.e. approximately 20% residual activity) was obtained with 2,000 or more equivalents of H2O2. Further inactivation was only induced at much higher H2O2 concentrations. Spectral changes during incubations of up to 5 days showed the presence of a compound III-like species whose abundance was correlated to the level of resistance observed. Inactivation was pH dependent, the enzyme being much more sensitive under acid conditions. A partition ratio (r1 approximately equals 1,140 at pH 6.5) between inactivation and catalysis was calculated from the data. The kinetics of inactivation followed single exponential time curves and were H2O2 concentration dependent. The apparent maximum rate constant of inactivation was lambdamax=3.56+/-0.07x10(-4)s(-1) and the H2O2 concentration required to give lambdamax/2 was K2=9.94+/-0.52 mM. The relationship lambdamax<ki has been shown to apply and thus the rate constant of inactivation has been calculated as ki=1.9x10(-3)s(-1). HRP-A2 possessed catalase-like oxygen gas-releasing activity, the catalytic constant being k3=2.2 s(-1), and the affinity for H2O2 as K2=23 mM. Catalase-like activity was pH dependent and favoured under more basic conditions. A mechanistic model has been developed and used to explain the behaviour of HRP-A2. The model suggests that, in common with HRP-C, mechanism-based (suicide) inactivation is being observed but that a fraction of the HRP-A2 is protected from inactivation in the form of a modified compound III species.

Catalase↗

PubMed2001

Time course equations of the amount of substance in a linear compartmental system and their computerized derivation.

In this contribution, we present the symbolic time course equations corresponding to a general model of a linear compartmental system, closed or open, with or without traps and with zero input. The steady state equations are obtained easily from the transient phase equations by setting the time --> infinity. Special attention has been given to the open systems, for which an exhaustive kinetic analysis has been developed to obtain important properties. Besides, the results have been particularized to open systems without traps and an alternative expression for the distribution function of exit times has been provided. We have implemented a versatile computer program, that is easy to use and with a user-friendly format of the input of data and the output of results. This computer program allows the user to obtain all the information necessary to derive the symbolic time course equations for closed or open systems as well as for the derivation of the distribution function of exit times.

Computer Simulation↗

PubMed2001

Kinetic analysis of enzyme systems with suicide substrate in the presence of a reversible, uncompetitive inhibitor.

We present a general kinetic analysis of enzyme catalyzed reactions evolving according to a Michaelis-Menten mechanism, in which an uncompetitive, reversible inhibitor acts. Simultaneously, enzyme inactivation is induced by an unstable suicide substrate, i.e. it is a Michaelis-Menten mechanism with double inhibition: one originating from the substrate and another originating from the reversible inhibitor. Rapid equilibrium of the reversible reaction steps involved is assumed and the time course equations for the reaction product have been derived under the assumption of limiting enzyme. The goodness of the analytical solutions has been tested by comparison with simulated curves obtained by numerical integration. A kinetic data analysis to determine the corresponding kinetic parameters from the time progress curve of the product is suggested.

Enzyme Inhibitors↗

PubMed2001

Kinetic analysis of enzyme systems with suicide substrate in the presence of a reversible competitive inhibitor, tested by simulated progress curves.

The use of suicide substrates remains a very important and useful method in enzymology for studying enzyme mechanisms and designing potential drugs. Suicide substrates act as modified substrates for the target enzymes and bind to the active site. Therefore the presence of a competitive reversible inhibitor decreases the rate of substrate-induced inactivation and protects the enzyme from this inactivation. This lowering on the inactivation rate has evident physiological advantages, since it allows the easy acquisition of experimental data and facilitates kinetic data analysis by providing another variable (inhibitor concentration). However despite the importance of the simultaneous action of a suicide substrate and a competitive reversible inhibition, to date no corresponding kinetic analysis has been carried out. Therefore we present a general kinetic analysis of a Michaelis-Menten reaction mechanism with double inhibition caused by both, a suicide substrate and a competitive reversible inhibitor. We assume rapid equilibrium of the reversible reaction steps involved, while the time course equations for the reaction product have been derived with the assumption of a limiting enzyme. The goodness of the analytical solutions has been tested by comparison with the simulated curves obtained by numerical integration. A kinetic data analysis to determine the corresponding kinetic parameters from the time progress curve of the product is suggested. In conclusion, we present a complete kinetic analysis of an enzyme reaction mechanism as described above in an attempt to fill a gap in the theoretical treatment of this type of system.

Binding Sites↗

PubMed2000

Stopped-flow and steady-state study of the diphenolase activity of mushroom tyrosinase.

The reaction of mushroom (Agaricus bisporus) tyrosinase with dioxygen in the presence of several o-diphenolic substrates has been studied by steady-state and transient-phase kinetics in order to elucidate the rate-limiting step and to provide new insights into the mechanism of oxidation of these substrates. A kinetic analysis has allowed for the first time the determination of individual rate constants for several of the partial reactions that comprise the catalytic cycle. Mushroom tyrosinase rapidly reacts with dioxygen with a second-order rate constant k(+8) = 2.3 x 10(7) M(-)(1) s(-)(1), which is similar to that reported for hemocyanins [(1.3 x 10(6))-(5.7 x 10(7)) M(-)(1) s(-)(1)]. Deoxytyrosinase binds dioxygen reversibly at the binuclear Cu(I) site with a dissociation constant K(D)(O)()2 = 46.6 microM, which is similar to the value (K(D)(O)()2 = 90 microM) reported for the binding of dioxygen to Octopus vulgaris deoxyhemocyanin [Salvato et al. (1998) Biochemistry 37, 14065-14077]. Transient and steady-state kinetics showed that o-diphenols such as 4-tert-butylcatechol react significantly faster with mettyrosinase (k(+2) = 9.02 x 10(6) M(-)(1) s(-)(1)) than with oxytyrosinase (k(+6) = 5.4 x 10(5) M(-)(1) s(-)(1)). This difference is interpreted in terms of differential steric and polar effects that modulate the access of o-diphenols to the active site for these two forms of the enzyme. The values of k(cat) for several o-diphenols are also consistent with steric and polar factors controlling the mobility, orientation, and thence the reactivity of substrates at the active site of tyrosinase.

Agaricus↗

PubMed2000

Kinetics of a self-amplifying substrate cycle: ADP-ATP cycling assay.

A kinetic study of an ATP-ADP amplification cyclic system involving the enzymes adenylate kinase, pyruvate kinase and L-lactate dehydrogenase has been made. The stoichiometry of the cycle is 2:1, because two molecules of ADP are synthesized from one each of ATP and AMP, and one molecule of ADP is converted back into one of ATP at each turn of the cycle. This results in a continuous exponential increase in the concentrations of ATP and ADP in the reaction medium, according to the equations obtained. This is therefore a substrate cycle that amplifies itself, the cycling rate increasing continuously with time. The background signal of the reagent was reduced by using apyrase to degrade ATP and ADP in the reagent, permitting detection limits as low as 16 pmol of ATP and/or ADP in a continuous spectrophotometric assay.

Adenosine Diphosphate↗

PubMed2000

Kinetic study of the oxidation of 3-hydroxyanisole catalysed by tyrosinase.

Tyrosinase hydroxylates 3-hydroxyanisole in the 4-position. The reaction product accumulates in the reaction medium with a lag time (tau) which diminishes with increasing concentrations of enzyme and lengthens with increasing concentrations of substrate, thus fulfilling all the predictions of the mechanism proposed by us for 4-hydroxyphenols. The kinetic constants obtained, kcatM = (46.87 +/- 2.06) s-1 and KmM = (5.40 +/- 0.60) mM, are different from those obtained with 4-hydroxyanisole, kcatM = (184.20 +/- 6.1) s-1 and KmM = (0.08 +/- 0.004) mM. The catalytic efficiency, kcatM/KmM is, therefore, 265.3 times greater with 4-hydroxyanisole. The possible rate-determining steps for the reaction mechanism of tyrosinase on 3- and 4-hydroxyanisole, based on the NMR spectra of both monophenols, are discussed. These possible rate-determining steps are the nucleophilic attack of hydroxyl's oxygen on the copper and the electrophilic attack of the peroxide on the aromatic ring. Both steps may be of similar magnitude, i.e. take place in the same time scale.

Agaricales↗