An experimental and theoretical study of the morphine binding capacity and kinetics of an engineered opioid receptor

Electrochemical real-time monitoring of ligand binding to an engineered opioid receptor specific for morphine is reported. In the particular systems studied, 90% of the binding was found to be completed after only 85-120 s. Thus, the binding kinetics has proven to be more rapid than previously believed. The observed association rate constant for the morphine binding reaction was calculated to be 215 M(-1)s(-1). A theoretical analysis of the experimental binding data suggested that the binding sites of the engineered opioid receptor could best be described by a model having two populations of binding sites: K(D)=40 microM (13 micromol/g) and K(D)=205 microM (29 micromol/g). Furthermore, a theoretical model was developed in order to explain the observed binding of the engineered opioid receptor. This model suggested that the binding sites on the polymer surface are up to 5.1A deep and they allow 100% of the ligand (morphine) to anchor itself into the site. The predicted theoretical maximum binding capacity for the reported receptor is calculated to be approximately 2 mmol/g polymer (based on an increase of cavity density).     

Structure-chiroptical properties relationship in clavams: an experimental and theoretical study

It is well known that the biological activity of clavams depends strongly on the absolute configuration at the ring junction carbon atom. Therefore, development of the efficient stereo-controlled synthetic methods for the new oxygen analogs of penams, and the structure-activity relationship studies call for a reliable determination of the absolute stereochemistry of newly synthesized compounds. Recently, we proposed an empirical helicity rule relating the configuration of the bridgehead carbon atom to the sign of the 240 nm band observed in the electronic circular dichroism (ECD) spectrum of clavams. In the present work, we investigate the validity of this structure-property relationship for several enantiomeric pairs of model compounds possessing an additional, interfering chromophore in the molecule. For this purpose a combination of the ECD spectroscopy and the time-dependent density functional theory (TD-DFT) is used. A comparison of the ECD spectra with the theoretical ones obtained by the TD-DFT calculations gives a reasonable interpretation of the Cotton effects observed in the 250-220 nm spectral range. Moreover, the calculations confirm validity of the helicity rule for systems studied here and demonstrate that ECD spectroscopy may be used as a highly sensitive probe of the three-dimensional molecular structure of clavams.     

Metachromasy: an experimental and theoretical reevaluation

Non-chromotropic substances such as fibrin and gelatin and most tissue and cellular structures stain orthochromatically with internal dye concentrations of such metachromatic dyes as methylene blue and toluidine blue which, if in solution, would be metachromatic. Therefore, at ordinary levels of staining these substances depress the natural tendency of these dyes to change color. However, at elevated levels of dye-binding metachromasy eventually occurs. This phenomenon is explained on the basis of the distribution of dye-binding sites. In these substrates, by contrast with chromotropic substances, many binding sites are too far removed for dye interaction, consequently the interaction frequency can become high enough to produce a color change only as saturation of the available sites is approached. It is also shown that the destruction of color is a characteristic of metachromasy and that water molecules intercalated between approximated dye ions are responsible for the loss and change of color. A concept of metachromasy is proposed in which the interaction between water molecules and suitably approximated dye ions plays an essential role. The experimental studies are described against a background of the history and evolution of ideas on metachromasy. The literature is reviewed and reassessed particularly from the physicochemical viewpoint.     

Isoelectrically trapped enzymatic bioreactors in a multimembrane cell coupled to an electric field: theoretical modeling and experimental validation with urease

A novel type of immobilized enzyme reactor operating under an electric field is here reported: a multicompartment immobilized enzyme reactor (MIER). In this experimental set-up, the enzyme and zwitterionic buffering ions are trapped in between two isoelectric membranes, having isoelectric point (pl) values so far apart as to trap the enzyme by an isoelectric mechanism, while allowing operation at pH optima, even when the latter pH value is quite removed from the enzyme pl. As an example, urease (pl 4.9) is trapped between a pl 4.0 and a pl 8.0 membranes, thus permitting operation (via suitable amphoteric ions buffering at pH 7.5) at the pH of optimum of activity (pH 7.5). The charged product (ammonium ions) quickly leaves the enzyme chamber under the influence of the electric field, thus allowing sustained activity for much longer time periods than in conventional reactors. As an example, while in a batch reactor 90% of original enzyme activity is lost in 200 min, only 2% activity is lost in the same period in the MIER reactor. As an additional bonus, the MIER reactor allows conversion rates of approximately 95% in a wide range of substrate concentrations, whereas batch-type reactors rarely achieve better than 50% conversion under comparable experimental conditions. (c) 1997 John Wiley & Sons, Inc.     

Turbidity as a probe of tubulin polymerization kinetics: a theoretical and experimental re-examination

We report here an examination of the validity of the experimental practice of using solution turbidity to study the polymerization kinetics of microtubule formation. The investigative approach proceeds via numerical solution of model rate equations to yield the time dependence of each microtubule species, followed by the calculation of the time- and wavelength-dependent turbidity generated by the calculated distribution of rod lengths. The wavelength dependence of the turbidity along the time course is analyzed to search for generalized kinetic regimes that satisfy a constant proportionality relationship between the observed turbidity and the weight concentration of polymerized tubulin. An empirical analysis, which permits valid interpretation of turbidity data for distributions of microtubules that are not long relative to the wavelength of incident light, is proposed. The basic correctness of the simulation work is shown by the analysis of the experimental time dependence of the turbidity wavelength exponent for microtubule formation in taxol-supplemented 0.1 M Pipes buffer (1 mM GTP, 1 mM EGTA, 1 mM MgSO4, pH 6.4). We believe that the general findings and principles outlined here are applicable to studies of other fibril-forming systems that use turbidity as a marker of polymerization progress.     

Peroxidase oxidation of lignin and its model compounds

The published information on the use of enzymes belonging to a large family of peroxidases of plant and fungal origin as the catalysts of lignin and its model compound oxidation by hydrogen peroxide are reviewed. The structures and the mechanism of the catalytic action of these enzymes are comparatively considered. The enzymes have similar structures; however, the enzymes of plant origin have higher stabilities and pH optima. It was concluded that further studies of the effect of the functional nature, polymolecular properties, and regularities of the redox conversions during the catalytic oxidation of plant lignins by plant peroxidases are promising.     

Enzyme reaction kinetics in organic solvents: A theoretical kinetic model and comparison with experimental observations

A theoretical kinetic model has been developed in order to describe the enzyme reaction in organic solvents. In this model the hydration of the enzyme molecule was examined and the equilibrium kinetic constants expressed in terms of thermodynamic activity. Analysis of a proposed kinetic model shows that the enzyme reaction rate in organic solvents is determined by two factors: substrate solvation and enzyme hydration, which are determined by the activity coefficient of the substrate and the water activity of the reaction media, respectively. The activity coefficient of the substrate and the water activity have been calculated using the UNIFAC equation to analyze the effects of organic solvents on the rate of enzyme reaction, and the results were compared with experimental data. Predictions of the proposed model were found to be in good agreement with previous experimental observations.     

Fluorescent sensors based on BODIPY derivatives for aluminium ion recognition: an experimental and theoretical study

Two BODIPY derivative sensors for metal ion recognition containing 10-(4-hydroxyphenyl) (L1) and 10-(3,4-dihydroxyphenyl) (L2) were synthesized in a one-pot reaction of benzaldehyde derivative and 2,4-dimethylpyrrole in the presence of trifluoroacetic acid as catalyst. The binding abilities between these sensors and 50 equivalents of Na⁺, K⁺, Ag⁺, Ca²⁺, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Cd²⁺, Pb²⁺, Al³⁺ and Cr³⁺ ions were studied using UV–vis and fluorescent spectroscopic methods. Of all the metal ions tested, Al³⁺ ion showed the greatest decrease in intensity in the spectra of the sensors, and therefore Al³⁺ ion forms the strongest complex. The binding abilities of BODIPY receptors with Na⁺, Ag⁺, Ca²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺ and Al³⁺ ions were also investigated using density functional theory (DFT) calculations at B3LYP/LanL2DZ theoretical level. The calculated results point to the same conclusion. DFT calculations also provided the HOMO–LUMO energy levels, which can explain the spectrum change upon complexation.

Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase

AAO (aryl-alcohol oxidase) provides H?O? in fungal degradation of lignin, a process of high biotechnological interest. The crystal structure of AAO does not show open access to the active site, where different aromatic alcohols are oxidized. In the present study we investigated substrate diffusion and oxidation in AAO compared with the structurally related CHO (choline oxidase). Cavity finder and ligand diffusion simulations indicate the substrate-entrance channel, requiring side-chain displacements and involving a stacking interaction with Tyr?2. Mixed QM (quantum mechanics)/MM (molecular mechanics) studies combined with site-directed mutagenesis showed two active-site catalytic histidine residues, whose substitution strongly decreased both catalytic and transient-state reduction constants for p-anisyl alcohol in the H502A (over 1800-fold) and H546A (over 35-fold) variants. Combination of QM/MM energy profiles, protonation predictors, molecular dynamics, mutagenesis and pH profiles provide a robust answer regarding the nature of the catalytic base. The histidine residue in front of the FAD ring, AAO His??2 (and CHO His???), acts as a base. For the two substrates assayed, it was shown that proton transfer preceded hydride transfer, although both processes are highly coupled. No stable intermediate was observed in the energy profiles, in contrast with that observed for CHO. QM/MM, together with solvent KIE (kinetic isotope effect) results, suggest a non-synchronous concerted mechanism for alcohol oxidation by AAO.     

A joint experimental and theoretical investigation of kinetics and mechanistic study in a synthesis reaction between triphenylphosphine and dialkyl acetylenedicarboxylates in the presence of benzhydrazide

Stable crystalline phosphorus ylides were obtained in excellent yields from the 1:1:1 addition reaction between triphenylphosphine (TPP) and dialkyl acetylenedicarboxylates, in the presence of NH-acids, such as benzhydrazide. To determine the kinetic parameters of the reactions, they were monitored by UV spectrophotometery. The second order fits were automatically drawn and the values of the second order rate constant (k₂) were calculated using standard equations within the program. At the temperature range studied the dependence of the second order rate constant (Ln k₂) on reciprocal temperature was compatible with Arrhenius equation. This provided the relevant plots to calculate the activation energy of all reactions. Furthermore, useful information were obtained from studies of the effect of solvent, structure of reactants (different alkyl groups within the dialkyl acetylenedicarboxylates) and also concentration of reactants on the rate of reactions. On the basis of experimental data the proposed mechanism was confirmed according to the obtained results and a steady state approximation and the first step (k₂) and third (k₃) steps of the reactions were recognized as the rate determining steps, respectively. In addition, three speculative proposed mechanisms were theoretically investigated using quantum mechanical calculation. The results, arising from the second and third speculative mechanisms, were far from the experimental data. Nevertheless, there was a good agreement between the theoretical kinetic data, emerge from the first speculative mechanism, and experimental kinetic data of proposed mechanism.

Peroxidase catalyzed oxidation of naturally-occurring phenols and hardwood lignins

Horseradish peroxidase and hydrogen peroxide form phenoxy radicals from 4-substituted-2,6-dimethoxyphenols, milled wood lignin and alkali lignins. A number of factors governing this reaction are examined. Side chain cleavage to quinones is the principal disproportionation reaction of these radicals. Catalysis by UV light and inhibition by quinones is observed. Aerobic oxidation of phenols is catalyzed by small amounts of hydrogen peroxide. Lignin substrates are degraded by the same oxidation mechanism as are the simple phenolic substrates.     

Electrical activity and metabolism in cardiac tissue: An experimental and theoretical study

Summary (1) Effects of the metabolic inhibitor 2,4-dinitrophenol (DNP) on electrical activity in frog atria were studied by means of the sucrose-gap technique and in tracer experiments. (2) Voltage-clamp studies of ionic membrane currents showed a suppression by DNP of peak Na inward current without marked changes in the kinetics of the Na-carrying system and an increase of steady state outward current to three to five times its normal value. In⁴²K tracer experiments, DNP increased K resting efflux by about 10% and decreased K influx by 25 to 30%. (3) The depression of Na inward current is regarded as being caused by a partial block of Na channels and an increase of internal Na concentration after inhibition of active Na extrusion. (4) The strong rise in outward current is probably not caused by a K current since K efflux fails to show a correspondingly large change. As a possible explanation for current and flux changes, an electrogenic K pump is discussed. (5) A mathematical model of a carrier system transporting a single ion species is described. The system is designed as a direct potential pump. Uphill transport requires an asymmetry of the rate constants governing the cyclic formation and breakdown of carrier-ion complex. The asymmetry is brought about by an input of metabolic energy. Reduction of energy input decreases the asymmetry and induces a carrier-mediated downhill ion movement, with corresponding changes in membrane current and ion fluxes. (6) A model of electrogenic K inward transport is calculated that approximately accounts for the steady state current and the K flux changes experimentally observed after inhibition.