DNA-modified electrodes. Part 6. A new method for the determination of binding constants and binding site sizes

A new method was developed to obtain the binding constant (K) and binding site size (n) for the interaction of DNA with other molecules using DNA-modified gold electrodes. This method is simple and microsample-consuming compared with conventional solution methods. A Q-basic program was designed to calculate K and n values. The results show that the K and n values obtained by the new method approach those obtained by conventional electrochemical methods, indicating the suitability of this method.     

Rapid screening of binding constants by calibrated competitive 1H NMR spectroscopy

A calibrated competitive NMR method has been developed that is appropriate for the rapid screening of binding constants. This method involves the initial characterisation of a receptor-substrate binding event for which the (1)H NMR spectrum of a given receptor (calibrant) is modified by the substrate of interest at a range of concentrations. For all subsequent "unknown" receptors, K(a) values are then determined by using a competition assay (in the presence of the calibrant receptor) by measuring a single standard (1)H NMR spectrum. This enables a rapid assessment of the recognition properties of a library of potential receptors. Only the calibrant receptor needs to be NMR active, while the library of putative receptors, as well as the substrate, can be NMR silent. This method assumes the formation of complexes of 1:1 stoichiometry. To demonstrate this methodology, the binding of a number of crown ether type compounds with K+ ions has been studied. Comparison of the binding strengths obtained by using this approach with those in the literature shows excellent agreement. A range of new compounds that have recently been synthesised within our group has also been screened in order to illustrate how this approach can rapidly assess binding ability. This method has significance for chemists working in the fields of combinatorial receptor/substrate design and supramolecular chemistry as a means of rapid optimisation of binding strength.     

A general mass spectrometry-based assay for the quantitation of protein-ligand binding interactions in solution

A new method that utilizes matrix-assisted laser desorption/ionization (MALDI) mass spectrometry and exploits the hydrogen/deuterium (H/D) exchange properties of proteins was developed for measuring the thermodynamic properties of protein-ligand complexes in solution. Dissociation constants (Kd values) determined by the method for five model protein-ligand complexes that included those with small molecules, nucleic acids, peptides, and other proteins were generally in good agreement with Kd values measured by conventional methods. Important experimental advantages of the described method over existing methods include: the ability to make measurements in a high-throughput and automated fashion, the ability to make measurements using only picomole quantitities of protein, and the ability to analyze either purified or unpurified protein-ligand complexes.     

Comparison between conventional and ultrasound accelerated Tessier sequential extraction schemes for metal fractionation in sewage sludge

Chemical sequential extraction for metal fractionation in sewage sludge using the Tessier method has been accelerated by ultrasound. The two sequential extraction schemes (conventional and ultrasound accelerated) were compared in terms of extraction efficiency, precision, treatment time and partitioning patterns of metals. Extractable contents of Cu, Cr, Ni, Pb and Zn were measured by flame atomic absorption spectrometry, and the analytical results obtained by the two procedures were statistically compared (P = 0.95). No significant differences were found in the two first fractions (i.e. exchangeable and carbonate-bound), however, in the third and fourth extracts (i.e. Fe-Mn oxides-bound and organic matter-bound) the extraction capability of the two methods differed significantly. Received: 15 June 1998 / Revised: 10 November 1998 / Accepted: 11 November 1998     

Comparison between conventional and ultrasound accelerated Tessier sequential extraction schemes for metal fractionation in sewage sludge

Chemical sequential extraction for metal fractionation in sewage sludge using the Tessier method has been accelerated by ultrasound. The two sequential extraction schemes (conventional and ultrasound accelerated) were compared in terms of extraction efficiency, precision, treatment time and partitioning patterns of metals. Extractable contents of Cu, Cr, Ni, Pb and Zn were measured by flame atomic absorption spectrometry, and the analytical results obtained by the two procedures were statistically compared (P = 0.95). No significant differences were found in the two first fractions (i.e. exchangeable and carbonate-bound), however, in the third and fourth extracts (i.e. Fe-Mn oxides-bound and organic matter-bound) the extraction capability of the two methods differed significantly. Received: 15 June 1998 / Revised: 10 November 1998 / Accepted: 11 November 1998     

Synthesis and binding properties of a noncovalent molecularly imprinted testosterone-specific polymer

In this study, molecular imprinting was used to develop a method based on noncovalent interactions for synthesis of a testosterone-specific polymer. The effect of the different template–monomer ratios, the particle sizes of polymers, and chromatographic mobile phases on steroid–polymer interactions are discussed. The polymer obtained was found to interact specifically with testosterone, while other steroids under study were eluted close to the void volume in the HPLC experiments. Batch rebinding studies in acetonitrile were undertaken to quantitatively evaluate the affinity of the polymer for testosterone. During this experiment, the testosterone concentration was measured in two ways: spectrophotometrically and by HPLC on a column with testosterone-specific imprinted polymer synthesized by us. Both methods resulted in similar values of association constants and the number of binding sites. However, the second method has obvious advantages when the analyzed solution contains a mixture of optically dense compounds. The results obtained focus on the two-point binding nature of the imprinted polymer–testosterone interaction and the significant role of hydrogen bonds between the OH group of testosterone and carboxy group of methacrylic acid residues inside specific recognition sites of the imprinted polymer. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 1725–1732, 1998     

Binding constant measurement by hyper-Rayleigh scattering: bilirubin-human serum albumin binding as a case study

In this paper, a new application of the hyper-Rayleigh scattering technique in determining multiple binding constants of a small molecule like bilirubin to a macromolecule like the protein human serum albumin has been demonstrated. Human serum albumin has two binding sites for bilirubin, and the binding constants have been measured by carrying out a second harmonic titration of the protein against bilirubin and vice versa. The measured binding constants K(1) = 1.5 +/- 0.43 x 10(7) M(-1) and K(2) = 1.01 +/- 0.16 x 10(6) M(-1) agree well with the reported values obtained by other methods.     

Investigation of drug-cyclodextrin complexes by a phase-distribution method: some theoretical and practical considerations

The purpose of the study was to evaluate an octanol-water phase distribution method for investigation of drug/cyclodextrin (D/CD) complexes and to compare stability constant values obtained by this method to values obtained by the phase solubility method. A general equation for determination of 1 : 1 D/CD complex stability constant (K1 : 1) from the slope of a phase-distribution diagram (a diagram of the reciprocal of the apparent partition coefficient vs. the total CD concentration) was derived. The equation accounted for the possible inclusion of the organic solvent in the CD cavity and the gradual saturation of the CD binding with increasing concentration of the guest compound. This method was used to determine K1 : 1 for 2-hydroxypropyl-beta-cyclodextrin (HPbetaCD) complexes of hydrocortisone, prednisolone, diazepam, beta-estradiol and diethylstilbestrol. These values were comparable to K1 : 1 values determined by the phase-solubility method. The phase-distribution method could also be applied to determine stability constants for the neutral and ionic forms of the weakly acidic drugs, naproxen and triclosan and the weakly basic drug lidocaine. The phase-distribution method is a very versatile and fast method and has the advantage, compared to the phase-solubility method, that it only requires very small drug samples. Thus, this method would be suitable for screening of new drug candidates.     

Minimising the risk of some systematic errors by the use of the single vessel principle for cold vapour atomic absorption spectrometric determination of mercury in biological solids

The suitability of the single vessel principle (performing all steps of an analytical procedure in one vessel) for cold vapour atomic absorption spectrometric determination of mercury in biological solids was evaluated. The single vessel method gave a lower mean blank level with better precision, hence lower detection limits, as compared to the conventional method. The determination of total mercury in biological standard reference materials by the single vessel method also produced significantly higher mercury values and better precision than the conventional method. However, the mercury concentrations obtained in certified reference materials by the use of both methods were close to the mean certified values. Moreover, the use of the single vessel method is cost effective, rapid and environment friendly. The use of the single vessel technique is therefore recommended for accurate and reliable determination of mercury in biological solids. Received: 15 December 1997 / Revised: 9 April 1998 / Accepted: 18 April 1998     

Interaction between natural organic matter (NOM) and polycyclic aromatic compounds (PAC) – comparison of fluorescence quenching and solid phase micro extraction (SPME)

The interaction of phenanthrene and 9-aminophenanthrene with natural organic matter (NOM) of different origin was investigated using the fluorescence quenching approach and the solid phase micro extraction method. The results of both methods are compared in terms of the influence of the concentration of the polycyclic aromatic compounds (PAC) as well as the concentration of the NOM on the observed binding constant. Due to the combination of steady-state and time-resolved fluorescence techniques it could be concluded that the observed fluorescence quenching was caused by a static interaction like a complex formation. While for phenanthrene both analytical methods showed no long term effects and the reaction equilibrium between NOM and phenanthrene was established within the first hour, for 9-aminophenanthrene a slow reaction kinetics (within days) was found indicating specific interactions between NOM and the amino group. Received: 12 November 1998 / Revised: 22 December 1998 / Accepted: 30 December 1998     

Experimental validation of theoretical potassium and sodium cation affinities of amides by mass spectrometric kinetic method measurements

In this study the theoretical Gaussian-2 K(+)/Na(+) binding affinities (enthalpies) at 0 K (in kJ mol(-1)) for six amides in the order: formamide (109.2/138.5) < N-methylformamide (117.7/148.6) < acetamide (118.7/149.5) < N,N-dimethylformamide (123.9/156.4) < N-methylacetamide (125.6/157.7) < N,N-dimethylacetamide (129.2/162.6), reported previously (Siu et al., J. Chem. Phys. 2001; 114: 7045-7051), were validated experimentally by mass spectrometric kinetic method measurements. By monitoring the collision-induced dissociation (CID) of K(+)/Na(+)-bound heterodimers of the amides, the relative affinities were shown to be accurate to within +/-2 kJ mol(-1). With these six theoretical K(+)/Na(+) binding affinities as reference values, the absolute K(+)/Na(+) affinities of imidazole, 1-methylimidazole, pyridazine and 1,2-dimethoxyethane were determined by the extended kinetic method, and found to be consistent (to within +/-9 kJ mol(-1)) with literature experimental values obtained by threshold-CID, equilibrium high-pressure mass spectrometry, and Fourier transform ion cyclotron resonance/ligand-exchange equilibrium methods. A self-consistent resolution is proposed for the inconsistencies in the relative order of K(+)/Na(+) affinities of amides reported in the literature. These two sets of validated K(+) and Na(+) affinity values are useful as reference values in kinetic method measurements of K(+)/Na(+) affinity of model biological ligands, such as the K(+) affinities of aliphatic amino acids.     

Anion binding studies of fluorinated expanded calixpyrroles

The anion binding properties of fluorinated calix[n]pyrroles (n = 4-6) in aprotic solvents (acetonitrile and DMSO) and modified reaction conditions allowing for the synthesis and isolation of the hitherto missing dodecafluorocalix[6]pyrrole from the condensation of 3,4-difluoro-1H-pyrrole and acetone are described. In acetonitrile solution containing 2% water, the association constants for the 1:1 binding interaction between octafluorocalix[4]pyrrole and chloride anion obtained with isothermal titration calorimetry (ITC) and (1)H NMR titration methods were found to match reasonably well. As compared to its nonfluorinated congener, octafluorocalix[4]pyrrole was found to display enhanced binding affinities for several representative anions in pure acetonitrile as judged from ITC analyses. Similar analyses of the fluorinated calix[n]pyrroles revealed an increase in the relative affinity for bromide over chloride with increasing macrocycle size, as manifest in a decrease in the binding ratio K(a(Cl))/K(a(Br)). Anion binding studies in the solid state, involving single-crystal X-ray diffraction analyses of the chloride and acetate anion complexes of octafluorocalix[4]pyrrole and decafluorocalix[5]pyrrole, respectively, confirmed the expected hydrogen bond interactions between the pyrrolic NH protons and the bound anions.     

Improved curve fitting procedures to determine equilibrium binding constants

For ligand-biomacromolecule titration experiments it has been traditional practice to extract parameters such as the equilibrium binding constant K and the number of bases per ligand binding site n with relatively labour intensive methods, usually based on single wavelength data, such as the difference method by Rodger and Nordén coupled together with a Scatchard plot. Presented in this paper are both the theory and a least squares fitting method to derive parameters such as K and n more directly from all spectral non-linear experimental data. Both the case of non competitive binding of a metal complex ligand to DNA and the case of displacement by a metal complex ligand of an ethidium marker attached to the DNA are considered. This work may be applied directly to reduce experimental data produced by a spectropolarimeter (for circular or linear dichroism) or a spectrophotometer (for fluorescence or UV-Vis spectroscopy).     

Modeling data from titration,amide H/D exchange,and mass spectrometry to obtain protein-ligand binding constants

We recently reported a new method for quantification of protein-ligand interaction by mass spectrometry, titration and H/D exchange (PLIMSTEX) for determining the binding stoichiometry and affinity of a wide range of protein-ligand interactions. Here we describe the method for analyzing the PLIMSTEX titration curves and evaluate the effect of various models on the precision and accuracy for determining binding constants using H/D exchange and a titration. The titration data were fitted using a 1:n protein:ligand sequential binding model, where n is the number of binding sites for the same ligand. An ordinary differential equation was used for the first time in calculating the free ligand concentration from the total ligand concentration. A nonlinear least squares regression method was applied to minimize the error between the calculated and the experimentally measured deuterium shift by varying the unknown parameters. A resampling method and second-order statistics were used to evaluate the uncertainties of the fitting parameters. The interaction of intestinal fatty-acid-binding protein (IFABP) with a fatty-acid carboxylate and that of calmodulin with Ca(2+) are used as two tests. The modeling process described here not only is a new tool for analyzing H/D exchange data acquired by ESI-MS, but also possesses novel aspects in modeling experimental titration data to determine the affinity of ligand binding.     

Determination of total iron in ground waters and multivitamin tablets using a solid-phase reactor with tiron immobilised on amberlite ion-exchange resin in a flow injection system

A method is described for the flow injection determination of total iron as Fe(III) using a solid-phase reactor containing disodium-1,2-dihydroxybenzene-3,5-disulphonate (tiron) as substrate. The iron(III) reacted with tiron to form a complex which absorbs strongly at 667 nm, where it was measured spectrophotometrically. The system has a linear range of 1 to 50 mg L^–1 with a detection limit of 0.67 mg L^–1. It is suitable for the determination of total iron in multivitamin tablets and iron-rich ground waters, with a relative standard deviation of better than 1.1%. The results obtained compared favourably with the certified values and a standard ICP-AES method. Received: 12 November 1997 / Revised: 9 March 1998 / Accepted: 15 March 1998     

Electrochemical assay of concanavalin A-ovalbumin binding on magnetic beads

To monitor protein-glycoprotein interactions on magnetic beads, the present study developed an electrochemical assay of the binding between concanavalin A (ConA) and ovalbumin (OVA). The system was a powerful model that could be used to evaluate cell junctions. ConA with an electroactive daunomycin was immobilized on 6 different sizes of magnetic beads (diameter: 1.0-8.9 μm) through a cross-linking agent. Six sizes of OVA-beads (diameter: 1.0-8.9 μm) were also prepared using a similar method. The binding was evaluated using an oxidation peak of ConA with daunomycin because ConA recognized OVA with α-mannose residues. When binding took place on the beads' surface, the peak current was decreased due to the electroactive moieties being covered with OVA. When ConA/daunomycin-OVA binding was evaluated, the change of the peak current obtained by the beads (diameter: 8.9 μm) modified with ConA and daunomycin was the greatest in the presence of OVA-modified beads (diameter: 2.5 μm). In contrast, particle agglomeration was observed for the smallest beads (diameter: 1.0 μm) with ConA/daunomycin and OVA. The results suggested that ConA-OVA binding depended on the size of beads. Thus, this method could be applied to measure protein-glycoprotein interactions on the cell surface.     

Average sequential water molecule binding enthalpies of M(H2O)(19-124)2+ (M = Co, Fe, Mn, and Cu) measured with ultraviolet photodissociation at 193 and 248 nm

The average sequential water molecule binding enthalpies to large water clusters (between 19 and 124 water molecules) containing divalent ions were obtained by measuring the average number of water molecules lost upon absorption of an UV photon (193 or 248 nm) and using a statistical model to account for the energy released into translations, rotations, and vibrations of the products. These values agree well with the trend established by more conventional methods for obtaining sequential binding enthalpies to much smaller hydrated divalent ions. The average binding enthalpies decrease to a value of ~10.4 kcal/mol for n > ~40 and are insensitive to the ion identity at large cluster size. This value is close to that of the bulk heat of vaporization of water (10.6 kcal/mol) and indicates that the structure of water in these clusters may more closely resemble that of bulk liquid water than ice, owing either to a freezing point depression or rapid evaporative cooling and kinetic trapping of the initial liquid droplet. A discrete implementation of the Thomson equation using parameters for liquid water at 0 °C generally fits the trend in these data but provides values that are ~0.5 kcal/mol too low.     

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a Lamarckian model of genetics, in which environmental adaptations of an individual's phenotype are reverse transcribed into its genotype and become heritable traits (sic). We consider three search methods, Monte Carlo simulated annealing, a traditional genetic algorithm, and the Lamarckian genetic algorithm, and compare their performance in dockings of seven protein–ligand test systems having known three-dimensional structure. We show that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTO DOCK , and that the Lamarckian genetic algorithm is the most efficient, reliable, and successful of the three. The empirical free energy function was calibrated using a set of 30 structurally known protein–ligand complexes with experimentally determined binding constants. Linear regression analysis of the observed binding constants in terms of a wide variety of structure-derived molecular properties was performed. The final model had a residual standard error of 9.11 kJ mol⁻¹ (2.177 kcal mol⁻¹) and was chosen as the new energy function. The new search methods and empirical free energy function are available in AUTO DOCK , version 3.0. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1639–1662, 1998     

Rapid determination of protein binding constant by a pressure-mediated affinity capillary electrophoresis method

A new pressure-mediated affinity capillary electrophoresis method for the rapid and accurate determination of drug-protein binding constants is described. A special combination of pressure and electrophoresis is used to shorten the electrophoresis and the overall analysis time to only a few minutes. At the same time, the suitability of this method is checked against a traditional fluorescence spectroscopy method. The binding constants of bovine serum albumin and a total of eight drugs with different pK(a) have been evaluated and compared with those determined by the fluorescence spectroscopy method and other methods in literature. The results indicate that the P-ACE method is well suited for the determination of binding constants with weak interaction (K(b) <10(5) M(-1)).     

Trace analysis of surfactants using chromatographic and electrophoretic techniques

Because of the widespread use, increased application of new formulations and immense impact on organisms and ecology surfactants are still in the focus of analytical chemistry. The development of methods with higher selectivity and lower detection limits is important to meet the requirements of greater responsibility for health of people and environment. Efficient separation methods, like HPLC, GC and CE, in combination with sensitive detection, like MS, are to be preferred over collective techniques which can suffer from interfering components. A review on trace analysis of ionic and neutral surfactants including sample preparation steps is presented, considering especially those methods which provide information about homologous and isomeric distribution of surfactant mixtures. Examples for the determination of linear alkylbenzene sulfonates in river water by HPLC and CE are discussed to show the capability of these methods for environmental analyses. As future trends increased applications of LC/MS (very high sensitivity) and also of CE (robustness and possibility for rapid method development) can be predicted. Received: 30 July 1998 / Revised: 28 October 1998 / Accetped: 1 November 1998