Quantifying Protein-Ligand Binding Constants using Electrospray Ionization Mass Spectrometry: A Systematic Binding Affinity Study of a Series of Hydrophobically Modified Trypsin Inhibitors

NanoESI-MS is used for determining binding strengths of trypsin in complex with two different series of five congeneric inhibitors, whose binding affinity in solution depends on the size of the P3 substituent. The ligands of the first series contain a 4-amidinobenzylamide as P1 residue, and form a tight complex with trypsin. The inhibitors of the second series have a 2-aminomethyl-5-chloro-benzylamide as P1 group, and represent a model system for weak binders. The five different inhibitors of each group are based on the same scaffold and differ only in the length of the hydrophobic side chain of their P3 residue, which modulates the interactions in the S3/4 binding pocket of trypsin. The dissociation constants (K_D) for high affinity ligands investigated by nanoESI-MS ranges from 15?nM to 450?nM and decreases with larger hydrophobic P3 side chains. Collision-induced dissociation (CID) experiments of five trypsin and benzamidine-based complexes show a correlation between trends in K_D and gas-phase stability. For the second inhibitor series we could show that the effect of imidazole, a small stabilizing additive, can avoid the dissociation of the complex ions and as a result increases the relative abundance of weakly bound complexes. Here the K_D values ranging from 2.9 to 17.6???M, some 1?C2 orders of magnitude lower than the first series. For both ligand series, the dissociation constants (K_D) measured via nanoESI-MS were compared with kinetic inhibition constants (K_i) in solution.     

Use of immobilized enzymes in chemical analysis

Immobilized enzymes are becoming increasingly popular as analytical reagents because of their reusability, stability, and sensitivity to many inhibitors that would seriously interfere in assays using soluble enzymes. In this article, some of the kinetic and catalytic effects of immobilized enzymes in analysis will be discussed. The shift of the activity-pH profile curves on immobilization, the changes in temperature dependence, the inhibitor constants (K_i), Michaelis constants (K_m), and the maximum velocity ( V_max), plus others, will be discussed. Finally, the use of these immobilized enzymes in fluorometric and electrochemical monitoring systems will be shown, and the future of these reagents in various areas will be discussed. A survey of enzyme electrodes will be presented as an example of the use of immobilized enzymes. Application of immobilized enzyme technology to the assay of BUN, glucose, uric acid, amino acids, ethanol, and other metabolites will be discussed.     

Study of affinity supports based on reactive polymers immobilized on silica: affinity constant determination from isocratic zonal elution.

Polymers bearing benzamidine moieties have been prepared from reactive copolymer containing chloroformate functions and deposited on porous silica matrices. These high-performance affinity chromatography supports were characterized by quantitative methods, which analyse the zonal elution behaviour of trypsin in the presence of a soluble competitor (L-arginine). The column loading capacity for trypsin was measured by the zonal elution method in mass overload conditions. On the basis of a Langmuir isotherm, the influence of the protein capacity and the concentration of the soluble ligand on the elution volume was studied for the determination of the binding constants. The plate heights determined for silica supports of various porosities and particle diameters show that the strong affinity interactions between trypsin and p-aminobenzamidine are mainly responsible for the low efficiencies observed.     

Immobilized enzymes as analytical reagents

Immobilized enzymes are becoming increasingly popular as analytical reagents because of their reusability, stability, and sensitivity to many inhibitors that would seriously interfere in assays using soluble enzymes. In this article, some of the kinetic and catalytic effects of immobilized enzymes in analysis will be discussed. The shift of the activity-pH profile curves on immobilization, the changes in temperature dependence. the inhibitor constants (K₁). Michaelis constants (K _m ), and the maximum velocity (V_max). plus others, will be discussed. Finally, the use of these immobilized enzymes in fluorometric and electrochemical monitoring systems will be shown, and the future of these reagents in various areas will be discussed. A survey of enzyme electrodes will be presented as an example of the use of immobilized enzymes. Application of immobilized enzyme technology to the assay of BUN, glucose, uric acid, amino acids, ethanol. and other metabolites will be discussed.     

Equilibrium in Saturated Ca(OH)2 Solutions: Parameters and Dissociation Constants

A new computer program has been developed for the calculation of pH, pOH, hydroxide ion concentration m _OH, species distribution coefficients _i, ionic activity coefficients _i ionic strength I, buffer capacity , solubility product K _s0, and the two dissociation constants, K _b1 and K _b2, corresponding, respectively, to first and second dissociation steps of Ca(OH)₂ in aqueous solution. Previously developed methodology, for the calculation of pH, _i, _i I, and parameters of pH buffer solutions, starting from the corresponding acidity constants, has been adapted for the case of aqueous Ca(OH)₂ solutions, for which the pertinent stoichiometric relationships are different from those applicable to mixtures of acids and their salts. The results show that, contrary to what is currently assumed, the first dissociation is far from complete. Values are given for the concentrations and activities of species Ca(OH)₂(aq), Ca(OH)⁺(aq), and Ca²⁺ (aq) in saturated calcium hydroxide solutions at 25°C.     

Design of active-site-directed fluorescent probes and their reactions with biopolymers

Fluorescent probes which are active-site-directed, reversible, competitive inhibitors of serum cholinesterase (ChE) enzymes have been designed and synthesized. Reversible inhibitors of enzyme active sites have a unique importance when they act as fluorescent probes, allowing fluorescence spectroscopic detection of conformation changes and activesite dynamics. 5-Dimethylamino-naphthalene-1-sulfonamido-N,N-dimethyl-n-propyl-amine and its aliphatic quaternary derivative are fluorescent probes for serum cholinesterase. The quaternary probe forms complexes with acetylcholinesterase (AChE). The dissociation constants K_d for the two probes with serum ChE are 6.0 × 10^?7 and 6.5 × 10^?7M. The inhibition constants K_i are 3.1 × 10^?6 and 6.3 × 10^?6M from the slopes of Lineweaver-Burk plots. The Michelis constant K_m for the enzyme was 8.8 × 10^?4M.     

Inhibition of Na+, K+-ATPase in the presence of crown ethers: modulation of ionic composition or pharmacological effects

It is believed that the biological effects of chelating agents such as crown ethers are largely related to their ability to form complexes with ions and/or to facilitate ion transport across membranes. Specific influences are rarely related. Here we present the evidence that even one of the simplest representatives of the crown ether super-family, 1,4,7,10,13,16-hexaoxacyclooctane (18-crown-6), is able to affect the activity of Na⁺, K⁺-ATPase directly. Using nonlinear regression fitting to kinetic data we have found that the crown ether diminishes the apparent Michaelis constant, K _m , and the maximal rate of ATP hydrolysis, V _m , acting as noncompetitive inhibitors. The apparent dissociation constants, K _i , for the crown interaction with the free ATPase and with the enzyme-substrate complex were established to be of 77 ± 3 mM and 21 ± 2 mM, respectively. So 18-crown-6 possesses weak but “direct” pharmacological activity on Na⁺, K⁺-ATPase hinders the formation of enzyme–substrate complex and detains the enzyme in this state.     

Acid-base and complexing properties of 10-carboxymethyl-9-acridone

Acid-base and complexing properties of 10-carboxymethyl-9-acridone in a multicomponent solvent H₂O-methanol-acetonitrile-dioxane were studied at 22°C, ionic strength I = 0.1 (NaClO₄), and different water-organic component ratios. The concentration protonation constants (logK _HL = 3.11), dissociation constants (pK _HL = 4.14), and stability constants of complexes (logK _MgL = 2.18, logK _CaL = 2.09, and logK _SrL = 1.96) were determined by extrapolation to zero content of organic solvent.     

Surface plasmon resonance study on binding interactions of multivalent cyclophane hosts with immobilized guests

Guest‐binding affinities of water‐soluble cyclophane heptadecamer (1) and pentamer (2) with immobilized guests such as 1‐pyrenylmethylamine (PMA) and 2‐(1‐ naphthyl)ethylamine (NEA) were investigated by surface plasmon resonance (SPR) measurements. As a typical example, the binding constants (K) for 1 and 2 with the immobilized PMA as a guest were evaluated to be 2.5 × 10⁷ and 2.7 × 10⁶ M^?1, respectively, and were much larger than that of a monocyclic reference cyclophane (K, 2.5 × 10⁴ M^?1). Interestingly, in the complexation of 1 and 2 with the immobilized guests, more favorable association and dissociation rate constant values (k_a and k_d, respectively) were observed in comparison with those for the monocyclic cyclophane, reflecting multivalent effects in macrocycles. The multivalent effects in macrocycles as well as molecular recognition abilities of the cyclophane oligomers were confirmed even when the guest molecules were immobilized on SPR sensor chip surfaces. Copyright © 2009 John Wiley & Sons, Ltd.     

Laws of complex formation in a series of azo-substituted pyrocatechol derivatives and their tin(II) complexes

Physicochemical properties of new reagents, azo-substituted pyrocatechol derivatives and their tin(II) complexes, are studied. The acid-base properties of the hydroxy groups (pK′_i, pK″_i), parameters of complex formation reactions (pH, temperature, time), and instability constants of the complexes formed (pK _i) are determined. Quantitative correlations between the dissociation constants (pK′_a) of the functional analytical group, and the electronic Hammett constant σ for a substituent (pK′_a-pH₅₀ of the complex formation reaction), as well as between pK′_a and instability constants of the complexes (pK _a), are established. The quantitative correlations established allow the prediction of the physicochemical properties of the reagents and tin(II) complexes with new reagents of this class with the same functional analytical group (FAG) but other substituents.     

Thermodynamic dissociation constants of risedronate using spectrophotometric and potentiometric pH-titration

Risedronate inhibits bone resorption in diseases like osteoporosis, Paget’s disease, tumor bone diseases or the malfunction of phosphocalcium metabolism. The acid-base properties of risedronate in an aqueous solution have been studied in a pH range from 2 to 12 and can be described in terms of four dissociation steps: pK _a,2, pK _a,4, pK _a,5 (related to the dissociation of POH groups) and pK _a,3 related to the dissociation of protonated amino group NH₃ ⁺. The mixed dissociation constants were determined at different ionic strengths I = 0.02 to 0.20 mol dm⁻³ KCl and of 25°C and 37°C using pH-spectrophotometric and pH-potentiometric titration methods. Determination of group parameters L ₀, H _T might lead to false estimates of common parameters p K _a;therefore, the computational strategy employed is important. A comparison between the two programs ESAB and HYPERQUAD demonstrated that the ESAB program provides a better fit of potentiometric titration curve. The thermodynamic dissociation constants pK _a^T were estimated by a nonlinear regression of (pK _a, I) data and a Debye-Hückel equation at 25°C and 37°C, pK _a,2^T = 2.37(1) and 2.44(1), pK _a,3^T = 6.29(3) and 6.26(1), pK _a,4^T = 7.48(1) and 7.46(2) and pK _a,5^T = 9.31(7) and 8.70(3) at 25°C and 37°C using pH-spectroscopic data and pK _a,2^T = 2.48(3) and 2.43(1), pK _a,3^T= 6.12(2) and 6.10(2), pK _a,4^T = 7.25(2) and 7.23(1) and pK _a,5^T = 12.04(5) and 11.81(2) at 25°C and 37°C. The ascertained estimates of three dissociation constants pK _a,3, pK _a,4, pK _a,5 are in agreement with the predicted values obtained using PALLAS      

The Reaction of Methyl Tosylate with Halide Ions in Pyridine-Dimethylformamide

The reactivity of the lithium halides in 83.3% pyridine-dimethylformamide changes from Cl^? > Br^? > I^? to Br^? > I^? to Br^? > I^? > Cl^? with increasing concentration of the salt from 0 to 0.35 M. This behaviour is explained by ion pairing which reduces the concentration of reactive free nucleophiles. Equilibrium constants K for ion pair dissociation and rate constants k₂ for the reaction of the free nucleophiles were determined from the variation of the observed rate constant with the total halide concentration and from conductivity measurements.     

Equilibria of formation and dehydration of the carbinolamine intermediate in the reaction of benzaldehyde with hydrazine

Measurement of polarographic limiting currents at equilibria made it possible at pH 3-7 to simultaneously determine concentrations of benzaldehyde, of its hydrazone and of the carbinolamine derivative. The dependence of concentration of carbinolamine at equilibrium on pH indicated presence of its di-, mono-, and unprotonated forms. Acid dissociation constants of the formation (pK_a¹≈3.2) of the diprotonated form and of the dissociation of the monoprotonated form of carbinolamine (pK_a²≈4.7) were estimated. The equilibrium constants of formation (K₁) and dehydration (K₂) of the carbinolamine intermediate were determined.     

DNA与金属锇配合物相互作用的表面电化学研究

采用自己建立的DNA表面电化学研究微量方法, 研究了单双链DNA与两种锇配合物(联吡啶锇和二氯菲咯啉锇)的相互作用. 研究发现, 两种锇配合物都是通过静电作用与DNA结合, 其作用方式不受溶液离子强度的影响. 并计算得到了联吡啶锇和二氯菲咯啉锇与dsDNA和ssDNA相互作用的多个热力学和动力学参数, 如结合常数K_3＋或K_2＋, 结合常数比K_3＋/K_2＋, 离子强度为零时的极限比 , 结合自由能ΔG_b, 解离速度常数k, 结合位点数s.     

Lipase immobilized on hydrophobic microporous polypropylene for the hydrolysis of palm kernel olein

Lipase (triacylglycerol ester hydrolase, EC 3.1.1.3) fromRhizopus arrhizus was immobilized in this work by adsorption on microporous polypropylene and employed for the lipolysis of palm kernel olein. The optimum operating temperature for the lipolysis reaction was determined. The reaction follows Michaelis-Menten kinetics with product competitive inhibition for substrate concentrations in the range of 0.175–0.877M. The apparentK _m and V_max were 0.42M and 691 U/mg protein, respectively. A dissociation constant of the enzymeproduct complex,K _I = 29.73 mM, for the product inhibition was also determined. Additionally, the time-courses of the reaction for various substrate concentrations were obtained and correlated sufficiently with those predicted from the theoretical rate equation for a period of up to 2 h. Experimental results indicated that discrepancies between the observed results and the predicted ones increase with reaction time.     

Bio-smart materials: kinetics of immobilized enzymes in p(HEMA)/p(pyrrole) hydrogels in amperometric biosensors

Various strategies are being pursued to confer the highly specific molecular recognition properties of bioactive molecules to the transducer action of inherently conductive polymers. We have successfully integrated inherently conductive polypyrrole within electrode-supported, UV cross-linked hydroxyethyl methacrylate (HEMA)-based hydrogels. These electroactive composites were used as matrixes for the physical immobilization of several oxidase enzymes to fabricate clinically important biosensors. Measurements were made of the amperometric responses via H₂O₂ oxidation for each biosensor. Apparent Michaelis constants, K_m(app), for glucose oxidase immobilized in p(HEMA) membranes and in p(HEMA)/p(Pyrrole) composite membranes were 13.8 and 43.7 mM respectively compared to 33 mM in solution. The inclusion of polypyrrole in the hydrogel network increased the thermal stability of the immobilized enzyme at 60°C by 30% and 40% compared to p(HEMA) membranes and solution phase respectively. The composite also yielded larger I_max values (19 μA/cm⁻²) for glucose biosensors compared to similar glucose biosensors fabricated without the conducting polymer (15 μA). K_m(app) values for cholesterol oxidase immobilized in the same composite films were ca. three orders of magnitude higher than the K_m for the soluble enzyme. The polypyrrole component is shown to reduce diffusive transport but to confer thermal stability to these biosensors.     

Gold(III) amine complexes in aqueous alkali solutions

The gold(III) 1,3-diaminopropane complex [Au(1,3-pn)(1,3-pn-H)]Cl₂ has been synthesized. Its dissociation constant has been determined: Au(1,3-pn)₂³⁺ = Au(1,3-pn-H)²⁺ + H⁺, logK _a1 = −7.03 ± 0.05 (I = 0.1 mol/L NaClO₄). Considerable spectral changes are observed for strong alkali solutions (pH 11–14) containing the monoamido forms of the gold(III) ethylenediamine, 1,3-diaminopropane, and diethylenetriamine complexes (Au(en)(en-H)²⁺, Au(1,3-pn)(1,3-pn-H)²⁺, Au(dien-H)OH⁺). These changes are attributed to the formation of the diamido species Au(en-H)₂⁺, Au(1,3-pn-H)₂⁺, and Au(dien-2H)OH⁰. The dissociation constants of the monoamido complexes have been determined: Au(en)(en-H)²⁺ (logK _a2 = −10.9 ± 0.1 at I = 0.001–0.01 mol/L NaCl); Au(1,3-pn)(1,3-pn-H)²⁺ (logK _a2 = −11.3 ± 0.1 at I = 0.1 mol/L NaCl); Au(dien-H)OH⁺ (logK _a2 = −12.4 ± 0.1 at I = 0.1 mol/L NaCl).     

Prompt and Slow Electron‐Detachment‐Dissociation/Electron‐Photodetachment‐Dissociation of a 21‐Mer Peptide

Electron detachment dissociation (EDD) and electron photodetachment dissociation (EPD) are relatively new dissociation methods that involve electron detachment followed by radical‐driven dissociation from multiply deprotonated species. EDD yields prompt dissociation whereas only electron detachment is obtained by EPD; subsequent vibrational activation of the charge‐reduced radical anion is required to obtain the product ions. Herein, the fragmentation patterns that were obtained by EDD and by vibrational activation of the charge‐reduced radical anions that were produced through EDD or EPD (activated‐EDD and activated‐EPD) were compared. The observed differences were related to the dissociation kinetics and/or the contribution of electron‐induced dissociation (EID). Time‐resolved double‐resonance experiments were performed to measure the dissociation rate constants of the EDD product ions. Differences in the formation kinetics were revealed between the classical EDD/EPD ′a^._i/′′x_j complementary ions and some ′a^._i/c_i/′′′z^._j product ions, which were produced with slower dissociation rate constants, owing to the presence of specific neighbouring side chains. A new fragmentation pathway is proposed for the formation of the slow‐kinetics ′a^._i ions.     

Predicting Properties of Iron(III) TAML Activators of Peroxides from Their III/IV and IV/V Reduction Potentials or a Lost Battle to Peroxidase

A cyclic voltammetry study of a series of iron(III) TAML activators of peroxides of several generations in acetonitrile as solvent reveals reversible or quasireversible Fe^III/IV and Fe^IV/V anodic transitions, the formal reduction potentials (E°′) for which are observed in the ranges 0.4–1.2 and 1.4–1.6 V, respectively, versus Ag/AgCl. The slope of 0.33 for a linear E°′(IV/V) against E°′(III/IV) plot suggests that the TAML ligand system plays a bigger role in the Fe^III/IV transition, whereas the second electron transfer is to a larger extent an iron-centered phenomenon. The reduction potentials appear to be a convenient tool for analysis of various properties of iron TAML activators in terms of linear free energy relationships (LFERs). The values of E°′(III/IV) and E°′(IV V⁻¹) correlate 1) with the pK_a values of the axial aqua ligand of iron(III) TAMLs with slopes of 0.28 and 0.06 V, respectively; 2) with the Stern–Volmer constants K_SV for the quenching of fluorescence of propranolol, a micropollutant of broad concern; 3) with the calculated ionization potentials of Fe^III and Fe^IV TAMLs; and 4) with rate constants k_I and k_II for the oxidation of the resting iron(III) TAML state by H₂O₂ and reactions of the active forms of TAMLs formed with donors of electrons S, respectively. Interestingly, slopes of log k_II versus E°′(III/IV) plots are lower for fast-to-oxidize S than for slow-to-oxidize S. The log k_I versus E°′(III/IV) plot suggests that the manmade TAML catalyst can never be as reactive toward H₂O₂ as a horseradish peroxidase enzyme.     

The solution chemistry of ethylmethylglyoxime : Part I. The proton complex

The solubility of ethylmethylglyoxime (EMG) was studied as a function of pH. The solubility K_sl in 0.1 M aqueous solution is 0.0132 ±0.0006 M. The distribution constants K_Dl of EMG between various organic solvents and 0.1 M aqueous solution were found to be —0.47 for chloroform, —0.51 for benzene, —1.10 for carbon tetrachloride and —1.83 for hexane. The acid dissociation constants were determined from potentiometric titrations; the values pK_a1=10.51 and pK_a2=12.02 were obtaining by fitting the experimental data to normalized curves. The UV spectra of 5·10^-5M EMG solutions of varying pH were measured between 210 and 290 nm. It is shown that H₂A has an absorption maximum at 226 nm and HA^-and A^2- have absorption maxima at nearly the same wavelengths, i.e. 258 and 266 nm, respectively. The spectra of HA^- and A^2- have approximately the same form. The data are compared with those of dimethylglyoxime (DMG). The distribution constants (org/aq) are 4–5 times higher for EMG. The acid dissociation constants are about the same for EMG and DMG, but EMG is more soluble in water than DMG (13.2 and 5.0 mmoles/l, respectively). The UV spectra of EMG and DMG are very similar.