Determination Of Dissociation Constants Research Articles

Evaluation of protein adsorption and preferred binding regions in multimodal chromatography using NMR

NMR titration experiments with labeled human ubiquitin were employed in concert with chromatographic data obtained with a library of ubiquitin mutants to study the nature of protein adsorption in multimodal (MM) chromatography. The elution order of the mutants on the MM resin was significantly different from that obtained by ion-exchange chromatography. Further, the chromatographic results with the protein library indicated that mutations in a defined region induced greater changes in protein affinity to the solid support. Chemical shift mapping and determination of dissociation constants from NMR titration experiments with the MM ligand and isotopically enriched ubiquitin were used to determine and rank the relative binding affinities of interaction sites on the protein surface. The results with NMR confirmed that the protein possessed a distinct preferred binding region for the MM ligand in agreement with the chromatographic results. Finally, coarse-grained ligand docking simulations were employed to study the modes of interaction between the MM ligand and ubiquitin. The use of NMR titration experiments in concert with chromatographic data obtained with protein libraries represents a previously undescribed approach for elucidating the structural basis of protein binding affinity in MM chromatographic systems.

A new sensitive method of dissociation constants determination based on the isohydric solutions principle

The paper provides a new formulation and analytical proposals based on the isohydric solutions concept. It is particularly stated that a mixture formed, according to titrimetric mode, from a weak acid (HX, C 0 mol/L) and a strong acid (HB, C mol/L) solutions, assumes constant pH, independently on the volumes of the solutions mixed, provided that the relation C 0 = C + C 2 · 10 p K 1 is valid, where p K 1 = −log K 1, K 1 the dissociation constant for HX. The generalized formulation, referred to the isohydric solutions thus obtained, was extended also to more complex acid–base systems. Particularly in the (HX, HB) system, the titration occurs at constant ionic strength ( I) value, not resulting from presence of a basal electrolyte. This very advantageous conjunction of the properties provides, among others, a new, very sensitive method for verification of p K 1 value. The new method is particularly useful for weak acids HX characterized by low p K 1 values. The method was tested experimentally on four acid–base systems (HX, HB), in aqueous and mixed-solvent media and compared with the literature data. Some useful (linear and hyperbolic) correlations were stated and applied for validation of p K 1 values. Finally, some practical applications of analytical interest of the isohydricity (pH constancy) principle as one formulated in this paper were enumerated, proving the usefulness of such a property which has its remote roots in the Arrhenius concept.

Microchip‐ESI‐MS determination of dissociation constant of the lysozyme–NAG3 complex

An on-line microfluidic system for determination of dissociation constants of enzyme/substrate weak interactions by nanoESI-MS is introduced. The microchip was designed to permit the enzyme and the substrate to mix by molecular diffusion in a pressure-driven laminar flow. Introduction of reagent solutions into the chip was an optimized combination of a micropump and an autosampler to enable automation of the measurements. The system performance was tested for monitoring of non-covalent interactions of hen egg white lysozyme with N-acetyl glucosamine oligomers. Dissociation constant (K(D)) of the hen egg white lysozyme-N-acetyl glucosamine oligomer complex was determined by non-linear regression analysis, and the range of K(D) values (39+/-6 x 10(-6) and 19.6+/-8 x 10(-6) M for manual and automated infusions, respectively) confirms the previously reported values. Such miniaturization of a continuous-flow enzyme assay system to a microfluidic format can maximize the capabilities of mass spectrometric detection, reduce the sample size and analysis time required, as well as the associated costs for on-line enzymatic kinetic studies.

Determination of Dissociation Constants of Hexanoic, Heptanoic, and Benzoic Acids to 673 K and 30 MPa by Potentiometric pH Measurements

Potentiometric pH measurements of 0.01 mol·kg−1 aqueous solutions of hexanoic, heptanoic, and benzoic acids in 0.1 mol·kg−1 NaCl media were performed using a flow-through electrochemical cell with two pressure-balanced hydrogen platinum electrodes. The dissociation constants of these carboxylic acids were determined on the basis of pH values measured at temperatures from (322 to 673) K and pressures of (23 and 30) MPa. The dissociation constants were consistent with the literature values determined from calorimetry, electrical conductivity, and potentiometry at temperatures up to 523 K. A simple Born model for describing temperature and pressure dependence of the dissociation constants was used to correlate the data.

Ligand–Receptor Binding Affinities from Saturation Transfer Difference (STD) NMR Spectroscopy: The Binding Isotherm of STD Initial Growth Rates

The direct evaluation of dissociation constants (K(D)) from the variation of saturation transfer difference (STD) NMR spectroscopy values with the receptor-ligand ratio is not feasible due to the complex dependence of STD intensities on the spectral properties of the observed signals. Indirect evaluation, by competition experiments, allows the determination of K(D), as long as a ligand of known affinity is available for the protein under study. Herein, we present a novel protocol based on STD NMR spectroscopy for the direct measurements of receptor-ligand dissociation constants (K(D)) from single-ligand titration experiments. The influence of several experimental factors on STD values has been studied in detail, confirming the marked impact on standard determinations of protein-ligand affinities by STD NMR spectroscopy. These factors, namely, STD saturation time, ligand residence time in the complex, and the intensity of the signal, affect the accumulation of saturation in the free ligand by processes closely related to fast protein-ligand rebinding and longitudinal relaxation of the ligand signals. The proposed method avoids the dependence of the magnitudes of ligand STD signals at a given saturation time on spurious factors by constructing the binding isotherms using the initial growth rates of the STD amplification factors, in a similar way to the use of NOE growing rates to estimate cross relaxation rates for distance evaluations. Herein, it is demonstrated that the effects of these factors are cancelled out by analyzing the protein-ligand association curve using STD values at the limit of zero saturation time, when virtually no ligand rebinding or relaxation takes place. The approach is validated for two well-studied protein-ligand systems: the binding of the saccharides GlcNAc and GlcNAcbeta1,4GlcNAc (chitobiose) to the wheat germ agglutinin (WGA) lectin, and the interaction of the amino acid L-tryptophan to bovine serum albumin (BSA). In all cases, the experimental K(D) measured under different experimental conditions converged to the thermodynamic values. The proposed protocol allows accurate determinations of protein-ligand dissociation constants, extending the applicability of the STD NMR spectroscopy for affinity measurements, which is of particular relevance for those proteins for which a ligand of known affinity is not available.

Determination of Alkalinity and dissociation constants of high salinity waters: use of F5BC titration function

Measurements of parameters expressed in terms of carbonic species such as Alkalinity and Acidity of saline waters do not analyze the influence of external parameters to the titration such as Total free and associated Carbonic Species Concentration, activity coefficient, ion pairing formation and Residual Liquid Junction Potential in pH measurements. This paper shows the development of F5BC titration function based on the titrations developed by Gran (1952) for the carbonate system of natural waters. For practical use, samples of saline waters from Pocinhos reservoir in Paraiba were submitted to titration and linear regression analysis. Results showed that F5BC involves F1x and F2x Gran functions determination, respectively, for Alkalinity and Acidity calculations without knowing “a priori” the endpoint of the titration. F5BC also allows the determination of the First and Second Apparent Dissociation Constant of the carbonate system of saline and high ionic strength waters.

Determination of Acidic Dissociation Constants of Glycine, Valine, Phenylalanine, Glycylvaline, and Glycylphenylalanine in Water Using ab Initio Methods

In this study, pKa values of glycine, valine, phenylalanine, glycylvaline, and glycylphenylalanine were determined in aqueous solution by an ab initio method. To explain the acidic dissociation constants obtained, we investigated the molecular conformations and solute−solvent interactions of the peptides and amino acid anions, using the density functional theory (DFT) method. Several ionization reactions and equilibria in protic solvents, which possess a high hydrogen-band-donor capability, are shown. The mentioned reactions and equilibria constitute the indispensable theoretical basis to calculate the acidity constants of glycine, valine, phenylalanine, glycylvaline, and glycylphenylalanine. Basis sets at the B3LYP/6-31+G(d) level of theory were used for calculations. Tomasi’s method was used to analyze the formation of intermolecular hydrogen bonds between the existent species and water molecules. In this way, it was determined that in alkaline aqueous solutions the cation, anion, and neutral species of...

Determination of Dissociation Constants of Folinic Acid (Leucovorin), 5-Fluorouracil, and Irinotecan in Hydro-organic Media by a Spectrophotometric Method

In this study, a multiwavelength spectrophotometric method was used for the determination of the dissociation constants of drugs used for treatment of colorectal cancer, folinic acid (leucovorin), 5-fluorouracil, and irinotecan, in water and acetonitrile−water binary mixtures up to a 0.50 volume fraction at 25 °C and an ionic strength of 0.1 mol·L−1 KCl. The absorbance/pH profiles were assessed and found to conform to those of polyprotic acids. Data evaluation was performed using the STAR software program which calculates stability constants and molar absorbances of the pure species by multilinear regression. A linear relationship between acidity constants and the mole fraction of acetonitrile in the solvent mixture was observed. The effect of solvent properties on acid−base behavior is discussed.

Determination of dissociation constants of species oxidizable in aqueous solution by air oxygen on an example of quercetin

The comparison of literature data on the dissociation constant of one of the most abundant natural flavonoids, e.g., quercetin, demonstrates their irreproducibility. The reason for this likely corresponds to the easiness of its oxidation by air oxygen during the titration process. To eliminate such problems, a modified version of potentiometric titration was proposed with bubbling a weak flow of an inert gas (nitrogen) through the solution to be titrated in the presence of minimal amounts of a nonionic surfactant. By virtue of the technique proposed, the values of pKa for quercetin were measured to be 6.62 ± 0.04 and 9.7 ± 0.3. The first one corresponds to the hydroxyl group in the γ-pyrone fragment of the molecule, while another agrees with the typical values of pKa for phenols.

Biochemical Characterization of ThiT from Lactococcus lactis: A Thiamin Transporter with Picomolar Substrate Binding Affinity

The putative thiamin transporter ThiT from Lactococcus lactis was overproduced in the membrane of lactococcal cells. In vivo transport assays using radiolabeled thiamin demonstrated that ThiT indeed was involved in thiamin transport. The protein was solubilized from the membranes and purified in detergent solution. Size exclusion chromatography coupled to static light scattering, refractive index, and UV absorbance measurements (SEC-MALLS) showed that ThiT is a monomer of 22.7 kDa in detergent solution. When the cells overexpressing ThiT had been cultivated in complex growth medium, all binding sites of the purified protein were occupied with substrate, which had copurified with the protein. MALDI-TOF mass spectrometry analysis confirmed that the copurified substance was thiamin. Substrate-depleted ThiT was obtained by expressing the protein in cells that were cultivated in chemically defined growth medium without thiamin. The intrinsic tryptophan fluorescence of substrate-depleted ThiT was strongly quenched upon thiamin binding. The quenching of the fluorescence was used to determine dissociation constants for thiamin and related compounds. ThiT had an unusually high affinity for thiamin (K(D) = 122 +/- 13 pM) and bound the substrate with a 1:1 (protein:ligand) stoichiometry. TPP, TMP, and pyrithiamin bound to ThiT with nanomolar affinity. A multiple sequence alignment of ThiT homologues revealed that well-conserved residues were clustered in a tryptophan-rich stretch comprising the loop between the predicted membrane spanning segments 5 and 6. Mutational analysis of the conserved residues in this region combined with binding assays of thiamin and related compounds was used to build a model of the high-affinity binding site. The model was compared with thiamin binding sites of other proteins and interpreted in terms of the transport mechanism.

Biophysical and X-ray Crystallographic Analysis of Mps1 Kinase Inhibitor Complexes,

The dual-specificity protein kinase monopolar spindle 1 (Mps1) is a central component of the mitotic spindle assembly checkpoint (SAC), a sensing mechanism that prevents anaphase until all chromosomes are bioriented on the metaphase plate. Partial depletion of Mps1 protein levels sensitizes transformed, but not untransformed, human cells to therapeutic doses of the anticancer agent Taxol, making it an attractive novel therapeutic cancer target. We have previously determined the X-ray structure of the catalytic domain of human Mps1 in complex with the anthrapyrazolone kinase inhibitor SP600125. In order to validate distinct inhibitors that target this enzyme and improve our understanding of nucleotide binding site architecture, we now report a biophysical and structural evaluation of the Mps1 catalytic domain in the presence of ATP and the aspecific model kinase inhibitor staurosporine. Collective in silico, enzymatic, and fluorescent screens also identified several new lead quinazoline Mps1 inhibitors, including a low-affinity compound termed Compound 4 (Cpd 4), whose interaction with the Mps1 kinase domain was further characterized by X-ray crystallography. A novel biophysical analysis demonstrated that the intrinsic fluorescence of SP600125 changed markedly upon Mps1 binding, allowing spectrophotometric displacement analysis and determination of dissociation constants for ATP-competitive Mps1 inhibitors. By illuminating the structure of the Mps1 ATP-binding site our results provide novel biophysical insights into Mps1-ligand interactions that will be useful for the development of specific Mps1 inhibitors, including those employing a therapeutically validated quinazoline template.

Synthesis of S‐Adenosyl‐L‐homocysteine Capture Compounds for Selective Photoinduced Isolation of Methyltransferases

Understanding the interplay of different cellular proteins and their substrates is of major interest in the postgenomic era. For this purpose, selective isolation and identification of proteins from complex biological samples is necessary and targeted isolation of enzyme families is a challenging task. Over the last years, methods like activity-based protein profiling (ABPP) and capture compound mass spectrometry (CCMS) have been developed to reduce the complexity of the proteome by means of protein function in contrast to standard approaches, which utilize differences in physical properties for protein separation. To isolate and identify the subproteome consisting of S-adenosyl-L-methionine (SAM or AdoMet)-dependent methyltransferases (methylome), we developed and synthesized trifunctional capture compounds containing the chemically stable cofactor product S-adenosyl-L-homocysteine (SAH or AdoHcy) as selectivity function. SAH analogues with amino linkers at the N6 or C8 positions were synthesized and attached to scaffolds containing different photocrosslinking groups for covalent protein modification and biotin for affinity isolation. The utility of these SAH capture compounds for selective photoinduced protein isolation is demonstrated for various methyltransferases (MTases) acting on DNA, RNA and proteins as well as with Escherichia coli cell lysate. In addition, they can be used to determine dissociation constants for MTase-cofactor complexes.

10.1007/s11178-008-1006-y

An empirical method was used to calculate 363 dissociation constants of 33 benzoic and acetic acid derivatives in 11 solvents. The relative error in the calculations did not exceed 9.5%, and the average error was no higher than 3%. The calculated values were compared with those obtained by quantum-chemical and other methods for determination of acid dissociation constants in different solvents.

Determination of Alkalinity and dissociation constants of high salinity waters: use of F5BC titration function

Measurements of parameters expressed in terms of carbonic species such as Alkalinity and Acidity of saline waters do not analyze the influence of external parameters to the titration such as Total free and associated Carbonic Species Concentration, activity coefficient, ion pairing formation and Residual Liquid Junction Potential in pH measurements. This paper shows the development of F5BC titration function based on the titrations developed by Gran (1952) for the carbonate system of natural waters. For practical use, samples of saline waters from Pocinhos reservoir in Paraiba were submitted to titration and linear regression analysis. Results showed that F5BC involves F1x and F2x Gran functions determination, respectively, for Alkalinity and Acidity calculations without knowing "a priori" the endpoint of the titration. F5BC also allows the determination of the First and Second Apparent Dissociation Constant of the carbonate system of saline and high ionic strength waters.

Determination of Acid Dissociation Constants of Compounds Active at Neuronal Nicotinic Acetylcholine Receptors by Means of Electrophoretic and Potentiometric Techniques

The dissociation constants of epiboxidine 2 and a series of bases active at neuronal nicotinic acetylcholine receptors were determined by means of potentiometric and electrophoretic methods, which gave values in good agreement. Although showing different features, the two techniques are complementary for dissociation constant determinations. The choice of the most suitable method is guided by the available amount of sample, its purity, and the time needed for the analysis. The experimental values were compared with the predictions obtained with ACD/pK(a) DB software.

Structure and Function of the PLAA/Ufd3-p97/Cdc48 Complex

PLAA (ortholog of yeast Doa1/Ufd3, also know as human PLAP or phospholipase A2-activating protein) has been implicated in a variety of disparate biological processes that involve the ubiquitin system. It is linked to the maintenance of ubiquitin levels, but the mechanism by which it accomplishes this is unclear. The C-terminal PUL (PLAP, Ufd3p, and Lub1p) domain of PLAA binds p97, an AAA ATPase, which among other functions helps transfer ubiquitinated proteins to the proteasome for degradation. In yeast, loss of Doa1 is suppressed by altering p97/Cdc48 function indicating that physical interaction between PLAA and p97 is functionally important. Although the overall regions of interaction between these proteins are known, the structural basis has been unavailable. We solved the high resolution crystal structure of the p97-PLAA complex showing that the PUL domain forms a 6-mer Armadillo-containing domain. Its N-terminal extension folds back onto the inner curvature forming a deep ridge that is positively charged with residues that are phylogenetically conserved. The C terminus of p97 binds in this ridge, where the side chain of p97-Tyr805, implicated in phosphorylation-dependent regulation, is buried. Expressed in doa1Δ null cells, point mutants of the yeast ortholog Doa1 that disrupt this interaction display slightly reduced ubiquitin levels, but unlike doa1Δ null cells, showed only some of the growth phenotypes. These data suggest that the p97-PLAA interaction is important for a subset of PLAA-dependent biological processes and provides a framework to better understand the role of these complex molecules in the ubiquitin system.

Design of O-Acetylserine Sulfhydrylase Inhibitors by Mimicking Nature

The inhibition of cysteine biosynthesis in prokaryotes and protozoa has been proposed to be relevant for the development of antibiotics. Haemophilus influenzae O-acetylserine sulfhydrylase (OASS), catalyzing l-cysteine formation, is inhibited by the insertion of the C-terminal pentapeptide (MNLNI) of serine acetyltransferase into the active site. Four-hundred MNXXI pentapeptides were generated in silico, docked into OASS active site using GOLD, and scored with HINT. The terminal P5 Ile accounts for about 50% of the binding energy. Glu or Asp at position P4 and, to a lesser extent, at position P3 also significantly contribute to the binding interaction. The predicted affinity of 14 selected pentapeptides correlated well with the experimentally determined dissociation constants. The X-ray structure of three high affinity pentapeptide-OASS complexes were compared with the docked poses. These results, combined with a GRID analysis of the active site, allowed us to define a pharmacophoric scaffold for the design of peptidomimetic inhibitors.

Ionic equilibrium in mixtures of protophobic and protophilic polar non‐hydrogen bond donor solvents: acids, salts, and indicators in acetone containing 5 mol% DMSO

AbstractProperties of a protophobic polar non‐HBD solvent can be strongly modified by introduction of a small amount of a protophilic polar non‐HBD solvent. In this paper, acetone (AC) with 5 mol% additive of DMSO, a solvent with $\varepsilon _{\rm r}^{{\rm 25}} = 22$, was considered as a media for acid–base reactions. Conductance was used for determination of dissociation constants of a set of salts, hydrogen chloride, and picric acid. The last‐named was also studied by UV‐vis spectroscopy. The introduction of 5 mol% of DMSO results in suppressing, to some extent, the homoconjugation processes in AC media as well as of proton hydration by (possible) traces of water. The dissociation of salicylic acid and 2,4‐dinitrophenol was examined utilizing quinhydrone electrodes in a cell with liquid junction. The pKa values of buffer acids and ${\rm p}a_{{\rm H}^ + }^* $ values of buffer solutions were calculated by taking into account the incomplete dissociation of salts. The response of the glass electrode appeared to be satisfactory, which allowed the estimation of the pKa value of benzoic acid. The apparent ionization constants of 22 acid–base indicators in buffer mixtures and perchloric acid solutions were determined in (AC + 5 mol% DMSO) using the spectrophotometric procedure. Copyright © 2009 John Wiley & Sons, Ltd.

Charge-scaled cavities in polarizable continuum model: Determination of acid dissociation constants for platinum-amino acid complexes

The main aim of this study is the calculation of acid dissociation constants of the products of cisplatin reaction with the amino acids cysteine and methionine. In the first step, a suitable procedure for the calculation of solvation Gibbs free energies is found, based on the comparison of the calculated and experimental pK(a)s of both amino acids and simple platinum complexes. The resulting approach combines the DFT/B3LYP density functional, 6-311++G(2df,2pd) basis set, the D-PCM formulation of the continuum solvation model, and modified UAHF cavities. Since the main area of applicability of the UAHF model is solvation of organic molecules, a minor modification of the UAHF algorithm was necessary to improve the accuracy when applying it to the transition metal complexes. Instead of the integer (or semi-integer) formal charges used in the original formulation, more realistic partial charges obtained from the electronic density using the NPA procedure are used to generate molecular cavity. All other parameters of the model remain unchanged. This simple modification of the UAHF model works markedly better than the original formulation. The root mean square error of calculated pK(a)s over a set of molecules including zwitterions and divalent diaquaplatinum cation is equal to 0.74. In the second step, pK(a)s of platinum amino-acid complexes with the total charge ranging from 0e to 2e were computed. It was found that the pK(a)s of all ionizable groups of both amino acids are highly variable among the complexes studied. They range from -5 (in complexes containing protonated thiol or carboxyl groups directly bonded to platinum) to 14 (in monodentate complexes containing a positively charged amino group, which is stabilized by intramolecular hydrogen bonds).

Proteomics strategy for quantitative protein interaction profiling in cell extracts

We report a proteomics strategy to both identify and quantify cellular target protein interactions with externally introduced ligands. We determined dissociation constants for target proteins interacting with the ligand of interest by combining quantitative mass spectrometry with a defined set of affinity purification experiments. We demonstrate the general utility of this methodology in interaction studies involving small-molecule kinase inhibitors, a tyrosine-phosphorylated peptide and an antibody as affinity ligands.