Interpretation and analysis of receptor binding experiments which yield non-linear Scatchard plots and binding constants dependent upon receptor concentration

Binding Characteristics Study of DNA based Aptamers for E. coli O157:H7

E. coli O157:H7 is a pathogenic bacterium producing verotoxins that could lead to serious complications such as hemolytic uremia syndrome. Fast detection of such pathogens is important. For rapid detection, aptamers are quickly gaining traction as alternative biorecognition molecules besides conventional antibodies. Several DNA aptamers have been selected for E. coli O157:H7. Nonetheless, there has not been a comparative study of the binding characteristics of these aptamers. In this work, we present a comprehensive analysis of binding characteristics including binding affinity (K_d) and binding capacity (B_max) of DNA-based aptamers for E. coli O157:H7 using qPCR. Our results show that aptamer E18R has the highest binding capacity to E. coli 157:H7 and the highest specificity over non-pathogenic E. coli strains K12 and DH5α. Our study also finds that the common biotin-tag modification at 5' end typically changes the binding capacity significantly. For most of the selected aptamers, the binding capacity after a biotin-tag modification decreases. There exists a discrepancy in the binding capability between the selected aptamer and the aptamer used for detection. Our study also shows that a lower concentration of Mg²⁺ ions in the binding buffer leads to a decrease in the binding capacity of E17F and E18R, while it does not affect the binding capacity of S1 and EcoR1.

Detection of Gram-negative bacterial outer membrane vesicles using DNA aptamers

Infection of various pathogenic bacteria causes severe illness to human beings. Despite the research advances, current identification tools still exhibit limitations in detecting Gram-negative bacteria with high accuracy. In this study, we isolated single-stranded DNA aptamers against multiple Gram-negative bacterial species using Toggle-cell-SELEX (systemic evolution of ligands by exponential enrichment) and constructed an aptamer-based detection tool towards bacterial secretory cargo released from outer membranes of Gram-negative bacteria. Three Gram-negative bacteria, Escherichia coli DH5α, E. coli K12, and Serratia marcescens, were sequentially incubated with the pool of random DNA sequences at each SELEX loop. Two aptamers selected, GN6 and GN12, were 4.2-times and 3.6-times higher binding to 10⁸ cells of Gram-negative bacteria than to Gram-positive bacteria tested, respectively. Using GN6 aptamer, we constructed an Enzyme-linked aptamer assay (ELAA) to detect bacterial outer membrane vesicles (OMVs) of Gram-negative bacteria, which contain several outer membrane proteins with potent immunostimulatory effects. The GN6-ELAA showed high sensitivity to detect as low as 25 ng/mL bacterial OMVs. Aptamers developed in this study show a great potential to facilitate medical diagnosis and early detection of bacterial terrorism, based on the ability to detect bacterial OMVs of multiple Gram-negative bacteria.

Determining the binding parameters from co-sedimentation assays

The stoichiometry n and the dissociation constant [Formula: see text] are key binding parameters characterizing the ligand-macromolecule interactions and equilibria. Equilibrium co-sedimentation experiments are performed in varying the concentration of one of the reactant while keeping constant that of the other reactant. The measured observable is the fraction [Formula: see text] of bound ligands when the ligand concentration is kept constant while that of macromolecules is varying whereas it is the macromolecule coverage [Formula: see text] with bound ligands when the ligand concentration is varying while that of macromolecules is kept constant. We have derived general expressions for [Formula: see text] and [Formula: see text] and subsequently showed that those expressions are in perfect agreement with simulations for a system of large ligands binding on macromolecules. Approximations have been developed to derive mathematical simple analytical expressions for [Formula: see text] and [Formula: see text] that can be used to fit the experimental data and thus extract, n and [Formula: see text] within the framework of equilibrium co-sedimentation assays. The method usefulness is illustrated and demonstrated by fitting the data from the literature using the derived formulas to determine the binding parameters.

A novel role for scavenger receptor B1 as a contributor to the capture of specific volatile odorants in the nasal cavity

Class B scavenger receptors, scavenger receptor B1 (SR-B1) and cluster of differentiation 36 (CD36), are broadly expressed cell-surface proteins and are believed to serve as multifaceted players in lipid and lipoprotein metabolism in mammals. Because of its ability to recognise distinct odour-active volatile compounds and its presence in murine olfactory epithelium, CD36 has recently emerged as a participant in the detection of odorants within the nasal cavity. However, there have been no attempts to assess whether SR-B1 has such a role. In this study, we performed a cell-free in-vitro assay utilising a peptide mimic of the receptor, and demonstrated that SR-B1 could recognise aliphatic aldehydes (e.g., tetradecanal), a distinct class of volatile odorants, as potential ligands. By reverse transcription-polymerase chain reaction and western immunoblot analyses, we detected the expression of SR-B1 mRNA and protein, respectively, in mouse olfactory tissue. Finally, we immunohistochemically mapped the distribution of SR-B1 in the surface layer of olfactory epithelium in vivo, which is the first line of odorant detection. These findings uncover a novel role for SR-B1 as a contributor to the capture of specific odorants in the nasal cavity of mammals.

Ligand binding studies by high speed centrifugal precipitation and linear spectral summation using ultraviolet-visible absorption spectroscopy

In ligand-protein binding experiments the major challenge is to separate bound from free ligand. Equilibrium and gel filtration separation techniques are often hampered by competition for the ligand and non-specific binding. Biophysical assays have attempted to circumvent this problem using titration calorimetry and spectroscopic methods. However, insoluble ligands require solvents that can overwhelm the discernible enthalpic changes of the protein and ligands. Spectroscopic methods are effective but may suffer from insensitivity (NMR) or the need for a lipid analog e.g., fluorescence and electron paramagnetic resonance. Our purpose is to compare the standard fluorescence assay to a technique we call high speed centrifugal precipitation. High speed centrifugal precipitation is suited to ligands that are insoluble in aqueous. The method permits separation of insoluble free ligand from that bound to the protein. The concentration of the each fraction can be precisely measured by absorbance spectrophotometry. A second technique, linear spectral summation has been published for protein-ligand associations using fluorescence of labeled ligands [1]. Here, the method is altered for use with ultraviolet-visible (UV-Vis) absorption spectroscopy. If the ligand complex shows a shift in the peak absorption of >8 nm, the bound and free concentrations can be measured simultaneously. The composite spectra of the samples are fit by linearly scaling UV-Vis absorption spectra of pure bound and free components at each point. •Ligand- protein binding kinetics is accessible with an ordinary spectrophotometer.•Concentrations are accurately measured from molar extinction coefficients.•The methods are ideal for lipid ligands that show absorption spectral peaks shifts in the bound and free states and/or are insoluble.

A Search for CD36 Ligands from Flavor Volatiles in Foods with an Aldehyde Moiety: Identification of Saturated Aliphatic Aldehydes with 9-16 Carbon Atoms as Potential Ligands of the Receptor

Volatile compounds with an aldehyde moiety such as (Z)-9-octadecenal are potential ligands for cluster of differentiation 36 (CD36), a transmembrane receptor that has recently been shown to play a role in mammalian olfaction. In this study, by performing an assay using a peptide mimic of human CD36, we aimed to discover additional ligands for the receptor from volatiles containing a single aldehyde group commonly found in human foods. Straight-chain, saturated aliphatic aldehydes with 9-16 carbons exhibited CD36 ligand activities, albeit to varying degrees. Notably, the activities of tridecanal and tetradecanal were higher than that of oleic acid, the most potent ligand among the fatty acids tested. Among the aldehydes other than aliphatic aldehydes, only phenylacetaldehyde showed a weak activity. These findings make a contribution to our knowledge of recognition mechanisms for flavor volatiles in foods with an aldehyde group.

Correcting binding parameters for interacting ligand-lattice systems

Binding of ligands to macromolecules is central to many functional and regulatory biological processes. Key parameters characterizing ligand-macromolecule interactions are the stoichiometry, inducing the number of ligands per macromolecule binding site, and the dissociation constant, quantifying the ligand-binding site affinity. Both these parameters can be obtained from analyses of classical saturation experiments using the standard binding equation that offers the great advantage of mathematical simplicity but becomes an approximation for situations of interest when a ligand binds and covers more than one single binding site on the macromolecule. Using the framework of car-parking problem with latticelike macromolecules where each ligand can cover simultaneously several consecutive binding sites, we showed that employing the standard analysis leads to underestimation of binding parameters, i.e., ligands appear larger than they actually are and their affinity is also greater than it is. Therefore, we have derived expressions allowing to determine the ligand size and true binding parameters (stoichiometry and dissociation constant) as a function of apparent binding parameters retrieved from standard saturation experiments.

Acute social defeat does not alter cerebral 5-HT2A receptor binding in male Wistar rats

It has been hypothesized that effects of uncontrollable stress on serotonin receptor expression contribute to the etiology of stress-related disorders like depression. While the serotonin-2A receptors (5-HT2A R) are thought to be important in this context, only few studies examined effects of stress on this receptor subtype. In this study, we therefore assessed acute and long-term changes in 5HT2A R binding after social defeat stress in rats. Male Wistar rats were subjected to social defeat by placing them in the home cage of an aggressive, dominant Long Evans rat. Acute social defeat suppressed growth, but did not affect anxiety-like behavior in an open field test. A positron emission tomography scan with the 5-HT2A R tracer [11C]MDL 100907 1 day and 3 weeks after defeat did not show significant changes in receptor binding. To verify these results, [3H]MDL 100907 binding assays were performed in homogenates of prefrontal cortex and hippocampus, which also did not indicate any changes in Bmax or Kd . These findings do not support the hypothesis that changes in 5-HT2A R function are a vital mechanism through which uncontrollable stress contributes to stress-related pathologies such as depression. It remains to be determined whether effects of stress on 5HT2A R binding depend on the nature of the stressor or on the characteristics of the rat strain.

Further validation of unsaturated long-chain fatty acids as inhibitors for oxidized low-density lipoprotein binding to CD36 via assays with synthetic CD36 peptide-cross-linked plates

We recently obtained evidence that unsaturated long-chain fatty acids (LCFAs) (e.g. oleic acid) inhibit binding of oxidized low-density lipoproteins (oxLDLs) to CD36. In the present study, we validated this prediction by examining inhibition by unsaturated LCFAs of Alexa-fluor-labeled oxLDL binding to multiwell plates onto which a synthetic CD36 peptide is covalently immobilized via thiol–maleimide coupling.

Unsaturated long-chain fatty acids inhibit the binding of oxidized low-density lipoproteins to a model CD36

Transmembrane protein CD36 binds multiple ligands, including oxidized low-density lipoproteins (oxLDLs) and long-chain fatty acids (LCFAs). Our aim was to determine whether LCFAs compete with oxLDLs for binding to CD36. We addressed this issue by examining the inhibitory effect of LCFAs against the binding of Alexa-fluor-labeled oxLDLs (AFL-oxLDL) to a synthetic peptide representing the oxLDL-binding site on CD36 (3S-CD36₁₅₀₋₁₆₈). All of the unsaturated LCFAs tested, inhibited the binding of AFL-oxLDL to 3S-CD36₁₅₀₋₁₆₈, albeit to varying degrees. For instance, the concentrations required for 50% inhibition of binding for oleic, linoleic, and α-linolenic acids were 0.25, 0.97, and 1.2 mM, respectively. None of the saturated LCFAs tested (e.g. stearic acid) exhibited inhibitory effects. These results suggest that at least unsaturated LCFAs can compete with oxLDLs for binding to CD36. The study also provides information on the structural requirements of LCFAs for inhibition of oxLDLs-CD36 binding.

A Novel Method for Determination of the Affinity of Protein: Protein Interactions in Homogeneous Assays

Nonradioactive homogeneous assays are widely used to screen for inhibitors of biomolecular interactions. To ensure optimal sensitivity for the detection of competitive inhibitors, reagent concentrations should be fixed at or below the KDof the protein-protein interaction. Accurate measurement of KDduring assay development is therefore critical. Although conventional methods work well with heterogeneous assays, they are generally unsatisfactory with homogeneous systems. Here the authors describe an alternative method to determine the KDof protein-protein interactions in homogeneous assays. The method uses a rearrangement of the Cheng-Prusoff equation: IC50= (([Ki]/KD) × [L]) + Ki. A competitive inhibitor is titrated into the ligand-receptor binding assay at a range of ligand concentrations and IC50values are calculated. Plotting measured IC50versus concentration of ligand gives a linear plot with y-intercept (Ki) and gradient (Ki/KD). KDis the affinity constant for the ligand-receptor interaction. Here the authors use homogeneous time-resolved fluorescence (HTRF®) in 2 model systems (TRAIL/TRAIL receptor 4 and OX40 ligand/OX40 receptor) and demonstrate that measured KDvalues calculated using the linearized Cheng-Prusoff plot compare favorably with those from independent experiments. The advantages and limitations of the method are discussed. ( Journal of Biomolecular Screening 2008:674-682)

Translational fusion of two beta-subunits of human chorionic gonadotropin results in production of a novel antagonist of the hormone

The strategy of translationally fusing the alpha- and beta-subunits of human chorionic gonadotropin (hCG) into a single-chain molecule has been used to produce novel analogs of hCG. Previously we reported expression of a biologically active single-chain analog hCGalphabeta expressed using Pichia expression system. Using the same expression system, another analog, in which the alpha-subunit was replaced with the second beta-subunit, was expressed (hCGbetabeta) and purified. hCGbetabeta could bind to LH receptor with an affinity three times lower than that of hCG but failed to elicit any response. However, it could inhibit response to the hormone in vitro in a dose-dependent manner. Furthermore, it inhibited response to hCG in vivo indicating the antagonistic nature of the analog. However, it was unable to inhibit human FSH binding or response to human FSH, indicating the specificity of the effect. Characterization of hCGalphabeta and hCGbetabeta using immunological tools showed alterations in the conformation of some of the epitopes, whereas others were unaltered. Unlike hCG, hCGbetabeta interacts with two LH receptor molecules. These studies demonstrate that the presence of the second beta-subunit in the single-chain molecule generated a structure that can be recognized by the receptor. However, due to the absence of alpha-subunit, the molecule is unable to elicit response. The strategy of fusing two beta-subunits of glycoprotein hormones can be used to produce antagonists of these hormones.

Biochemical and genetic characterizations of a novel human immunodeficiency virus type 1 inhibitor that blocks gp120-CD4 interactions

BMS-378806 is a recently discovered small-molecule human immunodeficiency virus type 1 (HIV-1) attachment inhibitor with good antiviral activity and pharmacokinetic properties. Here, we demonstrate that the compound targets viral entry by inhibiting the binding of the HIV-1 envelope gp120 protein to cellular CD4 receptors via a specific and competitive mechanism. BMS-378806 binds directly to gp120 at a stoichiometry of approximately 1:1, with a binding affinity similar to that of soluble CD4. The potential BMS-378806 target site was localized to a specific region within the CD4 binding pocket of gp120 by using HIV-1 gp120 variants carrying either compound-selected resistant substitutions or gp120-CD4 contact site mutations. Mapping of resistance substitutions to the HIV-1 envelope, and the lack of compound activity against a CD4-independent viral infection confirm the gp120-CD4 interactions as the target in infected cells. BMS-378806 therefore serves as a prototype for this new class of antiretroviral agents and validates gp120 as a viable target for small-molecule inhibitors.

Binding of hydrophobic ligands by Pseudomonas aeruginosa PA-I lectin

The ability of Pseudomonas aeruginosa PA-I lectin to bind the fluorescent hydrophobic probe, 2-(p-toluidinyl) naphthalene sulfonic acid (TNS), and adenine was examined by spectrofluorametry and equilibrium dialysis. Interaction of TNS with PA-I caused significant enhancement of TNS fluorescence. The Hill coefficient (3.8+/-0.3) and the dissociation constant (8.7+/-0.16 microM) showed that TNS probably bound to four high affinity hydrophobic sites per PA-I tetramer. Interactions between PA-I and adenine were examined by equilibrium dialysis using [3H] adenine. The results indicated the presence of at least two classes of binding sites--one high and four lower affinity sites per tetramer with dissociation constants of 3.7+/-1.5 and 42.6+/-1.2 microM, respectively. These were distinct from the TNS sites as titration of TNS-equilibrated PA-I with adenine caused TNS fluorescence enhancement. The titration curve confirmed the existence of two classes of adenine-binding sites. Conversely, when PA-I was first equilibrated with adenine and then titrated with TNS, no TNS-binding was registered. This may indicate that conformational rearrangements of the lectin molecule caused by adenine prevent allosterically TNS binding.

Equilibrium expert: an add-in to Microsoft Excel for multiple binding equilibrium simulations and parameter estimations

An add-in to Microsoft Excel was developed to simulate multiple binding equilibriums. A partition function, readily written even when the equilibrium is complex, describes the experimental system. It involves the concentrations of the different free molecular species and of the different complexes present in the experiment. As a result, the software is not restricted to a series of predefined experimental setups but can handle a large variety of problems involving up to nine independent molecular species. Binding parameters are estimated by nonlinear least-square fitting of experimental measurements as supplied by the user. The fitting process allows user-defined weighting of the experimental data. The flexibility of the software and the way it may be used to describe common experimental situations and to deal with usual problems such as tracer reactivity or nonspecific binding is demonstrated by a few examples. The software is available free of charge upon request.

SCATPLOT: a computer program for determination of binding parameters of non-linear non-cooperative ligand-substrate interactions

The importance of computer-assisted analysis of a non-linear binding phenomenon through Scatchard equation has been widely acknowledged. While several user-friendly softwares [LIGAND, SCTFIT, ALLFIT] are available for determining the binding parameters of nonlinear Scatchard phenomenon, there is no easily available software covering the class of phenomena described by the McGhee and von Hippel formalism [J. Mol. Biol. 86, 469-489 (1974)]. We report here user-friendly software, SCATPLOT, developed in Turbo BASIC, for the numerical estimation of binding parameters of a non-cooperative ligand-substrate interaction doing best fit to the experimental data on the basis of McGhee and von Hippel equation for a nonlinear Scatchard plot. A new parameter has also been incorporated to guide the process of least square analysis and subsequent determination of binding parameters.

Drug-protein binding sites. New trends in analytical and experimental methodology

In the last few years, continuous progress in instrumental analytical methodology has been achieved with a substantial increase in the number of new, more specific and more flexible methods for ligand-protein assays. In general, the methods used for drug-protein binding studies can be divided into two main groups: separation methods (enabling the calculation of binding parameters, i.e. the number of binding sites and their respective affinity constants) and non-separation methods (describing predominantly qualitative parameters of the ligand-protein complex). This review will be focussed particularly on recent trends in the development of drug-protein binding methods including stereoselective and non-stereoselective aspects using chromatography, capillary electrophoresis and microdialysis as compared to the "conventional approach" using equilibrium dialysis, ultrafiltration or size exclusion chromatography. The advantages and limitations of various methods will be discussed including a focus on "optimal" experimental strategies taking into account in vitro, ex vivo and/or in vivo studies. Furthermore, the importance of some particular aspects concerning the drug binding to proteins (covalent binding of drugs and metabolites, stereoselective interactions and evaluation of binding data) will be outlined in more detail.

An investigation of the use of nile red as a long-wavelength fluorescent probe for the study of alpha 1-acid glycoprotein-drug interactions

Spectrofluorimetry in the long-wavelength region of the electromagnetic spectrum (600-1000 nm) is a fairly recent development in photoluminescence spectroscopy, which has numerous advantages over measurements in the more conventional ultraviolet and visible spectral region. 9-Diethylamino-5H-benzophenoxazine-5-one (Nile Red) is an unchanged, hydrophobic molecule, and long-wavelength fluorescence of which is strongly influenced by the polarity of its environment. When Nile Red was added to solutions of alpha 1-acid glycoprotein (Orosomucoid. OMD), it showed an enhancement in fluorescence intensity and a shift to blue in emission wavelength, suggesting it was binding hydrophobically to a non-polar site on the protein. The association constant (12,261,000 +/- 900,000 M-1) and number of binding sites (0.746 +/- 0.044) were calculated for the probe. Upon addition of both acidic and basic drugs, the Nile Red fluorescence reverted to its unbound form, indicating that OMD probably has one high-affinity, wide and flexible binding area for such drugs. Possible enantiomeric selectivity was shown with ephedrine, and the association constant determined for a racemic mixture of propranolol was found to be comparable to other values obtained with alternative, more conventional techniques.

Stereoselective binding of isradipine to human plasma proteins

Isradipine (PN 200-110) is a highly potent calcium entry blocker with an asymmetrically substituted dihydropyridine ring (methyl- and isopropylester, respectively). The binding of the (+)-(S)-isradipine and (-)-(R)-isradipine to isolated human serum albumin (HSA, 30 mumol/l) and alpha 1-acid glycoprotein (AAG, 10 mumol/l) has been studied in vitro over a wide range of isradipine concentrations (0.06-20 mumol/l) using high-performance liquid chromatography (HPLC). HPLC experiments revealed that both isradipine enantiomers were bound to one class of high-affinity binding sites on the AAG molecule (n(S) = 0.83 +/- 0.05, Ka(S) = (1.33 +/- 0.25) x 10(6) l/mol, n(R) = 0.85 +/- 0.07, Ka(R) = (1.17 +/- 0.44) x 10(7) l/mol). The (R)-enantiomer also exhibited an interaction with the secondary low-affinity binding sites (n'Ka'(R) = (2.66 +/- 0.65) x 10(4) l/mol). In contrast, the pharmacologically more potent (+)-(S)-enantiomer was more strongly bound to HSA than its optical antipode (n(S) = 1.07 +/- 0.07, Ka(S) = (1.76 +/- 0.26) x 10(5) l/mol, nKa(R) = (3.62 +/- 0.06) x 10(4) l/mol). In general, the resulting binding characteristics of individual isradipine enantiomers showed stereoselectivity, but this was opposite for the two most important plasma binding proteins. The process of accumulation of isradipine by human platelets in the therapeutically relevant range (10-80 ng/ml) at 37 degrees C was devoid of stereoselectivity.