New capabilities in determining the binding parameters for ligand-receptor interaction

A new method for determining the binding parameters of ligand-receptor interaction is suggested. The method is based on the application of the so-called coordinate of dilution, suggested by us earlier. We demonstrated that it is possible to determine the binding characteristics of ligand-receptor interaction using either the measurement of the concentration of the ligand-receptor complex at a state of equilibrium or the concentration of free receptors at different dilutions of the studying ligand-receptor mixture. The method also allows the determination of the concentration of the ligand in a pre-existing ligand-receptor mixture without preliminary separation of the interacting counterparts. For this reason the suggested method could be especially useful when the studying very labile receptors for which purification from the corresponding ligand is very difficult or impossible.     

Analysis of ligand-receptor binding by the difference method

A new method has been proposed for analysis of experimental data on ligand-receptor binding at equilibrium. This method makes it possible to detect heterogeneity of a receptor system in cases where the contribution of the high-affinity site to total binding is rather small and the problem of graphic discrimination of a model cannot be solved unambiguously by other methods. The difference method permits us to exclude experiments on measuring nonspecific binding. A computer program for analysis of ligand-receptor binding has been worked out in which the difference method and traditional methods of binding isotherm analysis are realized. Numerical modeling has shown that the best strategy in experimental data processing is the treatment of total binding isotherms by both the difference method and regression analysis, including the nonspecific binding constant as one of the regression parameters.     

Tumor necrosis factor family ligand-receptor binding

Ligands and receptors of the tumor necrosis factor (TNF) superfamily have pivotal roles in the development and function of the immune system. The growing pool of data on TNF from structural and biochemical studies suggests that the higher order clustering of TNF family ligands could play an essential role in signal transduction initiation for this superfamily. The identification of new structural modules of TNF family receptors, as well as interaction modes between ligands and receptors, greatly expands our knowledge of how TNF family ligands and receptors determine specificity among diverse family members and between two closely related family members.     

A two-photon excitation fluorescence cross-correlation assay for a model ligand-receptor binding system using quantum dots

Two-photon excitation fluorescence cross-correlation spectroscopy (TPE-XCS) is a very suitable method for studying interactions of two distinctly labeled fluorescent molecules. As such, it lends itself nicely to the study of ligand-receptor interactions. By labeling the ligand with one color of fluorescent dye and the receptor with another, it is possible to directly monitor ligand binding rather than inferring binding by monitoring downstream effects. One challenge of the TPE-XCS approach is that of separating the signal due to the receptor from that of the ligand. Using standard organic fluorescent labels there is almost inevitably spectral cross talk between the detection channels, which must be accounted for in TPE-XCS data analysis. However, using quantum dots as labels for both ligand and receptor this limitation can be alleviated, because of the dot's narrower emission spectra. Using solely quantum dots as fluorescent labels is a novel approach to TPE-XCS, which may be generalizable to many pairs of interacting biomolecules after the proof of principle and the assessment of limitations presented here. Moreover, it is essential that relevant pharmacological parameters such as the equilibrium dissociation constant, K(d), can be easily extracted from the XCS data with minimal processing. Herein, we present a modified expression for fractional occupancy based on the auto- and cross-correlation decays obtained from a well-defined ligand-receptor system. Nanocrystalline semiconductor quantum dots functionalized with biotin (lambda(em) = 605 nm) and streptavidin (lambda(em) = 525 nm) were used for which an average K(d) value of 0.30 +/- 0.04 x 10(-9) M was obtained (cf. native system approximately 10(-15)). Additionally, the off-rate coefficient (k(off)) for dissociation of the two quantum dots was determined as 5 x 10(-5) s(-1). This off-rate is slightly larger than for native biotin-streptavidin (5 x 10(-6) s(-1)); the bulky nature of the quantum dots and restricted motion/orientation of functionalized dots in solution can account for differences in the streptavidin-biotin mediated dot-dot binding compared with those for native streptavidin-biotin.     

Consequences of neglecting the hemoglobin concentration on the determination of Adair binding constants

It is commonly believed that the tetrameric Adair constants for oxygen binding to human hemoglobin can be evaluated from a single oxygenation experiment at 'high' hemoglobin concentration without considering the consequence of the presence of alpha beta dimers. We present examples which demonstrate that this is a very dangerous assumption. Without a knowledge of the complete oxygenation-linked dimer-tetramer association reaction (alpha beta Xi----(alpha beta)2Xj), it is impossible to predict a priori how high of a hemoglobin concentration would be required to make this assumption. Furthermore, without a knowledge of the complete oxygenation-linked dimer-tetramer association reaction, it is impossible to predict a priori the direction and magnitude of the systematic errors which are induced by making this assumption.     

A ligand-receptor binding assay by receptor immobilization

Using transferrin-transferrin receptor binding as a model of ligand-receptor binding, we have developed a new and simple binding assay for the solubilized receptor. Solubilized membrane proteins containing transferrin receptor were immobilized by covalent binding to beads having chemical reactive epoxide groups, and then 125I-labeled transferrin was added to the beads. Dose-dependent, ligand-specific, and saturable binding of 125I-labeled transferrin to the immobilized membrane proteins were demonstrated and a Scatchard analysis derived affinity of Kd = 1.8 X 10(-9) M was obtained. These results indicate that the immobilization of receptors onto beads may be useful in a simple binding assay of the solubilized receptor.     

Mathematical modeling the kinetics of cell distribution in the process of ligand-receptor binding

A statistical approach is presented to model the kinetics of cell distribution in the process of ligand-receptor binding on cell surfaces. The approach takes into account the variation of the amount of receptors on cells assuming the homogeneity of monovalent binding sites and ligand molecules. The analytical expressions for the kinetics of cell distribution have been derived in the reaction-limited approximation. In order to demonstrate the applicability of the mathematical model, the kinetics of binding the rabbit, anti-mouse IgG with Ig-receptors of the murine hybridoma cells has been measured. Anti-mouse IgG was labeled with fluorescein isothiocyanate (FITC). The kinetics of cell distribution on ligand-receptor complexes was observed during the reaction process by real-time measuring of the fluorescence and light-scattering traces of individual cells with the scanning flow cytometer. The experimental data were fitted by the mathematical model in order to obtain the binding rate constant and the initial cell distribution on the amount of receptors.     

Minimal encounter time and separation determine ligand-receptor binding in cell adhesion

The binding properties of biomolecules play a crucial role in many biological phenomena, especially cell adhesion. Whereas the attachment kinetics of soluble proteins is considered well known, complex behavior arises when protein molecules are bound to the cell membrane. We probe the hidden kinetics of ligand-receptor bond formation using single-molecule flow chamber assays and Brownian dynamics simulations. We show that, consistent with our recently proposed hypothesis, association requires a minimum duration of contact between the reactive species. In our experiments, ICAM-1 anchored on a flat substrate binds to anti-ICAM-1 coated onto flowing microbeads. The interaction potential between bead and substrate is measured by microinterferometry and is used as an ingredient to simulate bead movement. Our simulation calculates the duration of ligand-receptor contacts imposed by the bead movement. We quantitatively predict the reduction of adhesion probability measured for shorter tether length of the ligand or if a repulsive hyaluronan layer is added onto the surface. To account for our results, we propose that bond formation may occur in our system by crossing of a diffusive plateau in the energy landscape, on the timescale of 5 ms and an energy barrier of 5 k_BT, before reaching the first detectable bound state. Our results show how to relate cell-scale behavior to the combined information of molecular reactivity and biomolecule submicron-scale environment.     

Dynamics of Fst for the island model

F(st) is a measure of genetic differentiation in a subdivided population. Sewall Wright observed that F(st)=1/1+2Nm in a haploid diallelic infinite island model, where N is the effective population size of each deme and m is the migration rate. In demonstrating this result, Wright relied on the infinite size of the population. Natural populations are not infinite and therefore they change over time due to genetic drift. In a finite population, F(st) becomes a random variable that evolves over time. In this work we ask, given an initial population state, what are the dynamics of the mean and variance of F(st) under the finite island model? In application both of these quantities are critical in the evaluation of F(st) data. We show that after a time of order N generations the mean of F(st) is slightly biased below 1/1+2Nm. Further we show that the variance of F(st) is of order 1/d where d is the number of demes in the population. We introduce several new mathematical techniques to analyze coalescent genealogies in a dynamic setting.     

Analysis of oxygen equilibria of the giant hemoglobin from the earthworm Eisenia foetida using the Adair model

Oxygen equilibrium curves of the giant hemoglobin from the earthworm Eisenia foetida were determined at various concentrations of cations. Using the Adair model of 12 oxygenation steps, we succeeded in fitting the data better than the simple concerted model (MWC model). Analysis of the Adair constants (K1 to K12) indicated that the increase in oxygen affinity occurs in the last six steps (K7 to K12) of the oxygen binding and that it is enhanced by increase in Ca2+ concentration. The Hill coefficient (nmax) at pH 7.5 attained a maximum value of 9.76 at 20 mM CaCl2. In the presence of physiological levels of Ca2+ (5 mM), the Bohr effect was similar to that seen in vertebrates. The data were consistent with the release of two Bohr protons being accompanied by the oxygen-linked binding of one Ca2+. Mg2+ and Na+ exerted a similar effect on the hemoglobin, though to a lesser extent. The stoichiometry of Ca2+ binding of the hemoglobin revealed the presence of two classes of binding sites, of which the affinities are high (Ka = 8.8 x 10(3) +/- 103 M-1) and low. The number of high affinity sites per heme was found to be 0.3, comparable to the number of oxygen-linked Ca2+ binding sites.     

Lanthanide-based luminescent assays for ligand-receptor interactions

The evaluation of receptor ligand interactions is important in the field of drug discovery and development. Currently these interactions are typically measured with cumbersome (low throughput) radiolabels. Higher throughput screens are available such as fluorescent measurements of G-protein coupled receptor-induced Ca2+ increases or fluorescence anisotropy, yet these have limited applicability and/or low signal to noise. Hence, there is a need to develop more widely applicable and more sensitive labels that can be used to monitor ligand-receptor interactions. Lanthanides provide an attractive alternative to the traditional labels used for monitoring ligand-receptor interactions. The incorporation of lanthanide labels into traditional assays used to assess receptor-ligand interactions can make these assays more affordable, less time consuming and amenable to automation. Lanthanides can be coupled to ligands and provide strong luminescent signals that can be detected using time-resolved fluorescence (TRF) methods. This approach takes advantage of the long fluorescence lifetime of the lanthanide and can detect less than one attomole of europium in a multiwell plate sample. This short review provides a basic introduction into lanthanides and TRF and describes some of the recent assays which have utilized lanthanides as labels to assess ligand-receptor interactions.     

Interrupting autocrine ligand-receptor binding: comparison between receptor blockers and ligand decoys.

Stimulation of cell behavioral functions by ligand/receptor binding can be accomplished in autocrine fashion, where cells secrete ligand capable of binding to receptors on their own surfaces. This proximal secretion of autocrine ligands near the surface receptors on the secreting cell suggests that control of these systems by inhibitors of receptor/ligand binding may be more difficult than for systems involving exogenous ligands. Hence, it is of interest to predict the conditions under which successful inhibition of cell receptor binding by the autocrine ligand can be expected. Previous theoretical work using a compartmentalized model for autocrine cells has elucidated the conditions under which addition of solution decoys for the autocrine ligand can interrupt cell receptor/ligand binding via competitive binding of the secreted molecules (Forsten, K. E., and D. A. Lauffenburger. 1992. Biophys. J. 61:1-12.) We now apply a similar modeling approach to examine the addition of solution blockers targeted against the cell receptor. Comparison of the two alternative inhibition strategies reveals that a significantly lower concentration of receptor blockers, compared to ligand decoys, will obtain a high degree of inhibition. The more direct interruption scheme characteristic of the receptor blockers may make them a preferred strategy when feasible.     

Evaluation of Adair binding constants from experimental data obtained with an Imai cell. Statistical weighting functions

One group of laboratories uses an 'even-weighted', or unweighted, nonlinear least-squares method for the analysis of experimental oxygen binding data obtained with an Imai oxygenation apparatus. Another group uses an 'end-weighted' nonlinear least-squares analysis. With end weighting each observation is assigned a statistical weight which is proportional to Y(1-Y), where Y is the fractional saturation. In this work we discuss statistical weighting functions as applied to the Imai oxygenation apparatus and then determined what are the best weighting factors for an actual series of published experiments. Based on these calculations, it is concluded that the 'best' weighting for the Imai oxygenation apparatus is a very small amount of end weighting. Furthermore, the amount of end weighting is so small that even weighting, or no weighting at all, is also appropriate.     

A computerized approach towards the estimation of binding parameters to characterize cooperative and non-cooperative multicomponent ligand-receptor interactions

A mathematical model has been developed to analyse multicomponent ligand-receptor interaction data directly from binding experiments without resorting to approximations such as linearization. This approach may be applied to analyze binding data for radioreceptor systems involving thyroid and steroid hormones, and drugs on neurotransmitters. Affinity constants, maximal binding capacity, cooperativity and nonspecific binding may be calculated for multiple binding systems.     

ELISA-based assay for scatchard analysis of ligand-receptor interactions

A simple, nonradioactive method is presented that can be used for performing large numbers of binding assays of cell membrane receptors with their ligands. The method adopts the simple membrane preparation and biotin-based quantitation methods of the semi-intact cell endocytosis assays. After binding of the biotinylated ligand to its receptors on the semi-intact cell membranes, a rapid centrifugation step separates the membranes from unbound ligand. Bound ligand is subsequently released by detergent, captured by a specific antibody coated on the surface of microwells, and quantitated with peroxidase-conjugated streptavidin in a colorimetric assay. Using this assay, Scatchard analysis was performed on the data for the specific binding of iron-loaded transferrin to its receptors on mouse fibroblasts and yieldedK _d values similar to those obtained with other published methods. The assay is sensitive, rapid, and also convenient, because aliquots of semi-intact cells can be stored frozen. The perforated plasma membrane of the cells offers the additional possibility of screening factors that interact with the cytoplasmic domain of the receptors for their possible effects on the parameters of the extracellular ligand-receptor interaction.     

Mutational analysis of the IFNAR1 binding site on IFNalpha2 reveals the architecture of a weak ligand-receptor binding-site

Type I interferons activate cellular responses by forming a ternary complex with two receptor components, IFNAR1 and IFNAR2. While the binding of the IFNAR2 receptor to interferon is of high affinity and well characterized, the binding to IFNAR1 is weak, transient, and poorly understood. Here, we mapped the complete binding region of IFNAR1 on IFNalpha2 by creating a panel of 21 single alanine mutant proteins, and determined their binding affinities. The IFNAR1 binding site on IFNalpha2 maps to the center of the B and C helices, opposite to the binding site for IFNAR2. No hot spots for binding were found in the interface, with individual mutations having an up to fivefold effect on binding. Of the nine residues that affected binding, three adjacent conserved residues, located on the B helix, conferred an increase in the binding affinity to IFNAR1, as well as an increase in the biological activity of the interferon mutant. This suggests that binding of alpha interferons to the IFNAR1 receptor is sub-optimal. A correlation between binding affinity and biological activity was found, albeit not across the whole range of affinities. In WISH cells, but not DAUDI cells, the anti-proliferative activity was markedly affected by fluctuations in the IFNalpha2 affinity towards the IFNAR1 receptor. On the other hand, the antiviral activity of interferons on WISH cells seems to change in accordance to the binding affinity towards IFNAR1 only as long as the binding affinity is not beyond twofold of the wild-type. In accordance, the biological roles of the two interferon-receptor subunits are discussed.     

Dynamics of the Goodwin-Trainor mechanochemical model

The dynamics of calcium in the cortical cytoplasm of plant cells has been modeled by Goodwin & Trainor (1985) using a mechanochemical field theory based on the interaction between calcium ions and the cytoskeleton. The resulting mathematical model is a system of two non-linear partial differential equations which rule the evolution of the free calcium concentration and of the cytogel strain field in the cytoplasm. According to the values of parameters such as: calcium diffusion coefficient, strength of the calcium-strain coupling, gel elasticity or total calcium concentration, this system may be stable or unstable around an homogeneous equilibrium state. With the aid of numerical simulations, various kinds of solutions have been observed. When inertial forces ar neglected or for low values of the gel density, most of the solutions are asymptotically stable and are reached after a more or less complex transient. But for higher values of the volumetric density more complex solutions may exist, periodic in time and space or eventually chaotic.

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Resume La dynamique du calcium dans le cytoplasme cortical des cellules végétales — principalement composé d'un gel d'actine enforcé par des microtubules—a été décrite par Goodwin et Trainor (1985) à l'aide d'un modèle de type mécano-chimique, sur la base d'une interaction entre l'ion calcium et le champ de déformation de ce cytogel. II en résulte un système parabolique non linéaire de deux équations aux dérivées partielles régissant l'évolution de la concentration en calcium libre et des déformations du cortex. Selon les valeurs de certains paramètres (coefficient de diffusion du calcium, elasticité du cytogel, coefficient de couplage calcium-déformation,...) ce système peut être en équilibre stable ou instable et dans ce cas présenter des solutions non-homogènes en espace. A l'aide de simulations numériques, divers types de solutions ont été observés, montrant ainsi les grandes possibilités qu'offre ce modèle. Au cours de ces simulations, il est apparu que, lorsque la densité volumique n'est pas négligée, des solutions pouvaient présenter une dynamique apparement complexe, de type périodique ou éventuellement chaotique (en espace et en temps).