A simple and convenient approach for evaluation of the parameters of ligand-receptor interaction. Receptor blocking index and its application

A new approach for determination of the parameters for ligand-receptor interaction, which is based on so-called dilution coordinates, was developed earlier. Equations that allow evaluation of not only the affinity of ligand-receptor interaction but also of the amount of free (or occupied by corresponding ligand) receptors were suggested. The most important advantage of this approach as compared with well-known methods is the ability to determine the binding parameters for ligand-receptor interaction even for the cases in which ligand and receptor are already present in a mixture and separation of counterparts from each other is technically difficult or even impossible. Due to this reason, the proposed approach can be especially useful for studying interactions between highly-labile biological receptors and corresponding ligands as found in vivo. In the present paper I continue to consider how to determine the binding parameters for a given ligand-receptor interaction if the value of receptor blocking index is determined experimentally.     

Enzymes as molecular automata: a stochastic model of self-oscillatory glycolytic cycles in cellular metabolism

A stochastic model based on the molecular automata approach was developed to simulate the cyclic dynamics of glycolysis-gluconeogenesis in cell energy metabolism. The stochastic algorithm, based on Gillespie's method, simulates the master equation associated with any network of enzymatically controlled reactions. This model of the glycolytic-gluconeogenetic cycle was developed by assembling the stochastic kinetic reactions controlled by two enzymes: phosphofructokinase (PFKase) and fructose-1, 6-biphosphatase (FBPase). In order to obtain the hysteresis behaviour predicted by classical Sel'kov analysis, a minimum complexity is required in the allosteric regulations. This implies that the FBPase cannot have a single binding site for its transition to the inactive state (a minimum of two or three binding sites is necessary). Given the multimeric structure of this enzyme, this kinetic hypothesis is tenable. Other possible applications of the stochastic automata approach for different cases of channels, receptors and enzymatic control are suggested.     

Kinetic analysis of [35S]dATP alpha S interaction with P2y(1) nucleotide receptor

The kinetics of 2'-deoxyadenosine-5'-O-(1-thiotriphosphate) ([(35)S]dATP alpha S) interaction with membrane fragments of transfected astrocytoma 1321N1 cells, expressing human P2Y(1) receptors, and the same wild-type cells, not expressing P2Y receptors were studied. Binding of this radioligand was observed with both types of membranes, but sites showing slow on-rate were found only on the transfected cells. These "slow" binding sites behaved as a kinetically homogeneous population and their interaction with the radioligand was shown to occur in two steps, R+A(K(A))<==>RA(k(i))<==>(k(-i))(RA), including the relatively slow isomerization of the complex RA into (RA). Evidence was obtained to assign the isomerized ("slow") binding sites on the transfected cells as P2Y(1) receptor sites, differentiated from other binding sites of non-receptor origin by kinetic analysis, and characterised by the kinetic parameters K(A)=59 +/- 19 nM, k(i)=(9.0 +/- 0.8)10(-3)s(-1) and k(-i)=(3.9 +/- 0.7)10(-3)s(-1). [(35)S]dATP alpha S binding, with kinetic criteria, can be of value for differentiation of the receptor sites from non-receptor sites and thus provides solid basis for radioligand assay of P2Y(1) receptors.     

Neurexin/Neuroligin Interaction Kinetics Characterized by Counting Single Cell-Surface Attached Quantum Dots

We report what to our knowledge is a new method to characterize kinetic rates between cell-surface-attached adhesion molecules. Cells expressing specific membrane receptors are surface-labeled with quantum dots coated with their respective ligands. The progressive diminution in the total number of surface-diffusing quantum dots tracked over time collectively reflects intrinsic ligand/receptor interaction kinetics. The probability of quantum dot detachment is modeled using a stochastic analysis of bond formation and dissociation, with a small number of ligand/receptor pairs, resulting in a set of coupled differential equations that are solved numerically. Comparison with the experimental data provides an estimation of the kinetic rates, together with the mean number of ligands per quantum dot, as three adjustable parameters. We validate this approach by studying the calcium-dependent neurexin/neuroligin interaction, which plays an important role in synapse formation. Using primary neurons expressing neuroligin-1 and quantum dots coated with purified neurexin-1β, we determine the kinetic rates between these two binding partners and compare them with data obtained using other techniques. Using specific molecular constructs, we also provide interesting information about the effects of neurexin and neuroligin dimerization on the kinetic rates. As it stands, this simple technique should be applicable to many types of biological ligand/receptor pairs.     

Real-time monitoring of the interactions of transforming growth factor-beta (TGF-beta ) isoforms with latency-associated protein and the ectodomains of the TGF-beta type II and III receptors reveals different kinetic models and stoichiometries of binding

Mature transforming growth factor-beta (TGF-beta) is proteolytically derived from the C terminus of a precursor protein. Latency-associated protein (LAP), the N-terminal remnant of the TGF-beta precursor, is able to bind and neutralize TGF-beta. Mature TGF-beta exerts its activity by binding and complexing members of two subfamilies of receptors, the type I and II receptors. In addition to these signaling receptors, TGF-beta can also interact with an accessory receptor termed the type III receptor. Using a surface plasmon resonance-based biosensor (BIAcore), we determined the mechanisms of interaction of four binding proteins (LAP, the type II and III receptor ectodomains (EDs), and a type II receptor ED/Fc chimera) with three TGF-beta isoforms, and we quantified their related kinetic parameters. Using global fitting based on a numerical integration data analysis method, we demonstrated that LAP and the type II receptor/Fc chimera interacted with the TGF-beta isoforms with a 1:1 stoichiometry. In contrast, the type II ED interactions with TGF-beta were best fit by a kinetic model assuming the presence of two independent binding sites on the ligand molecule. We also showed that the type III ED bound two TGF-beta molecules. Further experiments revealed that LAP was able to block the interactions of TGF-beta with the two EDs, but that the two EDs did not compete or cooperate with each other. Together, these results strongly support the existence of a cell-surface complex consisting of one type III receptor, two TGF-beta molecules, and four type II receptors, prior to the recruitment of the type I receptor for signal transduction. Additionally, our results indicate that the apparent dissociation rate constants are more predictive of the neutralizing potency of these TGF-beta-binding proteins (LAP, the type II and III receptor EDs, and the type II receptor/Fc chimera) than the apparent equilibrium constants.     

Reply to Claudio Cobelli and Gianna Toffolo,identifiability from parameter bounds. Structural and numerical aspects. Math. Biosci. 71:237–243 (1984)

We present an analysis of receptor mediated endocytosis which includes the following elements: ligand binding to receptors, interaction of the ligand-receptor complex with coated pits, internalization of coated pit contents, recycling of receptors, and degradation of ligand. The model accounts quantitatively for epidermal growth factor binding and clustering in coated pits at 4°C, for its internalization and degradation at 37°C, and for EGF receptor down-regulation. Steady state analysis of the model indicates that the slope and intercept of a Scatchard plot are functions of the kinetic parameters of the endocytic loop and do not necessarily reflect the affinity and number of receptors in metabolically active cells. Moreover, the model predicts that for homogeneous receptors, a Scatchard plot can be either linear or nonlinear, depending on the concentration of proteins in coated pits which interact with ligand-receptor complexes. A slight generalization of the model in which phorbol ester-receptor complexes compete with EGF-receptor complexes for the same coated pit proteins provides a quantitative explanation for the loss of the high affinity portion of the EGF Scatchard plot subsequent to preincubation with phorbol esters. This explanation leads to the prediction of a local homology between a portion of the phorbol ester receptor sequence and a portion of the EGF receptor sequence.     

Mechanism of lectin-cell interactions: thermodynamic and kinetic analysis of the binding of winged bean acidic lectin (WBA II) to human erythrocytes.

In order to identify the forces involved in the binding and to understand the mechanism involved, equilibrium and kinetic studies were performed on the binding of the winged bean acidic lectin to human erythrocytes. The magnitudes of delta S and delta H were positive and negative respectively, an observation differing markedly from the lectin-simple sugar interactions where delta S and delta H are generally negative. Analysis of the sign and magnitudes of these values indicate that ionic and hydrogen bonded interactions prevail over hydrophobic interactions resulting in net -ve delta H (-37.12 kJ.mol-1) and +ve delta S (14.4 J.mole-1 K-1 at 20 degrees C), thereby suggesting that this entropy driven reaction also reflects conformational changes in the lectin and/or the receptor. Presence of two kinds of receptors for WBA II on erythrocytes, as observed by equilibrium studies, is consistent with the biexponential dissociation rate constants (at 20 degrees C K1 = 1.67 x 10(-3) M-1 sec-1 and K2 = 11.1 x 10(-3) M-1 sec-1). These two rate constants differed by an order of magnitude accounting for the difference in the association constants of the two receptors of WBA II. However, the association process remains monoexponential suggesting no observable difference in the association rates of the lectin molecule with both the receptors, under the experimental conditions studied. The thermodynamic parameters calculated from kinetic data correlate well with those observed by equilibrium. A two-step binding mechanism is proposed based on the kinetic parameters for WBA II-receptor interaction.(ABSTRACT TRUNCATED AT 250 WORDS)     

Three classes of epidermal growth factor receptors on HeLa cells

The kinetics of 125I-labeled epidermal growth factor (EGF) binding to receptors on HeLa cells were investigated. Scatchard analysis revealed the presence of 22,000 high affinity receptors (Kd = 0.12 nM) and 25,000 low affinity receptors per cell (Kd = 9.2 nM). The kinetic analysis of EGF binding to high affinity receptors was performed with cells pretreated with the monoclonal antibody 2E9, which prevents specifically EGF binding to low affinity receptors. The study of EGF binding to only low affinity receptors was performed with cells pretreated with the phorbol ester phorbol 12-myristate 13-acetate, which induces a conversion of high affinity receptors to low affinity receptors. This kinetic analysis of EGF binding to HeLa cells revealed the presence of three types of receptors. High affinity receptors were found to consist of one receptor type (type I) with a kinetic association constant (kass) of 6.2 x 10(5) M-1.s-1 and a kinetic dissociation constant (kdis) of 3.5 x 10(-4) s-1. The low affinity receptors were found to consist of two kinetic distinguishable sites: type II or fast sites with kass = 3.3 x 10(6) M-1.s-1 and kdis = 8.1 x 10(-3) s-1 and the type III or slow sites with kass = 3.2 x 10(4) M-1.s-1 and kdis = 1.6 x 10(-4) s-1. The regulatory mechanism which may determine the EGF binding characteristics is discussed.     

Receptor binding oscillations]

A kinetic analysis of the delta-opiate receptor agonist, [3H] DADLE, binding to cell (NG108-15) suspensions has led to the discovery of a new periodic biological phenomenon, namely, receptor activity oscillations. The absence of oscillations for the antagonist binding to the receptors suggests that oscillations are generated only as a result of receptor signal transformation. The correlation between the quantitative characteristics of the kinetic curves and the experimental conditions points to the fact that receptor binding oscillations may be due either to the receptor binding to the G-protein or the interaction of the receptor (or G-protein) with microtubules.     

Semaphorin-7A Is an Erythrocyte Receptor for P. falciparum Merozoite-Specific TRAP Homolog,MTRAP

The motility and invasion of Plasmodium parasites is believed to require a cytoplasmic actin-myosin motor associated with a cell surface ligand belonging to the TRAP (thrombospondin-related anonymous protein) family. Current models of invasion usually invoke the existence of specific receptors for the TRAP-family ligands on the surface of the host cell; however, the identities of these receptors remain largely unknown. Here, we identify the GPI-linked protein Semaphorin-7A (CD108) as an erythrocyte receptor for the P. falciparum merozoite-specific TRAP homolog (MTRAP) by using a systematic screening approach designed to detect extracellular protein interactions. The specificity of the interaction was demonstrated by showing that binding was saturable and by quantifying the equilibrium and kinetic biophysical binding parameters using surface plasmon resonance. We found that two MTRAP monomers interact via their tandem TSR domains with the Sema domains of a Semaphorin-7A homodimer. Known naturally-occurring polymorphisms in Semaphorin-7A did not quantitatively affect MTRAP binding nor did the presence of glycans on the receptor. Attempts to block the interaction during in vitro erythrocyte invasion assays using recombinant proteins and antibodies showed no significant inhibitory effect, suggesting the inaccessibility of the complex to proteinaceous blocking agents. These findings now provide important experimental evidence to support the model that parasite TRAP-family ligands interact with specific host receptors during cellular invasion.     

The interaction of Fc alpha RI with IgA and its implications for ligand binding by immunoreceptors of the leukocyte receptor cluster

This study defines the molecular basis of the FcalphaRI (CD89):IgA interaction, which is distinct from that of the other leukocyte Fc receptors and their Ig ligands. A comprehensive analysis using both cell-free (biosensor) and cell-based assays was used to define and characterize the IgA binding region of FcalphaRI. Biosensor analysis of mutant FcalphaRI proteins showed that residues Y35, Y81, and R82 were essential for IgA binding, and R52 also contributed. The role of the essential residues (Y35 and R82) was confirmed by analysis of mutant receptors expressed on the surface of mammalian cells. These receptors failed to bind IgA, but were detected by the mAb MY43, which blocks IgA binding to FcalphaRI, indicating that its epitope does not coincide with these IgA binding residues. A homology model of the ectodomains of FcalphaRI was generated based on the structures of killer Ig-like receptors, which share 30-34% identity with FcalphaRI. Key structural features of killer Ig-like receptors are appropriately reproduced in the model, including the structural conservation of the interdomain linker and hydrophobic core (residues V17, V97, and W183). In this FcalphaRI model the residues forming the IgA binding site identified by mutagenesis form a single face near the N-terminus of the receptor, distinct from other leukocyte Fc receptors where ligand binding is in the second domain. This taken together with major differences in kinetics and affinity for IgA:FcalphaRI interaction that were observed depending on whether FcalphaRI was immobilized or in solution suggest a mode of interaction unique among the leukocyte receptors.     

Effect of ErbB2 coexpression on the kinetic interactions of epidermal growth factor with its receptor in intact cells.

We have extended the use of stopped-flow mixing and fluorescence anisotropy detection to investigate in real-time the effects of ErbB2 coexpression on the kinetic interactions of epidermal growth factor (EGF) with the EGF receptor. Using stable 32D-derived cell lines expressing both the EGF receptor and ErbB2, and fluorescein-labeled H22Y murine EGF (F-EGF), a series of association and dissociation experiments were performed in which the kinetic interaction of F-EGF with cells was monitored by observing time-dependent changes in fluorescence anisotropy following rapid mixing. Data were collected at various concentrations of F-EGF and multiple cell densities, using cells that express similar levels of the EGF receptor but different levels of ErbB2, and then analyzed by fitting to a two independent receptor-class model using global analysis techniques. The recovered kinetic parameters indicated that the coexpression of ErbB2 had relatively modest effects on recovered rate constants and calculated K(d) values, but a significant effect on the fraction of receptors associated with the high-affinity receptor class. This effect on the fraction of high-affinity receptors depended on the relative expression of ErbB2, as higher ErbB2 expression levels correlated with a larger fraction of high-affinity receptors. Further, the increase in the fraction of high-affinity receptors due to the presence of ErbB2 occurred without any change in the total number of EGF binding sites per cell. Thus, we have identified modulation of the relative populations of high- and low-affinity classes of EGF receptors as a consequence of coexpression of ErbB2 with the EGF receptor.     

A Mathematical Model for the Effects of HER2 Overexpression on Cell Proliferation in Breast Cancer

We present a mathematical model to study the effects of HER2 over-expression on cell proliferation in breast cancer. The model illustrates the proliferative behavior of cells as a function of HER2 and EGFR receptors numbers, and the growth factor EGF. This mathematical model comprises kinetic equations describing the cell surface binding of EGF growth factor to EGFR and HER2 receptors, coupled to a model for the dependence of cell proliferation rate on growth factor receptors binding. The simulation results from this model predict: (1) a growth advantage associated with excess HER2 receptors; (2) that HER2-over-expression is an insufficient parameter to predict the proliferation response of cancer cells to epidermal growth factors; and (3) the EGFR receptor expression level in HER2-over-expressing cells plays a key role in mediating the proliferation response to receptor-ligand signaling. This mathematical model also elucidates the interaction and roles of other model parameters in determining cell proliferation rate of HER2-over-expressing cells.     

Zinc nanoparticles interact with olfactory receptor neurons

Zinc metal nanoparticles strongly enhance odorant responses of olfactory receptor neurons. Olfactory receptors belong to the large superfamily of G-protein coupled receptors. A theoretical model based on experimental results explains a stoichiometry of metal nanoparticles receptor interaction. The model is similar to that used by A.V. Hill for the binding reaction between hemoglobin and oxygen. The model predicted that one metal nanoparticle binds two receptor molecules to create a dimer. This result is consistent with the evidence that many G-protein-coupled receptors form dimers or larger oligomers.     

Rate constants for binding, dissociation, and internalization of EGF: effect of receptor occupancy and ligand concentration

We measured the kinetic parameters for interaction of epidermal growth factor (EGF) with fetal rat lung (FRL) cells under two sets of experimental conditions and applied sensitivity analysis to see which parameters were well-defined. In the first set of experiments (method 1), the kinetics of internalization and dissociation of radiolabeled EGF were measured with a temperature-shift protocol in medium initially devoid of free ligand. The initial concentration of radiolabeled EGF bound to the cell surface corresponded to levels of receptor occupancy ranging from approximately 200 receptors per cell to approximately 18,000 receptors per cell, a level at which EGF binding approaches saturation. In the second set of experiments (method 2), carried out at a constant temperature, we began with no surface-bound or internalized ligand. The initial free ligand concentration was varied from 0.2 to 50 ng/mL. In both sets of experiments, we measured surface-bound, internalized, and free 125I-EGF as functions of time and evaluated the parameters of a mathematical model of endocytosis. Sensitivity analysis showed that three rate constants were well-defined in this combination of two experimental approaches: ke, the endocytic rate constant; ka, the association rate constant; and kd, the dissociation rate constant. The endocytic parameter ke was found to be independent of initial surface receptor occupancy (method 1); there was some indication that it increased with initial free ligand concentration in method 2. Neither kd nor ka was found to change with extent of initial surface receptor occupancy or initial free ligand concentration, respectively, a finding of significance, since diffusion theory predicts these parameters will vary with surface receptor occupancy.(ABSTRACT TRUNCATED AT 250 WORDS)     

Subunit Structure and Purification of Opioid Receptors

Abstract

Considerable evidence indicates the existence of multiple types of opioid receptors. The three major types have been named mu, delta and kappa. The earlier evidence was based on pharmacological as well as membrane binding experiments. This paper will emphasize more recent studies using solubilized opioid binding sites.

Several laboratories, including our own, have succeeded in separating kappa receptors from other types. A similar separation of mu from delta receptors has not yet been achieved. By crosslinking experiments with ¹²⁵I- human beta-endorphi we have been able to provide strong evidence for differences in molecular size between the major binding components of mu (65K) and delta (53K) receptors… It is not yet established whether the difference resides in the in the protein or carbohydrate portion of these glycoproteins. These results suggest that the three major types of opioid receptors represent distinct molecular entities.

An active opioid binding protein solubilized from bovine striatal membranes has been purified to apparent homogeneity. The major purification steps involve affinity chromatography and lectin chromatography on immobilized wheat germ agglutinin. The purified material gave a single band of molecular weight 65K Da on SDS-PAGE. Its specific activity for opioid binding was ca. 13000 pmol/mg protein and its properties are those of a component of the mu receptor.     

Determination of dependence of binding parameters on receptor occupancy

Measurements of the binding of ligand to receptors that are macromolecules, either free or components of biomembranes, often show deviation from what is expected of a simple reaction described by an association and a dissociation rate constant. A more versatile model and more discriminating experiments are required for a satisfactory explanation. This paper is based on a general model of the binding reaction in which the rate constants and equilibrium constant are dependent upon occupancy of receptors. The analysis of the model leads to three kinds of experiments: (1) equilibrium measurements which permit quantitative determination of a dissociation equilibrium parameter as a function of receptor occupancy; (2) measurements prior to equilibrium which yield the same information; and (3) measurements prior to equilibrium which reveal quantitatively the dependence of both association and dissociation rate parameters separately, on occupancy.     

Methyltransferase CheR binds to its chemoreceptor substrates independent of their signaling conformation yet modifies them differentially

Methylation of specific chemoreceptor glutamyl residues by methyltransferase CheR mediates sensory adaptation and gradient sensing in bacterial chemotaxis. Enzyme action is a function of chemoreceptor signaling conformation: kinase‐off receptors are more readily methylated than kinase‐on, a feature central to adaptational and gradient‐sensing mechanisms. Differential enzyme action could reflect differential binding, catalysis or both. We investigated by measuring CheR binding to kinase‐off and kinase‐on forms of Escherichia coli aspartate receptor Tar deleted of its CheR‐tethering, carboxyl terminus pentapeptide. This allowed characterization of the low‐affinity binding of enzyme to the substrate receptor body, otherwise masked by high‐affinity interaction with pentapeptide. We quantified the low‐affinity protein–protein interactions by determining kinetic rate constants of association and dissociation using bio‐layer interferometry and from those values calculating equilibrium constants. Whether Tar signaling conformations were shifted by ligand occupancy or adaptational modification, there was little or no difference between the two signaling conformations in kinetic or equilibrium parameters of enzyme‐receptor binding. Thus, differential methyltransferase action does not reflect differential binding. Instead, the predominant determinants of binding must be common to different signaling conformations. Characterization of the dependence of association rate constants on Deybe length, a measure of the influence of electrostatics, implicated electrostatic interactions as a common binding determinant. Taken together, our observations indicate that differential action of methyltransferase on kinase‐off and kinase‐on chemoreceptors is not the result of differential binding and suggest it reflects differential catalytic propensity. Differential catalysis rather than binding could well be central to other enzymes distinguishing alternative conformations of protein substrates.     

Harmonic oscillator model of the insulin and IGF1 receptors’ allosteric binding and activation

The insulin and insulin‐like growth factor 1 receptors activate overlapping signalling pathways that are critical for growth, metabolism, survival and longevity. Their mechanism of ligand binding and activation displays complex allosteric properties, which no mathematical model has been able to account for. Modelling these receptors’ binding and activation in terms of interactions between the molecular components is problematical due to many unknown biochemical and structural details. Moreover, substantial combinatorial complexity originating from multivalent ligand binding further complicates the problem. On the basis of the available structural and biochemical information, we develop a physically plausible model of the receptor binding and activation, which is based on the concept of a harmonic oscillator. Modelling a network of interactions among all possible receptor intermediaries arising in the context of the model (35, for the insulin receptor) accurately reproduces for the first time all the kinetic properties of the receptor, and provides unique and robust estimates of the kinetic parameters. The harmonic oscillator model may be adaptable for many other dimeric/dimerizing receptor tyrosine kinases, cytokine receptors and G‐protein‐coupled receptors where ligand crosslinking occurs.