On the detection of homotropic effects in enzymes of low co-operativity. Application to modified aspartate transcarbamoylase

In contrast with the ease of observing heterotropic effects in allosteric enzymes of low co-operativity, the detection of homotropic effects is often difficult. As a consequence, erroneous conclusions about the uncoupling of homotropic and heterotropic effects can result unless sensitive techniques are used for analyzing the kinetic data. Simulations of experiments as well as actual measurements on the allosteric enzyme, aspartate transcarbamoylase, of Escherichia coli and some of its modified forms, were performed in attempts to develop stringent diagnostic procedures for the detection of homotropic effects in enzymes of low co-operativity. The analyses show that direct saturation plots (velocity versus substrate concentration), double reciprocal plots, and Hill plots yield misleading results in that the co-operativity known to be present is not observed. In contrast, Eadie plots (velocity/substrate concentration versus velocity) are much more sensitive in revealing homotropic effects. Since the observed co-operativity depends on both the allosteric equilibrium constant, L, and the number of active sites, n, simulations were performed on the effect of those parameters. The maxima in the Eadie plots increased as L was lowered and conversely the maxima decreased as n was reduced. These changes were confirmed with a mutant aspartate transcarbamoylase which had the same specific activity as the wild-type enzyme and a lower value of L, and also with a hybrid enzyme containing fewer active sites and the same L value. Analogous experiments on nitrated aspartate transcarbamoylase derivatives of decreasing activity showed that Eadie plots were of value in distinguishing between the changes in L and n values resulting from the inactivation. Data from the literature were analyzed in the form of Eadie plots and in all cases homotropic effects were readily detectable for aspartate transcarbamoylase derivatives previously claimed to be devoid of co-operativity.     

Interaction of protein with a self-associating ligand. Deviation from a hyperbolic binding curve and the appearance of apparent co-operativity in the Scatchard plot

We derived a general formula to analyze a binding system in which a ligand self-associates, in terms of experimentally determinable quantities, i.e. r, the average number of bound ligands per protein molecule, and Lft, the total free ligand concentration, which are expressed as a ligand monomer unit. The limiting behaviors of the Scatchard plot (r/Lft vs r plot), that is, the intercepts on the r-axis and the r/Lft-axis, and the limiting slopes, are generally given. Three models that may be encountered are considered in detail. Numerical examples are also presented to illustrate how the self-association of a ligand affects the binding curves. The ligand self-association alone can cause deviation of the profile of the binding curve (r vs Lft plot) from a hyperbola, resulting in a nonlinear Scatchard plot. Therefore, analysis of the binding data without consideration of ligand self-association may lead to erroneous conclusions as to the numbers and classes of binding sites, co-operativity among the sites and binding parameter values.     

Cyclic nucleotide phosphodiesterase of rat pancreatic islets. Effects of Ca2+, calmodulin and trifluoperazine.

Cyclic nucleotide phosphodiesterase activity towards cyclic AMP and cyclic GMP was studied in extracts of rat islets of Langerhans. Biphasic Eadie plots [Eadie (1942) J. Biol. Chem. 146, 85-93] were obtained with either substrate suggesting the presence of both 'high'- and 'low'-Km components. The apparent Km values were 6.2 +/- 0.5 (n = 8) microM and 103.4 +/- 13.5 (6) microM for cyclic AMP and 3.6 +/- 0.3 (12) microM and 61.4 +/- 7.5 (13) microM for cyclic GMP. With cyclic AMP as substrate, phosphodeisterase activity was increased by calmodulin and Ca2+ and decreased by trifluoperazine, a specific inhibitor of calmodulin. With cyclic GMP as substrate, phosphodiesterase activity was decreased by omission of Ca2+ or addition of trifluoperazine. Addition of exogenous calmodulin had no effect on activity. The data suggest that Ca2+ may influence the islet content of cyclic AMP and cyclic GMP via effects on calmodulin-dependent cyclic nucleotide phosphodiesterase(s).     

Heterogeneities in EGF receptor density at the cell surface can lead to concave up scatchard plot of EGF binding

The mechanism responsible for the concave up nature of the Scatchard plot of epidermal growth factor (EGF) binding on EGF receptor (EGFR) has been a controversial issue for more than a decade. Past efforts to mechanistically simulate the concave up nature of the Scatchard plot of EGF binding have shown that negative cooperativity in EGF binding on an EGFR dimer or inclusion of some external site or binding event can describe this behavior. However, herein we show that heterogeneity in the density of EGFR due to localization in certain regions of the plasma membrane, which has been experimentally reported, can also lead to concave up shape of the Scatchard plot of the EGF binding on EGFR.     

Ligand-receptor interaction. Klotz-Hunston problem for two classes of binding sites and its solution

The problem of the affinity and quantity determination of two classes of binding sites for ligand-receptor interaction using either Scatchard or Klotz plots was considered. Klotz and Hunston previously solved this problem only for the case of a representation of experimental data using the Scatchard plot. Since their publication, it was the common view that only the use of the Scatchard plot allows solving this problem. However, in some cases, using the Klotz plot is more convenient for a representation of experimental data concerning ligand-receptor interaction, though usually, this plot was used only for the evaluation of receptor affinity with one class of binding sites. In the present paper, it was demonstrated that Klotz plot also could be used for the evaluation affinity and quantity of two classes of binding sites.     

A new measure of cooperativity in protein-ligand binding

An allosteric binding system consisting of a single ligand and a nondissociating macromolecule having multiple binding sites can be represented by a binding polynomial. Various properties of the binding process can be obtained by analyzing the coefficients of the binding polynomial and such functions as the binding curve and the Hill plot. The Hill plot has an asymptote of unit slope at each end and the departure of the slope from unity at any point can be used to measure the effective interaction free energy at that point. Of particular interest in detecting and measuring cooperativity are extrema of the Hill slope and its value at the half-saturation point. If the binding polynomial is symmetric, then there is an extremum of the Hill slope at the half-saturation point. This value, the Hill coefficient, is a convenient measure of cooperativity. The purpose of this paper is to express the Hill coefficient for symmetric binding polynomials in terms of the roots of the polynomial and to give an interpretation of cooperativity in terms of the geometric pattern of the roots in the complex plane. This interpretation is then applied to the binding polynomials for the MWC (Monod-Wyman-Changeux) and KNF (Koshland-Nemethy-Filmer) models.     

Identification of an atrial natriuretic peptide specific receptor in human kidney

A specific receptor for human atrial natriuretic peptide (h-ANP) was identified in the human kidney using the radioligand binding assay. Samples were prepared from non-malignant renal tissues obtained at nephrectomy of patients with renal carcinoma. Binding studies using [125I]hANP were performed at 0 degree C for 20 minutes and terminated by a rapid filtration technique. Scatchard plot analysis revealed [125I]hANP bound to a single class of binding site (Kd = 0.4 +/- 0.2 nM) with a density of 16 +/- 4 fmol/mg protein in the renal cortex (n = 7). The binding was rapid and maximal binding was obtained within 20 minutes after the start of incubation. Radioligand displacement was observed in a dose dependent fashion when cold hANP was entered into the reaction mixture. However, unrelated agents, such as angiotensin II or 1-epinephrine, did not affect the binding. This is the first time characterization of the hANP receptor in the human kidney has been conducted using a Scatchard plot analysis.     

Phenylmethylsulfonyl fluoride (PMSF) inhibits nerve growth factor binding to the high affinity (type I) nerve growth factor receptor

Dorsal root ganglia were extirpated from 9-day old embryonic chickens and solubilized in phosphate buffered saline containing 0.5% Noniodet P 40 detergent. When nerve growth factor binding studies are performed on these samples, the expected curvilinear Rosenthal (Scatchard) plot is obtained. However, when the solubilized cell sample is made 1-2 mM in phenylmethylsulfonyl fluoride and nerve growth factor binding is determined, a linear Rosenthal (Scatchard) plot is obtained. The equilibrium dissociation constant obtained from the slope of the line is 1.9 X 10(-9) M, identical to the equilibrium dissociation constant of the low affinity receptor. A similar phenomenon is observed when rat pheochromocytoma cells are solubilized in the non-ionic detergent and nerve growth factor binding is determined. No high affinity binding can be detected for either cell type when detergent solubilized cells are incubated with phenylmethylsulfonyl fluoride.     

Presence and binding characteristics of calcitriol receptors in human fetal gut

In the present study, we show for the first time the presence of calcitriol-specific binding sites in hypertonic extracts of cells isolated from human fetal small intestine and colon from 13-21 weeks of gestation. Woolf plot analysis of the binding characteristics revealed the presence of a single class of high affinity receptors. The presence of specific receptors for calcitriol in fetal intestine and colon opens interesting possibilities as to the role of this hormone in human gut development.     

Implications of epidermal growth factor (EGF) induced egf receptor aggregation.

To investigate the role of receptor aggregation in EGF binding, we construct a mathematical model describing receptor dimerization (and higher levels of aggregation) that permits an analysis of the influence of receptor aggregation on ligand binding. We answer two questions: (a) Can Scatchard plots of EGF binding data be analyzed productively in terms of two noninteracting receptor populations with different affinities if EGF induced receptor aggregation occurs? No. If two affinities characterize aggregated and monomeric EGF receptors, we show that the Scatchard plot should have curvature characteristic of positively cooperative binding, the opposite of that observed. Thus, the interpretation that the high affinity population represents aggregated receptors and the low affinity population nonaggregated receptors is wrong. If the two populations are interpreted without reference to receptor aggregation, an important determinant of Scatchard plot shape is ignored. (b) Can a model for EGF receptor aggregation and EGF binding be consistent with the "negative curvature" (i.e., curvature characteristic of negatively cooperative binding) observed in most Scatchard plots of EGF binding data? Yes. In addition, the restrictions on the model parameters required to obtain negatively curved Scatchard plots provide new information about binding and aggregation. In particular, EGF binding to aggregated receptors must be negatively cooperative, i.e., binding to a receptor in a dimer (or higher oligomer) having one receptor already bound occurs with lower affinity than the initial binding event. A third question we consider is whether the model we present can be used to detect the presence of mechanisms other than receptor aggregation that are contributing to Scatchard plot curvature. For the membrane and cell binding data we analyzed, the best least squares fits of the model to each of the four data sets deviate systematically from the data, indicating that additional factors are also important in shaping the binding curves. Because we have controlled experimentally for many sources of receptor heterogeneity, we have limited the potential explanations for residual Scatchard plot curvature.     

Effects of prenatal exposure to alcohol on the binding of H3-diazepam to the synaptic membranes of the cerebral hemisphere cortex at various stages of ontogenesis in the rat offspring

Exposure to ethanol during pregnancy results in the alteration of (3H)-diazepam binding to synaptosomal neocortical membranes from the rat offspring. In male rats, 14 days of age, binding level diminished to 11%. In two-month-old control rats Scatchard plot was biphasic. It has been shown that prenatal exposure to ethanol leads to changes in the nature of binding in two-month-old experimental animals, as compared with the control ones. Possible relationship is discussed between the brain benzodiazepine system disorders and behaviour.     

Comparison of acetylcholine and alpha-bungarotoxin binding sites in insects and vertebrates

1. The nervous tissue of locusts contains high affinity as well as low affinity binding sites for acetylcholine which display a similar nicotinic pharmacology. 2. Hill plot analysis indicated a non-cooperative binding of acetylcholine. 3. In membrane preparations from locust ganglia and mouse brain the number of binding sites for ACh was about ten fold lower than for BGTX, whereas in membranes from electric tissue both sites occurred in similar concentrations. 4. Drug binding studies suggest that the high affinity binding sites for ACh and BGTX in preparations from insect and mouse are different; whereas in electric tissue both sites are very similar. 5. Precipitation experiments using immobilized BGTX and specific antibodies indicated that in insect nervous tissue as in electric tissue the ACh and BGTX binding sites are located on the same receptor molecule and occupy distinct partially overlapping binding sites, whereas in the vertebrate brain both sites are located on distinct binding proteins.     

Some general aspects regarding the interpretation of binding data by means of a Scatchard plot

The question is quantitatively examined which general information can be obtained from experimental data of ligand binding to macromolecules if represented by a Scatchard plot. In particular, the curvature as well as the intercepts and slopes at both coordinate axes are analyzed assuming rather general conditions including cooperative behavior (with applications to some simplified cases of interest in practice). The results should provide a basis for attempts to elucidate the binding mechanism of a system encountered in experimental work.     

Albumin prevents nonspecific transferrin binding and iron uptake by isolated hepatocytes

Bovine serum albumin inhibits binding of transferrin by hepatocytes in suspension by 60-70%. Iron uptake is inhibited by less than 20%. A Scatchard analysis of the transferrin-binding data reveals a biphasic plot in the absence of bovine serum albumin, but a monophasic plot in the presence of bovine serum albumin. Bovine serum albumin inhibits low-affinity binding of transferrin (125000 molecules/cell), but has no effect on high-affinity binding (38000 molecules/cell). In pronase-treated cells, transferrin binding is reduced by 40%, and when bovine serum albumin is added, the binding is reduced by a further 40%. Corresponding figures for iron uptake are 70 and 10%, respectively. The results are strong evidence that the major part of iron uptake by hepatocytes occurs from transferrin bound to the plasma membrane transferrin receptor.     

Comparison of acetylcholine and α-bungarotoxin binding sites in insects and vertebrates

1. The nervous tissue of locusts contains high affinity as well as low affinity binding sites for acetylcholine which display a similar nicotinic pharmacology.2. Hill plot analysis indicated a non-cooperative binding of acetylcholine.3. In membrane preparations from locust ganglia and mouse brain the number of binding sites for ACh was about ten fold lower than for BGTX, whereas in membranes from electric tissue both sites occurred in similar concentrations.4. Drug binding studies suggest that the high affinity binding sites for ACh and BGTX in preparations from insect and mouse are different; whereas in electric tissue both sites are very similar.5. Precipitation experiments using immobilized BGTX and specific antibodies indicated that in insect nervous tissue as in electric tissue the ACh and BGTX binding sites are located on the same receptor molecule and occupy distinct partially overlapping binding sites, whereas in the vertebrate brain both sites are located on distinct binding proteins.     

Structure of a novel cofactor containing N-(7-mercaptoheptanoyl)-O-3-phosphothreonine

The cofactor required in the methylcoenzyme M methylreductase reaction was shown to be a large molecule with an Mr of 1149.21 in the free acid form. The cofactor, named MRF for methyl reducing factor, was identified from analyses by fast atom bombardment mass spectrometry and 1H, 13C, and 31P NMR spectroscopy as uridine 5'-[N-(7-mercaptoheptanoyl)-O-3-phosphothreonine-P-yl(2-acetamido- 2-deoxy- beta-mannopyranuronosyl)(acid anhydride)]-(1----4)-O-2-acetamido-2-deoxy- alpha-glucopyranosyl diphosphate. MRF contains N-(7-mercaptoheptanoyl)threonine O-3-phosphate (HS-HTP) [No11, K. M., Rinehart, K. L., Tanner, R. S., & Wolfe, R. S. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 4238-4242] and is linked to C-6 of 2-acetamido-2-deoxymannopyranuronic acid of the UDP-disaccharide through a carboxylic-phosphoric anhydride linkage. It is postulated that this bond is responsible for the instability of the molecule and its hydrolysis during isolation. Analyses of Eadie and Hofstee plots of the methylcoenzyme M methylreductase reaction indicate that MRF has a 6-fold lower Km(app) than HS-HTP and a 50% greater Vmax. This suggests that the UDP-disaccharide moiety may be of importance in the binding of MRF to the enzyme active site.     

Absence of positive co-operativity in the binding of 2,3,7,8-tetrachlorodibenzo-p-dioxin to its cytosolic receptor protein.

The role of positive co-operativity in stabilizing the binding of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) to the rat hepatic cytosolic TCDD receptor protein (Ah receptor) was investigated. The binding mechanism of TCDD was determined by kinetic means through equilibrium and saturation binding studies, and Scatchard and Hill plot analysis. In all studies, the slope of the Hill plot was close to 1.0, indicating the absence of positive co-operativity. Interpretation of the Scatchard plot was however complicated by the fact that both linear and nonlinear plots were experimentally obtained. The nonlinearity was shown to be an experimental artifact and a consequence not of co-operativity, but of high levels of nonspecific binding. The high level of nonspecific binding could be attributed to: (1) lipophilicity of the TCDD ligand, and (2) inefficient competition of receptor-bound [3H]TCDD. When nonspecific binding was minimized, the Scatchard slope was linear and in agreement with the Hill coefficient, thus indicating the lack of positive co-operativity in the binding of TCDD to the Ah receptor.     

Glutaraldehyde pretreatment blocks temperature-induced high-affinity [3H]tryptamine binding

The effect of glutaraldehyde (and Azure A) on temperature-sensitive high-affinity [3H]tryptamine binding was investigated in rat brain synaptic plasma membranes. In the 0.01-0.1% concentration range, the glutaraldehyde pretreatment preferentially inhibited only the above-mentioned portion of the binding, whereas the posttreatment of this reagent had no effect. On the other hand, in cases of pretreatment or posttreatment, a concentration of glutaraldehyde as high as 0.1% was inactive on the basal [3H]ligand binding capacity of the membranes (i.e., temperature-independent binding). Furthermore, it was revealed that the Scatchard plot of [3H]tryptamine binding in membranes pretreated with glutaraldehyde (0.05%) conformed to a straight line, as did a similar plot of temperature-independent binding. And, it was interesting to find that the binding parameters (KD and Bmax values) of both samples corresponded closely to each other. On the contrary, in all concentrations, Azure A affected nonspecifically both the temperature-dependent and the independent [3H]tryptamine binding to the same degree, regardless of whether or not there was pretreatment or posttreatment. All these observations clearly demonstrate that an appropriate concentration (0.01-0.1%) of glutaraldehyde pretreatment specifically blocks the temperature-induced allosteric modifications of high-affinity [3H]tryptamine binding sites.     

The Ca2+ binding to deionized monomerized and to retinal removed bacteriorhodopsin.

In our continuing effort to characterize the metal cation binding in bacteriorhodopsin (bR) using Ca(2+)-specific electrodes, potentiometric titration was carried out on deionized solubilized bR (containing monomeric units) and deionized bacterioopsin (bR with its retinal removed). Scatchard plots were analyzed. The monomer was found to have plots similar to those of the trimer, suggesting that the binding sites in bR are localized within the protein monomer unit and not between the molecules within the trimer structure. This also supports the previous assumption that the curvature in the Scatchard plot of regenerated bR is not due to cooperativity of metal cation within the trimer, but rather due to multiple sites. Recent studies further support the finding that the curved Scatchard plot is not due to the cooperativity between the metal ions in the two high affinity sites, wherever they are. The results of the analysis of the Scatchard plot for deionized bacterioopsin have shown a change in the binding characteristics of the high affinity but not the low affinity sites from that observed in bR. This result supports previous conclusions that metal cations in the high affinity sites are not far from the retinal cavity.     

Thermodynamic model of cooperativity in a dimeric protein: unique and independent parameters formulation.

A model of the cooperative interaction of ligand binding to a dimeric protein is presented based upon the unique and independent parameters (UIP) thermodynamic formulation (Gutheil and McKenna, Biophys. Chem. 45 (1992) 171-179). The analysis is developed from an initial model which includes coupled conformational and ligand binding equilibria. This completely general model is then restricted to focus on conformationally mediated cooperative interactions between the ligands and the expressions for the apparent ligand binding constant and the apparent ligand-ligand interaction constant are derived. The conditions under which there is no cooperative interaction between the ligands are found as roots to a polynomial equation. Consideration of the distribution of species among the various conformational states in this general model leads to a set of inequalities which can be represented as a two dimensional plot of boundaries. By superimposing a contour plot of the value of the apparent ligand-ligand interaction constant over the plot of boundaries a complete graphical representation of this system is achieved similar to a phase diagram. It is found that the parameter space homologous to Koshland-Nemethy-Filmer type of model is most consistent with both positive and negative cooperativity in this model. The maximal amount of positive and negative cooperativity are found to be simple functions of Kc, the equilibrium constant associated with the change of a subunit and ligand from the unligated to ligated conformation. It is shown that under certain limiting conditions the apparent allosteric interaction between ligands is equal to the conformational interaction between subunits. The methods presented are generally applicable to the theoretical analysis of thermodynamic interactions in complex systems.