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At least 217 records · Page 12Linked to original sources
PubMed1996

Competition BIAcore for measuring true affinities: large differences from values determined from binding kinetics.

In attempting to use the BIAcore instrument for the determination of binding constants of several haptens or peptides to different antibodies by measuring on- and off-rates, we found that neither the absolute nor the relative values of the binding constants corresponded to the measurements in solution. Even at the lowest coupling densities useful for measurements, rebinding and bivalency effects offset the measurements by a factor of up to 500. We caution therefore about using on- and off-rates for the determination of absolute or even relative binding constants without controlling for rebinding and avidity effects. Instead, we show that binding constants in solution can be reproduced well by using on-rate determinations of antibody preincubated with antigen, and we derive the conditions under which such an approach is valid.

Antibody Affinity↗
PubMed1981

Effect of pH on binding kinetics and biological effect of insulin in rat adipocytes.

The pH dependence of binding of [TyrA14-125I]monoiodoinsulin to isolated rat adipocytes was investigated at 37 degrees C. Although the amount of tracer bound at steady state at pH 7.8 was 6 times that at pH 6.8, the fractional degradation of receptor-bound iodoinsulin remained the same. The decreased binding at acidic pH could be accounted for by a decrease in the affinity. The pH-induced change in affinity was similar for iodoinsulin and insulin. The half-time of dissociation was not changed in the pH range 7.0 to 7.8. The presence of 25 nM insulin in the wash out medium caused a small increase in the dissociation of tracer independent of pH. Kinetic experiments revealed that the decreased affinity at acidic pH was mainly due to a decrease in the association rate constant. The decreased binding at acidic pH was reflected in a shift to the right of the insulin dose-response curve for initial rate of uptake of 3-O-[methyl-14C]glucose and the rate of conversion of glucose to lipids. It is concluded that the degradation of bound iodoinsulin is independent of pH (6.8 to 8.8), that the decreased binding at acidic pH is due to a decreased association rate constant, and that cells in acidic milieu are relatively insulin-resistant.

Adipose Tissue↗
PubMed1998

Immunopurification of human beta2-glycorprotein I with a monoclonal antibody selected for its binding kinetics using a surface plasmon resonance biosensor.

The beta2-glycoprotein I (beta2GPI)-binding properties of five murine monoclonal antibodies immobilized as capture antibodies were studied using surface plasmon resonance detection. The monoclonal antibody with the fastest dissociation kinetics (6F3) was selected for the development of an immunoaffinity chromatography procedure, assuming that its behaviour would be similar in both systems since the covalent coupling chemistries involved amino groups in both cases. Under our experimental conditions of a fast one-step procedure, beta2GPI was purified to homogeneity from human plasma with a yield of about 50%. Beta2GPI was eluted under fairly mild conditions, either at low pH or at high pH. The immunoadsorbent was used five times without any apparent loss of binding capacity. The immunopurified protein showed similar binding to cardiolipin-coated polystyrene wells as beta2GPI purified by conventional methods. However, differences in the pattern of immunoreactivity in relation to the purification procedure were observed by surface plasmon resonance using the monoclonal antibody with the highest association kinetics (9G1) immobilized on the sensor surface.

Animals↗
PubMed1989

A new method for measurements of plasma protein steroid-binding kinetics in human plasma at 37 C.

The equilibrium kinetics in vivo of free and protein-bound steroid hormone were examined at 37 C. Human plasma was pumped through a 1 m PVC catheter and tritiated steroid hormone continuously added at the inlet. The plasma was collected and rerun through a new catheter 24 h later. A significantly (P less than 0.05) higher uptake of steroid hormone was observed in the first parts of the catheter during the first passage when compared to the second passage. The results indicate that non-equilibrium conditions existed for testosterone (greater than 10 sec), estradiol (4 sec), estrone (greater than 2 sec), and estriol (greater than 2 sec) while no delay was observed for progesterone. The results indicate that the counter-current transfer between the testicular and ovarian vessels, respectively, may create a physiologically important, temporarily increased concentration of available hormones in the arterial blood supply to the organs.

Blood Proteins↗
PubMed1996

The cluster-arranged cooperative model: a model that accounts for the kinetics of binding to A1 adenosine receptors.

To explain the equilibrium binding and binding kinetics of ligands to membrane receptors, a number of models have been proposed, none of which is able to adequately describe the experimental findings, in particular the apparent negative cooperativity of ligand binding. In this paper, a new model, the cluster-arranged cooperative model, is presented whose main characteristic is that it explains the existence of negative cooperativity in the binding of ligands to the receptor molecule. The model is based on our findings of agonist binding to A1 adenosine receptors and of ligand-induced clustering of these receptors on the cell surface. The model assumes the existence of two conformational forms of the receptor in an equilibrium which depends on the concentration of the ligand. In this way, negative cooperativity is explained by the transmission of the information between receptor molecules through the structure of the membrane. The model is able to predict the thermodynamic binding and binding kinetics of [3H]-(R)-(phenylisopropyl)adenosine to A1 adenosine receptors in the presence and absence of guanylyl imidodiphosphate. In the presence of the guanine nucleotide analogue, the linear Scatchard plots obtained for [3H]-(R)-(phenylisopropyl)adenosine binding are explained by the disappearance of cooperativity, thus suggesting that G proteins are important for the existence of negative cooperativity in ligand binding. Among other predictions, the model justifies early events in homologous desensitization since high ligand concentrations would lead to the saturation of the receptor in a low-affinity conformation that does not signal. Our model can likely explain the behavior of a number of heptaspanning and tyrosine-kinase receptors exhibiting complex binding kinetics.

Animals↗
PubMed1993

Comparison of the membrane binding kinetics of bovine prothrombin and its fragment 1.

Total internal reflection fluorescence microscopy has been used to compare the membrane binding characteristics of fluorescein-labeled bovine prothrombin and fluorescein-labeled bovine prothrombin fragment 1. The Ca(2+)-dependent association of these proteins with quartz-supported planar membranes composed of mixtures of phosphatidylserine (2-10 mol%) and phosphatidylcholine was examined. Equilibrium binding measurements showed that the apparent equilibrium dissociation constants increased with decreasing molar fractions of phosphatidylserine and that the dissociation constants were somewhat lower for intact prothrombin. Kinetic measurements, using fluorescence photobleaching recovery, showed that the measured dissociation rates were approximately equivalent for prothrombin and fragment 1 and did not change with the protein solution concentration or the molar fraction of phosphatidylserine. The kinetic data also implied that the surface binding mechanism for both proteins is more complex than a simple reversible reaction between monovalent proteins and monovalent surface sites. Measured equilibrium and kinetic constants are reported and compared for prothrombin and fragment 1 on planar membranes.

Animals↗
PubMed1983

Immunoglobulin surface-binding kinetics studied by total internal reflection with fluorescence correlation spectroscopy.

An experimental application of total internal reflection with fluorescence correlation spectroscopy (TIR/FCS) is presented. TIR/FCS is a new technique for measuring the binding and unbinding rates and surface diffusion coefficient of fluorescent-labeled solute molecules in equilibrium at a surface. A laser beam totally internally reflects at the solid-liquid interface, selectively exciting surface-adsorbed molecules. Fluorescence collected by a microscope from a small, well-defined surface area approximately 5 micron2 spontaneously fluctuates as solute molecules randomly bind to, unbind from, and/or diffuse along the surface in chemical equilibrium. The fluorescence is detected by a photomultiplier and autocorrelated on-line by a minicomputer. The shape of the autocorrelation function depends on the bulk and surface diffusion coefficients, the binding rate constants, and the shape of the illuminated and observed region. The normalized amplitude of the autocorrelation function depends on the average number of molecules bound within the observed area. TIR/FCS requires no spectroscopic or thermodynamic change between dissociated and complexed states and no extrinsic perturbation from equilibrium. Using TIR/FCS, we determine that rhodamine-labeled immunoglobulin and insulin each nonspecifically adsorb to serum albumin-coated fused silica with both reversible and irreversible components. The characteristic time of the most rapidly reversible component measured is approximately 5 ms and is limited by the rate of bulk diffusion. Rhodamine-labeled bivalent antibodies to dinitrophenyl (DNP) bind to DNP-coated fused silica virtually irreversibly. Univalent Fab fragments of these same antibodies appear to specifically bind to DNP-coated fused silica, accompanied by a large amount of nonspecific binding. TIR/FCS is shown to be a feasible technique for measuring absorption/desorption kinetic rates at equilibrium. In suitable systems where nonspecific binding is low, TIR/FCS should prove useful for measuring specific solute-surface kinetic rates.

Animals↗
PubMed1985

Competitive binding kinetics in ligand-receptor-competitor systems. Rate parameters for unlabeled ligands for the formyl peptide receptor.

We describe the real-time kinetics of the competition of different ligands for the same receptor and use the computer routine SAAM to simulate this competition. Based on the simulation, we have developed two experimental approaches whereby the parameters of the interaction of nonlabeled ligands with their receptor can be detected; briefly, the analysis of the nonlabeled ligands depends on the perturbation of the kinetics of interaction of labeled ligands with the receptor with which they are in competition. The approach relies primarily upon an analysis of the kinetics of the competition between fluorescent and nonfluorescent ligands using a real-time, homogeneous binding assay in the fluorescence flow cytometer. A secondary approach depends upon an examination of the kinetic impact of antagonists on the responses of cells stimulated by agonists at the same receptor. Experimental verification of these approaches has been obtained using the N-formyl peptides (and their antagonists) which bind to receptors on human neutrophils and produce rapid cell stimulation. We find that agonistic N-formyl peptides have residence times of minutes while nonstimulatory antagonists have residence periods of, at most, a few seconds at these receptors. The limitations and general range of applicability of these procedures are discussed. The main advantage of these approaches is that they permit the evaluation of kinetic parameters of unlabeled ligands, even those which bind weakly or which have brief residence times--properties which make analyses by conventional methods difficult.

Binding, Competitive↗
PubMed1987

Isocyanide binding kinetics to monomeric hemoproteins. A study on the ligand partition between solvent and heme pocket.

The kinetics of methyl-, ethyl-, iso-propyl-, and ter-butyl-isocyanide binding to Aplysia limacina myoglobin (distal His----Lys) and the isolated beta chains from hemoglobin Zurich (distal His----Arg) have been investigated by flash photolysis at various temperatures above 0 degrees C. Sperm whale (Physter catodon) myoglobin and the isolated beta chains from normal adult hemoglobin have been used as references. In most reaction systems investigated the apparent extent of photolysis increases with temperature. For sperm whale myoglobin and the normal beta chains the increase is of the same magnitude and not correlated to the type of ligand used. On the contrary, for the two proteins lacking the distal histidine, the phenomenon is dependent on the size of the alkyl side chain of the ligand. The results, analyzed on the basis of the multibarrier model (Austin, R.H., K.W. Beeson, L. Eisenstein, H. Frauenfelder, and I.C. Gunsalus, 1975, Biochemistry, 16:5355-5373), suggest that the partition of the ligand molecules between the solvent and the heme pocket, occurring during the photolysis process, is primarily determined by interactions between the ligand and residues in the heme cavity rather than by diffusion through the protein matrix.

Animals↗
PubMed1992

Base mispair extension kinetics. Binding of avian myeloblastosis reverse transcriptase to matched and mismatched base pair termini.

We investigate the enzymatic basis for the inefficient extension of single base mismatches by DNA polymerase compared with the extension of correct base pairs. Inefficient mismatch extension could result from either a reduced binding of the enzyme to mispaired versus correctly paired DNA template-primer termini, or from a lowered intrinsic rate of extension of mispairs by a bound enzyme, or from a combination of both factors. Avian myeloblastosis reverse transcriptase is used to measure the affinities (equilibrium dissociation constants) for the four matched and twelve mismatched base pair configurations situated at a primer 3'-terminus. The binding affinities are analyzed by two different assays employing polyacrylamide gels. The first assay uses steady-state kinetics to measure the efficiency of elongating correct and incorrect base pairs and to evaluate the enzyme's dissociation constants for matched and mismatched termini. The estimated KD values obtained in the steady-state analysis fall within a range of approximately 0.1-20 nM. The efficiencies of extending two of the mispairs, G.G and C.C, are too low to allow a determination of KD by the kinetics method. The second assay uses equilibrium binding to measure the ratio of polymerase bound to matched compared with mismatched termini, KDright/KDwrong. The affinity ratios, including values for G.G and C.C mispairs, are in the range of about 0.4-4.2. While around 1 order of magnitude difference is observed in the relative binding affinities of the polymerase for matched and mismatched primer termini, the relative extension efficiencies vary over more than 5 orders of magnitude. Therefore, it appears that inefficient mismatch extension is caused primarily by a kinetic block inhibiting elongation from mispaired primer 3'-termini rather than to a difference in binding.

Avian Myeloblastosis Virus↗
PubMed1986

Stopped-flow fluorescence studies on binding kinetics of neurotoxins with acetylcholine receptor.

Acetylcholine receptor from Narke japonica electroplax exhibits a fluorescence change upon binding of snake neurotoxins. This fluorescence change primarily arises from the conformational change of the acetylcholine receptor and reflects the binding process of the toxin with the receptor. The time dependence of the fluorescence change has been monitored for 28 short neurotoxins and 8 long neurotoxins by using a stopped-flow technique. The steady-state fluorescence change is of the same order of magnitude for the short neurotoxins but varies among the long neurotoxins. Nha 10, a short neurotoxin with weak neurotoxicity, causes no fluorescence change in the receptor but can still bind to the receptor with sufficiently high affinity. The substitution of the conserved residue Asp-31 to Gly-31 in Nha is probably responsible for the reduced neurotoxicity. The rate constants for the binding of the neurotoxins to the receptor have been obtained by analyzing the transient fluorescence change. The rate constants show surprisingly a wide range of distribution: (1.0-20.5) X 10(6) M-1 s-1 for short neurotoxins and (0.26-1.9) X 10(6) M-1 s-1 for long neurotoxins. Examination of the relationship between the rate constants of fluorescence change of the short neurotoxins and their amino acid sequences, thermal stability, hydrogen-deuterium exchange behavior, overall net charge, etc. reveals the following. Positive charges on the side chains of residues 27 and 30 and overall net charge of the neurotoxin govern the magnitude of the binding rate of the neurotoxin with the receptor.

Amino Acid Sequence↗
PubMed2003

A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex.

NMR studies of the binding of a substrate to an inactive HIV-1 protease construct, containing an active site mutation PR(D25N), are reported. Substrate titration measurements monitored by HSQC spectra and a (15)N-edited NOESY experiment show that the chromogenic substrate analog of the capsid/p2 cleavage site binds to PR(D25N) with an equilibrium dissociation constant, K(D), of 0.27 +/- 0.05 mM, and upper limits of the association and dissociation rate constants, 2 x 10(4) M(-1)s(-1) and 10 s(-1), respectively, at 20 degrees C, pH 5.8. This association rate constant is not in the diffusion limit, suggesting that association is controlled by a rare event, such as opening of the protease flaps. Analysis of (15)N relaxation experiments reveals a slight reduction of S(2) values in the flap region, indicating a small increase in the amplitude of internal motion on the sub-nsec timescale. In addition, several residues in the flap region are mobile on the conformational exchange timescale, msec-microsec. Flap dynamics of the protease-substrate complex are compared with those of protease-inhibitor complexes, and the implications of these results for substrate-binding models are discussed.

HIV Protease↗
PubMed2000

Binding kinetics of soluble ligands to transmembrane proteins: comparing an optical biosensor and dynamic flow cytometry.

BACKGROUND: The kinetics of protein-protein interactions can be monitored with optical biosensors based on the principles of either surface plasmon resonance or mirror resonance. These methods are straightforward for soluble proteins, but not for proteins inserted in the plasma membrane. METHODS: We monitored with an IASys biosensor system, based on a resonant mirror: (1) the binding of cells to an immobilized ligand, (2) the binding of a soluble ligand to immobilized cells, and (3) the binding of a soluble ligand to immobilized plasma membrane vesicles. For comparison, the kinetics of fluorescent antibody binding to intact cells were measured by dynamic flow cytometry. RESULTS: With an optical biosensor, the useful configuration is the one based on immobilized plasma membrane vesicles. However, signals can be detected only for very abundant binding sites (>10(6) per cell). Dynamic flow cytometry allows the accurate determination of the k(on) and k(off) of antibody binding. The sensitivity of the method is two orders of magnitude better than with an optical biosensor. CONCLUSIONS: Although biosensors constitute a method of choice for measuring the interactions between soluble proteins, they are not well suited for measuring the interaction between soluble proteins and membrane-embedded proteins. On the contrary, flow cytometry is well suited for such an application, when it is used in a dynamic mode.

ADP-ribosyl Cyclase↗
PubMed1999

Determination of interaction mechanism of sensorgrams by analysis of binding kinetics.

We monitored the interactions between pairs of molecules where the antigen adenylate kinase (AK) was immobilized on the surface of a chip and the antibody against AK, McAb3D3, was in solution. The association data that we obtained were not always accurately described by the expected pseudo-first-order reaction mechanism. A better description of the association data was achieved with a double-exponential function. Various models were applied to describe these observations: mass transport-controlled processes, inhomogeneous immobilized ligands, or inhomogeneous soluble analytes. Inhomogeneous immobilized ligands seemed to be the most likely explanation for the observed biphasic association kinetics. We simulated the kinetics of the SPR signal under the above-mentioned conditions. Plots of dR/dt versus R of the association phase showed characteristic differences between those nonlinearities resulting from mass transport limitation and those from inhomogeneous ligands. The plots of dR/dt versus R of McAb3D3 binding to immobilized AK show positive curvatures, indicating that the observed biphasic association kinetics is due to the inhomogeneity of the immobilized ligands. This is consistent with the results obtained from the comparison of various model fittings.

Adenylate Kinase↗
PubMedDate not supplied

Neuroglobin ligand binding kinetics.

Neuroglobin, cytoglobin, and hemoglobins from Drosophila melanogaster and Arabidopsis thaliana were studied for their ligand binding properties versus temperature. These globins have a common feature of being hexacoordinated (via the distal histidine) under deoxy conditions, displaying and enhanced amplitude for the alpha absorption band at 560 nm. External ligands can bind, but the transition from the hexacoordinated form to the ligand (L) bound species is slow, as expected for a replacement reaction Fe-His <--> Fe <--> Fe-L. Histidine binding is on the order of 1 ms; dissociation times are variable, and may be as long as 1 s for the highest histidine affinities. Oxygen binds rapidly but dissociates slowly, requiring as much as 1 s. These rates would correspond to a very high affinity for the pentacoordinated form; however, competition with the distal histidine leads decreases the affinity for the external ligand. The observed oxygen affinity remains in the range of 1 to 10 mm Hg. The low oxygen dissociation indicates a stabilization via H-bonds as for certain globins from parasites (Ascaris, the trematodes). Other ligands such as CO, or CN for the ferric form, show a decreased affinity, since only the competition with the E7 histidine, but not the stabilizing H-bond, plays a role. In addition, the competitive internal ligand leads to a weaker observed temperature dependence of the ligand affinity, since the difference in equilibrium energy for the two ligands is much lower than that of ligand binding to pentacoordinated hemoglobin. This effect could be of biological relevance for certain organisms, since it would lead to an oxygen affinity that is nearly independent of temperature.

Animals↗