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PubMed1992

Biospecific interaction analysis using surface plasmon resonance detection applied to kinetic, binding site and concentration analysis.

A system for real-time biospecific interaction analysis using biosensor technology based on the optical phenomenon surface plasmon resonance is described. The biospecific interface is a sensor chip covered with a hydrogel matrix. One component of the interaction to be studied is immobilized covalently to the hydrogel and other interactants are passed over the chip in solution. The mass change at the sensor surface, reflecting the progress of the interaction studied, is monitored in real time. The technique, which does not require molecular labels for detection, can measure mass changes down to 10 pg/mm2. Repeated analyses can be performed on the same sensor chip. Applications shown include kinetic measurements, binding site analysis and concentration determination.

Antibodies, Monoclonal↗
PubMed1997

Effect of mobile phase composition on the binding kinetics of chiral solutes on a protein-based high-performance liquid chromatography column: interactions of D- and L-tryptophan with immobilized human serum albumin.

This work examined the kinetic interactions of chiral solutes on immobilized protein columns, using the binding of D- and L-tryptophan to human serum albumin as a model. Based on band-broadening studies and previous measurements of the association equilibrium constants (Ka) for this system, estimates were obtained for the dissociation and association rate constants (kd and ka) for D- and L-tryptophan under a variety of operating conditions. The relative importance of ka versus kd in creating changes in the overall binding affinity was then considered. For example, an increase in temperature from 4 to 45 degrees C gave a large change in ka for L-tryptophan that was due both to an increase in kd and to a decrease in ka, while ka and kd for D-tryptophan showed a parallel increase that led to a much smaller temperature dependence for Ka. Similar comparisons between ka, kd and Ka were performed over a range of pH values, ionic strengths and solvent polarities. It was also possible from these studies to examine the changes in enthalpy and entropy that accompanied the formation of the activated complex between human serum albumin and each solute. The results from this work were then used to illustrate the importance of kinetics and band-broadening in protein-based chiral separations, and an example was provided showing how this type of kinetic data might be used to help optimize such separations.

Chromatography, High Pressure Liquid↗
PubMed1980

hCG-Leydig cell functional binding kinetics: threshold and nonlinearity in response.

Functional kinetic methods, developed to measure the interaction of human chorionic gonadotropin (hCG) with rat Leydig-cell receptors, appear to be useful tools for correlating response with receptor occupancy. In the functional procedures, hCG was allowed to bind to the cells (period I), the free hormone was removed by washing and/or antiserum treatment (period II), and the response of the cells was measured at 37 degrees C (period III). Once initiated, the response to hCG was stable throughout period III. Assuming a one-to-one relationship between occupancy and response during period III, we estimated the rate of association to be 10(8) M-1/min at 37 degrees C with an activation energy of 14-17 kcal/mol. Removal of sialic acid from hCG increased this rate; removal of other carbohydrate residues decreased it. Similar values for the kinetics of binding were observed when either steroidogenesis or cyclic AMP accumulation was measured, suggesting that the same receptor may mediate both processes. Use of either functional or direct (i.e., 125I-labeled hCG) methods to estimate response as a function of occupancy gave equal results, suggesting that most binding sites were coupled to a response. Response was nonlinearly coupled to occupany. Threshold amounts of hormone-receptor complex (0.1% total receptors testosterone synthesis; 2.7% total receptors cyclic AMP accumulation) were required to induce any response. Increased stimulation required progressively larger increments of receptor occupancy. The threshold was inversely proportional to the efficacy of the hCG derivative used and was reduced by the presence of isobutylmethylxanthine.

Animals↗
PubMed1985

Potential antitumor agents. 44. Synthesis and antitumor activity of new classes of diacridines: importance of linker chain rigidity for DNA binding kinetics and biological activity.

Four classes of diacridines, joined at the 9-position by linker chains of varying length, rigidity, and polarity, were evaluated for DNA-binding properties and antitumor activity. Diacridines linked by flexible chains of varying polarity show relatively fast chromophore exchange kinetics among DNA binding sites but slower dissociation rates, suggesting the potential for considerable "creeping" of the drug along the helix, and are inactive in vivo. The exchange kinetics can be slowed dramatically by inclusion of positive charges in the side chain, but the resulting polycationic drugs are inactive in vivo, possibly due to poor distribution. Diacridines linked by a rigid, polar but neutral dicarbamoylpyrazole chain retain slow exchange kinetics, have a greatly reduced potential "creep rate", and possess good in vitro potency and significant in vivo antileukemic activity.

Acridines↗
PubMed2005

The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch.

Riboswitches are genetic control elements that usually reside in untranslated regions of messenger RNAs. These folded RNAs directly bind metabolites and undergo allosteric changes that modulate gene expression. A flavin mononucleotide (FMN)-dependent riboswitch from the ribDEAHT operon of Bacillus subtilis uses a transcription termination mechanism wherein formation of an RNA-FMN complex causes formation of an intrinsic terminator stem. We assessed the importance of RNA transcription speed and the kinetics of FMN binding to the nascent mRNA for riboswitch function. The riboswitch does not attain thermodynamic equilibrium with FMN before RNA polymerase needs to make a choice between continued transcription and transcription termination. Therefore, this riboswitch is kinetically driven, and functions more like a "molecular fuse." This reliance on the kinetics of ligand association and RNA polymerization speed might be common for riboswitches that utilize transcription termination mechanisms.

Bacillus subtilis↗
PubMed1999

The analysis of peptide affinity and its binding kinetics to DR1DW1 major histocompatibility complex protein.

The connection between experimentally measured values of ED50 (concentration of added peptide required to bind half of the protein), which characterize peptide-protein binding and the equilibrium dissociation constant of peptide-protein complex Kd (affinity) is considered. It is shown and confirmed by experimental studies that in certain cases, as a result of the absence of equilibrium in the system, the value of Kd could be much less than the experimental value of ED50, but not equal to that as commonly assumed. This is especially applicable to the formation of peptide-MHC complexes with low dissociation rates (strong binding), which may require longer time-intervals to reach equilibrium. Thus the search of the good binding peptides based on finding ones with the smallest measured values' of ED50 may result in missing the best binders with the lowest values of dissociation constant (highest affinity). To analyze the problem we considered the formal chemical kinetics of peptide-protein binding. Experimental studies of peptide binding was performed to obtain the parameters of the kinetic model. According to the predictions of the model, it was confirmed that peptide binding occurs through the preceding step, which is either a release of an endogenous peptide or some conformational change of the molecule. The half decay time for this process was determined to be approximately 3 h. Based on the model developed, a new effective method for determination of the dissociation rates of peptide-MHC complexes and the equilibrium dissociation constants Kd was proposed, which implies the comparison of binding levels (ED50) at different instants of time. This method works especially well for the peptide-MHC complexes with relatively slow dissociation rates (stable complexes), for which the direct off-rate measurements as well as obtaining equilibrium binding data to determine Kd are highly time consuming and not very reliable.

HLA Antigens↗
PubMed1997

Influence of extracellular K+ concentration on the time-course of Na+/K+-ATPase inhibition by cardiac glycosides with fast and low binding kinetics.

The magnitude of the K+ antagonism of cardiac glycoside binding to Na+/K+-ATPase prepared from porcine heart, was estimated from the enzyme activities determined in the presence of different concentrations of K+ ([K+]), ouabain, and alpha-methyl-digitoxigenin-glucoside, the latter showing a 30 fold greater dissociation rate than ouabain. An increase of [K+] (3-20 mmol/l) prolonged the half-lives of Na+/K+-ATPase inhibition and caused a rightward shift of the cardiac glycoside's dose-response curves by the same factor, almost maximal (4 fold) at 14 mmol/l K+. These data could be verified from the cardiac glycoside-elevated intravesicular Na+ concentrations of rat brain vesicles. These concentrations declined rapidly in brain vesicles treated with alpha-methyl-digitoxigenin-glucoside but not with ouabain after K+ was increased from 3.5 to 14 mM. The results suggest that the magnitude of the K+ antagonism under physiological conditions is only limited by the lifespan of the cardiac glycoside-binding E2P enzyme conformation reduced by K+.

Animals↗
PubMed1999

EMF signals and ion/ligand binding kinetics: prediction of bioeffective waveform parameters.

The kinetics of an electromagnetic field (EMF) target pathway are used to estimate frequency windows for EMF bioeffects. Ion/ligand binding is characterized via first order kinetics from which a specific electrical impedance can be derived. The resistance/capacitance properties of the binding pathway impedance, determined by the kinetics of the rate-determining step, define the frequency range over which the target pathway is most sensitive to external EMF. Applied signals may thus be configured such that their spectral content closely matches that of the target, using evaluation of the signal to thermal noise ratio to optimize waveform parameters. Using the approach proposed in this study, a pulsed radio frequency (PRF) waveform, currently employed clinically for soft tissue repair, was returned by modulation of burst duration, producing significant bioeffects at substantially reduced signal amplitude. Application is made to Ca2+/Calmodulin-dependent myosin phosphorylation, for which the binding time constants may be estimated from reported kinetics, neurite outgrowth from embryonic chick dorsal root explants and bone repair in a fracture model. The results showed that the retuned signal produced increased phosphorylation rates, neurite outgrowth and biomechanical strength that were indistinguishable from those produced by the clinical signal, but with a tenfold reduction in peak signal amplitude, approximately 800-fold reduction in average amplitude and approximately 10(6)-fold reduction in average power.

Algorithms↗
PubMed1996

Lorentz approach to static magnetic field effects on bound-ion dynamics and binding kinetics: thermal noise considerations.

The present study characterizes an ion-binding site, a molecular cleft in a signalling molecule such as calmodulin or troponin C, as a damped linear isotropic oscillator potential for small displacements about the origin. Quantitative assessments of the effects of thermal noise and exogenous static magnetic fields are made through a statistical mechanical treatment of the Lorentz-Langevin equation for an ion bound in a molecular cleft. Thermal noise causes a bound ion to be ejected from the site after a bound lifetime dependent upon the thermal noise spectral density. It is shown that the Lorentz-Langevin model requires values of the viscous damping parameter many orders of magnitude below those for bulk water in order to characterize the binding site and to obtain realistic lifetimes for a bound ion. The model predicts that milliTesla-range magnetic fields are required for static field effects on dissociation kinetics. The Lorentz equation also yields a classic coherent solution describing precession of the bound-ion oscillator orientation at the Larmor frequency. The bound-ion dynamics described by this coherent solution are sensitive to microTesla-range static magnetic fields in the presence of thermal noise. Numerical integration of the contribution of thermal noise forces to these dynamics is in good agreement with the results of statistical mechanical analysis, also producing realistic bound lifetimes for only very low viscous damping values. The mechanisms by which modulation of precessional motion might enable a signalling molecule such as calmodulin to detect an exogenous magnetic field are presently unclear.

Animals↗
PubMed1991

Structure-activity analysis of binding kinetics for NMDA receptor competitive antagonists: the influence of conformational restriction.

1. The kinetics of action of 17 structurally related NMDA receptor competitive antagonists were measured under voltage clamp in mouse hippocampal neurones. Analysis of the response to rapid changes in antagonist concentration during constant application of agonist was used to estimate microscopic association (kon) and dissociation (koff) rate constants for antagonist binding, assuming a two-equivalent site model for competitive antagonism. Dose-inhibition curves were analysed to estimate antagonist equilibrium dissociation constants. 2. For a series of 11 omega-phosphono, alpha-amino acids kon and koff varied 26 and 107 fold respectively. Rapid association and dissociation rate constants were obtained for flexible antagonist molecules such as D-2-amino-7-phosphonoheptanoic acid (D-AP7): kon 1.4 x 10(7) M-1 s-1; koff 20.3 s-1. For conformationally restrained molecules such as 3S,4aR,6S,8aR-6-phosphonomethyl-decahydroisoquinoline- 3-carboxylic acid (LY 235959), association and dissociation rate constants were much slower: kon 1.1 x 10(6) M-1 s-1; koff 0.2 s-1. For the D- and L-isomers of 3-(2-carboxypiperazin-4-yl)-propyl-1-phosphonic acid (CPP) estimates for kon were similar, but for the L-isomer koff was 10 fold faster than for the D-isomer. 3. For 2-amino-5-phosphonopentanoic acid (AP5) and its piperidine derivative cis-4-(phosphonomethyl)piperidine-2-carboxylic acid (CGS 19755), an increase in chain length of two methylene groups between the omega-phosphono and alpha-carboxylate moieties caused a 1.6 to 1.8 fold decrease in kon with little change in koff. In contrast, for AP5, CPP and its omega-carboxylate analogue, addition of a double bond close to the phosphonate moiety caused a 1.3 to 1.6 fold increase in kon. 4. For antagonists with an omega-tetrazole moiety, kon and koff were 2.8-4.6 times faster than for the parent omega-phosphono compounds. A similar, but smaller increase in kon and koff was observed for antagonists with an omega-carboxylate moiety. 5. The slow kinetics of action of potent NMDA receptor antagonists were not an artefact of buffered diffusion. In neurones equilibrated with 200 microM D-AP7, 2 microM LY 235959 and 10 microM NMDA, a transient agonist response was recorded following a rapid switch to D-AP7-free solution. This can only be explained by differences in the binding kinetics of AP7 and LY 235959, since at equilibrium, with these concentrations, either antagonist essentially eliminates the agonist response to 10 microM NMDA. 6. For all antagonists studied, the ratio koff/k0. was consistent with equilibrium Ki values obtained under similar experimental conditions, over a 40 fold range of potency. Comparison of these values with Ki estimates determined from both agonist ([3H]-glutamate), and antagonist ([3H]-CGS 19755 and [3H]- CPP) radioligand competition studies revealed good correlation between data from voltage clamp and binding experiments. However, Ki values obtained in antagonist binding assays showed on average 6.5 fold higher affinity than those obtained in voltage clamp experiments; in contrast Ki values obtained in agonist binding assays showed only 1.4 fold higher affinity. 7. The insights gained from our experiments may be of use for predicting the structural features required to generate more potent NMDA receptor antagonists, and suggest that novel acyclic compounds will have greater potential for high potency than derivatives of conformationally rigid compounds with piperazine, piperidine or bicyclic ring structures.

2-Amino-5-phosphonovalerate↗
PubMed1993

Variables influencing cell binding assays for antibody binding kinetics.

Owing to growing interest in the use of cell binding assays for quality testing of radiolabelled antibodies in radioimmunoscintigraphy, factors in the assay which might affect final outcome were evaluated in order to accumulate information for effective and reliable assay design. For unmodified antibody, magnitude of binding at certain antibody concentrations changed with alteration in number of target cells attached to the microtitre plate. The level of signal detection could either be enhanced or suppressed by changing the dilution of the enzyme-linked tester antibody as in the case of the enzyme-linked immunosorbent assay (ELISA). Accordingly, changes in either assay factor resulted in a shift in the slope of the binding curve even when the immunoreactivity of the antibody remained unchanged. A conventional technique of single cell preparation by trypsin-EDTA was investigated for the trypsin action on tumour cell antigenicity. No adverse effects could be observed if dissociated cells were incubated for 24 hours before the assay. Variation in number of target cells seemed to be a key factor in determining the power of the assay to reveal changes in the quality of the radiolabelled antibody. Our findings suggested the need to standardize factors such as the size of the seed, determination of plating efficiency and the time for culture in order to assure interassay reproducibility.

Antibodies↗
PubMed1998

Serum protein binding kinetics of phenytoin in monotherapy patients.

OBJECTIVES: To determine the binding characteristics of phenytoin to serum proteins in the Japanese population and to compare these with those reported by other investigators. METHOD: Serum samples examined in the study were obtained from 72 patients (35 males, 37 females) receiving phenytoin monotherapy. The patients' ages ranged from 1 to 73 years (1-15 years, 36 subjects; 16-44 years, 20 subjects; 45-64 years, 13 subjects; > or = 65 years, 3 subjects). RESULTS: The in vivo population binding parameters of phenytoin to serum proteins and theoretical minimal unbound serum phenytoin fraction (fu) were determined using the Scatchard equation. The association constant (K) was 0.020 1/micromol, while the total concentration of binding sites (n(Pt) was 556 micromol/l. The number of binding sites per albumin molecule (n) was 0.85, while binding ability (n.K) was 0.017 l/micromol. The fu was 0.083. The n.K is approximately 1.1 times higher in patients of Pospísil et al. (26) (i.e. 0.0191 l/micromol) than in all our patients. The association constant is approximately 1.1 times higher in our study than in the in vitro study of Monks et al. (23) (i.e. 0-0186 l/micromol), while n is similar between the two studies. The fu in our patients is similar to the unbound serum phenytoin fraction in adult patients receiving phenytoin therapy reported by Richens (2) (i.e. 0.1). CONCLUSION: Our results suggest that there may be small differences in the binding characteristics of phenytoin to serum proteins between Japanese and non-Japanese subjects. The unbound serum fraction of phenytoin in our patients with epilepsy can be assumed to be relatively constant in the therapeutic concentration range of phenytoin.

Adolescent↗
PubMed1997

Biphasic binding kinetics between FepA and its ligands.

The Escherichia coli FepA protein is an energy- and TonB-dependent, ligand-binding porin that functions as a receptor for the siderophore ferric enterobactin and colicins B and D. We characterized the kinetic and thermodynamic parameters associated with the initial, energy-independent steps in ligand binding to FepA. In vivo experiments produced Kd values of 24, 185, and 560 nM for ferric enterobactin, colicin B, and colicin D, respectively. The siderophore and colicin B bound to FepA with a 1:1 stoichiometry, but colicin D bound to a maximum level that was 3-fold lower. Preincubation with ferric enterobactin prevented colicin B binding, and preincubation with colicin B prevented ferric enterobactin binding. Colicin B release from FepA was unexpectedly slow in vivo, about 10-fold slower than ferric enterobactin release. This slow dissociation of the colicin B.FepA complex facilitated the affinity purification of FepA and FepA mutants with colicin B-Sepharose. Analysis of a fluorescent FepA derivative showed that ferric enterobactin and colicin B adsorbed with biphasic kinetics, suggesting that both ligands bind in at least two distinct steps, an initial rapid stage and a subsequent slower step, that presumably establishes a transport-competent complex.

Bacterial Outer Membrane Proteins↗
PubMed1997

Cytoskeletal protein binding kinetics at planar phospholipid membranes.

It has been hypothesized that nonspecific reversible binding of cytoskeletal proteins to lipids in cells may guide their binding to integral membrane anchor proteins. In a model system, we measured desorption rates k(off) (off-rates) of the erythrocyte cytoskeletal proteins spectrin and protein 4.1 labeled with carboxyfluorescein (CF), at two different compositions of planar phospholipid membranes (supported on glass), using the total internal reflection/fluorescence recovery after photobleaching (TIR/FRAP) technique. The lipid membranes consisted of either pure phosphatidylcholine (PC) or a 3:1 mixture of PC with phosphatidylserine (PS). In general, the off-rates were not single exponentials and were fit to a combination of fast, slow, and irreversible fractions, reported both separately and as a weighted average. By a variation of TIR/FRAP, we also measured equilibrium affinities (the ratio of surface-bound to bulk protein concentration) and thereby calculated on-rates, k(on). The average off-rate of CF-4.1 from PC/PS (approximately 0.008/s) is much slower than that from pure PC (approximately 1.7/s). Despite the consequent increase in equilibrium affinity at PC/PS, the on-rate at PC/PS is also substantially decreased (by a factor of 40) relative to that at pure PC. The simultaneous presence of (unlabeled) spectrin tends to substantially decrease the on-rate (and the affinity) of CF-4.1 at both membrane types. Similar experiments for CF-spectrin alone showed much less sensitivity to membrane type and generally faster off-rates than those exhibited by CF-4.1. However, when mixed with (unlabeled) 4.1, both the on-rate and off-rate of CF-spectrin decreased drastically at PC/PS (but not PC), leading to a somewhat increased affinity. Clearly, changes in affinity often involve countervailing changes in both on-rates and off-rates. In many of these studies, the effect of varying ionic strength and bulk concentrations was examined; it appears that the binding is an electrostatic attraction and is far from saturation at the concentrations employed. These results and the techniques implemented carry general implications for understanding the functional role of nonspecific protein binding to cellular lipid membranes.

Biophysical Phenomena↗
PubMed1998

Measuring two-dimensional receptor-ligand binding kinetics by micropipette.

We report a novel method for measuring forward and reverse kinetic rate constants, kf0 and kr0, for the binding of individual receptors and ligands anchored to apposing surfaces in cell adhesion. Not only does the method examine adhesion between a single pair of cells; it also probes predominantly a single receptor-ligand bond. The idea is to quantify the dependence of adhesion probability on contact duration and densities of the receptors and ligands. The experiment was an extension of existing micropipette protocols. The analysis was based on analytical solutions to the probabilistic formulation of kinetics for small systems. This method was applied to examine the interaction between Fc gamma receptor IIIA (CD16A) expressed on Chinese hamster ovary cell transfectants and immunoglobulin G (IgG) of either human or rabbit origin coated on human erythrocytes, which were found to follow a monovalent biomolecular binding mechanism. The measured rate constants are Ackf0 = (2.6 +/- 0.32) x 10(-7) micron 4 s-1 and kr0 = (0.37 +/- 0.055) s-1 for the CD16A-hIgG interaction and Ackf0 = (5.7 +/- 0.31) X 10(-7) micron 4 s-1 and kr0 = (0.20 +/- 0.042) s-1 for the CD16A-rIgG interaction, respectively, where Ac is the contact area, estimated to be a few percent of 3 micron 2.

Animals↗
PubMed1986

Effects of sodium and GTP on the binding kinetics of [3H]diprenorphine in NG 108-15 cell membranes.

Equilibrium binding isotherms of [3H]diprenorphine in membranes from NG 108-15 cells are consistent with a homogeneous population of binding sites. Upon addition of Na+, Mg2+ and GTP, only a 2-fold reduction in affinity with a minor decrease in the number of sites is observed. Dissociation curves of [3H]diprenorphine, however, are clearly biphasic: in the absence of Na+, Mg2+ and GTP, 80% of the bound ligand dissociates slowly with a t1/2 of 100 min, and only 20% rapidly (t1/2 4.5 min). In the presence of Mg2+, nearly all the binding is found in the slowly dissociating form. Upon the addition of either Na+ or GTP, 20-30% of the binding dissociates more rapidly. The rate constant of the rapidly dissociating form generated by Na+, however, is 2.5 times greater than that induced by the presence of GTP. Thus, the addition of both, Na+ and GTP, converts about 80% of the receptor into a very fast dissociating form (t1/2 1.7 min). Exposure of intact cells to pertussis toxin (10 ng/ml) or treatment of membranes with N-ethyl maleimide (500 microM), strongly reduces the proportion of the slowly dissociating component. Following these treatments, the effect of GTP is reduced or abolished, but that of Na+ remains unaffected. We conclude from these data that the effects of Na+ and GTP are not only distinct in site but also in mechanism of action and that there are three forms of opioid receptors that can be differentiated by their kinetic properties. The slowly dissociating receptor form requires a functional N unit.

Animals↗
PubMed1999

Methodological considerations for the human platelet 5-HT2A receptor binding kinetic assay.

Analysis of an extensive database of human platelet 5-HT2A receptor binding assays has been conducted in order to identify factors that may affect the assay results. Despite anecdotal reports that storage of frozen platelet pellets may affect 5-HT2A binding affinity and capacity, no quantitative study has been reported in the literature. Analysis of binding data for 373 frozen samples with a storage time up to three years is presented in this paper. It is shown that prolonged storage significantly decreases binding. The loss of binding capacity begins in the first six month of storage. Bmax declines by half after 17 month. The impact of storage time on the binding affinity is much smaller. There is only about 20% increase in the value of affinity K(D) during the half-life of Bmax. Differences in sample storage time may partly explain discrepancies in results between different research groups. Nonspecific binding due to binding to filter material diminishes accuracy and reliability of the binding assays as a result of a decrease in the ratio of specific to nonspecific ratio. A data analysis based on our suggested mathematical model shows that this effect depends on tissue concentration in test tube and becomes pronounced when the concentration is below 0.1 mg protein/ml (at 0.2 nM of ligand). Above 0.1 mg protein/ml, percentage of specific to total binding exceeds 65%, which is an acceptable level for the ratio. The majority of the binding studies reported in the literature employed a tissue concentration more than 0.5 mg/ml, well above the minimal limit sufficient for a reliable assay. However, development of microassays to conserve precious tissue must take the limit into consideration.

Blood Platelets↗