Kinetic Association Constants Research Articles

Interferometric detection of chloramphenicol via its immunochemical recognition at polymer-coated nano-corrugated surfaces

Three types of polymer-coated glass slides were prepared by acylation of their γ–aminopropyl derivatives with succinic anhydride or poly(p-nitrophenyl acylate) (PNPA) at various reaction times. The variations in duration of chemical adsorption of PNPA allowed control over nano-corrugation of the reactive surfaces employed for biosensing. The visually smooth and optically clear polymer-coated slides were used for immobilization of a conjugate of bovine serum albumin with chloramphenicol (CAP) and label-free measurement of concentration of this antibiotic. The sensor chips prepared in this way provided strong biosensing response due to fast biomolecular interactions and efficient competition of the target analyte during indirect immunoassay. The kinetics of formation and dissociation of immune complexes “conjugate-antibody” on the sensor chip surface was registered by the label-free methods of spectral-correlation and spectral-phase interferometry. The average thickness of immune complex adsorption layers was in the range of 5–12 nm. The highest value of kinetic association constant (kon = 5 × 104 M−1s−1) and the lowest equilibrium dissociation constant (Kdiss = 2 × 10-8 M−1) were achieved with the chips originated in the PNPA-coated slides, which were produced under short (2 min) polymer chemisorption and exhibited nano-corrugation almost unchanged with respect to the parent glass, according to the atomic-force microscopy. The detection limit for CAP detection was 80 pg/mL, and the dynamic range was 5 orders. The proposed methods for fabrication of sensor chips with nano-corrugated surface, the results of their characterization, as well as the developed assay can be employed for high-throughput recording of multiple molecular interactions by spectral interferometry and in a wide range of biosensing platforms for registration of biologically active compounds in medicine, veterinary, food control and ecological monitoring.

A new real-time method for investigation of affinity properties and binding kinetics of magnetic nanoparticles

A method for quantitative investigation of affinity constants of receptors immobilized on magnetic nanoparticles (MP) is developed based on spectral correlation interferometry (SCI). The SCI records with a picometer resolution the thickness changes of a layer of molecules or nanoparticles due to a biochemical reaction on a cover slip, averaged over the sensing area. The method is compatible with other types of sensing surfaces employed in biosensing. The measured values of kinetic association constants of magnetic nanoparticles are 4 orders of magnitude higher than those of molecular antibody association with antigen. The developed method also suggests highly sensitive detection of antigens in a wide dynamic range. The limit of detection of 92 pg/ml has been demonstrated for prostate-specific antigen (PSA) with 50-nm MP employed as labels, which produce 3-order amplification of the SCI signals. The calibration curve features high sensitivity (slope) of 3-fold signal raise per 10-fold increase of PSA concentration within 4-order dynamic range, which is an attractive compromise for precise quantitative and highly sensitive immunoassay. The proposed biosensing technique offers inexpensive disposable sensor chips of cover slips and represents an economically sound alternative to traditional immunoassays for disease diagnostics, detection of pathogens in food and environmental monitoring.

Measuring Kinetic Dissociation/Association Constants Between Lactococcus lactis Bacteria and Mucins Using Living Cell Probes

In this work we focused on quantifying adhesion between Lactococcus lactis, the model for lactic acid bacteria (LAB) and mucins. Interactions between two strains of L. lactis (IBB477 and MG1820 as control) and pig gastric mucin–based coating were measured and compared with the use of atomic force microscopy. Analysis of retraction force-distance curves shed light on the differential contributions of nonspecific and specific forces. An increased proportion of specific adhesive events was obtained for IBB477 (20% vs. 5% for the control). Blocking assays with free pig gastric mucin and its O-glycan moiety showed that oligosaccharides play a major (but not exclusive) role in L. lactis-mucins interactions. Specific interactions were analyzed in terms of kinetic constants. An increase in the loading rate of atomic force microscope tip led to a higher force between interacting biological entities, which was directly linked to the kinetic dissociation constant (Koff). Enhancing the contact time between the tip and the sample allowed an increase in the interaction probability, which can be related to the kinetic association constant (Kon). Variations in the loading rate and contact time enabled us to determine Kon (3.3 × 102 M−1·s−1) and Koff (0.46 s−1), and the latter was consistent with values given in the literature for sugar-protein interactions.

Biochemical characterization of DNA-binding proteins from Pyrobaculum aerophilum and Aeropyrum pernix

Several representatives of the Crenarchaeal branch of the Archaea contain highly abundant, small, positively charged proteins exemplified by the Sso7d protein from Sulfolobus solfataricus. These proteins bind to DNA in a non-sequence-specific manner. Using publicly available genomic sequence information, we identified a second class of small Crenarchaeal DNA-binding proteins represented by the Pyrobaculum aerophilum open reading frame 3192-encoded (Pae3192) protein and its paralogs. We investigated the biochemical properties of the Pae3192 protein and an orthologous protein (Ape1322b) from Aeropyrum pernix in side-by-side experiments with the Sso7d protein. We demonstrate that the recombinant Ape1322b, Pae3192 and Sso7d proteins bind to DNA and that the DNA-protein complexes formed are slightly different for each protein. We show that like Sso7d, Pae3192 constrains negative supercoils in DNA. In addition, we show that all three proteins raise the melting temperature of duplex DNA upon binding. Finally, we present the equilibrium affinity constants and kinetic association constants of each protein for single-stranded and double-stranded DNA.

Kinetic and equilibrium characterization of the interaction between bovine trypsin and I-ovalbumin

Serpins are a superfamily of structurally linked proteins with interesting functional properties. Most serpins act as proteinase suicide inhibitors and play a key role in a number of physiological processes. Structural flexibility properties make serpins extremely available to conformational transitions, often causing changes in protein function. Ovalbumin is a member of the serpin family that is not able to inhibit serine proteinases in its native form. In contrast, I-ovalbumin, the product of a heating transition, is a potent reversible serine proteinase inhibitor. In this paper, a detailed equilibrium and kinetic characterization of the interaction between the serpin ovalbumin and bovine trypsin, using a resonant mirror technique, is reported. This methodology revealed that the high affinity interaction between the two binding partners is characterized by high kinetic association constants and low kinetic dissociation constants. The modulation exerted by protons in solution, examined taking into account structural motifs characterizing the binding interface between the two macromolecules, suggests an interaction reminiscent of that observed for the binding of other serine proteases to their ligands.

Determination of binding constant of transcription factor myc-max/max-max and E-box DNA: the effect of inhibitors on the binding.

The truncated myc and max proteins, only containing basic regions and helix-loop-helix/zipper (b/HLH/Zip) regions were over-expressed in E. coli and used for the determination of the binding constant and of the inhibitory mechanism on myc-max (or max-max)-DNA complex formation. The association kinetic constants (k(1) and k(-1)) of truncated max-max or myc-max dimer and DNA were determined as k(1)=(1.7+/-0.6)x10(5) M(-1) s(-1), k(-1)=(3.4+/-1.2)x10(-2) s(-1) for max-max and DNA or k(1)=(2.1+/-0.7)x10(5) M(-1) s(-1), k(-1)=(3.2+/-1.4)x10(-2) s(-1) for myc-max and DNA. The equilibrium binding constant (K(1)) was determined using these kinetic parameters [K(XXD)=(7.8+/-2.6)x10(6) M(-1) for max-max and DNA or K(XYD)=(6.9+/-2.2)x10(6) M(-1) for myc-max and DNA]. The binding constants of myc-max or max-max dimer formation were K(XX)=(2.6+/-0.9)x10(5) M(-1) or K(XY)=(1.3+/-0.4)x10(4) M(-1), respectively. When truncated proteins were used, the max-max dimer formation was easier than the myc-max dimer formation, contrary to the physiologically determined case. This leads us to deduce that domains other than b/HLH/Zip are very important for the transcriptional regulatory activity in physiological conditions. The truncated myc and max proteins, which were expressed in E. coli and contained only b/HLH/Zip regions were also used for the screening of inhibitors of myc-max-DNA complex formation. A synthesized curcuminoid, 1,7-bis(4-methyl-3-nitrophenyl)-1,6-heptadiene-3,5-dione (curcuminoid 004), showed the most potent inhibition out of the synthesized curcuminoids, in competition with DNA. The dissociation constant of max-max dimer and the inhibitor was 9 microM, when investigated using in vitro expressed b/HLH/Zip dimer proteins. The curcuminoid 004 showed an inhibitory effect on the binding of myc-max protein to the E-box element in SNU16 cells, and suppressed the expression of myc target genes including ornithine decarboxylase (ODC), cdc25a and c-myc in myc over-expressed human stomach cancer cell line SNU16.

Influence of macroscopic and microscopic interactions on kinetic rate constants: I. Role of the extended DLVO theory in determining the kinetic adsorption constant of proteins in aqueous media, using von Smoluchowski’s approach

In the case of adsorption in an aqueous medium of a hydrophilic protein (e.g. human serum albumin (HSA)) onto a hydrophilic solid substratum such as a clean glass surface, one has to deal with a macroscopic-level repulsion between HSA and glass at (generally) the majority of orientations of the protein molecules, and also a microscopic-level attraction between HSA and glass at (generally) the minority of orientations of the protein molecules. The first phenomenon represents von Smoluchowski’s improbability of adhesion or adsorption and the second represents the probability of adhesion or adsorption [1]. Both contingencies have to be taken into account in determining von Smoluchowski’s net probability factor, f of the kinetic association constant, k a, pertaining to protein adsorption. In the exceptional case where both the protein and the solid substratum are hydrophobically/hydrophilically and electrostatically neutral, f=1, and the k a-value is only proportional to the diffusion coefficient of the protein [2]. In order to determine the contributions of both the macroscopic repulsion and the microscopic attraction pertaining to the kinetics of protein adsorption, an extended DLVO analysis (XDLVO) needs to be done on these interactions at all distances and at all protein orientations. The XDLVO analysis comprises the Lewis acid–base interaction energies as a function of distance, in addition to the Lifshitz–van der Waals and the electrokinetic interaction energies [2–5].

Measurements of the kinetic constants of protein adsorption onto silica particles

The early events pertaining to protein (human serum albumin: HSA) adsorption and desorption onto silica particles were studied employing real time, in situ measurements. The experimental method involved continuous measurements of the outflowing concentration of HSA with a fluorimeter, based on the natural fluorescence of the protein molecules. The adsorption (desorption) took place inside a well-stirred compartment, where particles were brought into contact by injection into a stream of a protein solution of known concentration. Intense mixing and sufficient protein supply rate allowed the process to take place solely under kinetic control. The acquired data were interpreted, according to a kinetic model, in terms of protein binding rates. From the latter, the kinetic association ( k a) and dissociation ( k d) constants were determined. To avoid the influence of steric hindrance, only data points obtained within the first 0.5 s of the initialization of the experiments were used. The experiments were performed at different protein concentrations, ranging from 7.25 nM to 14.5 μM. The real kinetic constants were determined by extrapolating the data obtained to zero protein concentration. Protein concentration effects were found to be pronounced in the determination of the kinetic association constant, producing values underestimated by as much as 30-fold for a 14.5 μM concentration. The concentration effect on the kinetic dissociation constant was not very significant: it was only of the order of a factor 2. The ratio of favorable to unfavorable protein orientations, also known as von Smoluchowski’s factor ( f), was found to be 0.064 for the system of silica and HSA. For HSA adsorbing onto silica particles, the following values were found: k a=4.529×10 6 l mol −1 s −1; k d=0.21 s −1. To convert from stirred to stationary conditions, both kinetic constants should be reduced by a factor 62.5, decreasing von Smoluchowski’s f factor to 0.001.

Kinetics and energetics of specific intermolecular interactions.

Taking into account the energy vs. distance functions of the aspecific (macroscopic) repulsion that usually prevails between antigen (Ag) and antibody (Ab) molecules in polar media, as well as the specific (microscopic) attraction between epitope and paratope of Ag and Ab, it proved possible to determine the kinetic constants (von Smoluchowski, 1917; Hammes, 1978) of Ag-Ab interactions, from the surface properties of Ag, Ab and the aqueous medium. The kinetic constants thus found correlate well with experimentally determined kinetic constants in comparable systems, and confirm the importance of the influence of the concentration of one of the reagents (e.g. the Ab) on the kinetic association constant (Van Regenmortel et al., 1994), which is largely due to steric hindrance. Applying the same energy vs. distance approach to the influence of temperature (T) on Ag-Ab reactions, it ensues that the familiar occurrence of an apparent 'enthalpy-entropy compensation' in aqueous media is in fact the relatively gratuitous outcome of a complex set of effects caused by an increase in T, on the total free energy, the hydration energy and, as a result, on the inter-epitope-paratope distance. A close correlation exists between the outcome of these surface-thermodynamic analyses and experimental results.

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.

Acridine dimers: influence of the intercalating ring and of the linking-chain nature on the equilibrium and kinetic DNA-binding parameters.

The rigidity of the linking chain of bifunctional intercalators in the ditercalinium series was shown to be critical for antitumor activity. In order to study the influence of the rigidity of the linking chain on the DNA-binding properties of DNA bifunctional intercalators, fluorescent 9-aminoacridine and 2-methoxy-6-chloro-9-aminoacridine analogues with chains of variable rigidity were synthesized. 1H-NMR studies show that the conformation of 9-aminoacridine dimers is almost independent of the nature of the linking chain. A strong self-stacking of the aromatic rings of the 2-methoxy-6-chloro-9-aminoacridine is observed for dimers with flexible chains but not for those with rigid chains. All the dimers having a linking chain long enough to bisintercalate in DNA according to the excluded site model are indeed bisintercalators. The kinetic association constant of all monomers and dimers for poly[d(A-T)].poly[d(A-T)] are in the same range (2-4 x 10(7) M-1 s-1). The large increase of DNA binding affinity observed for the dimers is always associated with the expected decrease of the dissociation rate constant. The effect of chain rigidity and pH on the calf thymus DNA binding of 9-aminoacridine and 2-methoxy-6-chloro-9-aminoacridine dimers is quite different. In the series of 9-aminoacridine the pKa of the dimers remains high and therefore no difference of DNA-binding affinity is observed between pH 5 and 7.4. The rigidity of the linking chain does not significantly alter the DNA-binding affinity. In the 2-methoxy-6-chloro-9-aminoacridine series, the pKa of all dimers became smaller than the physiological pH and a dramatic decrease of DNA-binding affinity is observed when the pH is increased from pH 5 to 7.4. This decrease appears significantly smaller for dimers with rigid chains. A similar dramatic decrease of binding affinity at pH 7.4 is not observed for poly[d(A-T)].poly[d(A-T)]. This factor makes these dimers strongly specific for the alternating polymer at pH 7.4.

Binding of a Tritiated Pepstatin Analog to Human Renin

The interaction between human renin and a potent pepstatin analog, SR 42128, has been investigated using binding studies. Binding and enzymatic assays were performed at pH 5.7 and pH 7.4. We found one specific inhibitor binding site per molecule of renin at both pH's. The dissociation constant (KD) obtained at equilibrium was 14-fold lower at pH 5.7 than at pH 7.4, showing a pH effect on binding of [3H]SR 42128. A similar decrease was measured in enzymatic studies. In nonequilibrium conditions, we demonstrated that only association kinetic constants have been affected by pH variations. Radioligands provided interesting tools to investigate enzyme-inhibitor relationships.

Study of protein association and micelle formation in surfactants by microcolumn exclusion chromatography

AbstractThe application of microcolumn exclusion chromatography to the determination of equilibrium and kinetic association constants for proteins is described. Taking phospholipase A2 as an example, the relationship between association and enzymatic activity was investigated. A procedure for determination of the critical concentration of micelle formation (CCM) in surfactants was developed.

Bacteriophage T7 E promoter: identification and measurement of kinetics of association with Escherichia coli RNA polymerase.

The initiation point for transcription from the Escherichia coli RNA polymerase E promoter on bacteriophage T7 has been determined to be at 36 835 base pairs (92.22 T7 units) from the left end of T7. The location was determined by RNA fingerprinting of a runoff transcription product. Kinetics of association for the E and the T7 A3 promoters were measured by using the abortive initiation assay for approach to steady-state turnover. The kinetic association constant, ka (=KBk2), for E was found to be over 10-fold slower than ka for A3. For the E promoter, ka = 1.2 X 10(6) M-1 s-1. For A3, we report ka greater than or equal to 4 X 10(7) M-1 s-1. This difference is due mostly to a 10-fold difference in the initial equilibrium constant, KB, for formation of the initial polymerase-promoter complex. The rate of isomerization, k2, of the initial complex to the open polymerase-promoter complex for the E promoter was only 2-fold slower than k2 for the A3 promoter. Various numerical methods for calculation of the kinetic parameters are discussed and compared. We argue that a nonlinear analysis provides the most reliable means of data analysis.

Microbore column exclusion chromatographic method for studying protein association and its relation with enzymatic activity

The principles of treating chromatographic data are considered to allow the determination of number of components, equilibrium and kinetic association constants of proteins by means of micro-column exclusion chromatography. The method is developed to study protein association in cases complicated by adsorption. The potentialities of the chromatographic method have been examined for the study of the mechanism of enzyme catalytic action.

A sensitive radioimmunoassay for vincristine and vinblastine

A rapid, sensitive and highly reproducible radioimmunoassay (RIA) has been devised for vincristine and vinblastine. These alkaloids bind to the antiserum very tightly with an association constant (Ka) of 5 x 10(9) M-1 as determined by Scatchard analysis. The kinetic association constant of the alkaloids, as determined by the 'on' and 'off' rates at 4 degrees C, is 30-fold higher than the Scatchard analysis value. At 4 degrees C, 80% of the alkaloid is bound to the antiserum within 20 min, and the remaining 20% reaches an equilibrium within 48-72 h. In the RIA procedure the amount of the alkaloid (1-2 ng) needed to compete for 50% binding remains unchanged when the reaction mixtures are incubated for 2, 4, or 20 h. By a modification of the RIA procedure, where the antiserum is first allowed to react with the unlabeled alkaloid followed by addition of the radiolabeled alkaloid, sensitivity of the assay has been increased five- to tenfold. Other drugs, such as adriamycin, CCNU, methyl CCNU, cyclophosphamide, 5-fluorouracil, heparin, hydrocortisone, prednisone, and nitrogen mustard do not interfere with the assay. This assay can thus be used to determine vincristine or vinblastine levels in 5 x 10(-10)--10(-9) M concentrations in biological fluids.