Single molecule studies of antibody-antigen interaction strength versus intra-molecular antigen stability

We investigated molecular recognition of antibodies to membrane-antigens and extraction of the antigens out of membranes at the single molecule level. Using dynamic force microscopy imaging and enzyme immunoassay, binding of anti-sendai antibodies to sendai-epitopes genetically fused into bacteriorhodopsin molecules from purple membranes were detected under physiological conditions. The antibody/antigen interaction strength of 70-170 pN at loading rates of 2-50 nN/second yielded a barrier width of x = 0.12 nm and a kinetic off-rate (corresponding to the barrier height) of k(off) = 6s(-1), respectively. Bacteriorhodopsin unfolding revealed a characteristic intra-molecular force pattern, in which wild-type and sendai-bacteriorhodopsin molecules were clearly distinguishable in their length distributions, originating from the additional 13 amino acid residues epitope in sendai purple membranes. The inter-molecular antibody/antigen unbinding force was significantly lower than the force required to mechanically extract the binding epitope-containing helix pair out of the membrane and unfold it (126 pN compared to 204 pN at the same loading rate), meeting the expectation that inter-molecular unbinding forces are weaker than intra-molecular unfolding forces responsible for stabilizing native conformations of proteins.     

Effect of detergents on antibody-antigen interaction.

The effect of the different detergent mixtures on immunodiffusion and immunoprecipitation was studied. The anionic detergent sodium dodecyl sulfate at concentrations above 0.2% ($\text{w}\text{v}$) inhibits the reaction between antigen and antibody by more than 90%. Nonionic detergents at a concentration of 1% ($\text{w}\text{v}$) have little or no detectable effect. In contrast, when we used mixtures of various concentrations of ionic and nonionic detergents the inhibitory effect of the ionic detergent decreased.     

Development of a label-free impedance biosensor for detection of antibody-antigen interactions based on a novel conductive linker

We developed a label-free impedance biosensor based on an innovative conductive linker for detecting antibody-antigen interactions. As the often used conventional long chain thiol is a poor conductor, it is not a suitable material for use in a faradaic biosensor. In this study, we adopted a thiophene-based conductive bio-linker to form a self-assembled monolayer and to immobilize the bio-molecules. We used cyclic voltammetry and impedance spectroscopy to verify the enhanced conductivity properties. Results showed that the electron transfer resistance of this new conductive linker was 3 orders of a magnitude lower than for a case using a conventional long chain thiol linker. With the decreased impedance (i.e. increased faradaic current), we can obtain a higher signal/noise ratio such that the detection limit is improved. Using fluorescence microscopy, we verified that our new conductive linker has a protein immobilization capability similar to a conventional long chain thiol linker. Also, using S100 proteins, we verified the protein interaction detection capability of our system. Our obtained results showed a linear dynamic range from 10 ng/ml to 10 μg/ml and a detection limit of 10 ng/ml. With our new conductive linker, an electrochemical impedance biosensor shows great potential to be used for point-of-care applications.     

Equilibrium and rapid kinetic studies on nocodazole-tubulin interaction

The interaction between nocodazole and calf brain tubulin in 10(-2) M sodium phosphate, 10(-4) M GTP, and 12% (v/v) dimethyl sulfoxide at pH 7.0 was studied. The number of binding sites for nocodazole was shown to be one per tubulin monomer of 50,000 as a result of equilibrium binding studies by gel filtration and spectroscopic techniques. The presence of microtubule-associated proteins did not significantly affect the binding of nocodazole to tubulin. The apparent equilibrium constant measured at 25 degrees C was (4 +/- 1) X 10(5) M-1. Temperature does not significantly affect the apparent equilibrium constant; hence, the binding of nocodazole to tubulin is apparently entropy driven. Stopped flow spectroscopy was employed to monitor the rate of nocodazole binding under pseudo first order conditions. The effects of temperature and nocodazole concentration were studied. The apparent rate constants were dependent on the concentration of nocodazole in a nonlinear manner. In conjunction with results from structural and thermodynamic studies the kinetic results were interpreted to suggest a mechanism of T + N in equilibrium with TN in equilibrium with T* N, where T and N are tubulin and nocodazole, respectively. T and T* represent two conformational states of tubulin. Furthermore, the kinetic data are consistent with the thermodynamic data only if a model of two parallel similar reactions were considered, one rapid and the other slow. The initial binding step for both the rapid and slow phases was characterized by identical binding constants; however, there was a significant difference in the rates of isomerization. Hence, nocodazole is potentially a useful probe for amplifying differences in solution properties of tubulin subspecies.     

Determination of interaction kinetic constants for HIV-1 protease inhibitors using optical biosensor technology

The interaction between HIV-1 protease and inhibitors has been studied with optical biosensor technology. Optimized experimental procedures and mathematical analysis permitted determination of association and dissociation rate constants. A sensor surface with native enzyme was unstable and exhibited a drift that was influenced by the binding of inhibitor. This was hypothesized to be due to a specific mechanism involving autoproteolysis and/or dimer dissociation. The use of a mutant predicted to be less susceptible to autoproteolysis (Q7K) than wild-type enzyme resulted in a minor effect on surface stability, while a completely stable surface was obtained by treatment of the immobilized enzyme with N-ethyl-N'-(dimethylaminopropyl)-carbodiimide and N-hydroxysuccinimide; the most stable surface was achieved by chemically modifying the Q7K enzyme. The stabilized surface was enzymatically active and the interaction with inhibitors was similar to that for native enzyme. Several of the inhibitors had very high association rates, and estimation of kinetic constants was therefore performed with a binding equation accounting for limited mass transport. Of the clinical inhibitors studied, saquinavir had the highest affinity for the enzyme, a result of the lowest dissociation rate. Although the dissociation rate for ritonavir was sixfold faster, the affinity was only twofold lower than that for saquinavir since the association rate was threefold faster. Nelfinavir and indinavir exhibited lower affinities relative to the other inhibitors, a consequence of a slower association for nelfinavir and a relatively fast dissociation for indinavir. These results show that biosensor-based interaction studies can resolve affinity into association and dissociation rates, and that these are characteristic parameters for the interaction between enzymes and inhibitors.     

Glycoprotein-protein interaction examined by kinetic studies of pyrene transfer

The transfer of pyrene between ₁-acid glycoprotein, acethylcholinesterase and sonicated liposomes was used to monitor glycoprotein-protein interaction on the lipid bilayer. When a density solution of glycoprotein or protein labeled with pyrene was mixed with unlabeled suspension of free-phospholipid liposomes, or suspensions containing the complexes of glycoprotein-lipid, protein-lipid, or glycoprotein-protein-lipid, pyrene excimer fluorescence increased with a half-time of approximately 30–50 msec. Since the increase in excimer fluorescence indicates an increase in the microscope concentrations of pyrene, the observed fluorescence change reflects pyrene transfer. The half-times for the increase in excimer fluorescence were determined in the presence of glycoprotein and protein in the liposomes. On the basis of the determined half-times it was concluded that both, glycoprotein and protein are bound on the lipid bilayer. Our data also suggest that the thickness of the lipid bilayer is significantly changed in this case. The observation suggests strongly that the limiting step in the transfer of pyrene is not the dissociation of pyrene, but the uptake of the pyrene monomers by the lipid phase.     

Electrochemical impedance characterization of antibody-antigen interaction with signal amplification based on polypyrrole-streptavidin

Streptavidin, as a dopant, has been incorporated into a polypyrrole film to bind biotinylated antibody onto the electrode surface. With four biotin binding sites, the incorporation of streptavdin, as confirmed by FTIR and impedance spectroscopy, provided a new method to amplify the response signal from antibody–antigen interaction. Biotinylated anti-goat IgG, as a probe, and goat IgG, as a target, were employed to evaluate the characteristics of the biosensor. With the amplification strategy, the detection sensitivity of the electrochemical impedance spectroscopy was significantly improved. A linear relationship between the charge transfer resistance change (ΔR_t) and the concentration of goat IgG ranging from 10 pg/ml to100 ng/ml was obtained.     

Comparison of biosensor platforms in the evaluation of high affinity antibody-antigen binding kinetics

The acquisition of reliable kinetic parameters for the characterization of biomolecular interactions is an important component of the drug discovery and development process. While several benchmark studies have explored the variability of kinetic rate constants obtained from multiple laboratories and biosensors, a direct comparison of these instruments' performance has not been undertaken, and systematic factors contributing to data variability from these systems have not been discussed. To address these questions, a panel of ten high-affinity monoclonal antibodies was simultaneously evaluated for their binding kinetics against the same antigen on four biosensor platforms: GE Healthcare's Biacore T100, Bio-Rad's ProteOn XPR36, ForteBio's Octet RED384, and Wasatch Microfluidics's IBIS MX96. We compared the strengths and weaknesses of these systems and found that despite certain inherent systematic limitations in instrumentation, the rank orders of both the association and dissociation rate constants were highly correlated between these instruments. Our results also revealed a trade-off between data reliability and sample throughput. Biacore T100, followed by ProteOn XPR36, exhibited excellent data quality and consistency, whereas Octet RED384 and IBIS MX96 demonstrated high flexibility and throughput with compromises in data accuracy and reproducibility. Our results support the need for a “fit-for-purpose” approach in instrument selection for biosensor studies.     

Equilibrium and kinetic studies on the interaction of tetracyclines with calcium and magnesium

The interaction of Ca2+ and Mg2+ with three Tetracycline antibiotics (tetracycline, chlorotetracycline, and oxytetracycline) has been investigated. Spectrophotometric measurements have been used to determine the apparent association constant for this interaction as a function of pH. It is shown that the results are consistent with a model in which the metal ion can form complexes with both the fully-deprotonated and mono-protonated forms of the Tetracycline. The temperature-jump relaxation method has been used to measure the kinetics of formation of the complexes of Mg2+ with the Tetracyclines. The results are compared with those of previous studies of Mg2+ complex formation reactions and it is shown that the data is consistent with the normal dissociative model. A possible role for metal ion chelation in the mechanism of antibacterial action of the Tetracyclines is discussed.     

Pregnancy zone protein, a proteinase binding alpha-macroglobulin. Stopped-flow kinetic studies of its interaction with chymotrypsin

Human pregnancy zone protein (PZP) is a major pregnancy-associated plasma protein, strongly related to alpha 2-macroglobulin (alpha 2M). The proteinase binding reaction of PZP is investigated using chymotrypsin as a model enzyme. The time-course of the interaction is studied by measuring the change in intrinsic protein fluorescence of PZP-chymotrypsin reaction mixtures as a function of time after rapid mixing in a stopped-flow apparatus. Titrations show the changes of fluorescence at equilibrium to correspond with the formation of a chymotrypsin-PZP(tetramer) species. The kinetic results show the formation of the species to take place in an overall second-order process dependent on the concentrations of chymotrypsin and of PZP(dimers), k = 5 x 10(5) M-1 x s-1. Reactions of PZP-thiol groups do not give rise to fluorescence changes. The fluorescence changes most likely reflect the formation of an intermediate with intact thiol esters. Further analysis of the kinetic results suggests that the chymotrypsin-PZP(tetramer) intermediate is formed in two reaction steps: (1) initially native PZP(dimers) are cleaved at bait regions by enzyme molecules, and that is the rate determining reaction of the fluorescence changes; (2) association with another PZP(dimer) or PZP(dimer)-chymotrypsin complex in a very fast reaction that leads to the formation of 1:1 -chymotrypsin-PZP(tetramer) intermediate, probably with intact thiol esters. The interactions studied apparently are established early in the path of the reaction and the fluorescence changes probably reflect noncovalent enzyme-PZP contacts, which are not changed when covalent binding occurs. Further, fluorescence changes are seen only in reactions of PZP with enzymes, not with methylamine.     

Application of an interferometric biosensor chip to biomonitoring an endocrine discruptor

RecombinantE. coli ACV 1003 (recA::lacZ) releasing β-galactosidase by a SOS regulon system, when exposed to DNA-damaging compounds, have been used to effectively monitor endocrine disruptors. Low enzyme activity of less than 10 units/mL, corresponding to a μg/L (ppb) range of an endocrine disruptor (tributyl tin, bisphenol A,etc.), can be rapidly determined, not by a conventional time-consuming and tedious enzyme assay, but by an alternative interferometric biosensor. Heavily boron-doped porous silicon for application as an interferometer, was fabricated by etching to form a Fabry-Perot fringe pattern, which caused a change in the refractive index of the medium including β-galactosidase. In order to enhance the immobilization of the porous silicon surface, a calyx crown derivative (ProLinker A) was applied, instead of a conventional biomolecular affinity method using biotin. This resulted in a denser linked formation. The change in the effective optical thickness versus β-galactosidase activity, showed a linear increase up to a concentration of 150 unit β-galactosidase/mL, unlike the sigmoidal increase pattern observed with the biotin.     

Tunable modulation of antibody-antigen interaction by protease cleavage of protein M

While immunoglobulins find ubiquitous use in biotechnology as static binders, recent developments have created proantibodies that enable orthogonal switch-like behavior to antibody function. Previously, peptides with low binding affinity have been genetically fused to antibodies, to proteolytically control binding function by blocking the antigen-binding site. However, development of these artificial blockers requires panning for peptide sequences that reversibly affect antigen affinity for each antibody. Instead, a more general strategy to achieve dynamic control over antibody affinity may be feasible using protein M (ProtM) from Mycoplasma genitalium, a newly identified polyspecific immunity evasion protein that is capable of blocking antigen binding for a wide range of antibodies. Using C-terminus truncation to identify ProtM variants that are still capable of binding to antibodies without the ability to block antigens, we developed a novel and universal biological switch for antibodies. Using a site-specifically placed thrombin cut site, antibody affinity can be modulated by cleavage of the two distinct antibody-binding and antigen-blocking domains of ProtM. Because of the high affinity of ProtM toward a large variety of IgG subtypes, this strategy may be used as a universal approach to create proantibodies that are conditionally activated by disease-specific proteases such as matrix metalloproteinases.     

Concerted kinetic folding of a multidomain ribozyme with a disrupted loop-receptor interaction

The free energy landscape for the folding of large, multidomain RNAs is rugged, and kinetically trapped, misfolded intermediates are a hallmark of RNA folding reactions. Here, we examine the role of a native loop-receptor interaction in determining the ruggedness of the energy landscape for folding of the Tetrahymena ribozyme. We demonstrate a progressive smoothing of the energy landscape for ribozyme folding as the strength of the loop-receptor interaction is reduced. Remarkably, with the most severe mutation, global folding is more rapid than for the wild-type ribozyme and proceeds in a concerted fashion without the accumulation of long-lived kinetic intermediates. The results demonstrate that a complex interplay between native tertiary interactions, divalent ion concentration, and non-native secondary structure determines the ruggedness of the energy landscape. Furthermore, the results suggest that kinetic folding transitions involving large regions of highly structured RNAs can proceed in a concerted fashion, in the absence of significant stable, preorganized tertiary structure.     

Control of antibody-antigen interaction using anion-induced conformational change in antigen peptide

The binding of a monoclonal antibody to an epitope peptide was controlled by the conformational change of the epitope peptide induced by anions. We synthesized peptides in which the epitope sequence DTYRYI for the monoclonal antibody AU1 is located between amphiphilic peptides (KKLL)n and (LLKK)n. In the absence of an appropriate anion, the peptide was in a random coil state and the epitope was linear. In contrast, in the presence of an appropriate anion, the peptide exhibited an anti-parallel alpha-helical structure and the epitope was subsequently 'bent'. In the presence of 41 microM triphosphate, the association constant between the antibody and the peptide was decreased by one order of magnitude in the case of n = 3 and at least three orders of magnitude in the case of n = 4 or 5. Oligo-DNAs, as anions, dissociated the antibody-peptide complex, whereas triphosphate did not. The DNA concentrations required for 50% dissociation of the antibody-peptide complex at pH 7.5 were 4x10(-8), 1x10(-7) and 6x10(-6) M for decamer, octamer and hexamer DNA, respectively.     

Spectral and kinetic studies on the interaction between oxyhaemoglobin and peroxynitrite: a comparison with hydrogen peroxide.

Interaction between oxyhaemoglobin and peroxynitrite was studied using stopped-flow rapid-scan spectrophotometry. The influence of pH, peroxynitrite concentration and temperature on the pseudo-first-order rate constants was studied and the activation energy calculated. The kinetic curve for the oxyhaemoglobin-peroxynitrite reaction showed that a fast reaction occurred in the initial seconds, followed by a slow process of decrease in absorbance. The biphasic reaction kinetics of oxyhaemoglobin with peroxynitrite or hydrogen peroxide demonstrated the existence of an intermediary species. For the first time a rapid-scan stopped-flow spectrophotometry study is presented, yielding spectral and kinetic data of the reaction.