Characterizing the interaction between aptamers and human IgE by use of surface plasmon resonance

Human immunoglobulin E (hIgE) is such an important protein, because of its involvement in allergic disease, that it is of significance to study the interactions between it and its recognizing elements. In this report an analytical strategy based on surface plasmon resonance (SPR) was developed to probe the pattern of interaction between hIgE and its recognizing molecules, including aptamers and antibodies. The affinity constants of hIgE for the antibody and the aptamer were compared first; the aptamer has more affinity than the antibody for human IgE. To study their pattern of interaction, three different binding approaches, including adding the antibody and the streptavidin-coupled aptamer to the sensing surface, were designed. The results showed that hIgE captured on the sensing surface could form a multivalent complex with the aptamer. An ELISA-like assay using the aptamer as both capture and detection probes was then developed. This work highlights an SPR method for characterizing the interaction between the protein and aptamers that is useful for study of biomolecular interaction patterns and binding properties. Figure Schematic diagram of the use of surface plasmon resonance for detection of the pattern of interaction of human IgE with its DNA aptamer and antibody     

Effect of the immobilisation of DNA aptamers on the detection of thrombin by means of surface plasmon resonance

We report a multichannel surface plasmon resonance (SPR) sensor for detection of thrombin via DNA aptamers immobilized on the SPR sensor surface. A detailed investigation of the effect of the immobilisation method on the interaction between thrombin and DNA aptamers is presented. Three basic approaches to the immobilisation of aptamers on the surface of the SPR sensor are examined: (i) immobilisation based on chemisorption of aptamers modified with SH groups, (ii) immobilisation of biotin-tagged aptamers via previously immobilized avidin, neutravidin or streptavidin molecular linkers, and (iii) immobilisation employing dendrimers as a support layer for subsequent immobilisation of aptamers. A level of nonspecific binding of thrombin to immobilized human serum albumin (HSA) for each of the immobilisation methods is determined. Immobilisation of aptamers by means of the streptavidin–biotin system yields the best results both in terms of sensor specificity and sensitivity.     

A novel low-cost and easy to develop functionalization platform. Case study: Aptamer-based detection of thrombin by surface plasmon resonance

A novel low-cost platform to assess biomolecular interactions was investigated using surface plasmon resonance and an aptamer-based assay for thrombin detection. Gold SPR surface functionalized with a carboxylated cross-linked BSA film (cBSA) and commercially available carboxymethylated dextran chip (CM5) were used as immobilization platforms for the thrombin binding aptamer. The high end commercial instrument Biacore 3000 and a custom made FIA set-up involving TI Spreeta sensor (TSPR2K23) were used to assess different concentrations of thrombin within the range 0.1-150 nM both in buffer and in a complex matrix (plasma) using the obtained aptasensors. Based on data derived from both CM5 and cBSA platforms, the cBSA aptasensor exhibited good selectivity, stability and regeneration ability, both in buffer and in complex matrices (plasma), comparable with CM5.     

Kinetics and enthalpy measurements of interaction between beta-amyloid and liposomes by surface plasmon resonance and isothermal titration microcalorimetry

The objective of this research is to understand the interaction mechanism of β-amyloid (Aβ) with cell and were basically divided into two parts. The first part focused on the time-dependent structural changes of Aβ (1-40) by circular dichroism (CD) spectroscopy, thioflavin T (ThT) fluorescence assay, and atomic force microscopy (AFM). The second part emphasized the kinetics and enthalpy of interaction between Aβ (1-40) and liposome by surface plasmon resonance (SPR) and isothermal titration microcalorimetry (ITC). Results obtained from CD, ThT and AFM confirmed the formation of 1 μm fibril after single day incubation. The driving force of kinetic interaction between Aβ and liposomes was revealed by SPR to be electrostatics. Further studies indicated that fresh Aβ has high GM1 affinity. Besides, addition of cholesterol to the liposome could alter membrane fluidity and affect the interactions of fresh Aβ with liposomes especially in the amount of Aβ absorbed and preserving the structure of liposome after adsorbing. Hydrophobicity was found to be the driving force leading to the interaction between Aβ fibrils and liposomes. These reactions are endothermic as supported by ITC measurements. When the composition of liposomes is zwitterionic lipids, the interaction of Aβ with liposomes is predominantly hydrophobic force. In contrast, the driving force of interaction of charged lipids with Aβ is electrostatic.     

Characterization of the 1st and 2nd EF-hands of NADPH oxidase 5 by fluorescence, isothermal titration calorimetry, and circular dichroism

Background

Superoxide generated by non-phagocytic NADPH oxidases (NOXs) is of growing importance for physiology and pathobiology. The calcium binding domain (CaBD) of NOX5 contains four EF-hands, each binding one calcium ion. To better understand the metal binding properties of the 1^st and 2^nd EF-hands, we characterized the N-terminal half of CaBD (NCaBD) and its calcium-binding knockout mutants.

Results

The isothermal titration calorimetry measurement for NCaBD reveals that the calcium binding of two EF-hands are loosely associated with each other and can be treated as independent binding events. However, the Ca²⁺ binding studies on NCaBD(E31Q) and NCaBD(E63Q) showed their binding constants to be 6.5 × 10⁵ and 5.0 × 10² M^-1 with ??Hs of -14 and -4 kJ/mol, respectively, suggesting that intrinsic calcium binding for the 1^st non-canonical EF-hand is largely enhanced by the binding of Ca²⁺ to the 2^nd canonical EF-hand. The fluorescence quenching and CD spectra support a conformational change upon Ca²⁺ binding, which changes Trp residues toward a more non-polar and exposed environment and also increases its ??-helix secondary structure content. All measurements exclude Mg²⁺-binding in NCaBD.

Conclusions

We demonstrated that the 1^st non-canonical EF-hand of NOX5 has very weak Ca²⁺ binding affinity compared with the 2^nd canonical EF-hand. Both EF-hands interact with each other in a cooperative manner to enhance their Ca²⁺ binding affinity. Our characterization reveals that the two EF-hands in the N-terminal NOX5 are Ca²⁺ specific.

Graphical abstract

     

Highly sensitive detection of human thrombin in serum by affinity capillary electrophoresis/laser-induced fluorescence polarization using aptamers as probes

The detection and quantification of disease-related proteins play critical roles in clinical practice and diagnostic assays. We present an affinity probe capillary electrophoresis/laser-induced fluorescence polarization (APCE/LIFP) assay for detection of human thrombin using a specific aptamer as probe. In the APCE/LIFP assay, the mobility and fluorescence polarization of complex are measured simultaneously during CE analysis. The affinity complex of human thrombin can be well separated from unbound aptamer on CE and clearly identified on the basis of its fluorescence polarization and migration. Because of the binding favorable G-quartet conformation potentially involved in the specific aptamer, it was assumed that monovalent and bivalent cations promoting the formation of a stable G quadruplex conformation in the aptamer may enhance the binding of the aptamer and thrombin. Therefore, we investigated the effects of various metal cations on the binding of human thrombin and the aptamer. Our results show that cations like K⁺ and Mg²⁺ could not stabilize the affinity complex. Without the use of typical cations, a highly sensitive assay of human thrombin was developed with the corresponding detection limits of 4.38 × 10⁻¹⁹ and 2.94 × 10⁻¹⁹ mol in mass for standard solution and human serum, respectively.     

Surface plasmon resonance, fluorescence, and circular dichroism studies for the characterization of the binding of BACE-1 inhibitors

The mechanism of action underlying β-secretase 1 (BACE-1) inhibition was characterized by a surface plasmon resonance (SPR) method using primary amino groups to immobilize OM99-2, a well-known highly potent peptidic BACE-1 inhibitor, on the carboxyl groups of the dextran layer of a sensor chip. The diluted BACE-1 was mixed with buffer or the test compound and the mixture was flushed through the chip. BACE-1 binding to the immobilized peptide inhibitor was quantified. This SPR method was used to identify BACE-1 inhibitor binding sites and the mechanism of action (competitive/noncompetitive) and to validate findings of fluorescence resonance energy transfer (FRET) inhibition studies. To support this, a multimethodological approach (circular dichroism and fluorescence spectroscopy) was applied in parallel to FRET inhibition studies to characterize the binding modes of peptidic and nonpeptidic BACE-1 inhibitors. Circular dichroism spectroscopy served to correlate the conformation of BACE-1 with enzymatic activity and to monitor secondary structure changes upon ligand binding. In a complementary approach, direct fluorescence spectroscopy was used to characterize different BACE-1 inhibitor binding sites. The influence of pH and inhibitors on BACE-1 secondary structure was also elucidated. This multimethodological approach was applied to identify binding modes of bis(7)-tacrine and myricetin in comparison with well-known peptidic inhibitors.

Interaction between PAMAM 4.5 dendrimer, cadmium and bovine serum albumin: a study using equilibrium dialysis, isothermal titration calorimetry, zeta-potential and fluorescence

Binding of Cd²⁺ by PAMAM 4.5 dendrimer was studied by equilibrium dialysis, isothermal titration calorimetry and zeta-potential measurement. The following binding parameters were obtained: n = 23.8 ± 9.5, K_b = 4.7 ± 0.9 × 10³ in water; and n = 41.3 ± 13.4, K_b = 2.1 ± 0.8 × 10³ in 0.15 mol/l phosphate-buffered saline. The location of the bound Cd²⁺ is discussed. The interactions between bovine serum albumin, PAMAM 4.5 dendrimer and cadmium were analyzed using fluorescence and equilibrium dialysis. The competition between Cd²⁺ binding to BSA and PAMAM 4.5 dendrimer was investigated. It is proposed that PAMAM 4.5 dendrimer could be successfully used for extracting Cd²⁺ from aqueous solutions (environmental protection).     

Affinity of aptamers binding 33-mer gliadin peptide and gluten proteins: Influence of immobilization and labeling tags

Aptamers are starting to increase the reagents tool box to develop more sensitive and reliable methods for food allergens. In most of these assays, aptamers have to be modified for detection and/or immobilization purposes. To take full advantage of their affinity, which decisively influence the detectability, these modifications must be faced rationally. In this work, a recently developed aptamer for an immunotoxic peptide of gliadin associated to celiac disease is used in different configurations and modified with various markers and anchored groups to evaluate the influence of such modifications on the real affinity. The interaction in solution with the peptide is strong for a relatively small molecule (K_d = 45 ± 10 nM, 17 °C) and slightly stronger than that for the immobilized intact protein due to a cooperative binding effect. Comparatively, while only minor differences were found when the peptide or the aptamer were immobilized, labeling with a biotin resulted preferable over fluorescein (K_d = 102 ± 11 vs 208 ± 54 nM, 25 °C). These findings are of prime importance for the design of an aptamer-based analytical method for gluten quantification.     

Study of donepezil binding to serum albumin by capillary electrophoresis and circular dichroism

The interaction between human serum albumin (HSA) and the acetylcholinesterase inhibitor donepezil, has been studied by means of capillary electrophoresis frontal analysis (CE/FA) and circular dichroism. CE/FA enabled rapid and direct estimation of the quantity of free donepezil present at equilibrium with a physiological level of serum albumin (600 mol L^–1). Application of Scatchard analysis enabled estimation of the binding parameters of HSA towards donepezil, such as association constant and number of binding sites on one protein molecule. Furthermore, due to enantioseparation ability shown by HSA on donepezil in CE mode, displacement experiments were carried out using ketoprofen and warfarin as coadditives to the HSA based running buffer. The addition of these compounds reduced the enantioresolution of donepezil by HSA only when used at high concentration. These data were confirmed and corroborated by circular dichroism (CD) experiments. Using CD, bilirubin was also applied as a ligand specific to site III of HSA. The observed behaviour suggested that donepezil could be considered a ligand with independent binding to sites I and II; although site III is not the highest affinity site, indirect interaction (i.e. cooperative binding) can be assumed.     

Microanalysis of the surface concentration of sulfate groups at polystyrene particle by isothermal titration calorimetry

 Microanalysis of sulfate groups at polystyrene particle surfaces, which were derived as persulfate initiator fragments, was carried out with isothermal titration calorimetry, and compared with a conventional conductometric titration. The quantitative analysis was possible even with an extremely small number of polystyrene particles have 10 μmol sulfate groups. Received: 15 December 1998 Accepted in revised form: 24 February 1999     

Study on the binding of puerarin to bovine serum albumin by isothermal titration calorimetry and spectroscopic approaches

The interaction of a flavonoid molecule (puerarin) with bovine serum albumin (BSA) was characterized by isothermal titration calorimetry (ITC), optical spectroscopic technique, and molecular modeling method under physiological conditions. The binding parameters for the reaction were calculated according to ITC experiments at different temperatures. The thermodynamic parameters, negative enthalpy changes (ΔH), and positive entropy (ΔS) indicated that the binding processes were entropically driven. The alterations of protein secondary structure in the presence of puerarin in aqueous solution were estimated by the evidences from FT-IR and CD spectroscopy with reductions of α-helices. On the basis of fluorescence resonance energy transfer (FRET) between excited tryptophan in BSA and BSA bound puerarin, the critical transfer distance and mean distance between tryptophan in BSA and puerarin were estimated.     

Hydrophobic interaction chromatography of proteins: Studies of unfolding upon adsorption by isothermal titration calorimetry

Heat of adsorption is an excellent measure for adsorption strength and, therefore, very useful to study the influence of salt and temperature in hydrophobic interaction chromatography. The adsorption of bovine serum albumin and β‐lactoglobulin to Toyopearl Butyl‐650 M was studied with isothermal titration calorimetry to follow the unfolding of proteins on hydrophobic surfaces. Isothermal titration calorimetry is established as an experimental method to track conformational changes of proteins on stationary phases. Experiments were carried out at two different salt concentrations and five different temperatures. Protein unfolding, as indicated by large changes of molar enthalpy of adsorption Δh_ads, was observed to be dependent on temperature and salt concentration. Δh_ads were significantly higher for bovine serum albumin and ranged from 578 (288 K) to 811 (308 K) kJ/mol for 1.2 mol/kg ammonium sulfate. Δh_ads for β‐lactoglobulin ranged from 129 kJ/mol (288 K) to 186 kJ/mol (308 K). For both proteins, Δh_ads increased with increasing temperature. The influence of salt concentration on Δh_ads was also more pronounced for bovine serum albumin than for β‐lactoglobulin. The comparison of retention analysis evaluated by the van't Hoff algorithm shows that beyond adsorption other processes occur simultaneously. Further interpretation such as unfolding upon adsorption needs other in situ techniques.     

Affinity capillary electrophoresis and isothermal titration calorimetry for the determination of fatty acid binding with beta-cyclodextrin

Affinity capillary electrophoresis (ACE) and isothermal titration calorimetry (ITC) were used to investigate the binding interaction between several fatty acids (FAs) and beta-cyclodextrin (beta-CD). Within each method, steps taken to obtain accurate binding constants are discussed. The stoichiometry of interaction was revealed to be 1:1 regardless of FA chain length. The binding constants obtained using ACE were: octanoate, 6.4x10(2); 2-octenoate, 4.7x10(2); decanoate, 3.7x10(3); 9-decenoate, 1.8x10(3) and dodecanote, 1.4x10(4). The binding constants obtained from ITC were of the same order of magnitude, but were consistently greater than those from ACE. Thermodynamic data obtained using ITC are used to explain the observed trends in binding strength.     

Investigation of the inclusion of the herbicide cycluron in native cyclodextrins by X-ray diffraction,nuclear magnetic resonance spectroscopy and isothermal titration calorimetry

The formation of inclusion complexes between the native cyclodextrins (CDs) and the urea herbicide cycluron has been investigated both in solution and in the solid state. Single-crystal X-ray structures of both the uncomplexed guest and the β-CD·cycluron complex were determined while powder X-ray diffraction was used to confirm complexation between γ-CD and cycluron in the solid state. Solution-state complexation between the herbicide and α-, β- and γ-CD was established using ¹H NMR spectroscopy and isothermal titration calorimetry (ITC). From the ¹H NMR spectroscopic studies 1:1 complex stoichiometry was indicated in all cases and association constant values (K) were determined as 228, 3254 and 155 for the complexes α-CD·cycluron, β-CD·cycluron and γ-CD·cycluron, respectively. Assigning a 1:1 host–guest ratio, the ITC technique produced K values of the same order as those determined using the spectroscopic method. The thermodynamic parameters ΔH, ΔS and ΔG obtained using ITC provide insights into the driving forces involved during complex formation.     

Rapid and efficient screening of adsorbent for oligopeptide using molecular docking and isothermal titration calorimetry

A rapid and efficient method based on molecular docking and isothermal titration calorimetry (ITC) was developed to identify effective adsorbents for the target peptide Ser‐Glu‐Ala‐Asp‐His (SEADH). Preliminary screening of five candidate adsorbents using molecular docking revealed that three suitable structures (A1, A2, and A3) either with or without coordination of Zn²⁺ should be effective. The three selected structures were then prepared and further screened by evaluating their affinities for the peptide SEADH using ITC. The screening results revealed that the adsorbent A2 coordinated with Zn²⁺ was the best adsorbent, and subsequent static adsorption experiments confirmed the reliability of the screening method. Further ITC analysis, combined with molecular docking, was performed to provide the possible adsorption mechanism.     

Modeling protein binding and elution over a chromatographic surface probed by surface plasmon resonance

Surface plasmon resonance (SPR) spectroscopy is used as a scaled-down, analytical, pseudo-chromatography tool for analyzing protein binding and elution over an ion-exchange surface under cyclic sorption conditions. A micrometric-scale adsorption surface was produced by immobilizing a typical ion exchange ligand – diethylaminoethyl (DEAE) – onto commercially available planar gold sensor chip surfaces pre-derivatized with a self-assembled monolayer of 11-mercaptoundecanoic acid with known density. An explicit mathematical formulation is provided for the deconvolution and interpretation of the SPR sensorgrams. An adsorption rate model is proposed to describe the SPR sensorgrams for bovine serum albumin, used here as model protein, when the DEAE surface is subjected to a cyclic series of binding and elution steps. Overall, we demonstrate that the adsorption rate model is capable of quantitatively describing BSA binding and elution for protein titers from dilute conditions up to overloaded conditions and a broad range of salt concentrations.     

Effect of surfactant type on surfactant-maltodextrin interactions: isothermal titration calorimetry, surface tensiometry, and ultrasonic velocimetry study

Isothermal titration calorimetry (ITC), surface tensiometry, and ultrasonic velocimetry were used to characterize surfactant-maltodextrin interactions in buffer solutions (pH 7.0, 10 mM NaCl, 20 mM Trizma base, 30.0 degrees C). Experiments were carried out using three surfactants with similar nonpolar tail groups (C12) but different charged headgroups: anionic (sodium dodecyl sulfate, SDS), cationic (dodecyl trimethylammonium bromide, DTAB), and nonionic (polyoxyethylene 23 lauryl ether, Brij35). All three surfactants bound to maltodextrin, with the binding characteristics depending on whether the surfactant headgroup was ionic or nonionic. The amounts of surfactant bound to 0.5% w/v maltodextrin (DE 5) at saturation were < 0.3 mM Brij35, approximately 1-1.6 mM SDS, and approximately 1.5 mM DTAB. ITC measurements indicated that surfactant binding to maltodextrin was exothermic. Surface tension measurements indicated that the DTAB-maltodextrin complex was more surface active than DTAB alone but that SDS- and Brij35- maltodextrin complexes were less surface active than the surfactants alone.