Analysis of kinetic data of antibody-antigen interaction from an optical biosensor by exponential curve fitting

Towards Early Diagnosis and Screening of Alzheimer's Disease Using Frequency Locked Whispering Gallery Mode Microtoroid Biosensors

Alzheimer's disease (AD) is a progressive form of dementia affecting almost 55 million people worldwide. It is characterized by the abnormal deposition of amyloid plaques and neurofibrillary tangles within the brain, leading to a pathological cascade of neuron degeneration and death as well as memory loss and cognitive decline. Amyloid beta (Aβ) is an AD biomarker present in cerebrospinal fluid and blood serum and correlates with the presence of amyloid plaques and tau tangles in the brain. Measuring the levels of Aβ can help with early diagnosis of AD, which is key for studying novel AD drugs and delaying the symptoms of dementia. However, this goal is difficult to achieve due to the low levels of AD biomarkers in biofluids. Here we demonstrate for the first time the use of FLOWER (frequency locked optical whispering evanescent resonator) for quantifying the levels of post-mortem cerebrospinal fluid (CSF) Aβ42 in clinicopathologically classified control, mild cognitive impairment (MCI), and AD participants. FLOWER is capable of measuring CSF Aβ42 (area under curve, AUC = 0.92) with higher diagnostic performance than standard ELISA (AUC = 0.82) and was also able to distinguish between control and MCI samples. Our results demonstrate the capability of FLOWER for screening CSF samples for early diagnosis of Alzheimer's pathology.

Sensitive operation of enzyme-based biodevices by advanced signal processing

Analytical devices that combine sensitive biological component with a physicochemical detector hold a great potential for various applications, e.g., environmental monitoring, food analysis or medical diagnostics. Continuous efforts to develop inexpensive sensitive biodevices for detecting target substances typically focus on the design of biorecognition elements and their physical implementation, while the methods for processing signals generated by such devices have received far less attention. Here, we present fundamental considerations related to signal processing in biosensor design and investigate how undemanding signal treatment facilitates calibration and operation of enzyme-based biodevices. Our signal treatment approach was thoroughly validated with two model systems: (i) a biodevice for detecting chemical warfare agents and environmental pollutants based on the activity of haloalkane dehalogenase, with the sensitive range for bis(2-chloroethyl) ether of 0.01–0.8 mM and (ii) a biodevice for detecting hazardous pesticides based on the activity of γ-hexachlorocyclohexane dehydrochlorinase with the sensitive range for γ-hexachlorocyclohexane of 0.01–0.3 mM. We demonstrate that the advanced signal processing based on curve fitting enables precise quantification of parameters important for sensitive operation of enzyme-based biodevices, including: (i) automated exclusion of signal regions with substantial noise, (ii) derivation of calibration curves with significantly reduced error, (iii) shortening of the detection time, and (iv) reliable extrapolation of the signal to the initial conditions. The presented simple signal curve fitting supports rational design of optimal system setup by explicit and flexible quantification of its properties and will find a broad use in the development of sensitive and robust biodevices.

Biomolecular Interaction Analysis Using an Optical Surface Plasmon Resonance Biosensor: The Marquardt Algorithm vs Newton Iteration Algorithm

Kinetic analysis of biomolecular interactions are powerfully used to quantify the binding kinetic constants for the determination of a complex formed or dissociated within a given time span. Surface plasmon resonance biosensors provide an essential approach in the analysis of the biomolecular interactions including the interaction process of antigen-antibody and receptors-ligand. The binding affinity of the antibody to the antigen (or the receptor to the ligand) reflects the biological activities of the control antibodies (or receptors) and the corresponding immune signal responses in the pathologic process. Moreover, both the association rate and dissociation rate of the receptor to ligand are the substantial parameters for the study of signal transmission between cells. A number of experimental data may lead to complicated real-time curves that do not fit well to the kinetic model. This paper presented an analysis approach of biomolecular interactions established by utilizing the Marquardt algorithm. This algorithm was intensively considered to implement in the homemade bioanalyzer to perform the nonlinear curve-fitting of the association and disassociation process of the receptor to ligand. Compared with the results from the Newton iteration algorithm, it shows that the Marquardt algorithm does not only reduce the dependence of the initial value to avoid the divergence but also can greatly reduce the iterative regression times. The association and dissociation rate constants, k_a, k_d and the affinity parameters for the biomolecular interaction, K_A, K_D, were experimentally obtained 6.969×10⁵ mL·g^-1·s^-1, 0.00073 s^-1, 9.5466×10⁸ mL·g^-1 and 1.0475×10^-9 g·mL^-1, respectively from the injection of the HBsAg solution with the concentration of 16ng·mL^-1. The kinetic constants were evaluated distinctly by using the obtained data from the curve-fitting results.

Interaction analysis between tmRNA and SmpB from Thermus thermophilus

Small protein B, SmpB, is a tmRNA-specific binding protein essential for trans-translation. We examined the interaction between SmpB and tmRNA from Thermus thermophilus, using biochemical and NMR methods. Chemical footprinting analyses using full-length tmRNA demonstrated that the sites protected upon SmpB binding are located exclusively in the tRNA-like domain (TLD) of tmRNA. To clarify the SmpB binding sites, we constructed several segments derived from TLD. Optical biosensor interaction analyses and melting profile analyses with mutational studies showed that SmpB efficiently binds to only a 30-nt segment that forms a stem and loop, with the 5' and 3' extensions composed of the D-loop and variable-loop analogues. The conserved sequences, 16UCGA and 319GAC, in the extensions are responsible for the SmpB binding. These results agree with the those visualized by the cocrystal structure of TLD and SmpB from Aquifex aeolicus. In addition, NMR chemical shift mapping analyses, using the 30-nt segment and (15)N-labeled SmpB, revealed the characteristic RNA binding mode. The hydrogen bond pattern around beta2 changes, with the Gly in beta2, which acts as a hinge, showing the largest chemical shift change. It appears that SmpB undergoes structural changes indicating an induced fit upon binding to the specific region of TLD.

Label-free detection with the resonant mirror biosensor

The resonant mirror (RM) biosensor is a leaky waveguide-based instrument that uses the evanescent field to probe changes in the refractive index at the sensing surface.The RM can therefore be used to monitor in real-time and label-free the interaction between an analyte in solution and its biospecific partner immobilized on the waveguide surface.The RM has been used in studying the interaction of a variety of moieties including proteins, carbohydrates, cells, nucleic acids and receptors, leading to applications in areas such as clinical diagnostics, homeland security, and pharmaceutical and biomolecular interactions. This chapter will review the principle of this biosensor, and the recent advances in instrumentation, different immobilization chemistries, and kinetic studies, as well as some applications.

Expression of the soluble extracellular domain of human thrombopoietin receptor using a maltose-binding protein-affinity fusion system

The thrombopoietin (TPO) receptor (Mpl) belongs to the family of ligand-dependent cytokine receptors and plays a functional role in regulating platelet production. The signaling capacity largely depends on the binding of TPO to the extracellular domains of the TPO receptor (Mpl-EC). Because the expression level of Mpl in human tissue is very low, studies on the functional and spatial characteristics of its ligand-binding sites have been limited. In the present study, we report the expression and purification of Mpl-EC as a fusion with the maltose-binding protein (MBP), designated MBP-Mpl-EC. MBP-Mpl-EC was expressed in the cytoplasm of Escherichia coli as a soluble fusion protein. Specific binding of TPO to purified MBP-Mpl-EC was demonstrated by a dot-blot assay and surface plasmon resonance. We conclude that bacterial expression of MBP-Mpl-EC yields large amounts of protein with correct folding and that it can be used for further structure and function analyses.

Kinetic analysis of interactions between bispecific monoclonal antibodies and immobilized antigens using a resonant mirror biosensor

A resonant mirror biosensor (IAsys) protocol is described for the comparative kinetic analysis of the ability of monoclonal antibodies (Mabs) and bispecific antibodies (Babs) to bind immobilized antigens. The protocol has been optimized and validated using the panel of affinity-purified antibodies, including two parental Mabs, one specific to human immunoglobulin G (hIgG) and another specific to horseradish peroxidase (HRP), and a Bab derived thereof by cell fusion (anti-hIgG/HRP Bab). The real-time kinetic analysis of antigen-antibody interactions using this protocol allows to demonstrate the differences in the avidity of bivalently binding Mabs and monovalent Babs. As shown in our previous study [J. Immunol. Methods 261 (2002) 103], the observed equilibrium association constants (Kass) determined by IAsys using this protocol yield figures almost overlapping with those obtained by solid-phase radioimmunoassay (RIA). The described protocol is suited for the investigation of the effects of valency on the binding properties of antibodies. It also may be applied for the selection of Mabs and Babs with desired features, for different fields of application.

Binding of Tamm-Horsfall protein to complement 1q and complement 1, including influence of hydrogen-ion concentration

The goal of this study was to further characterize the interaction between an abundant urinary glycoprotein, Tamm-Horsfall protein, and complement 1q to determine the robustness of this reaction under different environmental conditions (particularly pH) and to begin to determine the specificity of this reaction. The influence of pH coupled with ionic strength was evaluated with an ELISA that demonstrated immobilized Tamm-Horsfall protein bound complement 1q strongly with a KD in the nmol/L range from pH 9 to pH 5.5. Increasing the ionic strength from 10 mmol/L sodium chloride (NaCl) to 154 mmol/L NaCl decreased the affinity of Tamm-Horsfall protein for complement 1q slightly (2-7-fold) at pH 9 to pH 6.5. A resonant mirror biosensor was also utilized to evaluate the binding of Tamm-Horsfall protein to complement 1q at different pH values (pH 8.2-5.8). These studies indicated that, compared to at pH 8.2, Tamm-Horsfall protein bound complement 1q at pH 5.8 with an almost two-fold higher affinity (pH 8.2, KD = 5.1 nmol/L vs at pH 5.8, KD = 2.8 nmol/L) due to a faster association rate (pH 8.2 kass = 1.6 x 106 L/mol per s vs pH 5.8 kass = 2.9 x 106 L/mol per s). Surprisingly, the capacity of Tamm-Horsfall protein for complement 1q decreased significantly at pH 5.8, suggesting that a site for complement 1q binding to Tamm-Horsfall protein may be lost at the acidic pH. Biosensor studies also showed that Tamm-Horsfall protein bound the entire complement 1 complex with binding affinities and association rates similar to those obtained for complement 1q individually. This suggested that Tamm-Horsfall protein bound complement 1q at a site other than the region of its collagenous tail where C1r2 and C1s2 bind. By western blot analysis, it was demonstrated that Tamm-Horsfall protein bound preferentially to the C chain of complement 1q.

Kinetics of antigen binding to arrays of antibodies in different sized spots

A fluorescence-based array biosensor has been developed which can measure the binding kinetics of an antigen to an immobilized antibody in real time. A patterned array of antibodies immobilized on the surface of a planar waveguide was used to capture a Cy5-labeled antigen present in a solution that was continuously flowed over the surface. The CCD image of the waveguide was monitored continuously for 25 min. The resulting exponential rise in fluorescence signal was determined by image analysis software and fitted to a reaction-limited kinetics model, giving a kf of 3.6 x 10(5) M(-1) s(-1). Different spot sizes were then patterned on the surface of the waveguide using either a PDMS flow cell or laser exposure, producing width sizes ranging from 80 to 1145 microm. It was demonstrated that under flow conditions, the reduction of spot size did not alter the association rate of the antigen with immobilized antibody; however, as the spot width decreased to < 200 nm, the signal intensity also decreased.

New approaches for the analysis of molecular recognition using the IAsys evanescent wave biosensor

Trends in the analysis of molecular recognition using the IAsys evanescent wave biosensor are outlined. Diversification of sensor surface chemistry, an open cuvette format and the advent of robotics controlled by intelligent software are widening the range and throughput of applications. Analyses of binding and dissociation are now carried out across a wide spectrum of biomolecules, including protein, nucleic acid, carbohydrate and lipid. Determinations are obtained from a range of experimental formats. These include qualitative 'yes/no' screening assays, through semi quantitative ranking of kinetic association, dissociation and equilibrium constants for a family of binding partners, to deriving constants comparable with those which would be obtained in free solution. A dependence of the initial rate of biomolecular association on concentration allows analyte concentration to be measured--an increasingly common application class. This is often employed in situations where a rapid determination is required The ability to recover bound analyte from the sensor surface in sufficient amounts for subsequent characterization is opening up new routes to the parallel analysis of structure and function.

Determination of interactions between human thrombopoietin and its receptor MPL by yeast two-hybrid system and affinity biosensor

The binding of human thrombopoietin to the extracellular domain of its receptor MPL prompts a cascade transduction of intracellular signals, leading to the development of megakaryocyte precursors and the production of circulating platelets. We have used a yeast two-hybrid system to reveal, via in vivo interactions between different deletion constructs of MPL and thrombopoietin, that the extracellular subunit 1 of MPL is the ligand binding site and the N-terminal domain of thrombopoietin alone is sufficient for the binding. The extracellular portion of MPL was heterologously expressed in E. coli and its specific affinity with thrombopoietin was visualized in vitro by resonance mirror biosensor technique.

Bioprocess monitoring: an optical biosensor for rapid bioproduct analysis

The use of an optical biosensor for rapid bioproduct analysis is described. The biosensor, which is sensitive to changes in the concentration of bioproduct at its biologically active surface, has been shown to provide concentration data within 10 s of sample addition to the device. This has been achieved through the use of linear regression analysis to extract information from the early part of the biosensor interaction profiles. The system has been used to monitor both the production and purification of antibody fragments expressed during batch fermentation of recombinant Escherichia coli. Data obtained using the biosensor have been used to provide real-time profiles describing the location of antibody fragments during bioprocessing. Biosensor data have also been compared with those obtained from ELISA, the traditional method of retrospective analyses of samples collected during bioprocessing.

An optical biosensor for real-time chromatography monitoring: breakthrough determination

The use of an optical biosensor for immunorecognition of protein products during affinity chromatography is discussed to provide rapid data describing the loading and subsequent breakthrough, followed by elution and fraction collection. The optical biosensor works by following in real-time the interaction of soluble ligate with an appropriate ligand attached to the optically active surface. The initial rate of interaction between soluble ligate and immobilized ligand has been shown to correlate well with ligate concentration. This method of analysis has also been shown to agree well with ELISA, the traditionally employed technique for immunoassay of protein products lacking, for example, catalytic activity. Forward prediction, using models of the breakthrough fitted to the real-time data, has enabled the column saturation point to be determined before it has been reached, thus enabling appropriate action to ensure minimal loss of protein product while improving column utilization efficiency. The biosensor, operated within a flow injection analysis regime, has been demonstrated to provide concentration data within 10 s, with a total assay turnaround of 30 s.

Rapid monitoring of virus-like particles using an optical biosensor: a feasibility study

Virus-like particles (VLPs) are multimeric proteins expressed by Saccharomyces cerevisiae. The particles are approximately 80 nm in diameter and they are used as a framework for a range of biological products; for example as carriers of viral antigens. Rapid monitoring of purified VLPs was investigated using an optical biosensor. The aim was to develop an assay which may be employed for real-time bioprocess monitoring of VLPs. Problems of mass transfer of analyte were overcome through selection of a planar biosensor surface, in preference to the traditional polymer-coated surface. To prolong the surface activity for interaction analysis, a sandwich assay was developed which involved the use of a secondary capture species. It was shown that VLP concentration in pure solution could be determined within 10 min.

Covalent coupling of immunoglobulin G to a poly(vinyl)alcohol-poly(acrylic acid) graft polymer as a method for fabricating the interfacial-recognition layer of a surface plasmon resonance immunosensor

The synthesis of a terminally thiolated poly(vinyl)alcohol (PVA) grafted with Poly (acrylic acid) (PAA) side chains is described. The PVA-PAA graft polymer (PVAg) was end-tethered to silver surfaces via the terminal thiol functionality and the resultant mobile, hydrophilic polymer matrix exploited for the covalent immobilization of large quantities of polyclonal goat (anti-hIgG) antibody (IgG) with low levels of non-specific adsorption. An SPR immunosensor, fabricated with an IgG-PVA-silver interfacial layer proved capable of performing a sensitive label-free assay of human IgG antigen (hIgG) with minimal non-specific binding interference. A detection limit (DL) for hIgG from serum of 0.8 microgram/ml (5 nM) and an assay sensitivity of 0.66 ng hIgG/mm2/nM are reported.

Biosensors in immunology: the story so far

In conclusion, biosensors are versatile tools with a range of applications. With a thorough knowledge of possible artefacts and limitations, it possible to perform assays that were heretofore not practicable in immunology.

Modular structure of the trigger factor required for high activity in protein folding

The Escherichia coli trigger factor is a peptidyl-prolyl cis/trans isomerase (PPIase) which catalyzes proline-limited protein folding extremely well. It has been found associated with nascent protein chains as well as with the chaperone GroEL. The trigger factor utilizes protein regions outside the central catalytic domain for catalyzing refolding of unfolded proteins efficiently. Here we produced several fragments which encompass individual domains or combinations of the middle FKBP-like domain (M) with the N-terminal (N) and C-terminal (C) regions, respectively. These fragments appear to be stably folded. They show ordered structure and cooperative urea-induced unfolding transitions, and the far-UV CD spectrum of the intact trigger factor is well represented by the sum of the spectra of the fragments. This suggests that the native trigger factor shows a modular structure, which is composed of three fairly independent folding units. In the intact protein there is a slight mutual stabilization of these units. The high enzymatic activity in protein folding could not be restored by fusing alternatively the N or the C-terminal regions to the catalytic domain (in NM and MC constructs, respectively). Surprisingly, the high folding activity of the intact trigger factor has been regained partially by functional complementation of the overlapping NM and MC constructs.

Alkaline phosphatase-Strep tag fusion protein binding to streptavidin: resonant mirror studies

The properties of a fusion protein comprising a streptavidin recognition sequence (Strep tag) fused to the C terminus of Escherichia coli alkaline phosphatase are described. The catalytic properties were determined with p-nitrophenyl phosphate and compared to those of the native E. coli alkaline phosphatase. It was found that the Km values were similar in both cases (8 microM for transferase and 2 microM for hydrolase activities) whilst the Vmax values were lower for the fusion protein, possibly due to the presence of misfolded forms. An optical biosensor based on the resonant mirror was used to determine the binding kinetics between the fusion protein and the immobilised streptavidin. The association and dissociation rate constants were determined to be 2.1(+/-0.3) x 10(-2) microM(-1) s(-1) and 11(+/-0.2) x 10(-3) s(-1), respectively, which results in an equilibrium dissociation constant of 0.5 microM. This is larger than previously reported affinities based on titration calorimetry and may be a consequence of the presence of two streptavidin binding sequences on the dimeric alkaline phosphatase simultaneously binding to two subunits of streptavidin.