Biosensor-surface plasmon resonance methods for quantitative analysis of biomolecular interactions

TitrationAnalysis: a tool for high throughput binding kinetics data analysis for multiple label-free platforms

Label-free techniques including Surface Plasmon Resonance (SPR) and Biolayer Interferometry (BLI) are biophysical tools widely used to collect binding kinetics data of bimolecular interactions. To efficiently analyze SPR and BLI binding kinetics data, we have built a new high throughput analysis tool named the TitrationAnalysis. It can be used as a package in the Mathematica scripting environment and ultilize the non-linear curve-fitting module of Mathematica for its core function. This tool can fit the binding time course data and estimate association and dissociation rate constants ( k a and k d respectively) for determining apparent dissociation constant ( K D ) values. The high throughput fitting process is automatic, requires minimal knowledge on Mathematica scripting and can be applied to data from multiple label-free platforms. We demonstrate that the TitrationAnalysis is optimal to analyze antibody-antigen binding data acquired on Biacore T200 (SPR), Carterra LSA (SPR imaging) and ForteBio Octet Red384 (BLI) platforms. The k a , k d and K D values derived using TitrationAnalysis very closely matched the results from the commercial analysis software provided specifically for these instruments. Additionally, the TitrationAnalysis tool generates user-directed customizable results output that can be readily used in downstream Data Quality Control associated with Good Clinical Laboratory Practice operations. With the versatility in source of data input source and options of analysis result output, the TitrationAnalysis high throughput analysis tool offers investigators a powerful alternative in biomolecular interaction characterization.

Unique structural characteristics and biological activities of heparan sulfate isolated from the mantle of the scallop Chlamys farreri

Marine animals are a huge resource of various glycosaminoglycans (GAGs) with specific structures and functions. A large number of byproducts, such as low-edible mantle, are produced during the processing of Chlamys farreri, which is one of the most cultured scallops in China. In this study, a major GAG component was isolated from the mantle of C. farreri, and its structural characteristics and biological activities were determined in detail. Preliminary analysis by agarose electrophoresis combined with specific enzymatic degradation evaluations showed that this component was heparan sulfate and was named CMHS. Further analysis by HPLC and NMR revealed that CMHS has an average molecular weight of 35.9 kDa and contains a high proportion (80%) of 6-O-sulfated N-acetyl-D-glucosamine/N-sulfated-D-glucosamine (6-O-sulfated GlcNAc/GlcNS) residues and rare 3-O-sulfated β-D-glucuronic acid residues. Bioactivity analysis showed that CMHS has much lower anticoagulant activity than heparin and it can interact with various growth factors with high affinity. Moreover, CMHS binds strongly to the morphogen Wnt 3a to inhibit glypican-3-stimulated Wnt 3a signaling. Thus, the identification of CMHS with unique structural and bioactive features will provide a promising candidate for the development of GAG-type pharmaceutical products and promote the high-value utilization of C. farreri mantle.

Distributed interferometric fiber tip biosensors for a multi-channel and label-free biomolecular interaction analysis

This paper describes fabrication and implementation of distributed optical fiber tip biosensor probes for simultaneously measuring label-free biomolecular interactions at multiple locations. Biosensor probes at the tip of a single-mode fiber are Fabry-Perot etalons that are functionalized with a capture layer for a specific biomolecule. A coherence multiplexing method is implemented to separate data collected from distributed biosensors in a single data stream. Multiplexing is achieved by using fiber tip biosensors of varying etalon lengths with the same or different capture layers for each biosensing channel. Experiments demonstrating simultaneous multi-channel recording of protein-to-protein interaction sensorgrams with fiber tip biosensor probes are presented.

Parameter estimation and identifiability analysis for a bivalent analyte model of monoclonal antibody-antigen binding

Surface plasmon resonance (SPR) is an extensively used technique to characterize antigen-antibody interactions. Affinity measurements by SPR typically involve testing the binding of antigen in solution to monoclonal antibodies (mAbs) immobilized on a chip and fitting the kinetics data using 1:1 Langmuir binding model to derive rate constants. However, when it is necessary to immobilize antigens instead of the mAbs, a bivalent analyte (1:2) binding model is required for kinetics analysis. This model is lacking in data analysis packages associated with high throughput SPR instruments and the packages containing this model do not explore multiple local minima and parameter identifiability issues that are common in non-linear optimization. Therefore, we developed a method to use a system of ordinary differential equations for analyzing 1:2 binding kinetics data. Salient features of this method include a grid search on parameter initialization and a profile likelihood approach to determine parameter identifiability. Using this method we found a non-identifiable parameter in data set collected under the standard experimental design. A simulation-guided improved experimental design led to reliable estimation of all rate constants. The method and approach developed here for analyzing 1:2 binding kinetics data will be valuable for expeditious therapeutic antibody discovery research.

Self-assembled, Programmable DNA Nanodevices for Biological and Biomedical Applications

The broad field of structural DNA nanotechnology has diverged into various areas of applications ranging from computing, photonics, synthetic biology, and biosensing to in-vivo bioimaging and therapeutic delivery, to name but a few. Though the field began to exploit DNA to build various nanoscale architectures, it has now taken a new path to diverge from structural DNA nanotechnology to functional or applied DNA nanotechnology. More recently a third sub-branch has emerged-biologically oriented DNA nanotechnology, which seeks to explore the functionalities of combinatorial DNA devices in various biological systems. In this review, we summarize the key developments in DNA nanotechnology revealing a current trend that merges the functionality of DNA devices with the specificity of biomolecules to access a range of functions in biological systems. This review seeks to provide a perspective on the evolution and biological applications of DNA nanotechnology, where the integration of DNA structures with biomolecules can now uncover phenomena of interest to biologists and biomedical scientists. Finally, we conclude with the challenges, limitations, and perspectives of DNA nanodevices in fundamental and applied research.

Effect of strain on surface plasmon polaritons of a graphene cladded one-dimensional photonic crystal

We investigate the dispersion properties of TE-polarized surface plasmon polaritons at the interface of a strained graphene cladded one-dimensional photonic crystal and a homogeneous medium. The optical conductivity of graphene under uniform planar tension is numerically calculated using the perturbation theory and the nearest-neighbor tight-binding approximation. We show that the wavelength, propagation length, and penetration depth of the surface plasmon polaritons in the homogeneous environment and the photonic crystal depend on the magnitude and orientation of the applied strain. Depending on the magnitude and direction of the tension, a Van Hove singularity may appear at the electronic band structure of the graphene in the desired frequency interval. We show that the surface mode corresponding to the Van Hove singularity has the least propagation length. We also observe that strain only affects the penetration depth of the low-frequency surface plasmon polaritons in the homogeneous medium and the high-frequency surface plasmon polaritons in the photonic crystal.

Biosensor-Surface Plasmon Resonance: Label-Free Method for Investigation of Small Molecule-Quadruplex Nucleic Acid Interactions

Biosensor-surface plasmon resonance (SPR) technology is now well established as a quantitative approach for the study of nucleic acid interactions in real time, without the need for labeling any components of the interaction. The method provides real-time equilibrium and kinetic characterization for quadruplex DNA interactions and requires small amounts of materials and no external probe. A detailed protocol for quadruplex-DNA interaction analyses with a variety of binding molecules using biosensor-SPR methods is presented. Explanations of the SPR method with basic fundamentals for use and analysis of results are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples. Details of experimental design, quantitative and qualitative data analyses, and presentation are described. Some specific examples of small molecule-DNA quadruplex interactions are presented with results evaluated by both kinetic and steady-state SPR methods.

Biosensor-surface plasmon resonance: A strategy to help establish a new generation RNA-specific small molecules

Biosensor surface plasmon resonance (SPR) is a highly sensitive technique and is most commonly used to decipher the interactions of biological systems including proteins and nucleic acids. Throughout the years, there have been significant efforts to develop SPR assays for studying protein-protein interactions, protein-DNA interactions, as well as small molecules to target DNAs that are of therapeutic interest. With the explosion of discovery of new RNA structures and functions, it is time to review the applications of SPR to RNA interaction studies, which have actually extended over a long time period. The primary advantage of SPR is its ability to measure affinities and kinetics in real time, along with being a label-free technique and utilizing relatively small quantities of materials. Recently, developments that use SPR to analyze the interactions of different RNA sequences with proteins and small molecules demonstrate the versatility of SPR as a powerful method in the analysis of the structure-function relationships, not only for biological macromolecules but also for potential drug candidates. This chapter will guide the reader through some background material followed by an extensive assay development to dissect the interactions of small molecules and RNA sequences using SPR as the critical method. The protocol includes (i) fundamental concepts of SPR, (ii) experimental design and execution, (iii) the immobilization of RNA using the streptavidin-biotin capturing method, and (iv) affinities and kinetics analyses of the interactions using specific example samples. The chapter also contains useful notes to address situations that might arise during the process. This assay demonstrates SPR as a valuable quantitative method used in the search for potential therapeutic agents that selectively target RNA.

Two distinct conformations of factor H regulate discrete complement-binding functions in the fluid phase and at cell surfaces

Factor H (FH) is the major regulator of C3b in the alternative pathway of the complement system in immunity. FH comprises 20 short complement regulator (SCR) domains, including eight glycans, and its Y402H polymorphism predisposes those who carry it to age-related macular degeneration. To better understand FH complement binding and self-association, we have studied the solution structures of both the His-402 and Tyr-402 FH allotypes. Analytical ultracentrifugation revealed that up to 12% of both FH allotypes self-associate, and this was confirmed by small-angle X-ray scattering (SAXS), MS, and surface plasmon resonance analyses. SAXS showed that monomeric FH has a radius of gyration (Rg ) of 7.2-7.8 nm and a length of 25 nm. Starting from known structures for the SCR domains and glycans, the SAXS data were fitted using Monte Carlo methods to determine atomistic structures of monomeric FH. The analysis of 29,715 physically realistic but randomized FH conformations resulted in 100 similar best-fit FH structures for each allotype. Two distinct molecular structures resulted that showed either an extended N-terminal domain arrangement with a folded-back C terminus or an extended C terminus and a folded-back N terminus. These two structures are the most accurate to date for glycosylated full-length FH. To clarify FH functional roles in host protection, crystal structures for the FH complexes with C3b and C3dg revealed that the extended N-terminal conformation accounted for C3b fluid-phase regulation, the extended C-terminal conformation accounted for C3d binding, and both conformations accounted for bivalent FH binding to glycosaminoglycans on the target cell surface.

Surface Plasmon Resonance kinetic analysis of the interaction between G-quadruplex nucleic acids and an anti-G-quadruplex monoclonal antibody

BACKGROUND

G-quadruplexes (G4s) are nucleic acids secondary structures formed in guanine-rich sequences. Anti-G4 antibodies represent a tool for the direct investigation of G4s in cells. Surface Plasmon Resonance (SPR) is a highly sensitive technology, suitable for assessing the affinity between biomolecules. We here aimed at improving the orientation of an anti-G4 antibody on the SPR sensor chip to optimize detection of binding antigens.

METHODS

SPR was employed to characterize the anti-G4 antibody interaction with G4 and non-G4 oligonucleotides. Dextran-functionalized sensor chips were used both in covalent coupling and capturing procedures.

RESULTS

The use of two leading molecule for orienting the antibody of interest allowed to improve its activity from completely non-functional to 65% active. The specificity of the anti-G4 antobody for G4 structures could thus be assessed with high sensitivity and reliability.

CONCLUSIONS

Optimization of the immobilization protocol for SPR biosensing, allowed us to determine the anti-G4 antibody affinity and specificity for G4 antigens with higher sensitivity with respect to other in vitro assays such as ELISA. Anti-G4 antibody specificity is a fundamental assumption for the future utilization of this kind of antibodies for monitoring G4s directly in cells.

GENERAL SIGNIFICANCE

The heterogeneous orientation of amine-coupling immobilized ligands is a general problem that often leads to partial or complete inactivation of the molecules. Here we describe a new strategy for improving ligand orientation: driving it from two sides. This principle can be virtually applied to every molecule that loses its activity or is poorly immobilized after standard coupling to the SPR chip surface.

Noble metal nanostructures in optical biosensors: Basics, and their introduction to anti-doping detection

Nanotechnology has illustrated significant potentials in biomolecular-sensing applications; particularly its introduction to anti-doping detection is of great importance. Illicit recreational drugs, substances that can be potentially abused, and drugs with dosage limitations according to the prohibited lists announced by the World Antidoping Agency (WADA) are becoming of increasing interest to forensic chemists. In this review, the theoretical principles of optical biosensors based on noble metal nanoparticles, and the transduction mechanism of commonly-applied plasmonic biosensors are covered. We review different classes of recently-developed plasmonic biosensors for analytic determination and quantification of illicit drugs in anti-doping applications. The important classes of illicit drugs include anabolic steroids, opioids, stimulants, and peptide hormones. The main emphasis is on the advantages that noble metal nano-particles bring to optical biosensors for signal enhancement and the development of highly sensitive (label-free) biosensors. In the near future, such optical biosensors may be an invaluable substitute for conventional anti-doping detection methods such as chromatography-based approaches, and may even be commercialized for routine anti-doping tests.

Kinetic analysis of IgM monoclonal antibodies for determination of dengue sample concentration using SPR technique

Surface plasmon resonance (SPR) sensing is recently emerging as a valuable technique for measuring the binding constants, association and dissociation rate constants, and stoichimetry for a binding interaction kinetics in a number of emerging biological areas. This technique can be applied to the study of immune system diseases in order to contribute to improved understanding and evaluation of binding parameters for a variety of interactions between antigens and antibodies biochemically and clinically. Since the binding constants determination of an anti-protein dengue antibody (Ab) to a protein dengue antigen (Ag) is mostly complicated, the SPR technique aids a determination of binding parameters directly for a variety of particular dengue Ag_Ab interactions in the real-time. The study highlights the doctrine of real-time dengue Ag_Ab interaction kinetics as well as to determine the binding parameters that is performed with SPR technique. In addition, this article presents a precise prediction as a reference curve for determination of dengue sample concentration.

Exploring the Association of Surface Plasmon Resonance with Recombinant MHC:Ig Hybrid Protein as a Tool for Detecting T Lymphocytes in Mice Infected with Leishmania (Leishmania) amazonensis

A surface plasmon resonance- (SPR-) based recognition method applying H-2 L^d:Ig/peptides complexes for ex vivo monitoring cellular immune responses during murine infection with Leishmania (Leishmania) amazonensis is described. Lymphocytes from lesion-draining popliteal lymph nodes were captured on a carboxylated sensor chip surface previously functionalized with H-2 L^d:Ig (DimerX) protein bound to synthetic peptides derived from the COOH-terminal region of cysteine proteinase B of L. (L.) amazonensis. In computational analysis, these peptides presented values of kinetic constants favorable to form complexes with H-2 L^d at neutral pH, with a Gibbs free energy ΔG° < 0. The assayed DimerX:peptide complexes presented the property of attaching to distinct T lymphocytes subsets, obtained from experimentally infected BALB/c mice, in each week of infection, thus indicating a temporal variation in specific T lymphocytes populations, each directed to a different COOH-terminal region-derived peptide. The experimental design proposed herein is an innovative approach for cellular immunology studies of a neglected disease, providing a useful tool for the analysis of specific T lymphocytes subsets.

An unexpected use of ferrocene. A scanning electrochemical microscopy study of a toll-like receptor array and its interaction with E. coli

Toll-like receptor microarrays were investigated by scanning electrochemical microscopy with enhanced contrast from using ferrocene derivatives.

Bloch Surface Wave-Coupled Emission at Ultra-Violet Wavelengths

The interaction of fluorophores with nearby metallic structures is now an active area of research. Dielectric photonic structures offer some advantages over plasmonic structures, namely small energy losses and less quenching. We describe a dielectric one-dimensional photonic crystal (1DPC), which supports Bloch surface waves (BSWs) from 280 to 440 nm. This BSW structure is a quartz slide coated with alternating layers of SiO2 and Si3N4. We show that this structure displays BSWs and that the near-UV fluorophore, 2-aminopurine (2-AP), on the top surface of the structure couples with the BSWs. Fluorophores do not have to be inside the structure for coupling and show a narrow angular distribution, with an angular separation of wavelengths. The Bloch wave-coupled emission (BWCE) radiates through the dielectric layer. These BSW structures, with useful wavelength range for detection of intrinsic protein and cofactor fluorescence, provide opportunities for novel optical configurations for bioassays with surface-localized biomolecules and for optical imaging using the coupled emission.

Cannabinoid Receptor Interacting Protein 1a Competition with β-Arrestin for CB1 Receptor Binding Sites

Cannabinoid receptor interacting protein 1a (CRIP1a) is a CB₁ receptor (CB₁R) distal C-terminal-associated protein that alters CB₁R interactions with G-proteins. We tested the hypothesis that CRIP1a is capable of also altering CB₁R interactions with β-arrestin proteins that interact with the CB₁R at the C-terminus. Coimmunoprecipitation studies indicated that CB₁R associates in complexes with either CRIP1a or β-arrestin, but CRIP1a and β-arrestin fail to coimmunoprecipitate with each other. This suggests a competition for CRIP1a and β-arrestin binding to the CB₁R, which we hypothesized could attenuate the action of β-arrestin to mediate CB₁R internalization. We determined that agonist-mediated reduction of the density of cell surface endogenously expressed CB₁Rs was clathrin and dynamin dependent and could be modeled as agonist-induced aggregation of transiently expressed GFP-CB₁R. CRIP1a overexpression attenuated CP55940-mediated GFP-CB₁R as well as endogenous β-arrestin redistribution to punctae, and conversely, CRIP1a knockdown augmented β-arrestin redistribution to punctae. Peptides mimicking the CB₁R C-terminus could bind to both CRIP1a in cell extracts as well as purified recombinant CRIP1a. Affinity pull-down studies revealed that phosphorylation at threonine-468 of a CB₁R distal C-terminus 14-mer peptide reduced CB₁R-CRIP1a association. Coimmunoprecipitation of CB₁R protein complexes demonstrated that central or distal C-terminal peptides competed for the CB₁R association with CRIP1a, but that a phosphorylated central C-terminal peptide competed for association with β-arrestin 1, and phosphorylated central or distal C-terminal peptides competed for association with β-arrestin 2. Thus, CRIP1a can compete with β-arrestins for interaction with C-terminal CB₁R domains that could affect agonist-driven, β-arrestin-mediated internalization of the CB₁R.

Semi-continuous, real-time monitoring of protein biomarker using a recyclable surface plasmon resonance sensor

Although label-free immunosensors based on, for example, surface plasmon resonance (SPR) provide advantages of real-time monitoring of the analyte concentration, its application to routine clinical analysis in a semi-continuous manner is problematic because of the high cost of the sensor chip. The sensor chip is in most cases regenerated by employing an acidic pH. However, this causes gradual deterioration of the activity of the capture antibody immobilized on the sensor surface. To use sensor chips repeatedly, we investigated a novel surface modification method that enables regeneration of the sensor surface under mild conditions. We introduced a monoclonal antibody (anti-CBP Ab) that detects the conformational change in calcium binding protein (CBP) upon Ca²⁺ binding (>1mM). To construct a regenerable SPR-based immunosensor, anti-CBP Ab was first immobilized on the sensor surface, and CBP conjugated to the capture antibody (specific for creatine kinase-MB isoform (CK-MB); CBP-CAb) then bound in the presence of Ca²⁺. A serum sample was mixed with the detection antibody to CK-MB, which generated an SPR signal proportional to the analyte concentration. After each analysis, the sensor surface was regenerated using medium (pH 7) without Ca²⁺, and then adding fresh CBP-CAb in the presence of Ca²⁺ for the subsequent analysis. Analysis of multiple samples using the same sensor was reproducible at a rate >98.7%. The dose-response curve was linear for 1.75-500.75ng/mL CK-MB, with an acceptable coefficient of variation of <8.8%. The performance of the immunosensor showed a strong correlation with that of the Pathfast reference system (R²>96%), and exhibited analytical stability for 1 month. To our knowledge, this is the first report of a renewal of a sensor surface with fresh antibody after each analysis, providing high consistency in the assay during a long-term use (e.g., a month at least).

DNA templated self-assembly of gold nanoparticle clusters in the colorimetric detection of plant viral DNA using a gold nanoparticle conjugated bifunctional oligonucleotide probe

The DNA templated self-assembly of gold nanoparticles clustered in different configurations (nn = 2–∞) was investigated in the colorimetric detection of ToLCNDV DNA using a gold nanoparticle conjugated bifunctional oligonucleotide probe.

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.

Quantitative Investigation of Protein-Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance

Biosensor-surface plasmon resonance (SPR) technology has emerged as a powerful label-free approach for the study of nucleic acid interactions in real time. The method provides simultaneous equilibrium and kinetic characterization for biomolecular interactions with low sample requirements and without the need for external probes. A detailed and practical guide for protein-DNA interaction analyses using biosensor-SPR methods is presented. Details of SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips and samples, experimental design, quantitative and qualitative data analyses and presentation. A specific example of the interaction of a transcription factor with DNA is provided with results evaluated by both kinetic and steady-state SPR methods.

Unexpected DNA affinity and sequence selectivity through core rigidity in guanidinium-based minor groove binders

In this paper we report the design and biophysical evaluation of novel rigid-core symmetric and asymmetric dicationic DNA binders containing 9H-fluorene and 9,10-dihydroanthracene cores as well as the synthesis of one of these fluorene derivatives. First, the affinity toward particular DNA sequences of these compounds and flexible core derivatives was evaluated by means of surface plasmon resonance and thermal denaturation experiments finding that the position of the cations significantly influence the binding strength. Then their affinity and mode of binding were further studied by performing circular dichroism and UV studies and the results obtained were rationalized by means of DFT calculations. We found that the fluorene derivatives prepared have the ability to bind to the minor groove of certain DNA sequences and intercalate to others, whereas the dihydroanthracene compounds bind via intercalation to all the DNA sequences studied here.

Analysis of PNA hybridization by surface plasmon resonance

Reactions templated by a specific nucleic acid sequence have emerged as an attractive strategy for nucleic acid sensing. The Staudinger reaction using an azide-quenched fluorophore and a phosphine is particularly well suited by virtue of its bioorthogonality and biocompatibility. The reaction is promoted by a complementary nucleic acid that aligns the phosphine with the azide-quenched fluorophore. Cellular RNAs can catalyze the Staudinger reaction, and signal amplification can be achieved through multiple turnover of the template. Peptide nucleic acids (PNAs) provide a convenient platform for the preparation of specific probes as they combine desirable hybridization properties, robust synthesis, ease of fluorophore conjugation, and high biochemical stability. Herein, we describe protocols for fast fluorescent detection of miRNAs in human cells with PNA-based probes via reductive unquenching of bis-azidorhodamine by trialkylphosphine.

Novel insights into amylin aggregation

Amylin is a peptide that aggregates into species that are toxic to pancreatic beta cells, leading to type II diabetes. This study has for the first time quantified amylin association and dissociation kinetics (association constant (ka ) = 28.7 ± 5.1 L mol-1 s-1 and dissociation constant (kd ) = 2.8 ± 0.6 ×10-4 s-1) using surface plasmon resonance (SPR). Thus far, techniques used for the sizing of amylin aggregates do not cater for the real-time monitoring of unconstrained amylin in solution. In this regard we evaluated recently innovated nanoparticle tracking analysis (NTA). In addition, both SPR and NTA were used to study the effect of previously synthesized amylin derivatives on amylin aggregation and to evaluate their potential as a cell-free system for screening potential inhibitors of amylin-mediated cytotoxicity. Results obtained from NTA highlighted a predominance of 100-300 nm amylin aggregates and correlation to previously published cytotoxicity results suggests the toxic species of amylin to be 200-300 nm in size. The results seem to indicate that NTA has potential as a new technique to monitor the aggregation potential of amyloid peptides in solution and also to screen potential inhibitors of amylin-mediated cytotoxicity.

Application of atomic force microscopy for characteristics of single intermolecular interactions

Atomic force microscopy (AFM) can be used to make measurements in vacuum, air, and water. The method is able to gather information about intermolecular interaction forces at the level of single molecules. This review encompasses experimental and theoretical data on the characterization of ligand-receptor interactions by AFM. The advantage of AFM in comparison with other methods developed for the characterization of single molecular interactions is its ability to estimate not only rupture forces, but also thermodynamic and kinetic parameters of the rupture of a complex. The specific features of force spectroscopy applied to ligand-receptor interactions are examined in this review from the stage of the modification of the substrate and the cantilever up to the processing and interpretation of the data. We show the specificities of the statistical analysis of the array of data based on the results of AFM measurements, and we discuss transformation of data into thermodynamic and kinetic parameters (kinetic dissociation constant, Gibbs free energy, enthalpy, and entropy). Particular attention is paid to the study of polyvalent interactions, where the definition of the constants is hampered due to the complex stoichiometry of the reactions.

Sensitive and continuous screening of inhibitors of β-site amyloid precursor protein cleaving enzyme 1 (BACE1) at single SPR chips

The development of new methods that meet the demand of high-throughput, high-fidelity screening of hit compounds is important to researching modalities of important diseases such as neurological disorders, HIV, and cancer. A surface plasmon resonance- (SPR-) based method capable of continuously screening enzyme inhibitors at a single chip with antibody-amplified signal enhancement has been developed. The proof of concept is demonstrated by monitoring the cleavage of chip-confined peptide substrates [a segment of the amyloid precursor protein (APP) with the Swiss mutation] by β-site APP-cleaving enzyme 1 (BACE1). In the presence of a noninhibitor, BACE1 clips the peptide substrate at the cleavage site, detaching a fragment that is homologous to the N-terminus of the amyloid beta (Aβ) peptide. Consequently, a subsequent injection of the Aβ antibody does not lead to any molecular recognition or SPR signal change at the chip. In contrast, suppression of the BACE1 activity by a strong inhibitor leaves the peptide substrate intact, and the subsequent antibody attachment produces an easily detectable SPR signal. Compared to the widely used FRET (fluorescence resonance energy transfer) assay, the method reported here is more cost-effective, as unlabeled peptide is used as the BACE1 substrate. Furthermore, the assay is faster (each screening cycle lasts for ca. 1.5 h) and can be continuously carried out at a single, regenerable SPR chip for more than 30 h. Consequently, excellent reproducibility (RSD < 5%) and throughput can be attained. Two inhibitors were screened, and their half-maximal inhibitory concentrations (IC50) determined by the SPR method were in excellent agreement with values deduced from ELISA and mass spectrometry.

Bivalent and co-operative binding of complement factor H to heparan sulfate and heparin

FH (Factor H) with 20 SCR (short complement regulator) domains is a major serum regulator of complement, and genetic defects in this are associated with inflammatory diseases. Heparan sulfate is a cell-surface glycosaminoglycan composed of sulfated S-domains and unsulfated NA-domains. To elucidate the molecular mechanism of binding of FH to glycosaminoglycans, we performed ultracentrifugation, X-ray scattering and surface plasmon resonance with FH and glycosaminoglycan fragments. Ultracentrifugation showed that FH formed up to 63% of well-defined oligomers with purified heparin fragments (equivalent to S-domains), and indicated a dissociation constant K(d) of approximately 0.5 μM. Unchanged FH structures that are bivalently cross-linked at SCR-7 and SCR-20 with heparin explained the sedimentation coefficients of the FH-heparin oligomers. The X-ray radius of gyration, R(G), of FH in the presence of heparin fragments 18-36 monosaccharide units long increased significantly from 10.4 to 11.7 nm, and the maximum lengths of FH increased from 35 to 40 nm, confirming that large compact oligomers had formed. Surface plasmon resonance of immobilized heparin with full-length FH gave K(d) values of 1-3 μM, and similar but weaker K(d) values of 4-20 μM for the SCR-6/8 and SCR-16/20 fragments, confirming co-operativity between the two binding sites. The use of minimally-sulfated heparan sulfate fragments that correspond largely to NA-domains showed much weaker binding, proving the importance of S-domains for this interaction. This bivalent and co-operative model of FH binding to heparan sulfate provides novel insights on the immune function of FH at host cell surfaces.

Increasing throughput of surface plasmon resonance-based biosensors by multiple analyte injections

Surface plasmon resonance-based biosensors are now acknowledged as robust and reliable instruments to determine the kinetic parameters related to the interactions between biomolecules. These kinetic parameters are used in screening campaigns: there is a considerable interest in reducing the experimental time, thus improving the throughput of the surface plasmon resonance assays. Kinetic parameters are typically obtained by analyzing data from several injections of a given analyte at different concentrations over a surface where its binding partner has been immobilized. It has been already proven that an iterative optimization approach aiming at determining optimal analyte injections to be performed online can significantly reduce the experimentation time devoted to kinetic parameter determination, without any detrimental effect on their standard errors. In this study, we explore the potential of this iterative optimization approach to further reduce experiment duration by combining it with the simultaneous injection of two analytes.

High DNA affinity of a series of peptide linked diaromatic guanidinium-like derivatives

In this paper we report the design and synthesis of a new family of asymmetric peptide linked diaromatic dications as potent DNA minor groove binders. These peptide-linked compounds, with a linear core, displayed a much larger affinity than other guanidinium-like derivatives from the same series with curved cores. As a first screening, the DNA affinity of these structures was evaluated by means of thermal denaturation experiments, finding that the nature of the cation (guanidinium vs 2-aminoimidazolinium) significantly influenced the binding strength. Their binding affinity was assessed by implementing further biophysical measurements such as surface plasmon resonance and circular dichroism. In particular, it was observed that compounds 6, 7, and 8 displayed both a strong binding affinity and significant selectivity for AT oligonucleotides. In addition, the thermodynamics of their binding was evaluated using isothermal titration calorimetry, indicating that the binding is derived from favorable enthalpic and entropic contributions.

A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness

In cell signaling systems, the abundances of signaling molecules are generally thought to determine the response to stimulation. However, the kinetics of molecular processes, for example receptor trafficking and protein turnover, may also play an important role. Few studies have systematically examined this relationship between the resting state and stimulus-responsiveness. Fewer still have investigated the relative contribution of steady-state concentrations and reaction kinetics. Here we describe a mathematical framework for modeling the resting state of signaling systems. Among other things, this framework allows steady-state concentration measurements to be used in parameterizing kinetic models, and enables comprehensive characterization of the relationship between the resting state and the cellular response to stimulation.

Leishmania (Viannia) braziliensis: insights on subcellular distribution and biochemical properties of heparin-binding proteins

Leishmaniasis is a vector-borne disease and an important public health issue. Glycosaminoglycan ligands in Leishmania parasites are potential targets for new strategies to control this disease. We report the subcellular distribution of heparin-binding proteins (HBPs) in Leishmania (Viannia) braziliensis and specific biochemical characteristics of L. (V.) braziliensis HBPs. Promastigotes were fractionated, and flagella and membrane samples were applied to HiTrap Heparin affinity chromatography columns. Heparin-bound fractions from flagella and membrane samples were designated HBP Ff and HBP Mf, respectively. Fraction HBP Ff presented a higher concentration of HBPs relative to HBP Mf, and SDS-PAGE analyses showed 2 major protein bands in both fractions (65 and 55 kDa). The 65 kDa band showed gelatinolytic activity and was sensitive to inhibition by 1,10-phenanthroline. The localization of HBPs on the promastigote surfaces was confirmed using surface plasmon resonance (SPR) biosensor analysis by binding the parasites to a heparin-coated sensor chip; that was inhibited in a dose-dependent manner by pre-incubating the parasites with variable concentrations of heparin, thus indicating distinct heparin-binding capacities for the two fractions. In conclusion, protein fractions isolated from either the flagella or membranes of L. (V.) braziliensis promastigotes have characteristics of metallo-proteinases and are able to bind to glycosaminoglycans.

Understanding the DNA binding of novel non-symmetrical guanidinium/2-aminoimidazolinium derivatives

Biophysical studies have been carried out on a family of asymmetric guanidinium-based diaromatic derivatives to assess their potential as DNA minor groove binding agents. To experimentally assess the binding of these compounds to DNA, solution phase biophysical studies have been performed. Thus, surface plasmon resonance, UV-visible spectroscopy and circular and linear dichroism have been utilized to evaluate binding constants, stoichiometry and mode of binding. In addition, the thermodynamics of the binding process have been determined by using isothermal titration calorimetry. These results show significant DNA binding affinity that correlates with the expected 1 : 1 binding ratio usually observed for minor groove binders. Moreover, a simple computational approach has been devised to assess the potential as DNA binders of this family of compounds.

Interface design and multiplexed analysis with surface plasmon resonance (SPR) spectroscopy and SPR imaging

Ever since the advent of surface plasmon resonance (SPR) and SPR imaging (SPRi) in the early 1990s, their use in biomolecular interaction analysis (BIA) has expanded phenomenally. An important research area in SPR sensor development is the design of novel and effective interfaces that allow for the probing of a variety of chemical and biological interactions in a highly selective and sensitive manner. A well-designed and robust interface is a necessity to obtain both accurate and pertinent biological information. This review covers the recent research efforts in this area with a specific focus towards biointerfaces, new materials for SPR biosensing, and novel array designs for SPR imaging. Perspectives on the challenges ahead and next steps for SPR technology are discussed.

Unravelling protein–protein interactions between complement factor H and C-reactive protein using a multidisciplinary strategy

Experimental studies of protein–protein interactions are very much affected by whether the complexes are fully formed (strong, with nanomolar dissociation constants) or partially dissociated (weak, with micromolar dissociation constants). The functions of the complement proteins of innate immunity are governed by the weak interactions between the activated proteins and their regulators. Complement is effective in attacking pathogens, but not the human host, and imbalances in this process can lead to disease conditions. The inherent complexity in analysing complement interactions is augmented by the multivalency of its main regulator, CFH (complement factor H), for its physiological or pathophysiological ligands. The unravelling of such weak protein–protein or protein–ligand interactions requires a multidisciplinary approach. Synchrotron X-ray solution scattering and constrained modelling resulted in the determination of the solution structure of CFH and its self-associative properties, whereas AUC (analytical ultracentrifugation) identified the formation of much larger CFH multimers through the addition of metals such as zinc. The ligands of CFH, such as CRP (C-reactive protein), also undergo self-association. The combination of X-rays and AUC with SPR (surface plasmon resonance) proved to be essential to identify CRP self-association and revealed how CFH interacts with CRP. We show that CRP unexpectedly binds to CFH at two non-contiguous sites and explain its relevance to age-related macular degeneration.

Correlation between the composition of multivalent antibody conjugates with colloidal gold nanoparticles and their affinity

Interactions between multivalent preparations of antibodies (conjugated with colloidal gold nanoparticles (GNP) as a carrier system) and a multivalent ligand were investigated. The aim of the present study was to reveal the relationship between the affinity of the conjugate and its composition (i.e., the valency). Surface plasmon resonance was applied to study the affinity and the kinetics of the interaction of multivalent conjugates and multivalent virus (on the example of the plum pox virus (PPV)). Three monoclonal antibodies against PPV were prepared. Five GNP preparations with an average particle size in the range from 5 to 60nm (according to electron microscopy measurements) were obtained. The series of preparations allowed us to synthesize GNP-antibody conjugates with different surface areas for immobilization of antibodies, and, consequently, conjugates with different valencies. It was shown that the affinity of the conjugates changes with size of colloidal carriers (i.e. with the valency of the conjugates). The affinity of the virus-antibody interaction (antibodies with affinities of 1.46.10(-8)M and 1.73.10(-8)M) is one to three orders of magnitude lower (depending on the valency of the conjugate) compared to that of the interactions of the virus with GNP conjugates (conjugates with the affinity varying from 1.69.10(-9) to 7.02.10(-12)M and from 2.39.10(-9) to 2.62.10(-11)M, respectively). An increase in the conjugate size leads to an increase in its affinity. The similar trends were observed for the potato virus X.

Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'

Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.

The effects of hairpin loops on ligand-DNA interactions

Hairpin nucleic acids are frequently used in physical studies due to their greater thermal stability compared to their equivalent duplex structures. They are also good models for more complex loop-containing structures such as quadruplexes, i-motifs, cruciforms, and molecular beacons. Although a connecting loop can increase stability, there is little information on how the loop influences the interactions of small molecules with attached base-paired nucleic acid regions. In this study, the effects of different hairpin loops on the interactions of A/T specific DNA minor groove binding agents with a common stem sequence have been investigated by spectroscopic and surface plasmon resonance (SPR) biosensor methods. The results indicate that the hairpin loop has little influence on the specific site interactions on the stem but significantly affects nonspecific binding. The use of a non-nucleotide loop (with a reduced negative charge) not only enhances the thermal stability of the hairpin but also reduces the nonspecific binding at the loop without compromising the primary binding affinity on the stem.

Assessment of the pre-clinical immunogenicity of a new VEGF receptor Fc-fusion protein FP3 with ELISA and BIACORE

PURPOSE

A new VEGF receptor fusion protein FP3 was shown to have promising antitumor potency better than Bevacizumab. Characterization of its immune response is essential to the safe and effective administration in clinical trials. In this study, both BIACORE and ELISA assays were employed to assess pre-clinical immunogenicity of FP3 in monkeys.

EXPERIMENTAL DESIGN

Serum samples from 20 rhesus monkeys were analyzed for the generation of anti-FP3 antibody after intravenous administration of three doses of FP3 (n = 6 per group) or buffer control (n = 2). Sera samples were obtained at 2, 4, 6, 8, 10 weeks after the first administration.

RESULTS

It showed BIACORE presented linear correlation with the dilution of anti-FP3 antibody and the results of ELISA. Two weeks after the initial FP3 injection, anti-FP3 antibody was detected in about 20% FP3-treated monkeys. The ratio of positive samples and the titer of antibody increased along with the FP3-treatment time. Six weeks following FP3 injection almost all the samples were anti-FP3 antibody positive. Moreover, the titer of anti-FP3 antibody but not the ratio of positive samples was also enhanced when the dose of FP3 was elevated. Furthermore, the immunoglobulin types and subclasses of anti-FP3 antibody serum components were mainly identified as IgG1 and IgG4, not IgM. Serum antibodies are characterized that they could not block FP3 binding to VEGF and were non-neutralizing.

CONCLUSIONS

Our data implied that proteins with full human sequences may also have the potential to induce immune response in rhesus monkeys, and BIACORE could be an effective approach to detect the immunogenicity of protein therapeutics in clinic.

C-reactive protein exists in an NaCl concentration-dependent pentamer-decamer equilibrium in physiological buffer

C-reactive protein (CRP) is an acute phase protein of the pentraxin family that binds ligands in a Ca(2+)-dependent manner, and activates complement. Knowledge of its oligomeric state in solution and at surfaces is essential for functional studies. Analytical ultracentrifugation showed that CRP in 2 mM Ca(2+) exhibits a rapid pentamer-decamer equilibrium. The proportion of decamer decreased with an increase in NaCl concentration. The sedimentation coefficients s(20,w)(0) of pentameric and decameric CRP were 6.4 S and in excess of 7.6 S, respectively. In the absence of Ca(2+), CRP partially dissociates into its protomers and the NaCl concentration dependence of the pentamer-decamer equilibrium is much reduced. By x-ray scattering, the radius of gyration R(G) values ranged from 3.7 nm for the pentamer to above 4.0 nm for the decamer. An averaged K(D) value of 21 microM in solution (140 mM NaCl, 2 mM Ca(2+)) was determined by x-ray scattering and modeling based on crystal structures for the pentamer and decamer. Surface plasmon resonance showed that CRP self-associates on a surface with immobilized CRP with a similar K(D) value of 23 microM (140 mM NaCl, 2 mM Ca(2+)), whereas CRP aggregates in low salt. It is concluded that CRP is reproducibly observed in a pentamer-decamer equilibrium in physiologically relevant concentrations both in solution and on surfaces. Both 2 mM Ca(2+) and 140 mM NaCl are essential for the integrity of CRP in functional studies and understanding the role of CRP in the acute phase response.