Surface plasmon resonance: towards an understanding of the mechanisms of biological molecular recognition

Identification of protein-protein interactions by surface plasmon resonance followed by mass spectrometry

Elucidation of the function and meaning of the protein networks can be useful in the understanding of many pathological processes and the identification of new therapeutic targets. This unit describes an approach to discover protein-protein interactions by coupling surface plasmon resonance to mass spectrometry. Briefly, a protein is covalently bound to a sensor chip, which is then exposed to brain extracts injected over the surface via a microfluidic system. This allows the monitoring in real-time of the interactions between the immobilized ligand and the extracts. Interacting proteins from the extracts are then recovered, trypsinized, and identified using mass spectrometry. The data obtained are searched against a sequence database using the Mascot software. To exclude nonspecific interactors, control experiments using blank sensor chips, and/or randomized peptides, are performed. The protocol presented here does not require specific labeling or modification of proteins and can be performed in <4 days.

Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications

The congruent development of computational technology, bioinformatics and analytical instrumentation makes proteomics ready for the next leap. Present-day state of the art proteomics grew from a descriptive method towards a full stake holder in systems biology. High throughput and genome wide studies are now made at the functional level. These include quantitative aspects, functional aspects with respect to protein interactions as well as post translational modifications and advanced computational methods that aid in predicting protein function and mapping these functionalities across the species border. In this review an overview is given of the current status of these aspects in plant studies with special attention to non-genomic model plants.

Surface plasmon resonance analysis of interactions between diacylglycerol acyltransferase and its interacting molecules

To measure the interactions of diacylglycerol acyltransferase (DGAT) by surface plasmon resonance (SPR), we immobilized Saccharomyces cerevisiae DGAT2 encoded by DGA1 on a BIACORE sensor chip surface. We used N-terminally truncated Dga1p with a FLAG tag at the C-terminus, which was purified to apparent homogeneity, maintaining significant DGAT activity (Kamisaka et al., Appl. Microbiol. Biotechnol., 88, 105-115 (2010)). Truncated Dga1p with a FLAG tag was immobilized with an anti-FLAG antibody that had been coupled with an L1 chip surface consisting of a carboxymethyl dextran matrix with additional hydrophobic alkane groups. The Dga1p-immobilized chip surface was analyzed for interactions of Dga1p with oleoyl-CoA, its substrate, and anti-Dga1p IgG, its interacting protein, by SPR. The binding of these analytes with the Dga1p-immobilized chip surface was specific, because butyryl-CoA, which cannot be used as a substrate for DGAT, and anti-glyceraldehyde-3-phosphate dehydrogenase IgG, did not induce any signals on SPR. Furthermore, injection of organic compounds such as xanthohumol, a DGAT inhibitor, into the Dga1p-immobilized chip surface induced significant SPR signals, probably due to interaction with DGAT. Another DGAT inhibitor, piperine, did not induce SPR signals on application, but induced them due to piperine on application together with oleoyl-CoA, in which piperine can be incorporated into the micelles of oleoyl-CoA. The results indicate that the Dga1p-immobilized L1 chip surface recognized DGAT inhibitors. Taking all this together, SPR measurement using the Dga1p-immobilized L1 chip surface provided a useful system to elucidate the structure-function relationships of DGAT and screen DGAT inhibitors.

State of the art in tumor antigen and biomarker discovery

Our knowledge of tumor immunology has resulted in multiple approaches for the treatment of cancer. However, a gap between research of new tumors markers and development of immunotherapy has been established and very few markers exist that can be used for treatment. The challenge is now to discover new targets for active and passive immunotherapy. This review aims at describing recent advances in biomarkers and tumor antigen discovery in terms of antigen nature and localization, and is highlighting the most recent approaches used for their discovery including “omics” technology.

Dispersions based on noble metal nanoparticles-DNA conjugates

Many biomolecules have specific binding properties in the nanostructure formation; they are attractive materials for nanotechnology. One such promising construction material for growing a well-defined nanostructure is deoxyribonucleic acid, due to its π-electron hydrophobic core and predictable recognition attributed to the specificity of Watson-Crick base-pairing. Hydrogen bonding provides the specificity behind the matching of complementary pairs of single-stranded (ss) DNA to hybridize into a double strand (ds) of helical DNA. The double-helical structure of DNA is determined by a subtle balance of noncovalent interactions among the DNA building blocks. The most prominent role is played by the interactions between the DNA bases, where two binding motifs can be recognized: planar hydrogen bonding and vertical stacking. DNA-based nanotechnology has generated interest in a number of applications due to the specificity, programmability, and reproducibility of DNA interaction with noble metal nanoparticles. 5' and 3' thiol moieties are used to prepare composite DNAs, DNA-gold nanoparticle conjugates and nanostructures with a variety of nanoparticle-based DNA assays. Particularly, color changes induced by the association of nanometer-sized gold particles provide a basis of a simple yet highly selective method for detecting specific biological reactions between anchored ligand molecules and receptor molecules in the milieu. Colloidal noble metal nanoparticles, in particular, have found application in a variety of assay formats in which analyte binding is coupled to particle adsorption. The extreme sensitivity of the bandwidth, the peak height, and the position of the absorption (or scattering) maximum of surface plasmon resonance spectra to environmental changes have prompted the development of approaches directly monitor the DNA hybridization. The same features that make DNA an effective molecule for the storage of genetic information also render it useful as an engineering material for the construction of smart objects at the nanometer scale because of its ability to self organize into desired structures via the specific hybridization of complementary sequences. Biocompatibility between gold nanomaterials and biological scaffolding is crucial to the development of smart biomaterials. These DNA/metal colloids are interesting for their fundamental properties as well as for applications in nanomaterials science and nanobiotechnology.

Protein-protein binding affinities in solution determined by electrospray mass spectrometry

Electrospray ionization (ESI) allows the transfer of multi-protein complexes into the gas phase, thereby providing a simple approach for monitoring the stoichiometry of these noncovalent assemblies by mass spectrometry (MS). It remains unclear, however, whether the measured ion abundance ratios of free and bound species are suitable for determining solution-phase binding affinities (K(d) values). Many types of mass spectrometers employ rf-only quadrupoles as ion guides. This work demonstrates that the settings used for these devices are a key factor for ensuring uniform transmission behavior, which is a prerequisite for meaningful affinity measurements. Using bovine β-lactoglobulin and hemoglobin as model systems, it is demonstrated that under carefully adjusted conditions the "direct" ESI-MS approach is capable of providing K(d) values that are in good agreement with previously published solution-phase data. Of the several ion sources tested, a regular ESI emitter operated with pressure-driven flow at 1 μL min(-1) provided the most favorable results. Potential problems in these experiments include conformationally-induced differences in ionization efficiencies, inadvertent collision-induced dissociation, and ESI-induced clustering artifacts. A number of simple tests can be conducted to assess whether or not these factors are prevalent under the conditions used. In addition, the fidelity of the method can be scrutinized by performing measurements over a wide concentration range. Overall, this work supports the viability of the direct ESI-MS approach for determining binding affinities of protein-protein complexes in solution.

Analysis of protein-ligand interactions by fluorescence polarization

Quantification of the associations between biomolecules is required both to predict and understand the interactions that underpin all biological activity. Fluorescence polarization (FP) provides a nondisruptive means of measuring the association of a fluorescent ligand with a larger molecule. We describe an FP assay in which binding of fluorescein-labeled inositol 1,4,5-trisphosphate (IP(3)) to N-terminal fragments of IP(3) receptors can be characterized at different temperatures and in competition with other ligands. The assay allows the standard Gibbs free energy (ΔG°), enthalpy (ΔH°) and entropy (ΔS°) changes of ligand binding to be determined. The method is applicable to any purified ligand-binding site for which an appropriate fluorescent ligand is available. FP can be used to measure low-affinity interactions in real time without the use of radioactive materials, it is nondestructive and, with appropriate care, it can resolve ΔH° and ΔS°. The first part of the protocol, protein preparation, may take several weeks, whereas the FP measurements, once they have been optimized, would normally take 1-6 h.

Surface plasmon resonance spectroscopy: a new lead in studying the membrane binding of amyloidogenic transthyretin

Surface plasmon resonance (SPR) employs the optical principle of SPR to measure changes in mass on a sensor chip surface in real time. Surface chemistry has been developed which enables the immoblization of lipid bilayers and determination of protein-membrane interactions in real time. In the last decade, the plasma membrane has been demonstrated to play an important role in amyloidogenesis and cytotoxicity induced by amyloidogenic proteins. SPR provides an ideal way to study the membrane binding of amyloidogenic proteins. In this chapter, we describe the application of SPR to the study of amyloidogenic transthyretin binding to the plasma membrane and artificial lipid bilayers.

Protein microarrays: novel developments and applications

Protein microarray technology possesses some of the greatest potential for providing direct information on protein function and potential drug targets. For example, functional protein microarrays are ideal tools suited for the mapping of biological pathways. They can be used to study most major types of interactions and enzymatic activities that take place in biochemical pathways and have been used for the analysis of simultaneous multiple biomolecular interactions involving protein-protein, protein-lipid, protein-DNA and protein-small molecule interactions. Because of this unique ability to analyze many kinds of molecular interactions en masse, the requirement of very small sample amount and the potential to be miniaturized and automated, protein microarrays are extremely well suited for protein profiling, drug discovery, drug target identification and clinical prognosis and diagnosis. The aim of this review is to summarize the most recent developments in the production, applications and analysis of protein microarrays.

Ultrasensitively sensing acephate using molecular imprinting techniques on a surface plasmon resonance sensor

An ultrathin molecularly imprinted polymer film was anchored on an Au surface for fabricating a surface plasmon resonance sensor sensitive to acephate by a surface-bound photo-radical initiator. The polymerization in the presence of acephate resulted in a molecular-imprinted matrix for the enhanced binding of acephate. Analysis of the SPR wavenumber changes in the presence of different concentrations of acephate gave a calibration curve that included the ultrasensitive detection of acephate by the imprinted sites in the composite, K(ass) for the association of acephate to the imprinted sites, 7.7×10(12) M(-1). The imprinted ultrathin film revealed impressive selectivity. The selectivity efficiencies for acephate and other structurally related analogues were 1.0 and 0.11-0.37, respectively. Based on a signal to noise ratio of 3, the detection limits were 1.14×10(-13) M for apple sample and 4.29×10(-14) M for cole sample. The method showed good recoveries and precision for the apple and cole samples spiked with acephate solution. This suggests that a combination of SPR sensing with MIP film is a promising alternative method for the detection of organophosphate compounds.

Flavonoids as protein kinase inhibitors for cancer chemoprevention: direct binding and molecular modeling

Protein kinases play crucial roles in the regulation of multiple cell signaling pathways and cellular functions. Deregulation of protein kinase function has been implicated in carcinogenesis. The inhibition of protein kinases has emerged as an important target for cancer chemoprevention and therapy. Accumulated data revealed that flavonoids exert chemopreventive effects through acting at protein kinase signaling pathways, more than as conventional hydrogen-donating antioxidants. Recent studies show that flavonoids can bind directly to some protein kinases, including Akt/protein kinase B (Akt/PKB), Fyn, Janus kinase 1 (JAK1), mitogen-activated protein kinase kinase 1 (MEK1), phosphoinositide 3-kinase (PI3K), mitogen-activated protein (MAP) kinase kinase 4 (MKK4), Raf1, and zeta chain-associated 70-kDa protein (ZAP-70) kinase, and then alter their phosphorylation state to regulate multiple cell signaling pathways in carcinogenesis processes. In this review, we report recent results on the interactions of flavonoids and protein kinases, especially their direct binding and molecular modeling. The data suggest that flavonoids act as protein kinase inhibitors for cancer chemoprevention that were thought previously as conventional hydrogen-donating antioxidant. Moreover, the molecular modeling data show some hints for creating natural compound-based protein kinase inhibitors for cancer chemoprevention and therapy.

Aptamer-based molecular recognition for biosensor development

Nucleic acid aptamers are an emerging class of synthetic ligands and have recently attracted significant attention in numerous fields. One is in biosensor development. In principle, nucleic acid aptamers can be discovered to recognize any molecule of interest with high affinity and specificity. In addition, unlike most ligands evolved in nature, synthetic nucleic acid aptamers are usually tolerant of harsh chemical, physical, and biological conditions. These distinguished characteristics make aptamers attractive molecular recognition ligands for biosensing applications. This review first concisely introduces methods for aptamer discovery including upstream selection and downstream truncation, then discusses aptamer-based biosensor development from the viewpoint of signal production.

Protein-protein interactions and selection: array-based techniques for screening disease-associated biomarkers in predictive/early diagnosis

There has been considerable interest in recent years in the development of miniaturized and parallelized array technology for protein-protein interaction analysis and protein profiling, namely 'protein-detecting microarrays'. Protein-detecting microarrays utilize a wide variety of capture agents (antibodies, fusion proteins, DNA/RNA aptamers, synthetic peptides, carbohydrates, and small molecules) immobilized at high spatial density on a solid surface. Each capture agent binds selectively to its target protein in a complex mixture, such as serum or cell lysate samples. Captured proteins are subsequently detected and quantified in a high-throughput fashion, with minimal sample consumption. Protein-detecting microarrays were first described by MacBeath and Schreiber in 2000, and the number of publications involving this technology is rapidly increasing. Furthermore, the first multiplex immunoassay systems have been cleared by the US Food and Drug Administration, signaling recognition of the usefulness of miniaturized and parallelized array technology for protein detection in predictive/early diagnosis. Although genetic tests still predominate, with further development protein-based diagnosis will become common in clinical use within a few years.

Surface plasmon resonance biosensorics in urine proteomics

Surface plasmon resonance (SPR) is a novel biophysical detection method. In combination with sophisticated surface chemistries and sensing instrumentations, SPR biosensors are approved as tools for molecular interaction studies. SPR plays also a role in interaction proteomics. Once being detected in urine, SPR helps to unravel the functions of new proteins. Due to its outstanding analytical characteristics, SPR also moves more and more into the realm of quantitative analyses in the clinical laboratory. Complex urine determinations of proteins and/or metabolites will bring the SPR biosensor both to the core lab and to point-of-care-testing.This review delineates first the optical phenomena of SPR near to the gold surface, and also the main features of bioconjugation chemistry on a solid-state surface. Then the kinetic calculation of molecular interaction analysis using SPR is introduced. In order to portray the capability of the method, new applications in urine proteomics and proteinuria diagnostics are finally described in detail.

Surface plasmon resonance spectroscopy in determination of the interactions between amyloid beta proteins (Abeta) and lipid membranes

Surface plasmon resonance (SPR) spectroscopy is emerging as a useful tool for determination of molecular interactions in real time. Studies on the molecular pathogenesis of amyloidoses have shown that the plasma membrane plays an important role in amyloidogenesis and cytotoxicity induced by amyloidogenic proteins. By immobilizing lipid bilayers on a sensor chip surface, SPR spectroscopy has been employed to examine the binding of amyloidogenic proteins, such as amyloid beta protein (Abeta), to a variety of lipid membranes, and it provided new insights into the molecular interactions between these amyloidogenic proteins and membranes. In this chapter, we describe the application of SPR spectroscopy to the determination of the binding of Abeta to lipid membranes.

A generalized model of maximizing the sensitivity in intensity-interrogation surface plasmon resonance biosensors

Intensity interrogation of surface plasmon resonance (IISPR) biosensors possesses the greatest sensitivity beyond other interrogations and is operated at a fixed incident angle to enable real-time analysis without time delay, so that it promises excellent performance in biological/chemical detection and SPR imaging systems. Here we provide a general model to describe its sensitivity based on Lorentz equation and unveil the relation between the sensitivity and the metal thickness. This model presents the dependency between sensitivity and metal thickness, and the optimal thickness of gold layers to maximize the sensitivity in our experiment is 53 nm that agrees well in both measurement and simulation. This general model can be further applied in other intensity-interrogation SPR configurations as a design rule for sensing and imaging applications.

Cellular assays as portals to seven-transmembrane receptor-based drug discovery

As technology advances to the point at which various behaviours of seven-transmembrane (7TM) receptors (also known as G protein-coupled receptors (GPCRs)) can be observed individually, it is clear that, rather than being 'on-off' switches, 7TM receptors are more akin to 'microprocessors' of information. This has introduced the phenomenon of functional selectivity, whereby certain ligands initiate only portions of the signalling mechanisms mediated by a given receptor, which has opened new horizons for drug discovery. The need to discover new 7TM receptor-ligand behaviours and quantify the effect of the drug on these complex systems, to guide medicinal chemistry, puts the pharmacological assay into the spotlight. This Perspective outlines the return to whole-system assays from reductionist recombinant systems, and discusses how the efficacy of a drug is linked to the particular assay used to observe its effects. It also highlights how these new assays are adding value to the drug discovery process.

Autoantibodies to glucose‐6‐phosphate isomerase are elevated in the synovial fluid of rheumatoid arthritis patients

OBJECTIVE

This study investigated whether anti-glucose-6-phosphate isomerase (GPI) antibody in the synovial fluid is specifically related to human rheumatoid arthritis (RA).

METHODS

Synovial fluid was collected from patients with RA, osteoarthritis (OA), gout, Behcet's disease, or ankylosing spondylitis. GPI-binding activity was measured in the synovial fluid using a surface plasmon resonance (SPR) biosensor.

RESULTS

The mean level of anti-GPI signal in the synovial fluid of RA patients was significantly elevated compared with that of OA patients (2.84 +/- 1.41 AU versus 1.19 +/- 0.42 AU, respectively; p < 0.0001). Anti-GPI signals in the synovial fluids of patients with non-rheumatoid arthritis, such as gout, Behcet's disease, or ankylosing spondylitis were significantly lower than in the synovial fluid of RA patients (p < 0.005), and were similar to those of OA patients.

CONCLUSION

Our study indicates that anti-GPI antibody in the synovial fluid is specifically related to RA, and suggests that GPI and its autoantibody might be important in the pathogenesis of human RA.

Surface Plasmon Resonance-Based Molecular Detection of Hb S [β6(A3)Glu→Val, GAG→GTG] at the Gene Level

The surface plasmon resonance (SPR) approach, being a relatively novel biophysical method, is used to detect many different targets by biomolecular interaction. The SPR system uses optical and evanescent wave phenomenon. This approach does not need any labels, such as enzymes or isotopes, and the monitored interactions are in real time. In DNA-DNA interaction, the SPR approach is Tm-independent. Here we report our preliminary results for the molecular detection of the Hb S (GAG -->GTG) mutation at codon 6 of the human beta-globin gene. Our preliminary results show that the SPR approach could be applied as an inexpensive and fast routine test system for the molecular diagnosis of abnormal hemoglobins (Hbs), especially in premarital screening programs.

Trinity DNA detection platform by ultrasmooth and functionalized PEDOT biointerfaces

An oligonucleotide-grafted poly(3,4-ethylenedioxythiophene) (PEDOT) thin film is developed for three DNA biosensor detection methods, including fluorescence, quartz crystal microbalance, and electrochemical methods. By electrocopolymerization of hydroxyl-functionalized EDOT and carboxylic-functionalized EDOT in microemulsion solutions, ultrasmooth films with a controlled surface density of carboxylic groups are created. The probe oligonucleotides are immobilized on PEDOT thin films by using a N-hydroxysuccinimide and 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide hydrochloride coupling method. By monitoring the DNA hybridization efficiency on thin films with different oligonucleotide densities, the optimized density for DNA hybridization is obtained. The feasibility and limitation of using this platform for electrochemical detection are also discussed.

Nucleic Acid-based Detection of Bacterial Pathogens Using Integrated Microfluidic Platform Systems

The advent of nucleic acid-based pathogen detection methods offers increased sensitivity and specificity over traditional microbiological techniques, driving the development of portable, integrated biosensors. The miniaturization and automation of integrated detection systems presents a significant advantage for rapid, portable field-based testing. In this review, we highlight current developments and directions in nucleic acid-based micro total analysis systems for the detection of bacterial pathogens. Recent progress in the miniaturization of microfluidic processing steps for cell capture, DNA extraction and purification, polymerase chain reaction, and product detection are detailed. Discussions include strategies and challenges for implementation of an integrated portable platform.

Low-avidity HPA-1a alloantibodies in severe neonatal alloimmune thrombocytopenia are detectable with surface plasmon resonance technology

BACKGROUND

Fetal and neonatal alloimmune thrombocytopenia (FNAIT) is mostly caused by maternal alloantibodies directed against the human platelet alloantigen (HPA)-1a. Currently, the serologic diagnosis of FNAIT is based on the characterization of the HPA alloantibodies in monoclonal antibody-based antigen-capture assays (e.g., MAIPA assay). Accumulated current evidence indicated that such assays may overlook some HPA-1a antibodies.

STUDY DESIGN AND METHODS

This study employed surface plasmon resonance (SPR) technology using immunoaffinity-purified glycoprotein IIb/IIIa isoforms immobilized on biosensor chips to study the binding kinetics of HPA-1a alloantibodies from different FNAIT cases in real time.

RESULTS

Analysis of HPA-1a alloantibodies from FNAIT cases (n = 9) in SPR showed a moderate relative response (22.2-69.7 resonance units [RU]) and slow antibody dissociation. After the dissociation phase, varying amounts of bound antibodies (41%-79%) remained on the chip. In contrast in HPA-1a alloantibodies from a patient suffering from posttransfusion purpura, a high relative response (approximately 490 RU) was observed at the end of the association phase and no dissociation of antibody binding was detectable. Of particular relevance, by the use of this SPR technique, HPA-1a alloantibodies were detected in two severe FNAIT cases that had determined as false negative by MAIPA assay. In SPR, these HPA-1a alloantibodies showed low-avidity nature characterized by gradual dissociation of antibody during the association phase and complete detachment of antibody binding after the dissociation phase. This high "off-rate" character of low-avidity HPA-1a alloantibodies indicates that such antibody binding is easily detachable by the extensive washing procedure of the MAIPA.

CONCLUSIONS

Our results demonstrated that the SPR method can facilitate the diagnosis of clinically relevant low-avidity HPA-1a antibodies.

Identifying residues in antigenic determinants by chemical modification

Chemical modification of the side chains of amino acid residues was one of the first methods developed to investigate epitopes in protein antigens. The principle of the method is that alteration of the structure of a key residue of an epitope by a chemical modification will alter reactivity with antibody by affecting either specificity or avidity or both. Chemical modification has the advantage that it can be applied to discontinuous as well as continuous epitopes and may be of value in identifying cryptic epitopes. We consider here the several recent studies that have applied site-specific chemical modification to the identification of epitopes on antigens, including the use of formaldehyde, glutaraldehyde, and acid anhydrides, to produce allergoids where determinants important to reaction with IgE are modified but the ability to elicit an IgG response is retained. It is noteworthy that modification of amino groups with charge reversal appears to be the most useful approach. The approach to the use of site-specific chemical modification as a tool for the study of protein function is discussed, and emphasis is placed on the necessity to (1) validate the specificity of modification and (2) assess potential conformational change that may occur secondary to modification. Finally, a list of chemical reagents used for protein modification is presented, together with properties and references to use.

Interference terahertz label-free imaging for protein detection on a membrane

We demonstrate a highly sensitive imaging method combined a terahertz time-domain spectroscopy and an interference effect for label-free protein detection on a polyvinylidene difluoride membrane. The method is based on terahertz time-domain spectroscopy and uses an interference effect. Biotin is linked to the membrane using poly ethylene glycol or poly ethylene glycol methyl ether to prevent it from being washed off. Binding of the biotin with streptavidin is then observed by measuring the terahertz signal change due to the variation of the membrane refractive index. We demonstrate the detection of the binding streptavidin protein in gradually decreasing concentrations, down to 27 ng mm-2, using the image recorded at 1.5 THz.

Improvement of photoaffinity SPR imaging platform and determination of the binding site of p62/SQSTM1 to p38 MAP kinase

p38 mitogen-activated protein kinase (MAPK) is a member of the serine/threonine kinases and is activated in response to stress stimuli, such as cytokines, ultraviolet irradiation, heat shock, and osmotic shock. We revealed in a previous report that p62/SQSTM1, known to participate in proteasomal or autophagosomal protein degradation and cytokine receptor signal transduction pathways, binds to p38 to regulate specifically. Herein, we describe the improvement of the photoaffinity-thiol linker of our SPR imaging platform, which enabled us to determine the binding site of p62 to p38. SPR imaging experiments using a new photoaffinity linker 2 to immobilize the peptides derived from p62 on gold substrate indicate that the domain comprising amino acids 164-190 of p62 binds to p38 directly. These SPR analysis data and empirical biologic data reveal that the binding site of p62 to p38 is the domain corresponding to 173-182.

Label-free detection of biomolecular interactions in real time with a nano-porous silicon-based detection method

BACKGROUND

We describe a biosensor platform for monitoring molecular interactions that is based on the combination of a defined nano-porous silicon surface, coupled to light interferometry. This platform allows the label-free detection of protein-protein and protein-DNA interactions in defined, as well as complex protein mixtures. The silicon surface can be functionalized to be compatible with traditional carboxyl immobilization chemistries, as well as with aldehyde-hydrazine bioconjugation chemistries.

RESULTS

We demonstrate the utility of the new platform in measuring protein-protein interactions of purified products in buffer, in complex mixtures, and in the presence of different organic solvent spikes, such as DMSO and DMF, as these are commonly used in screening chemical compound libraries.

CONCLUSION

Nano-porous silicon, when combined with white light interferometry, is a powerful technique for the measurement of protein-protein interactions. In addition to studying the binary interactions of biomolecules in clean buffer systems, the newly developed surfaces are also suited for studying interactions in complex samples, such as plasma.

Functional characterisation of Fab'-fragments self-assembled onto hydrophilic gold surfaces

Antibody Fab'-fragments have been immobilised on hydrophilic gold by direct self-assembly, and embedded in a matrix of non-ionic hydrophilic polymers, tris(hydroxymethyl)methylacrylamide, carrying lipoate terminal linking groups. Different polymers were synthesised, and co-adsorbed or post-adsorbed between the antibody fragments in order to optimise the antigen binding. Various factors were investigated that influence the activity of the immobilised Fab'-fragments for binding of the antigen, human IgG. The Fab'-fragments were immobilised in dense layers close to monolayer coverage, and the stoichiometric efficiency of immobilisation was up to 30%, with the human IgG also approaching monolayer coverage. The cleaning of the gold surface was a crucial factor in preservation of activity. Besides the usual treatment in hot ammonia/peroxide solution, hot DMSO appeared to be highly effective as a cleaning agent.

The Drosophila IKK-related kinase (Ik2) and Spindle-F proteins are part of a complex that regulates cytoskeleton organization during oogenesis

Background

IkappaB kinases (IKKs) regulate the activity of Rel/NF-kappaB transcription factors by targeting their inhibitory partner proteins, IkappaBs, for degradation. The Drosophila genome encodes two members of the IKK family. Whereas the first is a kinase essential for activation of the NF-kappaB pathway, the latter does not act as IkappaB kinase. Instead, recent findings indicate that Ik2 regulates F-actin assembly by mediating the function of nonapoptotic caspases via degradation of DIAP1. Also, it has been suggested that ik2 regulates interactions between the minus ends of the microtubules and the actin-rich cortex in the oocyte. Since spn-F mutants display oocyte defects similar to those of ik2 mutant, we decided to investigate whether Spn-F could be a direct regulatory target of Ik2.

Results

We found that Ik2 binds physically to Spn-F, biomolecular interaction analysis of Spn-F and Ik2 demonstrating that both proteins bind directly and form a complex. We showed that Ik2 phosphorylates Spn-F and demonstrated that this phosphorylation does not lead to Spn-F degradation. Ik2 is localized to the anterior ring of the oocyte and to punctate structures in the nurse cells together with Spn-F protein, and both proteins are mutually required for their localization.

Conclusion

We conclude that Ik2 and Spn-F form a complex, which regulates cytoskeleton organization during Drosophila oogenesis and in which Spn-F is the direct regulatory target for Ik2. Interestingly, Ik2 in this complex does not function as a typical IKK in that it does not direct SpnF for degradation following phosphorylation.

Biosensor analyses of serum autoantibodies: application to antiphospholipid syndrome and systemic lupus erythematosus

Autoimmune disorders are rare human diseases characterized by the presence of circulating autoantibodies that bind the body's own structural compounds as target antigens. The detection of autoantibodies is important for the diagnostic process. Immunofluorescence and immunoassay methods do not allow a reliable characterization of binding characteristics. Therefore, novel analytical techniques should be considered. This review describes the application of surface plasmon resonance biosensor systems for the diagnosis of autoimmune disorders. The covalent attachment of native antigens to the sensor chip is a suitable method for obtaining highly reproducible analyses of autoantibodies, allowing the evaluation of kinetic rate and affinity constants, and it may enable the identification of disease-relevant autoantibodies linked to disease progression. The autoantibody microarray is another future-oriented technique. Patterns of differential antigen recognition should allow early diagnosis. This is due to the fact that a broad range of autoreactive B cell responses in autoimmune disorders can only be mirrored by including a sufficient number of antigens in a microarray format.