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

Nanotechnology-Based Surface Plasmon Resonance Affinity Biosensors for In Vitro Diagnostics

In the last decades, in vitro diagnostic devices (IVDDs) became a very important tool in medicine for an early and correct diagnosis, a proper screening of targeted population, and also assessing the efficiency of a specific therapy. In this review, the most recent developments regarding different configurations of surface plasmon resonance affinity biosensors modified by using several nanostructured materials for in vitro diagnostics are critically discussed. Both assembly and performances of the IVDDs tested in biological samples are reported and compared.

Efficient Qualitative and Quantitative Determination of Antigen-induced Immune Responses

To determine the effectiveness of immunization strategies used in therapeutic antibody or vaccine development, it is critical to assess the quality of immunization-induced polyclonal antibody responses. Here, we developed a workflow that uses sensitive methods to quantitatively and qualitatively assess immune responses against foreign antigens with regard to antibody binding affinity and epitope diversity. The application of such detailed assessments throughout an immunization campaign can significantly reduce the resources required to generate highly specific antibodies. Our workflow consists of the following two steps: 1) the use of surface plasmon resonance to quantify antigen-specific antibodies and evaluate their apparent binding affinities, and 2) the recovery of serum IgGs using an automated small scale purification system, followed by the determination of their epitope diversity using hydrogen deuterium exchange coupled with mass spectrometry. We showed that these methods were sensitive enough to detect antigen-specific IgGs in the nanogram/μl range and that they provided information for differentiating the antibody responses of the various immunized animals that could not be obtained by conventional methods. We also showed that this workflow can guide the selection of an animal that produces high affinity antibodies with a desired epitope coverage profile, resulting in the generation of potential therapeutic monoclonal antibody clones with desirable functional profiles. We postulate that this workflow will be an important tool in the development of effective vaccines to combat the highly sophisticated evasion mechanisms of pathogens.

Current Experimental Methods for Characterizing Protein-Protein Interactions

Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.

Current Experimental Methods for Characterizing Protein-Protein Interactions

Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.

Role of lectin microarrays in cancer diagnosis

The majority of cell differentiation associated tumor markers reported to date are either glycoproteins or glycolipids. Despite there being a large number of glycoproteins reported as candidate markers for various cancers, only a handful are approved by the US Food and Drug Administration. Lectins, which bind to the glycan part of the glycoproteins, can be exploited to identify aberrant glycosylation patterns, which in turn would help in enhancing the specificity of cancer diagnosis. Although conventional techniques such as HPLC and MS have been instrumental in performing the glycomic analyses, these techniques lack multiplexity. Lectin microarrays have proved to be useful in studying multiple lectin-glycan interactions in a single experiment and, with the advances made in the field, hold a promise of enabling glycomic profiling of cancers in a fast and efficient manner.

Preliminary Therapy Evaluation of (225)Ac-DOTA-c(RGDyK) Demonstrates that Cerenkov Radiation Derived from (225)Ac Daughter Decay Can Be Detected by Optical Imaging for In Vivo Tumor Visualization

The theranostic potential of ²²⁵Ac-based radiopharmaceuticals continues to increase as researchers seek innovative ways to harness the nuclear decay of this radioisotope for therapeutic and imaging applications. This communication describes the evaluation of ²²⁵Ac-DOTA-c(RGDyK) in both biodistribution and Cerenkov luminescence imaging (CLI) studies. Initially, La-DOTA-c(RGDyK) was prepared as a non-radioactive surrogate to evaluate methodologies that would contribute to an optimized radiochemical synthetic strategy and estimate the radioactive conjugate's affinity for α_vβ₃, using surface plasmon resonance spectroscopy. Surface plasmon resonance spectroscopy studies revealed the IC₅₀ and K_i of La-DOTA-c(RGDyK) to be 33 ± 13 nM and 26 ± 11 nM, respectively, and suggest that the complexation of the La³⁺ ion to the conjugate did not significantly alter integrin binding. Furthermore, use of this surrogate allowed optimization of radiochemical synthesis strategies to prepare ²²⁵Ac-DOTA-c(RGDyK) with high radiochemical purity and specific activity similar to other ²²⁵Ac-based radiopharmaceuticals. This radiopharmaceutical was highly stable in vitro. In vivo biodistribution studies confirmed the radiotracer's ability to target α_vβ₃ integrin with specificity; specificity was detected in tumor-bearing animals using Cerenkov luminescence imaging. Furthermore, tumor growth control was achieved using non-toxic doses of the radiopharmaceutical in U87mg tumor-bearing nude mice. To our knowledge, this is the first report to describe the CLI of α_vβ₃⁺ tumors in live animals using the daughter products derived from ²²⁵Ac decay in situ. This concept holds promise to further enhance development of targeted alpha particle therapy.

Far-field measurements of vortex beams interacting with nanoholes

We measure the far-field intensity of vortex beams going through nanoholes. The process is analyzed in terms of helicity and total angular momentum. It is seen that the total angular momentum is preserved in the process, and helicity is not. We compute the ratio between the two transmitted helicity components, γ_m,p. We observe that this ratio is highly dependent on the helicity (p) and the angular momentum (m) of the incident vortex beam in consideration. Due to the mirror symmetry of the nanoholes, we are able to relate the transmission properties of vortex beams with a certain helicity and angular momentum, with the ones with opposite helicity and angular momentum. Interestingly, vortex beams enhance the γ_m,p ratio as compared to those obtained by Gaussian beams.

High-throughput measurement of drug–cyclodextrin kinetic rate constants by a small molecule microarray using surface plasmon resonance imaging

A high-throughput methodology for the measurement of drug–CD kinetic rate constants.

Determination of the effective index and thickness of biomolecular layer by Fano resonances in gold nanogrid array

We present an accurate method to determine the effective refractive index and thickness of biomolecular layer by using Fano resonance modes in dual-period gold nanogrid arrays. The effective refractive index changes along the x and y directions are simultaneously measured and obtained by using a modified dispersion relation. The thickness of the surface layer is calculated by a three-layer waveguide equation without any fitting parameters. The accuracy of the proposed method is verified by comparing the results with the known coated dielectric layer and self-assembly layers. The applications of this method and nanogrid chips for determining the thickness and surface concentration of antigen/antibody interactions are demonstrated.

SPR Biosensor Probing the Interactions between TIMP-3 and Heparin/GAGs

Tissue inhibitor of metalloproteinases-3 (TIMP-3) belongs to a family of proteins that regulate the activity of matrix metalloproteinases (MMPs), which can process various bioactive molecules such as cell surface receptors, chemokines, and cytokines. Glycosaminoglycans (GAGs) interact with a number of proteins, thereby playing an essential role in the regulation of many physiological/patho-physiological processes. Both GAGs and TIMP/MMPs play a major role in many cell biological processes, including cell proliferation, migration, differentiation, angiogenesis, apoptosis, and host defense. In this report, a heparin biosensor was used to map the interaction between TIMP-3 and heparin and other GAGs by surface plasmon resonance spectroscopy. These studies show that TIMP-3 is a heparin-binding protein with an affinity of ~59 nM. Competition surface plasmon resonance analysis indicates that the interaction between TIMP-3 and heparin is chain-length dependent, and N-sulfo and 6-O-sulfo groups (rather than the 2-O-sulfo groups) in heparin are important in the interaction of heparin with TIMP-3. Other GAGs (including chondroitin sulfate (CS) type E (CS-E)and CS type B (CS-B)demonstrated strong binding to TIMP-3, while heparan sulfate (HS), CS type A (CSA), CS type C (CSC), and CS type D (CSD) displayed only weak binding affinity.

The Cerebro-oculo-facio-skeletal Syndrome Point Mutation F231L in the ERCC1 DNA Repair Protein Causes Dissociation of the ERCC1-XPF Complex

The ERCC1-XPF heterodimer, a structure-specific DNA endonuclease, is best known for its function in the nucleotide excision repair (NER) pathway. The ERCC1 point mutation F231L, located at the hydrophobic interaction interface of ERCC1 (excision repair cross-complementation group 1) and XPF (xeroderma pigmentosum complementation group F), leads to severe NER pathway deficiencies. Here, we analyze biophysical properties and report the NMR structure of the complex of the C-terminal tandem helix-hairpin-helix domains of ERCC1-XPF that contains this mutation. The structures of wild type and the F231L mutant are very similar. The F231L mutation results in only a small disturbance of the ERCC1-XPF interface, where, in contrast to Phe(231), Leu(231) lacks interactions stabilizing the ERCC1-XPF complex. One of the two anchor points is severely distorted, and this results in a more dynamic complex, causing reduced stability and an increased dissociation rate of the mutant complex as compared with wild type. These data provide a biophysical explanation for the severe NER deficiencies caused by this mutation.

The blood clotting Factor XIIIa forms unique complexes with amyloid-beta (Aβ) and colocalizes with deposited Aβ in cerebral amyloid angiopathy

AIMS

Cerebral amyloid angiopathy (CAA) is a key pathological hallmark of Alzheimer's disease (AD) characterized by accumulation of amyloid-beta (Aβ) protein in blood vessel walls. CAA impairs vessel functioning, affects blood brain barrier integrity and accelerates cognitive decline of AD patients. Unfortunately, mechanisms underlying Aβ deposition in the vessel wall remain largely unknown. Factor XIIIa (FXIIIa) is a blood-derived transglutaminase crucial in blood coagulation by cross-linking fibrin molecules. Evidence is mounting that blood-derived factors are present in CAA and may play a role in protein deposition in the vessel wall. We therefore investigated whether FXIIIa is present in CAA and if FXIIIa cross-link activity affects Aβ aggregation.

METHODS

Using immunohistochemistry, we investigated the distribution of FXIIIa, its activator thrombin and in situ FXIIIa activity in CAA in post-mortem AD tissue. We used surface plasmon resonance and Western blot analysis to study binding of FXIIIa to Aβ and the formation of FXIIIa-Aβ complexes, respectively. In addition, we studied cytotoxicity of FXIIIa-Aβ complexes to cerebrovascular cells.

RESULTS

FXIIIa, thrombin and in situ FXIIIa activity colocalize with the Aβ deposition in CAA. Furthermore, FXIIIa binds to Aβ with a higher binding affinity for Aβ1-42 compared with Aβ1-40 . Moreover, highly stable FXIIIa-Aβ complexes are formed independently of FXIIIa cross-linking activity that protected cerebrovascular cells from Aβ-induced toxicity in vitro.

CONCLUSIONS

Our data showed that FXIIIa colocalizes with Aβ in CAA and that FXIIIa forms unique protein complexes with Aβ that might play an important role in Aβ deposition and persistence in the vessel wall.

Sensitive detection of a tumor marker, α-fetoprotein, with a sandwich assay on a plasmonic chip

Two types of plasmonic silver- and gold-coated grating biosensor chips (plasmonic chip) were applied in the detection of α-fetoprotein (AFP) with a sandwich imunoassay and surface plasmon field-enhanced fluorescence. On the plasmonic chip, unlabeled marker in the sandwich immunoassay was first quantitatively detected over a wide range between 10(-12) and 10(-8) g/mL. The affinity constants between AFP and anti-AFP antibody, which were obtained by fitting the experimental data to the Langmuir isotherm adsorption curve, were 1 × 10(8) g(-1) mL regardless of the kind of metal in the plasmonic chips. Although the fluorescence intensity on the silver plasmonic chip was 5 times larger than that on the gold plasmonic chip, the limit of detection (LOD) was on the order of 10(-11) g/mL and not improved with a silver plasmonic chip. Herein, we used a new setup that generated less dispersions of both the fluorescence intensity for nonspecific adsorption and the background (optical blank) signal and improved the LOD of AFP to 4 pg/mL (55 fM) with the silver plasmonic chip. With the highly sensitive detection in the sandwich immunoassay, the development of a plasmonic chip for clinical diagnosis by a blood test is promising.

Ligand-detected relaxation dispersion NMR spectroscopy: dynamics of preQ1-RNA binding

An NMR-based approach to characterizing the binding kinetics of ligand molecules to biomolecules, like RNA or proteins, by ligand-detected Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments is described. A (15)N-modified preQ1 ligand is used to acquire relaxation dispersion experiments in the presence of low amounts of the Fsu class I preQ1 aptamer RNA, and increasing ligand concentrations to probe the RNA small molecule interaction. Our experimental data strongly support the conformational selection mechanism postulated. The approach gives direct access to two parameters of a ligand-receptor interaction: the off rate and the population of the small molecule-receptor complex. A detailed description of the kinetics underlying the ligand binding process is of crucial importance to fully understanding a riboswitch's function and to evaluate potential new antibiotics candidates targeting the noncoding RNA species. Ligand-detected NMR relaxation dispersion experiments represent a valuable diagnostic tool for the characterization of binding mechanisms.

CD36 binds oxidized low density lipoprotein (LDL) in a mechanism dependent upon fatty acid binding

The association of unesterified fatty acid (FA) with the scavenger receptor CD36 has been actively researched, with focuses on FA and oxidized low density lipoprotein (oxLDL) uptake. CD36 has been shown to bind FA, but this interaction has been poorly characterized to date. To gain new insights into the physiological relevance of binding of FA to CD36, we characterized FA binding to the ectodomain of CD36 by the biophysical method surface plasmon resonance. Five structurally distinct FAs (saturated, monounsaturated (cis and trans), polyunsaturated, and oxidized) were pulsed across surface plasmon resonance channels, generating association and dissociation binding curves. Except for the oxidized FA HODE, all FAs bound to CD36, with rapid association and dissociation kinetics similar to HSA. Next, to elucidate the role that each FA might play in CD36-mediated oxLDL uptake, we used a fluorescent oxLDL (Dii-oxLDL) live cell assay with confocal microscopy imaging. CD36-mediated uptake in serum-free medium was very low but greatly increased when serum was present. The addition of exogenous FA in serum-free medium increased oxLDL binding and uptake to levels found with serum and affected CD36 plasma membrane distribution. Binding/uptake of oxLDL was dependent upon the FA dose, except for docosahexaenoic acid, which exhibited binding to CD36 but did not activate the uptake of oxLDL. HODE also did not affect oxLDL uptake. High affinity FA binding to CD36 and the effects of each FA on oxLDL uptake have important implications for protein conformation, binding of other ligands, functional properties of CD36, and high plasma FA levels in obesity and type 2 diabetes.

Universal screening platform using three-dimensional small molecule microarray based on surface plasmon resonance imaging

Herein we report a potent methodology for drug screening on a three-dimensional (3D) surface using a carbene based photo-cross-linking reaction.

Rapid and sensitive PCR-dipstick DNA chromatography for multiplex analysis of the oral microbiota

A complex of species has been associated with dental caries under the ecological hypothesis. This study aimed to develop a rapid, sensitive PCR-dipstick DNA chromatography assay that could be read by eye for multiplex and semiquantitative analysis of plaque bacteria. Parallel oligonucleotides were immobilized on a dipstick strip for multiplex analysis of target DNA sequences of the caries-associated bacteria, Streptococcus mutans, Streptococcus sobrinus, Scardovia wiggsiae, Actinomyces species, and Veillonella parvula. Streptavidin-coated blue-colored latex microspheres were to generate signal. Target DNA amplicons with an oligonucleotide-tagged terminus and a biotinylated terminus were coupled with latex beads through a streptavidin-biotin interaction and then hybridized with complementary oligonucleotides on the strip. The accumulation of captured latex beads on the test and control lines produced blue bands, enabling visual detection with the naked eye. The PCR-dipstick DNA chromatography detected quantities as low as 100 pg of DNA amplicons and demonstrated 10- to 1000-fold higher sensitivity than PCR-agarose gel electrophoresis, depending on the target bacterial species. Semiquantification of bacteria was performed by obtaining a series of chromatograms using serial 10-fold dilution of PCR-amplified DNA extracted from dental plaque samples. The assay time was less than 3 h. The semiquantification procedure revealed the relative amounts of each test species in dental plaque samples, indicating that this disposable device has great potential in analysis of microbial composition in the oral cavity and intestinal tract, as well as in point-of-care diagnosis of microbiota-associated diseases.

High-mode spoof SPP of periodic metal grooves for ultra-sensitive terahertz sensing

We report terahertz surface plasmon resonance (SPR) sensing based on prism-coupling to the spoof surface plasmon polariton (SSPP) mode existing on periodically grooved metal films. It was demonstrated that, except for the fundamental mode of the SSPP, there was also a higher mode SSPP wave when the depth of groove was larger. Both fundamental and high-order modes of SSPP could be used for terahertz sensing. We compared the performance of different modes of SSPP on the sensing sensitivity using both reflection amplitude and phase-jump information. The results indicated that the gap distance between the prism base and the metal film had a significant influence on the reflectivity of SPR sensing by affecting the coupling efficiency of an evanescent wave to an SSPP wave; also, high-order mode SSPP-based sensing had a high sensitivity of up to 2.27 THz/RIU, which nearly doubled the sensitivity of the fundamental mode. The application of high-mode SSPP has enormous potential for ultra-sensitive SPR sensing in the terahertz regime.

Cardiovascular disease detection using bio-sensing techniques

Universally, cardiovascular disease (CVD) is recognised as the prime cause of death with estimates exceeding 20 million by 2015 due to heart disease and stroke. Facts regarding the disease, its classification and diagnosis are still lacking. Hence, understanding the issues involved in its initiation, its symptoms and early detection will reduce the high risk of sudden death associated with it. Biosensors developed to be used as rapid screening tools to detect disease biomarkers at the earliest stage and able to classify the condition are revolutionising CVD diagnosis and prognosis. Advances in interdisciplinary research areas have made biosensors faster, highly accurate, portable and environmentally friendly diagnostic devices. The recent advances in microfluidics and the advent of nanotechnology have resulted in the development of improved diagnostics through reduction of analysis time and integration of several clinical assays into a single, portable device as lab-on-a-chip (LOC). The development of such affinity based systems is a major drive of the rapidly growing nanotechnology industry which involves a multidisciplinary research effort encompassing nanofluidics, microelectronics and analytical chemistry. This review summarised the classification of CVD, the biomarkers used for its diagnosis, biosensors and their application including the latest developments in the field of heart-disease detection.

Exopolysaccharides isolated from hydrothermal vent bacteria can modulate the complement system

The complement system is involved in the defence against bacterial infection, or in the elimination of tumour cells. However, disturbances in this system contributes to the pathogenesis of various inflammatory diseases. The efficiency of therapeutic anti-tumour antibodies is enhanced when the complement system is stimulated. In contrast, cancer cells are able to inhibit the complement system and thus proliferate. Some marine molecules are currently being developed as new drugs for use in humans. Among them, known exopolyssacharides (EPSs) generally originate from fungi, but few studies have been performed on bacterial EPSs and even fewer on EPSs extracted from deep-sea hydrothermal vent microbes. For use in humans, these high molecular weight EPSs must be depolymerised. Furthermore, the over-sulphation of EPSs can modify their biological activity. The aim of this study was to investigate the immunodulation of the complement system by either native or over-sulphated low molecular weight EPSs isolated from vent bacteria in order to find pro or anti-activators of complement.

Real-time quantification of proteins secreted by artificial connective tissue made from uni- or multidirectional collagen I scaffolds and oral mucosa fibroblasts

Previously, we found that oral autologous artificial connective tissue (AACT) had a different protein secretion profile to that of clot-embedded AACT. Other oral mucosa substitutes, having different cell types and scaffolds, had dissimilar secretion profiles of proteins (including that for AACT) that influence healing outcome; thus, to ascertain the profiles of factors secreted by artificial tissue and whether they are influenced by their microstructure might help in understanding their bioactivity. An important component of tissue microstructure is the fiber orientation of the scaffold used for manufacturing it. This work developed a surface plasmon resonance (SPR) methodology to quantify factors secreted by oral artificial connective tissue (ACT) in culture medium, and a method to manufacture unidirectional laminar collagen I scaffolds. The SPR methodology was used for assessing differences in the protein secretion profile of ACT made with collagen scaffolds having different fiber orientation (unidirectional vs multidirectional). Oral fibroblasts seeded onto unidirectional scaffolds increased the secretion of six factors involved in modulating healing compared to those seeded onto multidirectional scaffolds. Histological analysis of uni- and multidirectional ACT showed that cells differ in their alignment and morphology. This SPR-methodology led to nanoscale detection of paracrine factors and might be useful to study biomarkers of three-dimensional cell growth, cell differentiation, and wound-healing progression.

Mass spectrometry-based approaches to protein–ligand interactions

One of the greatest current challenges in proteomics is to develop an understanding of cellular communication and regulation processes, most of which involve noncovalent interactions of proteins with various binding partners. Mass spectrometry plays an important role in all aspects of these research efforts. This article provides a survey of mass spectrometry-based approaches for exploring protein-ligand interactions. A wide array of techniques is available, and the choice of method depends on the specific problem at hand. For example, the high-throughput screening of compound libraries for binding to a specific receptor requires different approaches than structural studies on multiprotein complexes. This review is directed to readers wishing to obtain a concise yet comprehensive overview of existing experimental techniques. Specific emphasis is placed on emerging methods that have been developed within the last few years.

Examining the interactions of the splicing factor MBNL1 with target RNA sequences via a label-free, multiplex method

The near-ubiquity of the involvement of RNA in crucial biological processes is accepted. It is important, therefore, to study and understand the biophysical principles that regulate the function of RNA and its interactions with other molecules (e.g., proteins and antibiotics). Methods enabling the high-throughput determination of RNA-protein binding kinetics and thermodynamics would greatly accelerate understanding of these interactions. To that end, we describe the development of a real-time biomolecular interaction analysis platform based on arrayed imaging reflectometry (AIR) for multiplex analysis of RNA-protein interactions. We demonstrate the use of aqueous AIR by measuring the binding kinetics between muscleblind-like 1 (MBNL1), a splicing regulator protein that plays a pivotal role in the Myotonic Dystrophies and Huntington's Disease, and several of its RNA targets simultaneously on a microarrayed chip. Using this approach, we observe that the kinetics of MBNL1 binding isolated CUG and repeat CUG RNA sequences (as models for "normal" and "pathogenic" RNA, respectively) are different even though their steady state binding constants are similar. The ability to compare binding kinetics between RNA sequences rapidly and easily may provide insight into the molecular basis of MBNL1-RNA binding, and more generally suggests that AIR can be a powerful tool to enable the label-free, real-time analysis of biomolecular interactions in a high-throughput format.

Type 1 and Type 2 scenarios in hydrogen exchange mass spectrometry studies on protein–ligand complexes

Ligand binding to a protein can elicit a wide range of responses when studied by HDX mass spectrometry.

Detection of protective antigen, an anthrax specific toxin in human serum by using surface plasmon resonance

In this study, surface plasmon resonance (SPR) technology was used for the sensitive detection of protective antigen (PA), an anthrax specific toxin in spiked human serum samples. A monoclonal antibody raised against Bacillus anthracis PA was immobilized on carboxymethyldextran-modified gold chip, and its interaction with PA was characterized in situ by SPR. By using kinetic evaluation software, KD (equilibrium constant) and Bmax (maximum binding capacity of analyte) were found to be 20 fM and 18.74 m°, respectively. The change in Gibb's free energy (∆G= -78.04 kJ/mol) confirmed the spontaneous interaction between antigen and antibody. The assay could detect 1 pg/mL purified PA. In PA-spiked human serum samples, 10 pg/mL of PA could be detected. Presence of PA in blood samples serves as an important early diagnostic marker for B. anthracis infections. Thus, SPR test can be a sensitive assay for detection of anthrax at early stages of infection.

Gold nanolayer and nanocluster coatings induced by heat treatment and evaporation technique

The paper is focused on the preparation and surface characterization of gold coatings and nanostructures deposited on glass substrate. Different approaches for the layer preparation were applied. The gold was deposited on the glass with (i) room temperature, (ii) glass heated to 300°C, and (iii) the room temperature-deposited glass which was consequently annealed to 300°C. The sheet resistance and concentration of free carriers were determined by the van der Pauw method. Surface morphology was characterized using an atomic force microscopy. The optical properties of gold nanostructures were measured by UV-vis spectroscopy. The evaporation technique combined with simultaneous heating of the glass leads to change of the sheet resistance, surface roughness, and optical properties of gold nanostructures. The electrically continuous layers are formed for significantly higher thickness (18 nm), if the substrate is heated during evaporation process. The annealing process influences both the structure and optical properties of gold nanostructures. The elevated temperature of glass during evaporation amplifies the peak of plasmon resonance in the structures, the surface morphology being significantly altered.

Site-specific peptide and protein immobilization on surface plasmon resonance chips via strain-promoted cycloaddition

Surface plasmon resonance (SPR) is a powerful label-free diagnostic tool to study biomolecular interactions. However, one of the drawbacks of SPR is the lack of controlled immobilization of ligands on the sensor surface. We have developed a modular platform for the fast, reagent-free and site-specific immobilization of azide-containing ligands by strain-promoted cycloaddition onto a cyclooctyne-modified SPR sensor surface. The usefulness of the concept was shown in a study with a papain model system, and up to 150 experiments were performed without loss of surface quality. Furthermore, azide-containing green fluorescent protein (GFP) was also effectively immobilized. Taken together, cyclooctyne-modified SPR chips enable smooth and site-selective immobilization of ligands and prove to be more robust than traditionally functionalized systems.

Quantitative analysis of JAK binding using isothermal titration calorimetry and surface plasmon resonance

Janus Kinases (JAKs) are the key effector kinases that initiate intracellular signalling cascades in response to cytokines and growth factors. As such, a large number of cytoplasmic proteins interact with JAKs both as substrates and as components of regulatory machinery designed to ensure correct activation and termination of signalling. In vitro techniques such as Isothermal Titration Calorimety and Surface Plasmon Resonance are valuable methods to verify and quantify the interaction between JAK and potential binding partners or substrates. Here we describe protocols that exploit both of these in vitro techniques in order to more fully understand the intracellular JAK signalling network.

Evaluating Inhibition of the Epidermal Growth Factor (EGF)-Induced Response of Mutant MCF10A Cells with an Acoustic Sensor

Many cancer treatments rely on inhibition of epidermal growth factor (EGF)-induced cellular responses. Evaluating drug effects on such responses becomes critical to the development of new cancer therapeutics. In this report, we have employed a label-free acoustic sensor, the quartz crystal microbalance with dissipation monitoring (QCM-D), to track the EGF-induced response of mutant MCF10A cells under various inhibitory conditions. We have identified a complex cell de-adhesion process, which can be distinctly altered by inhibitors of signaling pathways and cytoskeleton formation in a dose-dependent manner. The dose dependencies of the inhibitors provide IC₅₀ values which are in strong agreement with the values reported in the literature, demonstrating the sensitivity and reliability of the QCM-D as a screening tool. Using immunofluorescence imaging, we have also verified the quantitative relationship between the ΔD-response (change in energy dissipation factor) and the level of focal adhesions quantified with the areal density of immunostained vinculin under those inhibitory conditions. Such a correlation suggests that the dynamic restructuring of focal adhesions can be assessed based on the time-dependent change in ΔD-response. Overall, this report has shown that the QCM-D has the potential to become an effective sensing platform for screening therapeutic agents that target signaling and cytoskeletal proteins.

Layer-by-layer coating of alginate matrices with chitosan-alginate for the improved survival and targeted delivery of probiotic bacteria after oral administration

The oral administration of probiotic bacteria has shown potential in clinical trials for the alleviation of specific disorders of the gastrointestinal tract. However, cells must be alive in order to exert these benefits. The low pH of the stomach can greatly reduce the number of viable microorganisms that reach the intestine, thereby reducing the efficacy of the administration. Herein, a model probiotic, Bifidobacterium breve, has been encapsulated into an alginate matrix before coating in multilayers of alternating alginate and chitosan. The intention of this formulation was to improve the survival of B. breve during exposure to low pH and to target the delivery of the cells to the intestine. The material properties were first characterized before in vitro testing. Biacore™ experiments allowed for the polymer interactions to be confirmed; additionally, the stability of these multilayers to buffers simulating the pH of the gastrointestinal tract was demonstrated. Texture analysis was used to monitor changes in the gel strength during preparation, showing a weakening of the matrices during coating as a result of calcium ion sequestration. The build-up of multilayers was confirmed by confocal laser-scanning microscopy, which also showed the increase in the thickness of coat over time. During exposure to in vitro gastric conditions, an increase in viability from <3 log(CFU) per mL, seen in free cells, up to a maximum of 8.84 ± 0.17 log(CFU) per mL was noted in a 3-layer coated matrix. Multilayer-coated alginate matrices also showed a targeting of delivery to the intestine, with a gradual release of their loads over 240 min.

Plasmoelectronics: coupling plasmonic excitation with electron flow

Explorations of the coupling of light and charge via localized surface plasmons have led to the discovery that plasmonic excitation can influence macroscopic flows of charge and, conversely, that charging events can change the plasmonic excitation. We discuss recent theory and experiments in the emerging field of plasmoelectronics, with particular emphasis on the application of these materials to challenges in nanotechnology, energy use, and sensing.

Open-ITC: an alternate computational approach to analyze the isothermal titration calorimetry data of complex binding mechanisms

Isothermal titration calorimetry (ITC) is an important technique used in quantitatively analyzing the global mechanism of protein-protein or protein-ligand interactions through thermodynamic measurements. Among different binding mechanisms, the parallel and ligand induced protein oligomerization mechanisms are technically difficult to analyze compared with a sequential binding mechanism. Here, we present a methodology implemented as a program "Open-ITC" that eliminates the need for exact analytical expressions for free ligand concentrations [L] and mole fractions of bound ligand θ that are required for the thermogram analysis. Adopting a genetic algorithm-based optimization, the thermodynamic parameters are determined, and its standard error is evaluated at the global minimum by calculating the Jacobian matrix. This approach yielded a statistically consistent result for a single-site and a two-site binding protein-ligand system. Further, a comparative simulation of a two-step sequential, a parallel, and a ligand induced oligomerization model revealed that their mechanistic differences are discernable in ITC thermograms, only if the first binding step is weaker compared with the second binding step (K(1) <K(2)). We find this to be valid even for the cases where the enthalpies of each of the binding process did not vary significantly.

PROTEIN–PROTEIN INTERACTIONS AS NEW TARGETS FOR DRUG DESIGN: VIRTUAL AND EXPERIMENTAL APPROACHES

Protein–protein and protein–ligand interactions play a central role in biochemical reactions, and understanding these processes is an important task in different fields of biomedical science and drug discovery. Proteins often work in complex assemblies of several macromolecules and small ligands. The structural and functional description of protein–protein interactions (PPI) is very important for basic-, as well as applied research. The interface areas of protein complexes have unique structure and properties, so PPI represent prospective targets for a new generation of drugs. One of the key targets of PPI inhibitors are oligomeric enzymes. This report shows interactive links between virtual and experimental approaches in a total pipeline "from gene to drug" and using Surface Plasmon Resonance technology for experimentally assessing PPI. Our research is conducted on two oligomeric enzymes — HIV-1 protease (HIVp) (homo-dimer) and bacterial L-asparaginase (homo-tetramer). Using methods of molecular modeling and computational alanine scanning we obtained structural and functional description of PPI in these two enzymes. We also presented a real example of application of integral approach in searching inhibitors of HIVp dimerization — from virtual database mining up to experimental testing of lead compounds.

Analysis of IP3 receptors in and out of cells

BACKGROUND

Inositol 1,4,5-trisphosphate receptors (IP3R) are expressed in almost all animal cells. Three mammalian genes encode closely related IP3R subunits, which assemble into homo- or hetero-tetramers to form intracellular Ca2+ channels.

SCOPE OF THE REVIEW

In this brief review, we first consider a variety of complementary methods that allow the links between IP3 binding and channel gating to be defined. How does IP3 binding to the IP3-binding core in each IP3R subunit cause opening of a cation-selective pore formed by residues towards the C-terminal? We then describe methods that allow IP3, Ca2+ signals and IP3R mobility to be examined in intact cells. A final section briefly considers genetic analyses of IP3R signalling.

MAJOR CONCLUSIONS

All IP3R are regulated by both IP3 and Ca2+. This allows them to initiate and regeneratively propagate intracellular Ca2+ signals. The elementary Ca2+ release events evoked by IP3 in intact cells are mediated by very small numbers of active IP3R and the Ca2+-mediated interactions between them. The spatial organization of these Ca2+ signals and their stochastic dependence on so few IP3Rs highlight the need for methods that allow the spatial organization of IP3R signalling to be addressed with single-molecule resolution.

GENERAL SIGNIFICANCE

A variety of complementary methods provide insight into the structural basis of IP3R activation and the contributions of IP3-evoked Ca2+ signals to cellular physiology. This article is part of a Special Issue entitled Biochemical, biophysical and genetic approaches to intracellular calcium signaling.

Advances in localized surface plasmon resonance spectroscopy biosensing

In recent years, localized surface plasmon resonance (LSPR) spectroscopy advancements have made it a sensitive, flexible tool for probing biological interactions. Here, we describe the basic principles of this nanoparticle-based sensing technique, the ways nanoparticles can be tailored to optimize sensing, and examples of novel LSPR spectroscopy applications. These include detecting small molecules via protein conformational changes and resonance LSPR spectroscopy, as well as coupling LSPR with mass spectrometry to identify bound analytes. The last few sections highlight the advantages of single nanoparticle LSPR, in that it lowers limits of detection, allows multiplexing on the nanometer scale, and enables free diffusion of sensors in solution. The cases discussed herein illustrate creative ways that LSPR spectroscopy has been improved to achieve new sensing capabilities.