Biosensor chip mass spectrometry: a chip-based proteomics approach

Opportunities and Challenges for Biosensors and Nanoscale Analytical Tools for Pandemics: COVID-19

Biosensors and nanoscale analytical tools have shown huge growth in literature in the past 20 years, with a large number of reports on the topic of 'ultrasensitive', 'cost-effective', and 'early detection' tools with a potential of 'mass-production' cited on the web of science. Yet none of these tools are commercially available in the market or practically viable for mass production and use in pandemic diseases such as coronavirus disease 2019 (COVID-19). In this context, we review the technological challenges and opportunities of current bio/chemical sensors and analytical tools by critically analyzing the bottlenecks which have hindered the implementation of advanced sensing technologies in pandemic diseases. We also describe in brief COVID-19 by comparing it with other pandemic strains such as that of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) for the identification of features that enable biosensing. Moreover, we discuss visualization and characterization tools that can potentially be used not only for sensing applications but also to assist in speeding up the drug discovery and vaccine development process. Furthermore, we discuss the emerging monitoring mechanism, namely wastewater-based epidemiology, for early warning of the outbreak, focusing on sensors for rapid and on-site analysis of SARS-CoV2 in sewage. To conclude, we provide holistic insights into challenges associated with the quick translation of sensing technologies, policies, ethical issues, technology adoption, and an overall outlook of the role of the sensing technologies in pandemics.

Quantification of Recombinant Products in Yeast

Quantification of various proteins expressed in yeast can be performed by different methods. In this respect, classical as well as advanced techniques can be applied, where the analysis of crude supernatants is of special interest in screening but also manufacturing.The following chapter addresses the analytical background of the introduced methods followed by specific recommendations for the quantification of different products of industrial interest. The method portfolio includes electrophoresis, chromatography, and ELISA as classical techniques, but also biosensor-based, microfluidic and automated, miniaturized methods are introduced. Furthermore, individual strengths and perceived limitations are summarized.Although prominent examples are described, it should be noted that individual modifications are required according to host and cultivation mode.

Label-free detection and identification of protein ligands captured by receptors in a polymerized planar lipid bilayer using MALDI-TOF MS

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) coupled with affinity capture is a well-established method to extract biological analytes from complex samples followed by label-free detection and identification. Many bioanalytes of interest bind to membrane-associated receptors; however, the matrices and high-vacuum conditions inherent to MALDI-TOF MS make it largely incompatible with the use of artificial lipid membranes with incorporated receptors as platforms for detection of captured proteins and peptides. Here we show that cross-linking polymerization of a planar supported lipid bilayer (PSLB) provides the stability needed for MALDI-TOF MS analysis of proteins captured by receptors embedded in the membrane. PSLBs composed of poly(bis-sorbylphosphatidylcholine) (poly(bis-SorbPC)) and doped with the ganglioside receptors GM1 and GD1a were used for affinity capture of the B subunits of cholera toxin, heat-labile enterotoxin, and pertussis toxin. The three toxins were captured simultaneously, then detected and identified by MS on the basis of differences in their molecular weights. Poly(bis-SorbPC) PSLBs are inherently resistant to nonspecific protein adsorption, which allowed selective toxin detection to be achieved in complex matrices (bovine serum and shrimp extract). Using GM1-cholera toxin subunit B as a model receptor-ligand pair, we estimated the minimal detectable concentration of toxin to be 4 nM. On-plate tryptic digestion of bound cholera toxin subunit B followed by MS/MS analysis of digested peptides was performed successfully, demonstrating the feasibility of using the PSLB-based affinity capture platform for identification of unknown, membrane-associated proteins. Overall, this work demonstrates that combining a poly(lipid) affinity capture platform with MALDI-TOF MS detection is a viable approach for capture and proteomic characterization of membrane-associated proteins in a label-free manner.

Enabling systems biology approaches through microfabricated systems

With the experimental tools and knowledge that have accrued from a long history of reductionist biology, we can now start to put the pieces together and begin to understand how biological systems function as an integrated whole. Here, we describe how microfabricated tools have demonstrated promise in addressing experimental challenges in throughput, resolution, and sensitivity to support systems-based approaches to biological understanding.

Quantum dots: synthesis, bioapplications, and toxicity

This review introduces quantum dots (QDs) and explores their properties, synthesis, applications, delivery systems in biology, and their toxicity. QDs are one of the first nanotechnologies to be integrated with the biological sciences and are widely anticipated to eventually find application in a number of commercial consumer and clinical products. They exhibit unique luminescence characteristics and electronic properties such as wide and continuous absorption spectra, narrow emission spectra, and high light stability. The application of QDs, as a new technology for biosystems, has been typically studied on mammalian cells. Due to the small structures of QDs, some physical properties such as optical and electron transport characteristics are quite different from those of the bulk materials.

MALDI-ToF mass spectrometry for studying noncovalent complexes of biomolecules

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been demonstrated to be a valuable tool to investigate noncovalent interactions of biomolecules. The direct detection of noncovalent assemblies is often more troublesome than with electrospray ionization. Using dedicated sample preparation techniques and carefully optimized instrumental parameters, a number of biomolecule assemblies were successfully analyzed. For complexes dissociating under MALDI conditions, covalent stabilization with chemical cross-linking is a suitable alternative. Indirect methods allow the detection of noncovalent assemblies by monitoring the fading of binding partners or altered H/D exchange patterns.

Matrices for Sensors from Inorganic, Organic, and Biological Nanocomposites

Matrices and sensors resulting from inorganic, organic and biological nanocomposites are presented in this overview. The term nanocomposite designates a solid combination of a matrix and of nanodimensional phases differing in properties from the matrix due to dissimilarities in structure and chemistry. The nanoocomposites chosen for a wide variety of health and environment sensors consist of Anodic Porous Allumina and P450scc, Carbon nanotubes and Conductive Polymers, Langmuir Blodgett Films of Lipases, Laccases, Cytochromes and Rhodopsins, Three-dimensional Nanoporous Materials and Nucleic Acid Programmable Protein Arrays.

Production of reliable MALDI spectra with quality threshold clustering of replicates

We present the first application of the quality threshold (QT) clustering algorithm to mass spectrometry (MS) data. The unique abilities of QT clustering to yield precision nodes that are commensurate with the mass measurement precision of the instrument are exploited to generate a consensus spectrum out of multiple replicate spectra. The spectral dot product and confidence intervals are used as a tool for evaluating the similarity and reproducibility between the consensus and replicates. The method is equally applicable to high and low resolution measurements. This paper demonstrates applications to linear spectra from a matrix assisted laser desorption ionization (MALDI) time of flight (TOF) instrument as well as peptide fragmentation data obtained from a TOF/TOF after unimolecular decomposition. The advantages of clustering to mitigate the inherent precision the shortcomings of MALDI data are discussed.

Identification and characterization of an inhibitory fibroblast growth factor receptor 2 (FGFR2) molecule, up-regulated in an Apert Syndrome mouse model

AS (Apert syndrome) is a congenital disease composed of skeletal, visceral and neural abnormalities, caused by dominant-acting mutations in FGFR2 [FGF (fibroblast growth factor) receptor 2]. Multiple FGFR2 splice variants are generated through alternative splicing, including PTC (premature termination codon)-containing transcripts that are normally eliminated via the NMD (nonsense-mediated decay) pathway. We have discovered that a soluble truncated FGFR2 molecule encoded by a PTC-containing transcript is up-regulated and persists in tissues of an AS mouse model. We have termed this IIIa–TM as it arises from aberrant splicing of FGFR2 exon 7 (IIIa) into exon 10 [TM (transmembrane domain)]. IIIa–TM is glycosylated and can modulate the binding of FGF1 to FGFR2 molecules in BIAcore-binding assays. We also show that IIIa–TM can negatively regulate FGF signalling in vitro and in vivo. AS phenotypes are thought to result from gain-of-FGFR2 signalling, but our findings suggest that IIIa–TM can contribute to these through a loss-of-FGFR2 function mechanism. Moreover, our findings raise the interesting possibility that FGFR2 signalling may be a regulator of the NMD pathway.

Incubated protein reduction and digestion on an electrowetting-on-dielectric digital microfluidic chip for MALDI-MS

Localized heating of droplets on an electrowetting-on-dielectric (EWOD) chip has been implemented and shown to accelerate trypsin digestion reaction rates, sample drying, and matrix crystallization for matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Achieving this involved extending the functionality of previous EWOD droplet-based techniques by developing a multifunctional electrode with closed-loop temperature control, while minimizing overall system complexity and addressing challenges associated with rapid evaporation. For the EWOD chip design, we discuss the performance of multifunctional surface electrodes for actuation, localized Joule heating, and thermistic temperature sensing. Furthermore, a hydrophilic pattern is formed in the multifunctional electrode to control the location of an evaporating droplet on the electrode. To demonstrate the capabilities and limitations of this technique, we performed three experiments and measured the results using MALDI-MS: (i) insulin disulfide reductions in dithiothreitol (DTT) over a range of heater temperatures (22-70 °C) to show how reaction rates can be affected by thermal control, (ii) insulin disulfide reductions at 130 °C in dimethyl sulfoxide (DMSO) to demonstrate a reaction in a high boiling point solvent, and (iii) tryptic digestions of cytochrome c at 22 and 40 °C to show that heated droplets can yield reasonably higher peptide sequence coverage than unheated droplets. Although they do not decouple the effects of changing temperatures and concentrations, these experiments verified that thermal cycling by EWOD electrodes accelerates reaction rates in liquid droplets in air.

Integration of SPR biosensors with mass spectrometry (SPR-MS)

The combination of surface plasmon resonance (SPR) and mass spectrometry (MS) creates a comprehensive protein investigation approach wherein SPR is employed for protein quantification and MS is utilized to structurally characterize the proteins. In such, MS utterly complements the SPR detection and reveals intrinsic protein structural modifications that go unregistered via the SPR detection. Protein complexes and non-specific binding can also be delineated via the SPR-MS approach. Described here are the protocols and know-how for successful and reproducible integration of SPR and MS. The individual steps of the entire SPR-MS process are illustrated via an example showing analysis of myoglobin from human plasma.

Kinetic binding analysis of aptamers targeting HIV-1 proteins by a combination of a microbalance array and mass spectrometry (MAMS)

An enhanced chip-based detection platform was developed by integrating a surface acoustic wave biosensor of the Love-wave type with protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). The system was applied to characterize the interaction of aptamers with their cognate HIV-1 proteins. The aptamers, which target two proteins of HIV-1, were identified using an automated in vitro selection platform. For aptamers S66A-C6 and S68B-C5, which target the V3 loop of the HIV-1 envelope protein gp120, KD values of 406 and 791 nM, respectively, were measured. Aptamer S69A-C15 was shown to bind HIV-1 reverse transcriptase (HIV-1 RT) with a KD value of 637 nM when immobilized on the biosensor surface. HIV-1 RT was identified with high significance using MALDI-ToF MS even in crude protein mixtures. The V3-loop of gp120 could be directly identified when using chip-bound purified protein samples. From crude protein mixtures, it could be identified indirectly with high significance via its fusion-partner glutathione-S-transferase (GST). Our data show that the combination of the selectivity of aptamers with a sensitive detection by MS enables the reliable and quantitative analysis of kinetic binding events of protein solutions in real time.

Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry

Sample preparation and fractionation technologies are one of the most crucial processes in proteomic analysis and biomarker discovery in solubilized samples. Chromatographic or electrophoretic proteomic technologies are also available for separation of cellular protein components. There are, however, considerable limitations in currently available proteomic technologies as none of them allows for the analysis of the entire proteome in a simple step because of the large number of peptides, and because of the wide concentration dynamic range of the proteome in clinical blood samples. The results of any undertaken experiment depend on the condition of the starting material. Therefore, proper experimental design and pertinent sample preparation is essential to obtain meaningful results, particularly in comparative clinical proteomics in which one is looking for minor differences between experimental (diseased) and control (nondiseased) samples. This review discusses problems associated with general and specialized strategies of sample preparation and fractionation, dealing with samples that are solution or suspension, in a frozen tissue state, or formalin-preserved tissue archival samples, and illustrates how sample processing might influence detection with mass spectrometric techniques. Strategies that dramatically improve the potential for cancer biomarker discovery in minimally invasive, blood-collected human samples are also presented.

A radioisotope label-free alpha-bungarotoxin-binding assay using BIAcore sensor chip technology for real-time analysis

alpha-Bungarotoxin (alpha-bgtx)-binding proteins, including certain nicotinic acetylcholine receptors and acetylcholine-binding proteins (AChBPs), are frequently characterized with radioisotope-labeled alpha-bgtx-binding assays. Such assays, however, preclude investigations of binding interactions in real time and are hampered by the inconveniences associated with radioisotope-labeled reagents. We used surface plasmon resonance-based technology (BIAcore) to investigate the binding of recombinant AChBP to CM-5 sensor chip surfaces with directly immobilized alpha-bgtx. We validated our BIAcore results by comparing the same biological samples using the traditional (125)I-labeled alpha-bgtx-binding assay. An alpha-bgtx sensor chip, as described here, enables detailed, real-time, radioisotope-free interaction studies that can greatly facilitate the characterization of novel alpha-bgtx-binding proteins and complexes.

Surface plasmon resonance mass spectrometry in proteomics

Due to the enormous complexity of the proteome, focus in proteomics shifts more and more from the study of the complete proteome to the targeted analysis of part of the proteome. The isolation of this specific part of the proteome generally includes an affinity-based enrichment. Surface plasmon resonance (SPR), a label-free technique able to follow enrichment in real-time and in a semiquantitative manner, is an emerging tool for targeted affinity enrichment. Furthermore, in combination with mass spectrometry (MS), SPR can be used to both selectively enrich for and identify proteins from a complex sample. Here we illustrate the use of SPR-MS to solve proteomics-based research questions, describing applications that use very different types of immobilized components: such as small (drug or messenger) molecules, peptides, DNA and proteins. We evaluate the current possibilities and limitations and discuss the future developments of the SPR-MS technique.

Automated SPR-LC-MS/MS system for protein interaction analysis

We have developed a novel automated system to analyze protein complexes by integrating a surface plasmon resonance (SPR) biosensor with highly sensitive nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS). A His-tagged protein, which is also tagged with FLAG and biotinylated sequences, was expressed in mammalian cells. After purification by using the His tag from the cell lysate, the sample protein mixture was applied to an SPR biosensor and the protein complex was captured on the sensor chip. The automated SPR-LC-MS/MS was then performed: (1) two-step on-chip purification of the protein complex by using the FLAG and the biotinylated tags, (2) on-chip protease digestion of the complex, and (3) online nanoflow LC-MS/MS analysis of the resulting peptide fragments for protein identification. All of these processes could be monitored in real-time by the SPR biosensor. We validated the performance of the system using either FK506-binding protein 52 kDa (FKBP52) or ribosomal protein S19 (rpS19) as bait. Thus, the fully automated SPR-LC-MS/MS system appeared to be a powerful tool for functional proteomics studies, particularly for snapshot analysis of functional cellular complexes and machines.

Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomics analysis

The routine detection of low abundance components in complex samples for detailed proteomics analysis continues to be a challenge. Whilst the potential of multidimensional chromatographic fractionation for this purpose has been proposed for some years, and was used effectively for the purification to homogeneity of trace components in bulk biological samples for N-terminal sequence analysis, its practical application in the proteomics arena is still limited. This article reviews some of the recent data using these approaches, including the use of microaffinity purification as part of multidimensional protocols for downstream proteomics analysis.

Potential of label-free detection in high-content-screening applications

The classical approach of high-content screening (HCS) is based on multiplexed, functional cell-based screening and combines several analytical technologies that have been used before separately to achieve a better level of automation (scale-up) and higher throughput. New HCS methods will help to overcome the bottlenecks, e.g. in the present development chain for lead structures for the pharmaceutical industry or during the identification and validation process of new biomarkers. In addition, there is a strong need in analytical and bioanalytical chemistry for functional high-content assays which can be provided by different hyphenated techniques. This review discusses the potential of a label-free optical biosensor based on reflectometric interference spectroscopy (RIfS) as a bridging technology for different HCS approaches. Technical requirements of RIfS are critically assessed by means of selected applications and compared to the performance characteristics of surface plasmon resonance (SPR) which is currently the leading technology in the area of label-free optical biosensors.

An integrated microfluidic chip for the analysis of biochemical reactions by MALDI mass spectrometry

Using an integrated microfluidic chip combined with mass spectrometry is an attractive method for parallel and multiple analyses because of its inherent simplicity, low sample consumption, and high sensitivity. To realize an effective microfluidic chip for the rapid analysis of biochemical reactions by matrix assisted laser desorption/ionization (MALDI)-mass spectrometry (MS), the basic operations on microfluids, namely loading, metering, cutting, transporting, mixing, and injecting, must be integrated. This study describes an integrated microfluidic chip with MALDI-MS that performs the on-chip analysis of biochemical reactions, such as enzymatic reactions. For on-chip multiple reactions, we present sequential fluidic manipulations with nanoliter-sized droplets, based on the precise control of wettability and the capillary pressure of a microchannel. The microfluidic chip we have developed successfully performed biochemical reactions and can dispense a droplet of a few hundred nanoliters on the MALDI target plate according to the designed multiple reaction procedure. Finally, the MS spectrum showed accurate and clear characteristic peaks for reaction products. Our investigations into reaction efficiency showed that the microfluidic chip could reduce the reaction time to one third, and the volume to one hundredth, of off-chip methods using conventional labware such as the micropipette and Eppendorf tube.

Development of surface plasmon resonance mass spectrometry array platform

Protein microarrays are the format of choice for high-throughput, high-content protein interaction analysis. In most of the array formats, reporter molecules are used in multistep detection of the protein interactions. Among the few existing label-free detection approaches, surface plasmon resonance (SPR) and mass spectrometry (MS) stand out as most promising for utilization in protein microarrays, albeit both have been used only sporadically for high-content protein arrays. Shown here for the first time is the combination of SPR and MS detection on a single high-content protein microarray. Antibodies to five human plasma proteins were arrayed in a 10 x 10 spot arrangement on a chemically activated gold-coated glass chip. Binding of proteins to their corresponding antibodies was monitored via SPR imaging across the entire surface of the chip. Following protein affinity retrieval, the chip was overlaid with MALDI matrix and MS analyzed, producing protein-specific mass spectra from distinct spots on the array. The SPR-MS dual detection is well suited for high-content protein microarrays and comprehensive protein analysis-from quantitative assessment of the protein concentration to detection of structural protein variants arising from genetic variations and postexpression processing.

Mass spectrometry-based immunoassays for the next phase of clinical applications

Recent applications of affinity mass spectrometry into clinical laboratories brought a renewed interest in immunoaffinity mass spectrometry as a more specific affinity method capable of selectively targeting and studying protein biomarkers. In mass spectrometry-based immunoassays, proteins are affinity retrieved from biological samples via surface-immobilized antibodies, and are then detected via mass spectrometric analysis. The assays benefit from dual specificity, which is brought about by the affinity of the antibody and the protein mass readout. The mass spectrometry aspect of the assays enables single-step detection of protein isoforms and their individual quantification. This review offers a comprehensive review of mass spectrometry-based immunoassays, from historical perspectives in the development of the immunoaffinity mass spectrometry, to current applications of the assays in clinical and population proteomic endeavors. Described in more detail are two types of mass spectrometry-based immunoassays, one of which incorporates surface plasmon resonance detection for protein quantification. All mass spectrometry-based immunoassays offer high-throughput targeted protein investigation, with clear implications in clinical research, encompassing biomarker discovery and validation, and in diagnostic settings as the next-generation immunoassays.

How to comprehensively analyse proteins and how this influences nutritional research

Proteomics, the comprehensive analysis of a protein complement in a cell, tissue or biological fluid at a given time, is a key platform within the "omic" technologies that also encompass genomics (gene analysis), transcriptomics (gene expression analysis) and metabolomics (metabolite profiling). This review summarises protein pre-separation, identification, quantification and modification/interaction analysis and puts them into perspective for nutritional R and D. Mass spectrometry has progressed with regard to mass accuracy, resolution and protein identification performance. Separation, depletion and enrichment techniques can increasingly cope with complexity and dynamic range of proteomic samples. Hence, proteomic studies currently provide a broader, albeit still incomplete, coverage of a given proteome. Proteomics adapted and applied to nutrition and health should demonstrate ingredient efficacy, deliver biomarkers for health and disease disposition, help in differentiating dietary responders from non-responders, and discover bioactive food components.

Identification and characterization of DNA-binding proteins by mass spectrometry

Mass spectrometry is the most sensitive and specific analytical technique available for protein identification and quantification. Over the past 10 years, by the use of mass spectrometric techniques hundreds of previously unknown proteins have been identified as DNA-binding proteins that are involved in the regulation of gene expression, replication, or DNA repair. Beyond this task, the applications of mass spectrometry cover all aspects from sequence and modification analysis to protein structure, dynamics, and interactions. In particular, two new, complementary ionization techniques have made this possible: matrix-assisted laser desorption/ionization and electrospray ionization. Their combination with different mass-over-charge analyzers and ion fragmentation techniques, as well as specific enzymatic or chemical reactions and other analytical techniques, has led to the development of a broad repertoire of mass spectrometric methods that are now available for the identification and detailed characterization of DNA-binding proteins. These techniques, how they work, what their requirements and limitations are, and selected examples that document their performance are described and discussed in this chapter.

Protein-sensing assay formats and devices

Proteins are used as biocatalysts, therapeutic or diagnostic agents, and as such they are biotechnological products. Moreover, they are biomarkers for health states, diseases or toxic or other adverse effects, and the intracellular protein network is essential for the adaptation of an organism to its environment. Thus, there is a strong need for analytical methods for protein determination, which allow not only to indicate the presence of a protein, but also its concentration, covalent modification and activity, and corresponding developments of new methods experienced strong support. Among those methods only those were considered here, which are based on affinity reactions between an immobilized capture agent, such as an antibody or a receptor, and the target protein. Immobilization methods range from adsorption on hydrophobic materials, in membranes or gels to covalent binding and bioaffinity reactions, such as the oriented immobilization of antibodies on protein A/G layers. The applicability of the various methods is dependent on physical and chemical properties of the immobilization substrate and of the capture agent, i.e. the presence of surface charges, hydrophobic areas or functional groups for chemical coupling. The choice of the immobilization substrate is influenced by the combination of the assay and detection principle, which meets best the practical requirements. Assay formats range from direct, label-free one-step detection of the affinity reaction between the capture agent and the target protein to multi-step procedures, such as an enzyme-tracer-based sandwich assays. Each approach has its particular advantages and disadvantages with respect to the complexity of the assay, i.e. number of required reagents and of incubation steps, the possible degree of automation, assay time, availability of suitable reagents, required sample volume, sensitivity and specificity, including the possibility to determine several proteins simultaneously. No general recommendation for the "best choice" was given in this contribution, but examples were chosen, which illustrate the potential of the different systems.

Proteomics-on-a-chip: the challenge to couple lab-on-a-chip unit operations

This review describes a vision of a proteomics-on-a-chip device to separate, detect and identify the proteome. It guides the reader towards a development strategy, avoiding some of the pitfalls. It also describes the current state-of-the-art developments in proteomic analysis including available technologies, current market issues, the elements of an envisaged proteomics-on-a-chip device, the required microfabrication processes and the integration of the elements into one device. Address-flow microfluidics is a tool for connecting separation and detection platforms. The final section contains an expert opinion on the recommended development strategies, benefits of proteomics-on-a-chip in the life sciences and the anticipated market.

Biomolecular interaction analysis under electrophoretic flow conditions

Combining the advantages of electrophoresis with the advantages of biomolecular interaction analysis (BIA) enables the biospecific detection of separated molecules; for example it permits differentiation between a complementary single-stranded DNA and a single nucleotide polymorphism. In order to integrate these two techniques, it is necessary to investigate whether it is possible to detect a biomolecular interaction under electrophoretic flow conditions. To this end a novel detection system was developed for electrophoresis that utilizes a label-free and time-resolved detection technique: reflectometric interference spectroscopy (RIfS). The biological functions of important analytes were investigated using this system. Although RIfS can be used as a postcolumn detector, it is also possible to use it to detect relevant substances under electrophoretic flow conditions. DNA-LNA, biotin-streptavidin and protein-protein interactions were detected using this coupled electrophoresis-RIfS set-up.

Cholesterol modulated antibody binding in supported lipid membranes as determined by total internal reflectance microscopy on a microfabricated high-throughput glass chip

A high-throughput microfabricated all-glass microchip, lipid biochip, was created and used to measure fluorescently tagged antibody binding to dinitrophenol (DNP) haptens in planar supported phospholipid/cholesterol lipid bilayers as a function of cholesterol-to-lipid molar ratio (X(CHOL)). Multiple parallel microchannels etched in the lipid biochip allowed simultaneous measurement of antibody binding to hapten-containing and hapten-free lipid bilayers, for a range of aqueous antibody concentrations. Specific and nonspecific antibody binding to the supported lipid bilayers was determined from the internally calibrated intensity of the surface fluorescence using total internal reflectance fluorescence (TIRF) microscopy. The TIRF intensity data of the specific antibody binding were fitted to the Langmuir isotherm and Hill equation models to determine the apparent dissociation constant K(d), the maximum fluorescence parameter F(infinity), and binding cooperativity n. As X(CHOL) increased from 0 to 0.50, K(d) exhibited a minimum of approximately 4 microM and n reached a maximum of approximately 2.2 at X(CHOL) approximately 0.20. However, F(infinity) appeared to be insensitive to the cholesterol content. The nonspecific binding fraction (NS), defined as the ratio of the TIRF intensity for hapten-free bilayers to that with hapten, showed a minimum of approximately 0.08 also at X(CHOL) approximately 0.20. The results suggest that cholesterol regulates the specific binding affinity and cooperativity, as well as suppresses nonspecific binding of aqueous antibody to a planar supported lipid bilayer surface at an optimal cholesterol content of X(CHOL) approximately 0.20. Interestingly, for X(CHOL) approximately 0.40, NS reached a maximum of approximately 0.57, suggesting significant packing defects in the lipid bilayer surface, possibly as a result of lipid domain formation as predicted by the lipid superlattice model. We conclude that cholesterol plays a significant role in regulating both specific and nonspecific antibody/antigen binding events on the lipid bilayer surface and that our lipid biochip represents a new and useful high-resolution microfluidic device for measuring lipid/protein surface binding activities in a parallel and high-throughput fashion.

Reflectometric interference spectroscopy combined with MALDI-TOF mass spectrometry to determine quantitative and qualitative binding of mixtures of vancomycin derivatives

This paper describes the combination of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with label free bio-interaction analysis based on reflectometric interference spectroscopy (RIfS). The potential of this concerted approach is demonstrated by measuring the binding properties of different vancomycin-type glycopeptide antibiotic mixtures. Although RIfS is sensitive and does not require use of a label, it cannot determine which components of a mixture have bound to the surface after incubation. Fortunately, each bound species has a unique mass that can, afterwards, be determined by mass spectrometry. Thus, the screening capability of RIfS is combined with the identification capability of mass spectrometry.

Proteomics in developmental toxicology

The objective of this presentation is to review the major proteomic technologies available to developmental toxicologists and, when possible, to provide examples of how various proteomic technologies have been used in developmental toxicology or toxicology in general. The field of proteomics is too broad for us to go into great depth about each technology, so we have attempted to provide brief overviews supplemented with many references that cover the subjects in more detail. Proteomics tools produce a global view of complex biological systems by examining complex protein mixtures using large-scale, high-throughput technologies. These technologies speed up the process of protein separation, quantification, and identification. As an important complement to genomics, proteomics allows for the examination of the entire complement of proteins in an organism, tissue, or cell-type. Current proteomics technologies not only identify protein expression, but also post-translational modifications and protein interactions. The field of proteomics is expanding rapidly to provide greater volume and quality of protein information to help understand the multifaceted nature of biological systems.

Creating nanoscopic collagen matrices using atomic force microscopy

The atomic force microscope (AFM) is introduced as a biomolecular manipulation machine capable of assembling biological molecules into well-defined molecular structures. Native collagen molecules were mechanically directed into well-defined, two-dimensional templates exhibiting patterns with feature sizes ranging from a few nanometers to several hundreds of micrometers. The resulting nanostructured collagen matrices were only approximately 3-nm thick, exhibited an extreme mechanical stability, and maintained their properties over the time range of several months. Our results directly demonstrate the plasticity of biological assemblies and provide insight into the physical mechanisms by which biological structures may be organized by cells in vivo. These nanoscopic templates may serve as platforms on non-biological surfaces to direct molecular and cellular processes.

Proteomic studies of human and other vertebrate muscle proteins

This review summarizes results of some systemic studies of muscle proteins of humans and some other vertebrates. The studies, started after introduction of two-dimensional gel electrophoresis of O'Farrell, were significantly extended during development of proteomics, a special branch of functional genomics. Special attention is paid to analysis of characteristic features of strategy for practical realization of the systemic approach during three main stages of these studies: pre-genomic, genomic (with organizational registration of proteomics), and post-genomic characterized by active use of structural genomics data. Proteomic technologies play an important role in detection of changes in isoforms of various muscle proteins (myosins, troponins, etc.). These changes possibly reflecting tissue specificity of gene expression may underline functional state of muscle tissues under normal and pathological conditions, and such proteomic analysis is now used in various fields of medicine.

Genomic and Proteomic Profiles of Heart Disease

Genomics and proteomics are becoming powerful tools for profiling diseased states. The human genome is estimated to encode 30,000 to 40,000 genes, generating more than 100,000 functionally distinct proteins. Microarray data are available for multiple models of heart disease as well as for diseased and failing human hearts. Similarly, two-dimensional gel data banks of normal and diseased myocardium from multiple species are published and are available on the Internet. The combined technologies are beginning to provide new insights into the causes and pathways of cardiac dysfunction. This article reviews the novel findings that have been acquired from genomic and proteomic screens of diseased hearts in animal models and humans.