Detection and Quantification of On-Chip Phosphorylated Peptides by Surface Plasmon Resonance Imaging Techniques Using a Phosphate Capture Molecule

Validity of the cell-extracted proteome as a substrate pool for exploring phosphorylation motifs of kinases

Three representative protein kinases with different substrate preferences, ERK1 (Pro-directed), CK2 (acidophilic), and PKA (basophilic), were used to investigate phosphorylation sequence motifs in substrate pools consisting of the proteomes from three different cell lines, MCF7 (human mammary carcinoma), HeLa (human cervical carcinoma), and Jurkat (human acute T-cell leukemia). Specifically, recombinant kinases were added to the cell-extracted proteomes to phosphorylate the substrates in vitro. After trypsin digestion, the phosphopeptides were enriched and subjected to nanoLC/MS/MS analysis to identify their phosphorylation sites on a large scale. By analyzing the obtained phosphorylation sites and their surrounding sequences, phosphorylation motifs were extracted for each kinase-substrate proteome pair. We found that each kinase exhibited the same set of phosphorylation motifs, independently of the substrate pool proteome. Furthermore, the identified motifs were also consistent with those found using a completely randomized peptide library. These results indicate that cell-extracted proteomes can provide kinase phosphorylation motifs with sufficient accuracy, even though their sequences are not completely random, supporting the robustness of phosphorylation motif identification based on phosphoproteome analysis of cell extracts as a substrate pool for a kinase of interest.

Surface Plasmon Resonance (SPR) biosensor for detection of mycotoxins: A review

Mycotoxin is one of the most important natural pollutants, which poses a global threat to food safety. However, the pollution of mold in food production is inevitable. The detection technology of mycotoxins in food production is an important means to prevent the damage of mycotoxins, so rapid detection and screening to avoid pollution diffusion is essential. The focus of this review is to update the literature on the detection of mycotoxins by surface plasmon resonance (SPR) technology, rather than just traditional chromatographic methods. As a relatively novel and simple analytical method, SPR has been proved to be fast, sensitive and label-free, and has been widely used in real-time qualitative and quantitative analysis of various pollutants. This paper aims to give a broad overview of the sensors for detection and analysis of several common mycotoxins.

Recent Progress in Fluorescent Chemosensors for Protein Kinases

Protein kinases are involved in almost all biological activities. The activities of different kinases reflect the normal or abnormal status of the human body. Therefore, detecting the activities of different kinases is important for disease diagnosis and drug discovery. Fluorescent probes offer opportunities for studying kinase behaviors at different times and spatial locations. In this review, we summarize different kinds of fluorescent chemosensors that have been used to detect the activities of many different kinases.

History of Phos-tag technology for phosphoproteomics

Phos-tag is a functional molecule that selectively captures a phosphate monoester dianion in neutral aqueous solutions. The affinity of Phos-tag for phosphate monoester dianions is more than 10,000 times greater than that for other anions present in living organisms, such as carboxylic acid anions. We have developed and applied useful techniques for phosphoproteomics based on Phos-tag. This review describes the history of Phos-tag development and outlines three main technologies that have been put to practical use. The first is a technique to separate and concentrate phosphopeptides and phosphoproteins using a Phos-tag derivative with a hydrophilic chromatography carrier (Phos-tag polymer beads). The second is a technology to detect phosphopeptides and phosphoproteins on various arrays using Phos-tag biotin. The third is a technique to separate and detect phosphoproteins by electrophoresis using Phos-tag acrylamide. We hope that these three technologies will make a significant contribution to phosphoproteomics and, ultimately, to life science research. SIGNIFICANCE: The authors found that a dinuclear metal complex of 1,3-bis[bis(pyridin-2-ylmethyl)-amino]propan-2-olato acted as a novel phosphate-binding tag nanomolecule, Phos-tag, in an aqueous solution under near physiological conditions. The metal complex having a vacancy on two metal ions is suitable for the access of a phosphomonoester dianion (R-OPO₃^2-) as a bridging ligand. A dinuclear zinc(II) complex (Zn²⁺-Phos-tag) strongly binds to a p-nitrophenyl phosphate dianion (K_d = 2.5 × 10^-8 M) at a neutral pH. The anion selectivity indexes against SO₄^2-, CH₃COO^-, Cl^-, and the bisphenyl phosphate monoanion at 25 °C are 5.2 × 10³, 1.6 × 10⁴, 8.0 × 10⁵, and > 2 × 10⁶, respectively. We have been involved in developing technologies by using the Phos-tag molecule and its derivatives to permit the analysis of phosphorylated biomolecules. To date, Phos-tag technology has contributed to the development of several procedures for phosphoproteomics, including a phosphate-affinity chromatography technique for the separation and enrichment of phosphopeptides and phosphoproteins, a wide variety of microarray/on-chip techniques for the detection of protein phosphorylation, and a phosphate-affinity electrophoresis technique for the detection of shifts in the mobilities of phosphoproteins. In this review article, the authors introduce the impact of Phos-tag-based technological advances for phosphoproteomics.

Determining Protein Phosphorylation Status Using Antibody Arrays and Phos-Tag Biotin

We describe here a standard protocol for determining the phosphorylation status of protein multiplexes using antibody arrays and a biotinylated Phos-tag with a dodeca(ethylene glycol) spacer (Phos-tag Biotin). The procedure is based on an antibody microarray technique used in conjunction with an enhanced chemiluminescence system, and it permits the simultaneous and highly sensitive detection of multiple phosphoproteins in a cell lysate. By using this procedure, we have demonstrated the quantitative detection of the entire phosphorylation status of a target protein involved in intracellular signaling.

Rational Design of Functional Peptide-Gold Hybrid Nanomaterials for Molecular Interactions

Gold nanoparticles (AuNPs) have been extensively used for decades in biosensing-related development due to outstanding optical properties. Peptides, as newly realized functional biomolecules, are promising candidates of replacing antibodies, receptors, and substrates for specific molecular interactions. Both peptides and AuNPs are robust and easily synthesized at relatively low cost. Hence, peptide-AuNP-based bio-nano-technological approaches have drawn increasing interest, especially in the field of molecular targeting, cell imaging, drug delivery, and therapy. Many excellent works in these areas have been reported: demonstrating novel ideas, exploring new targets, and facilitating advanced diagnostic and therapeutic technologies. Importantly, some of them also have been employed to address real practical problems, especially in remote and less privileged areas. This contribution focuses on the application of peptide-gold hybrid nanomaterials for various molecular interactions, especially in biosensing/diagnostics and cell targeting/imaging, as well as for the development of highly active antimicrobial/antifouling coating strategies. Rationally designed peptide-gold nanomaterials with functional properties are discussed along with future challenges and opportunities.

Zinc(ii) and copper(ii) complexes as tools to monitor/inhibit protein phosphorylation events

A perspective on the advance of copper(ii) and zinc(ii) complexes of varied ligand architectures as binders of phosphorylated peptides/proteins and as sensors of phosphorylation reactions is presented.

Photoelectrochemical biosensor for protein kinase A detection based on carbon microspheres, peptide functionalized Au-ZIF-8 and TiO2/g-C3N4

In this work, a novel and sensitive photoelectrochemical (PEC) strategy was designed for protein kinase A (PKA) detection, comprising carbon microsphere (CMS) modified ITO electrode, TiO₂ as the phosphate group recognition material and graphite-carbon nitride (g-C₃N₄) as photoactive material. For the first time, gold nanoparticle decorated zeolitic imidazolate frameworks (Au-ZIF-8) was employed to fabricate biosensor for PKA activity assay with the function of substrate peptide immobilization and signal amplification. Firstly, substrate peptides were assembled on the Au-ZIF-8/CMS/ITO surface through the covalent bonding between the gold nanoparticles (AuNPs) and sulfydryl groups of the peptides. Then, in the presence of ATP, phosphorylation of the substrate peptide was achieved under PKA catalysis. Finally, TiO₂-g-C₃N₄ composites were further modified on the electrode surface based on bonding between TiO₂ and phosphate groups created via phosphorylation of the peptide (yielding TiO₂-g-C₃N₄/P-peptide/Au-ZIF-8/CMS/ITO), which is different with our previous work by directly immobilizing g-C₃N₄ composite on electrode surface. The developed method showed a wide linear range from 0.05-50 U mL^-1. The detection limit was 0.02 U mL^-1 (S/N = 3). The constructed biosensor exhibited high detection specificity for PKA. In addition, the wide applicability of this biosensor was demonstrated by evaluating the inhibition ability of ellagic acid towards PKA.

Ultrasensitive Detection of Bacterial Protein Toxins on Patterned Microarray via Surface Plasmon Resonance Imaging with Signal Amplification by Conjugate Nanoparticle Clusters

Sensitive detection and monitoring of biological interactions in a high throughput, multiplexed array format has numerous advantages. We report here a method to enhance detection sensitivity in surface plasmon resonance (SPR) spectroscopy and SPR imaging via the effect of accumulation of conjugated nanoparticles of varying sizes. Bacterial cholera toxin (CT) was chosen for the demonstration of enhanced immunoassay by SPR. After immobilization of CT on a gold surface, specific recognition is achieved by biotinylated anti-CT. The signal is amplified by the attachment of biotinylated 20 nm AuNP via streptavidin bridge, followed by attachment of 5 nm streptavidin-functionalized Fe₃O₄NP to the AuNP-biotin surface. The continuous surface binding of two differently sized conjugated nanoparticles effectively increases their packing density on surface and significantly improves SPR detection sensitivity, allowing quantitative measurement of CT at very low concentration. The dense packing of conjugated nanoparticles on the surface was confirmed by atomic force microscopy characterization. SPR imaging of the immunoassay for high-throughput analysis utilized an Au-well microarray that attenuated the background resonance interference on the resulting images. A calibration curve of conjugated nanoparticle binding signal amplification for CT detection based on surface coverage has been obtained that shows a correlation in a range from 6.31 × 10^-16 to 2.51 × 10^-13 mol/cm² with the limit of detection of 5.01 × 10^-16 mol/cm². The absolute quantity of detection limit using SPR imaging was 0.25 fmol. The versatile nanoparticles and biotin-streptavidin interaction used here should allow adaptation of this enhancement method to many other systems that include DNA, RNA, peptides, and carbohydrates, opening new avenues for ultrasensitive analysis of biomolecules.

Dual Kretschmann and Otto configuration fiber surface plasmon resonance biosensor

We present a dual-resonance fiber surface plasmon resonance (SPR) sensor for biological analysis. The sensing element was fabricated by sequentially sputtering layers of indium tin oxide (ITO) (100 nm thickness) and Au (35 nm thickness) on the surface of an optical fiber. The refractive index dispersion effect of ITO material led to resonances in the near infrared and visible wavelength regions. The refractive index of ITO is larger than the optical fiber in visible spectral area (400 to 733nm), such that the structure is a typical Kretschmann configuration surface plasmon resonance sensor. However, an Otto configuration is observed in the near infrared area (NIR) due to the ITO refractive index being smaller than the fiber core. We characterized the sensor performance by measuring bulk refractive index (RI) sensitivity in the two configurations, which were 1345 nm/RIU in the Kretschmann configuration and 1100 nm/RIU in the Otto configuration. In addition, this sensor was applied for real-time and label-free monitoring of the IgG/anti-IgG biomolecular interaction. As a robust and ultra-compact SPR sensor, which possesses wide detection range and is highly sensitive, this fiber SPR sensor can be applied for real-time biological analysis and monitoring.

Effect of Linker Length on Cell Capture by Poly(ethylene glycol)-Immobilized Antimicrobial Peptides

Development of antimicrobial peptide (AMP)-functionalized materials has renewed interest in using poly(ethylene glycol) (PEG)-mediated linking to minimize unwanted interactions while engendering the peptides with sufficient flexibility and freedom of movement to interact with the targeted cell types. While PEG-based linkers have been used in many AMP-based materials, the role of the tether length has been minimally explored. Here, we assess the impact of varying the length of PEG-based linkers on the binding of bacterial cells by surface-immobilized AMPs. While higher surface densities of immobilized AMPs were observed using shorter PEG linkers, the increased density was insufficient to fully account for the increased binding activity of peptides. Furthermore, effects were specific to both the peptide and cell type tested. These results suggest that simple alterations in linking strategies-such as changing tether length-may result in large differences in the surface properties of the immobilized AMPs that are not easily predictable.

Potentiometric sensing of aqueous phosphate by competition assays using ion-exchanger doped-polymeric membrane electrodes as transducers

Using Zn(2+)-BPMP or Cu(2+)-BPMP as a receptor and o-mercaptophenol as an indicator, potentiometric sensing of aqueous phosphate by competition assays was achieved. With attractive features of portability, low cost and resistance to interference from turbidity and color, this sensor was successfully used for phosphate detection in biological and water samples.

Peptide Arrays on Planar Supports

On a past volume of this monograph we have reviewed general aspects of the varied technologies available to generate peptide arrays. Hallmarks in the development of the technology and a main sketch of preparative steps and applications in binding assays were used to walk the reader through details of peptide arrays. In this occasion, we resume from that work and bring in some considerations on quantitative evaluation of measurements as well as on selected reports applying the technology.

A tool for the selective sequestration of ATP and PPi to aid in-solution phosphopeptide detection assays

The presence of small phospho-anions, such as PPi and ATP in protein samples often complicates the robust detection of phosphoproteins by metal-based chemosensors and receptors. We herein report the development of a bis(Zn(2+)-cyclen)-triethylbenzene scaffold which can selectively sequester PPi and ATP without affecting the detection of a di-phosphorylated peptide by a ProxyPhos chemosensor.

Phosphopeptide Detection with Biotin-Labeled Phos-tag

Protein kinases are widely considered to be invaluable target enzymes for drug discovery and for diagnosing diseases and assessing their prognosis. Effective analytical techniques for measuring the activities of cellular protein kinases are therefore required for studies in the field of phosphoproteomics. We have recently developed a highly sensitive microarray-based technique for tracing the activities of protein kinases. A series of peptides that are specific substrates of various protein kinases are immobilized on a glass slide and subjected to phosphorylation by cell lysates. The resulting phosphorylated forms of the various peptides are then selectively and simultaneously detected by using a phosphate-binding tag molecule, biotin-labeled Phos-tag, bound to horseradish peroxidase-conjugated streptavidin. Enhanced chemiluminescence signals can then be readily detected by using an automatic image analyzer. In this chapter, we describe a standard protocol for detecting phosphopeptides by biotin-labeled Phos-tag. We also describe a microarray system for high-throughput profiling of intracellular protein kinase activities. The Phos-tag-based method is expected to be useful in the rapid detection of the complex range of phosphorylation reactions involved in cellular signaling events, and it has potential applications in high-throughput screening of kinase activators or inhibitors.

Compact multi-channel surface plasmon resonance sensor for real-time multi-analyte biosensing

A compact multi-channel surface plasmon resonance (SPR) biosensor is demonstrated based on a tablet as the measurement platform. The SPR biosensor employs a bundle of fiber-optic SPR sensors as the multiplexed sensing elements that are illuminated by a light-emitting diode (LED) plane light source and detected by a cordless camera. The multi-channel SPR biosensor was based on optical fiber components for precise, label-free and high-throughput detection without the use of complex, specialized or fragile instrumentation that would require optical calibration. The reference and control channels compensated for the fluctuation of the LED light source and the bulk refractive index, increasing the accuracy and reliability of the biosensor. The multi-channel SPR biosensor was applied for multi-analyte biosensing of immunoglobulin G (IgG) and concanavalin A (Con A). The channels functionalized with staphylococcal protein A (SPA) and ribonuclease B (RNase B) only showed relative intensity responses to their corresponding analytes. Moreover, the multi-channel SPR sensors responded to the specific detection of IgG and Con A with an approximately linear relative intensity response to the analyte concentration. Hence, multiple analytes were simultaneously and quantitatively detected with the multi-channel SPR biosensor. This compact, cost-effective multi-channel SPR biosensor is adapted for point-of-care tests, which are important in healthcare and environmental monitoring and for biomolecular interaction analysis.

Surface Plasmon Resonance Biosensor Based on Smart Phone Platforms

We demonstrate a fiber optic surface plasmon resonance (SPR) biosensor based on smart phone platforms. The light-weight optical components and sensing element are connected by optical fibers on a phone case. This SPR adaptor can be conveniently installed or removed from smart phones. The measurement, control and reference channels are illuminated by the light entering the lead-in fibers from the phone’s LED flash, while the light from the end faces of the lead-out fibers is detected by the phone’s camera. The SPR-sensing element is fabricated by a light-guiding silica capillary that is stripped off its cladding and coated with 50-nm gold film. Utilizing a smart application to extract the light intensity information from the camera images, the light intensities of each channel are recorded every 0.5 s with refractive index (RI) changes. The performance of the smart phone-based SPR platform for accurate and repeatable measurements was evaluated by detecting different concentrations of antibody binding to a functionalized sensing element, and the experiment results were validated through contrast experiments with a commercial SPR instrument. This cost-effective and portable SPR biosensor based on smart phones has many applications, such as medicine, health and environmental monitoring.

Neutral Phosphate-Affinity SDS-PAGE system for profiling of protein phosphorylation

In this chapter, we describe a standard protocol for phosphate-affinity SDS-PAGE that uses a dizinc(II) complex of the phosphate-binding molecule Phos-tag in conjunction with a neutral-pH gel system (Zn(2+-)Phos-tag SDS-PAGE) to detect shifts in the mobilities of phosphoproteins. A previous protocol for affinity electrophoresis that uses polyacrylamide-bound Mn(2+)-Phos-tag and Laemmli's buffer system under conditions of alkaline pH has limitations in separating certain phosphoproteins. The current protocol provides major improvements in separation and detection of various phosphorylated protein species. We here introduce two neutral-pH gel systems buffered with Bis-Tris-HCl and Tris-AcOH, respectively, for Zn(2+)-Phos-tag SDS-PAGE, and we also discuss their characteristics on the basis of comparative studies on phosphorylation profiling of proteins with a wide range of molecular masses. Each analytical procedure, from the beginning of gel preparation to the end of electrophoresis, requires 2.5-5 h with either buffer system.

Protein recognition using synthetic small-molecular binders toward optical protein sensing in vitro and in live cells

This review describes the recognition and sensing techniques of proteins and their building blocks by use of small synthetic binders.

Advances in Phos-tag-based methodologies for separation and detection of the phosphoproteome

This review article describes analytical techniques based on the phosphate-binding tag molecule "Phos-tag", which is an alkoxide-bridged dinuclear metal complex with 1,3-bis(pyridin-2-ylmethylamino)propan-2-olate, for studying the protein phosphorylome. The dinuclear zinc(II) complex forms a stable 1:1 complex with a phosphate monoester dianion in an aqueous solution under conditions of neutral pH. By using a series of functional Phos-tag derivatives, our group has developed novel techniques that are useful in studies on kinomics and phosphoproteomics. Among the derivatives, a series of biotinylated Phos-tag derivatives have been used as molecular tools in applications such as Western blotting for comprehensive detection of phosphorylated proteins and in highly sensitive peptide microarray-based techniques for the detection of kinase activities in biological samples. The review also gives an outline of phosphate affinity electrophoresis, in which immobilized Phos-tag molecules in a general polyacrylamide gel are used to separate proteins and detect differences in their phosphorylation status. This technique permits quantitative analyses of multiple phosphorylation statuses of individual cellular proteins and their time-dependent changes. Conventional mass spectrometry-based shotgun techniques used in phosphoproteomics detect the phosphorylation modification of proteins in peptide fragments, whereas the Phos-tag electrophoresis technique permits the direct analysis of the phosphorylation status of full-length proteins. The technique therefore provides a greater understanding of the detailed properties of particular proteins involved in specific physiological and pathological events. This article is part of a Special Issue entitled: Medical Proteomics.

A signal "on" photoelectrochemical biosensor for assay of protein kinase activity and its inhibitor based on graphite-like carbon nitride, Phos-tag and alkaline phosphatase

A highly sensitive and selective photoelectrochemical (PEC) biosensor is fabricated for the detection of protein kinase activity based on visible-light active graphite-like carbon nitride (g-C3N4) and the specific recognition utility of Phos-tag for protein kinase A (PKA)-induced phosphopeptides. For assembling the substrate peptides, g-C3N4 and gold nanoparticles (g-C3N4-AuNPs) complex is synthesized and characterized. When the immobilized peptides on g-C3N4-AuNPs modified ITO electrode are phosphorylated under PKA catalysis, they can be specifically identified and binded with biotin functionalized Phos-tag (Phos-tag-biotin) in the presence of Zn(2+). Then, through the specific interaction between biotin and avidin, avidin functionalized alkaline phosphatase (avidin-ALP) is further assembled to catalyze its substrate of l-ascorbic acid-2-phosphate trisodium salt (AAP) to produce electron donor of ascorbic acid (AA), resulting an increased photocurrent compared with the absence of phosphorylation event. Based on the specific identification effect of Phos-tag, the fabricated biosensor presents excellent selectivity for capturing the phosphorylated serine residues in the substrate peptides. With the good photoactivity of g-C3N4 and ALP-catalyzed signal amplification, the fabricated biosensor presents high sensitivity and low detection limit (0.015 unit/mL, S/N = 3) for PKA. The applicability of this PEC biosensor is further testified by the evaluation of PKA inhibition by HA-1077 with the IC50 value of 1.18μM. This new strategy is also successfully applied to detect the change of PKA activity in cancer cell lysate with and without drug stimulation. Therefore, the developed PEC method has great potential in screening of kinase inhibitors and highly sensitive detection of kinase activity.

Enzymatic reactions on immobilised substrates

This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.

A novel quantitative kinase assay using bacterial surface display and flow cytometry

The inhibition of tyrosine kinases is a successful approach for the treatment of cancers and the discovery of kinase inhibitor drugs is the focus of numerous academic and pharmaceutical laboratories. With this goal in mind, several strategies have been developed to measure kinase activity and to screen novel tyrosine kinase inhibitors. Nevertheless, a general non-radioactive and inexpensive approach, easy to implement and adapt to a range of applications, is still missing. Herein, using Bcr-Abl tyrosine kinase, an oncogenic target and a model protein for cancer studies, we describe a novel cost-effective high-throughput screening kinase assay. In this approach, named the BacKin assay, substrates displayed on a Bacterial cell surface are incubated with Kinase and their phosphorylation is examined and quantified by flow cytometry. This approach has several advantages over existing approaches, as using bacteria (i.e. Escherichia coli) to display peptide substrates provides a self renewing solid support that does not require laborious chemical strategies. Here we show that the BacKin approach can be used for kinetic and mechanistic studies, as well as a platform to characterize and identify small-molecule or peptide-based kinase inhibitors with potential applications in drug development.

A Phos-tag-based magnetic-bead method for rapid and selective separation of phosphorylated biomolecules

A simple and efficient method based on magnetic-bead technology has been developed for the separation of phosphorylated and nonphosphorylated low-molecular-weight biomolecules, such as nucleotides, phosphorylated amino acids, or phosphopeptides. The phosphate-binding site on the bead is an alkoxide-bridged dinuclear zinc(II) complex with 1,3-bis(pyridin-2-ylmethylamino)propan-2-olate (Phos-tag), which is linked to a hydrophilic cross-linked agarose coating on a magnetic core particle. All steps for the phosphate-affinity separation are conducted in buffers of neutral pH with 50 μL of the magnetic beads in a 1.5-mL microtube. The entire separation protocol for phosphomonoester-type compounds, from addition to elution, requires less than 12 min per sample if the buffers and the zinc(II)-bound Phos-tag magnetic beads have been prepared in advance. The phosphate-affinity magnetic beads are reusable at least 15 times without a decrease in their phosphate-binding ability and they are stable for three months in propan-2-ol.

Anion recognition and sensing with Zn(II)-dipicolylamine complexes

This critical review covers the developments in anion recognition and sensing using Zn(II)-dipicolylamine functionalized receptors over the past decade with emphasis on recent rapid advances in the last five years.

Deciphering enzyme function using peptide arrays

Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.

Reusable amperometric biosensor for measuring protein tyrosine kinase activity

This work presents a simple, low-cost and reusable label-free method for detecting protein tyrosine kinase activity using a tyrosinase-based amperometric biosensor (tyrosine kinase biosensor). This method is based on the observation that phosphorylation can block the tyrosinase-catalyzed oxidation of tyrosine or tyrosyl residue in peptides. Therefore, the activity of p60c-src protein tyrosine kinase (Src) on the developed tyrosine kinase biosensor could be quickly determined when its specific peptide substrate, p60c-src substrate I, was used. The tyrosine kinase biosensor was highly sensitive to the activity of Src with a linear dynamic range of 1.9-237.6 U/mL and the lowest detection limit of 0.23 U/mL. Interestingly, the tyrosine kinase activity can be measured using the developed tyrosine kinase biosensor repetitively without regeneration. The inhibitory effect of various kinase inhibitors on the Src activity could be determined on the tyrosine kinase biosensor. Src-specific inhibitors, PP2 and Src inhibitor I, effectively suppressed Src activity, whereas PD153035, an inhibitor of the epidermal growth factor receptor, was ineffective. Staurosporine, a universal kinase inhibitor, inhibited Src activity in an ATP concentration-dependent manner. These results suggests that the activities of tyrosine kinases and their behaviors toward various reagents can be effectively measured using the developed tyrosine kinase biosensor.

Patterned resonance plasmonic microarrays for high-performance SPR imaging

We report a novel optical platform based on SPR generation and confinement inside a defined three-dimensional microwell geometry that leads to background resonance-free SPR images. The array shows an exceptionally high signal-to-noise ratio (S/N > 80) for imaging analysis and subnanometric thickness resolution. An angular sensitivity of 1°/0.01 RIU has been achieved and the signal to background ratio (S/B) improves to 20, 1 order of magnitude higher than that of the best literature results. The design proves effective for probing-supported lipid membrane arrays in real time with a thickness resolution of 0.24 nm and allows for imaging analysis of microfluidic circuits where resonant spots are separated by only one pixel (∼7 μm). The high image quality and unique chip geometry open up new avenues for array screening and biomicrofluidics using SPRi detection.

Substrate screening of protein kinases: detection methods and combinatorial peptide libraries

The study of protein kinases has become a matter of great importance in the development of new drugs for the treatment of diseases, including cancer and inflammation. Substrate screening is the first step in the fundamental investigation of protein kinases and the development of inhibitors for use in drug discovery. Towards this goal, various studies have been reported regarding the development of phospho-peptide detection methods and the screening of phosphorylated peptide sites by protein kinases. This review introduces the detection methods for phosphorylation events using the reagents with (γ(32)P)ATP, ligand-linked ATP, phospho-peptide-specific antibodies and metal chelating compounds. Chemical modification methods using β-elimination for the detection of phospho-Ser/Thr peptides are introduced as well. In addition, the implementations of combinatorial peptide libraries for screening peptide substrates of protein kinases are discussed. The phage display approach has been suggested as an alternative method of using synthetic peptides for screening the substrate specificities of protein kinase. However, a solid phase assay using a peptide library-bound polymer resin or a peptide-arrayed glass chip is preferred for high throughput screening (HTS).

Single-step kinase inhibitor screening using a peptide-modified gold nanoparticle platform

Two complementary formats for kinase inhibitor screening are presented in which peptide-modified gold nanoparticles are enzymatically phosphorylated and rapidly aggregate on a surface or in solution by action of phosphospecific antibodies. The simple and rapid colourimetric response of the assays makes them an attractive approach for drug-screening applications.

A magnetic bead-based protein kinase assay with dual detection techniques

A novel magnetic bead-based protein kinase assay was developed using MALDI-TOF mass spectrometry (MALDI-TOF MS) and immunochemifluorescence as two independent detection techniques. Abltide substrate was immobilized onto magnetic beads via noncovalent biotin-streptavidin interactions. This noncovalent immobilization strategy facilitated peptide release and allowed MALDI-TOF MS analysis of substrate phosphorylation. The use of magnetic beads provided rapid sample handling and allowed secondary analysis by immunochemifluorescence to determine the degree of substrate phosphorylation. This dual detection technique was used to evaluate the inhibition of c-Abl kinase by imatinib and dasatinib. For each inhibitor, IC₅₀ (half-maximal inhibitory concentration) values determined by these two different detection methods were consistent and close to values reported in the literature. The high-throughput potential of this new approach to kinase assays was preliminarily demonstrated by screening a chemical library consisting of 31 compounds against c-Abl kinase using a 96-well plate. In this proof-of-principle experiment, both MALDI-TOF MS and immunochemifluorescence were able to compare inhibitor potencies with consistent values. Dual detection may significantly enhance the reliability of chemical library screening and identify false positives and negatives. Formatted for 96-well plates and with high-throughput potential, this dual detection kinase assay may provide a rapid, reliable, and inexpensive route to the discovery of small-molecule drug leads.

Phosphate-affinity polyacrylamide gel electrophoresis for SNP genotyping

We introduce a genotyping method which relies on the use of a 1:1 mixture of 5'-phosphate-labeled and nonlabeled allele-specific primers for polymerase chain reaction (PCR). The method is based on the difference in mobility of the phosphorylated and nonphosphorylated PCR products (possessing the same number of base pairs) during phosphate-affinity polyacrylamide gel electrophoresis (PAGE). The phosphate-affinity site in the gel is represented by an immobilized phosphate-binding tag molecule [i.e., a polyacrylamide-bound dizinc(II) complex], which selectively captures the 5'-phosphate-labeled allele-specific product compared with the corresponding nonlabeled one. The DNA migration bands obtained can be visualized by ethidium bromide staining. We demonstrate the genotyping of a single-nucleotide polymorphism reported in a human cardiac sodium channel gene, SCN5A, using the phosphate-affinity PAGE.