Monitoring selectivity in kinase-promoted phosphorylation of densely packed peptide monolayers using label-free electrochemical detection

Using a Single Peptide to Electrochemically Sense Multiple Kinases

Kinases are responsible for regulating cellular and physiological processes, and abnormal kinase activity is associated with various diseases. Therefore, kinases are being used as biomarkers for disease and developing methods for their sensing is highly important. Usually more than one kinase is involved in phosphorylating a target protein. However, kinase detection methods usually detect the activity of only one specific kinase. Here we describe an electrochemical kinase sensing tool for the selective detection of two kinases using the same target peptide. We demonstrate the sensing of kinases ERK2 and PKCδ. This is based on a single sensing element, a peptide that contains two distinct phosphorylation sites of these two kinases. Reversibility experiments with alkaline phosphatase and reaction with the electrochemically active ferrocene-labeled ATP showed that the mechanism of sensing is by detecting the enzymatic phosphorylation. Our approach can be further utilized to develop devices for the detection of multiple kinases and can be expanded to other types of enzymes involved in disease.

Electrochemical biosensors based on peptide-kinase interactions at the kinase docking site

Kinases are important cancer biomarkers and are conventionally detected based on their catalytic activity. Kinases regulate cellular activities by phosphorylation of motif-specific multiple substrate proteins, resulting in a lack of selectivity of activity-based kinase biosensors. We present an alternative approach of sensing kinases based on the interactions of their allosteric docking sites with a specific partner protein. The new approach was demonstrated for the ERK2 kinase and its substrate ELK-1. A peptide derived from ELK-1 was bound to a gold electrode and ERK2 sensing was performed by electrochemical impedance spectroscopy. We performed a detailed analysis of the interaction between the ELK-1 peptide and the kinase on gold surfaces. Atomic force microscopy, variable angle spectroscopic ellipsometry, X-ray Photoelectron Spectroscopy, and polarization modulation IR reflection-absorption spectroscopy analysis of the gold surface revealed the adsorbed layer of the ERK2 on the peptide monolayer. The sensors showed a high level of target selectivity for ERK2 compared to the p38γ kinase and BSA. ERK2 was detected in its cellular concentration range, 0.5-2.0 μM, and the limit of detection was calculated to be 0.35 μM. Using the flexibility of peptide design, our method is generic for developing sensitive and substrate-specific biosensors and other disease-related enzymes based on their interactions.

Effect of Interfacial Properties on Impedimetric Biosensing of the Sialylation Process with a Biantennary N-Glycan-Based Monolayer

Sensing enzymatic sialylation provides new tools for the evaluation of pathological events and pathogen invasion. Enzymatic sialylation is usually monitored via fluorescence or metabolic labeling, which requires relatively large amounts of the glycan substrate with limited availability. Using a label-free biosensor requires smaller quantities of substrates because the interactions induce measurable changes to an interface, which can be translated into a signal. The downside of label-free biosensors is that they are very sensitive to changes at the interface, and the properties of the surface layer can play a major role. Electrochemical impedance spectroscopy was used here to follow the enzymatic sialylation of a biantennary N-glycan acceptor in mixed monolayers. The surfaces contained either neutral, positively or negatively charged, or zwitterionic functional groups. The systems were characterized by contact potential difference, ellipsometry, and contact angle analyses. We found that the characteristics of the mixed monolayer have a profound effect on the biosensing of the enzymatic sialylation. Positively charged layers were found to adsorb the enzyme under the reaction conditions. Negatively charged and zwitterionic surfaces were nonresponsive to enzymatic sialylation. Only the neutral mixed monolayers provided signals that were related directly to enzymatic sialylation. This work demonstrates the importance of appropriate interface properties for monitoring enzymatic sialylation processes.

Electrochemical distinction of neuronal and neuroblastoma cells via the phosphorylation of the cellular extracellular membrane

In this contribution we establish a proof of concept method for monitoring, quantifying and differentiating the extracellular phosphorylation of Human SHSY5Y undifferentiated neuronal cells and neuroblastoma cells by three prominent ectokinases PKA, PKC and Src. Herein it is demonstrated that a combination of different experimental techniques, including fluroesence microscopy, quartz crystal microscopy (QCM) and electrochemistry, can be used to detect extracellular phosphorylation levels of neuronal and neuroblastoma cells. Phosphorylation profiles of the three ectokinases, PKA, PKC and Src, were investigated using fluorescence microscopy and the number of phosphorylation sites per kinase was estimated using QCM. Finally, the phosphorylation of the extracellular membrane was determined using electrochemistry. Our results clearly demonstrate that the extracellular phosphorylation of neuronal cells differs significantly in terms of its phosphorylation profile from diseased neuroblastoma cells and the strength of surface electrochemical techniques in the differentiation process. We reveal that using electrochemistry, the percent compositions of neuronal and neuroblastoma cells can also be identified.

Electrochemical detection of kinase by converting homogeneous analysis into heterogeneous assay through avidin-biotin interaction

In the classical heterogeneous electrochemical assay, phosphorylation of peptide substrate is usually performed on the solid-liquid surface. However, immobilization of probe on the solid surface may limit the interaction between the reaction site of probe and the active center of kinase due to the steric hindrance effect. In this work, we proposed a heterogeneous electrochemical method for kinase detection, in which the probe is immobilization-free during the phosphorylation reaction. A biotinylated peptide was used as the kinase substrate. After phosphorylation, the biotinylated phosphopeptide was captured by the neutravidin (NA)-modified electrode through the avidin-biotin interaction. The phosphate groups on the electrode surface were then recognized by the conjugates preformed between biotinylated Phos-tag™ (Bio-tag-Phos) and ferrocene (Fc)-capped NA-modified gold nanoparticle (Fc-AuNP-NA). The method integrates the advantages of homogeneous reaction and heterogeneous detection with high simplicity, sensitivity and specificity. The strategy can be applied to design other heterogeneous biosensors without the immobilization of probe during the enzyme catalyzed reaction.

Electrochemical detection of neuronal extracellular phosphorylation by PKA, PKC and Src

The focus of this work described here is to establish a method for monitoring and quantifying the extracellular phosphorylation of Human SHSY5Y undifferentiated neuronal cells by three ectokinases PKA, PKC and Src; these are kinases that are known to be present in the extracellular matrix. Here is demonstrated that a combination of different experimental techniques, including microscopy and electrochemistry, can be used to detect extracellular phosphorylations. Phosphorylation profiles of the three ectokinases, PKA, PKC and Src, were investigated using fluorescence microscopy and the number of phosphorylation sites per kinase was estimated using QCM. Finally, the phosphorylation of the extracellular membrane was determined using electrochemistry. Our results clearly demonstrate the extracellular phosphorylation of neuronal cells and the strength of surface electrochemical techniques in the investigation of cellular phosphorylation.

Multiphosphorylated peptides: importance, synthetic strategies, and applications for studying biological mechanisms

Advances in the synthesis of multiphosphorylated peptides and peptide libraries: tools for studying the effects of phosphorylation patterns on protein function and regulation.

Direct Assembly and Metal-Ion Binding Properties of Oxytocin Monolayer on Gold Surfaces

Peptides are very common recognition entities that are usually attached to surfaces using multistep processes. These processes require modification of the native peptides and of the substrates. Using functional groups in native peptides for their assembly on surfaces without affecting their biological activity can facilitate the preparation of biosensors. Herein, we present a simple single-step formation of native oxytocin monolayer on gold surface. These surfaces were characterized by atomic force spectroscopy, spectroscopic ellipsometry, and X-ray photoelectron spectroscopy. We took advantage of the native disulfide bridge of the oxytocin for anchoring the peptide to the Au surface, while preserving the metal-ion binding properties. Self-assembled oxytocin monolayer was used by electrochemical impedance spectroscopy for metal-ion sensing leading to subnanomolar sensitivities for zinc or copper ions.

Diversification of Device Platforms by Molecular Layers: Hybrid Sensing Platforms, Monolayer Doping, and Modeling

Inorganic materials such as semiconductors, oxides, and metals are ubiquitous in a wide range of device technologies owing to the outstanding robustness and mature processing technologies available for such materials. However, while the important contribution of inorganic materials to the advancement of device technologies has been well established for decades, organic-inorganic hybrid device systems, which merge molecular functionalities with inorganic platforms, represent a newer domain that is rapidly evolving at an increasing pace. Such devices benefit from the great versatility and flexibility of the organic building blocks merged with the robustness of the inorganic platforms. Given the overwhelming wealth of literature covering various approaches for modifying and using inorganic devices, this feature article selectively highlights some of the advances made in the context of the diversification of devices by surface chemistry. Particular attention is given to oxide-semiconductor systems and metallic surfaces modified with organic monolayers. The inorganic device components, such as semiconductors, metals, and oxides, are modified by organic monolayers, which may serve as either active, static, or sacrificial components. We portray research directions within the broader field of organic-inorganic hybrid device systems that can be viewed as specific examples of the potential of such hybrid device systems given their comprehensive capabilities of design and diversification. Monolayer doping techniques where sacrificial organic monolayers are introduced into semiconducting elements are reviewed as a specific case, together with associated requirements for nanosystems, devices, and sensors for controlling doping levels and doping profiles on the nanometric scale. Another series of examples of the flexibility provided by the marriage of organic functional monolayers and inorganic device components are represented by a new class of biosensors, where the organic layer functionality is exploited in a functioning device for sensing. Considerations for relying on oxide-terminated semiconductors rather than the pristine semiconductor material as a platform both for processing and sensing are discussed. Finally, we cover aspects related to the use of various theoretical and computational approaches to model organic-inorganic systems. The main objectives of the topics covered here are (i) to present the advances made in each respective domain and (ii) to provide a comprehensive view of the potential uses of organic monolayers and self-assembly processes in the rapidly evolving field of molecular-inorganic hybrid device platforms and processing methodologies. The directions highlighted here provide a perspective on a future, not yet fully realized, integrated approach where organic monolayers are combined with inorganic platforms in order to obtain versatile, robust, and flexible systems with enhanced capabilities.

Tailor-Made Functional Peptide Self-Assembling Nanostructures

Noncovalent interactions are the main driving force in the folding of proteins into a 3D functional structure. Motivated by the wish to reveal the mechanisms of the associated self-assembly processes, scientists are focusing on studying self-assembly processes of short protein segments (peptides). While this research has led to major advances in the understanding of biological and pathological process, only in recent years has the applicative potential of the resulting self-assembled peptide assemblies started to be explored. Here, major advances in the development of biomimetic supramolecular peptide assemblies as coatings, gels, and as electroactive materials, are highlighted. The guiding lines for the design of helical peptides, β strand peptides, as well as surface binding monolayer-forming peptides that can be utilized for a specific function are highlighted. Examples of their applications in diverse immerging applications in, e.g., ecology, biomedicine, and electronics, are described. Taking into account that, in addition to extraordinary design flexibility, these materials are naturally biocompatible and ecologically friendly, and their production is cost effective, the emergence of devices incorporating these biomimetic materials in the market is envisioned in the near future.

Oxytocin-Monolayer-Based Impedimetric Biosensor for Zinc and Copper Ions

Zinc and copper are essential metal ions for numerous biological processes. Their levels are tightly maintained in all body organs. Impairment of the Zn²⁺ to Cu²⁺ ratio in serum was found to correlate with many disease states, including immunological and inflammatory disorders. Oxytocin (OT) is a neuropeptide, and its activity is modulated by zinc and copper ion binding. Harnessing the intrinsic properties of OT is one of the attractive ways to develop valuable metal ion sensors. Here, we report for the first time an OT-based metal ion sensor prepared by immobilizing the neuropeptide onto a glassy carbon electrode. The developed impedimetric biosensor was ultrasensitive to Zn²⁺ and Cu²⁺ ions at physiological pH and not to other biologically relevant ions. Interestingly, the electrochemical impedance signal of two hemicircle systems was recorded after the attachment of OT to the surface. These two semicircles suggest two capacitive regions that result from two different domains in the OT monolayer. Moreover, the change in the charge-transfer resistance of either Zn²⁺ or Cu²⁺ was not similar in response to binding. This suggests that the metal-dependent conformational changes of OT can be translated to distinct impedimetric data. Selective masking of Zn²⁺ and Cu²⁺ was used to allow for the simultaneous determination of zinc to copper ions ratio by the OT sensor. The OT sensor was able to distinguish between healthy control and multiple sclerosis patients diluted sera samples by determining the Zn/Cu ratio similar to the state-of-the-art techniques. The OT sensor presented herein is likely to have numerous applications in biomedical research and pave the way to other types of neuropeptide-derived sensors.

Copper Induced Conformational Changes of Tripeptide Monolayer Based Impedimetric Biosensor

Copper ions play a major role in biological processes. Abnormal Cu²⁺ ions concentrations are associated with various diseases, hence, can be used as diagnostic target. Monitoring copper ion is currently performed by non-portable, expensive and complicated to use equipment. We present a label free and a highly sensitive electrochemical ion-detecting biosensor based on a Gly-Gly-His tripeptide layer that chelate with Cu²⁺ ions. The proposed sensing mechanism is that the chelation results in conformational changes in the peptide that forms a denser insulating layer that prevents RedOx species transfer to the surface. This chelation event was monitored using various electrochemical methods and surface chemistry analysis and supported by theoretical calculations. We propose a highly sensitive ion-detection biosensor that can detect Cu²⁺ ions in the pM range with high SNR parameter.

Atomic force microscopy characterization of kinase-mediated phosphorylation of a peptide monolayer

We describe the detailed microscopic changes in a peptide monolayer following kinase-mediated phosphorylation. A reversible electrochemical transformation was observed using square wave voltammetry (SWV) in the reversible cycle of peptide phosphorylation by ERK2 followed by dephosphorylation by alkaline phosphatase. A newly developed method for analyzing local roughness, measured by atomic force microscope (AFM), showed a bimodal distribution. This may indicate either a hole-formation mechanism and/or regions on the surface in which the peptide changed its conformation upon phosphorylation, resulting in increased roughness and current. Our results provide the mechanistic basis for developing biosensors for detecting kinase-mediated phosphorylation in disease.

Semiconductor technology in protein kinase research and drug discovery: sensing a revolution

Since the discovery of protein kinase activity in 1954, close to 600 kinases have been discovered that have crucial roles in cell physiology. In several pathological conditions, aberrant protein kinase activity leads to abnormal cell and tissue physiology. Therefore, protein kinase inhibitors are investigated as potential treatments for several diseases, including dementia, diabetes, cancer and autoimmune and cardiovascular disease. Modern semiconductor technology has recently been applied to accelerate the discovery of novel protein kinase inhibitors that could become the standard-of-care drugs of tomorrow. Here, we describe current techniques and novel applications of semiconductor technologies in protein kinase inhibitor drug discovery.

Revealing the role of catechol moieties in the interactions between peptides and inorganic surfaces

Catechol (1,2-dihydroxy benzene) moieties are being widely used today in new adhesive technologies. Understanding their mechanism of action is therefore of high importance for developing their applications in materials science. This paper describes a single-molecule study of the interactions between catechol-related amino acid residues and a well-defined titanium dioxide (TiO2) surface. It is the first quantified measurement of the adhesion of these residues with a well-defined TiO2 surface. Single-molecule force spectroscopy measurements with AFM determined the role of different substitutions of the catechol moiety on the aromatic ring in the adhesion to the surface. These results shed light on the nature of interactions between these residues and inorganic metal oxide surfaces. This information is important for the design and fabrication of catechol-based materials such as hydrogels, coatings, and composites. Specifically, the interaction with TiO2 is important for the development of solar cells.

Integrating proteomics with electrochemistry for identifying kinase biomarkers

We present an integrated approach for highly sensitive identification and validation of substrate-specific kinases as cancer biomarkers. Our approach combines phosphoproteomics for high throughput cancer-related biomarker discovery from patient tissues and an impedimetric kinase activity biosensor for sensitive validation. Using non-small-cell lung cancer (NSCLC) as a proof-of-concept study, label-free quantitative phosphoproteomic analysis of a pair of cancerous and its adjacent normal tissues revealed 198 phosphoproteins that are over-phosphorylated in NSCLC. Among the differentially regulated phosphorylation sites, the most significant alteration was in residue S165 in the Hepatoma Derived Growth Factor (HDGF) protein. Hence, HDGF was selected as a model system for the electrochemical studies. Further motif-based analysis of this altered phosphorylation site revealed that extracellular-signal-regulated kinase 1/2 (ERK1/2) are most likely to be the corresponding kinases. For validation of the kinase-substrate pair, densely packed peptide monolayers corresponding to the HDGF phosphorylation site were coupled to a gold electrode. Phosphorylation of the monolayer by ERK2 and dephosphorylation by alkaline phosphatase (AP) were detected by electrochemical impedance spectroscopy (EIS) and surface roughness analysis. Compared to other methods for quantification of kinase concentration, this label-free electrochemical assay offers the advantages of ultra-sensitivity as well as higher specificity for the detection of cancer-related kinase-substrate pair. With implementation of multiple kinase-substrate biomarker pairs, we expect this integrated approach to become a high throughput platform for discovery and validation of phosphorylation-mediated biomarkers.

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.