Colorimetric and electrochemical determination of the activity of protein kinase based on retarded particle growth due to binding of phosphorylated peptides to DNA – capped silver nanoclusters

Zr4+-mediated DNAzyme-driven DNA walker amplification strategy for electrochemical assay of protein kinase a activity and inhibition

Protein kinase A (PKA) can regulate many cellular biological processes by phosphorylation substrate peptide or protein. Sensitive detection of PKA activity is critical for the PKA-related drug discovery and disease diagnosis. A new electrochemical biosensing method was developed for detection of PKA activity based on Zr⁴⁺-mediated DNAzyme-driven DNA walker signal amplification strategy. In this strategy, the special designed substrate peptide and a thiolated methylene blue-labeled hairpin DNA (MB-hpDNA) containing a single ribonucleic acid group (rA) could be anchored on the surface of gold electrode by Au-S bond. In the presence of adenosine triphosphate (ATP) and PKA, substrate peptide was phosphorylated and linked with walker DNA (WD) via the robust phosphate-Zr⁴⁺-phosphate chemistry. The linked WD hybridized with the loop region of MB-hpDNA to form a Mn²⁺-dependent deoxynuclease (DNAzyme), which cleaved the MB-hpDNA into MB-labeled fragment releasing away from electrode surface, resulting in a dramatic decrease of electrochemical signal and providing an electrochemical sensing platform for PKA activity detection. The response signal of the developed biosensor is proportional to the logarithm of PKA concentration in the range of 0.05 U mL^-1 to 100 U mL^-1, with a detection limit of 0.017 U mL^-1 at a signal to noise ratio of 3. Furthermore, the proposed method can also be applied for the evaluation of PKA inhibition and PKA activity assay in cell samples. Therefore, the proposed biosensor shows great promise as a universal tool for diagnostics and drug discovery of PKA-related diseases.

Phosphoproteome Analysis Using Two-Dimensional Electrophoresis Coupled with Chemical Dephosphorylation

Protein phosphorylation is a reversible post-translational modification (PTM) with major regulatory roles in many cellular processes. However, the analysis of phosphoproteins remains the most challenging barrier in the prevailing proteome research. Recent technological advances in two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MS) have enabled the identification, characterization, and quantification of protein phosphorylation on a global scale. Most research on phosphoproteins with 2-DE has been conducted using phosphostains. Nevertheless, low-abundant and low-phosphorylated phosphoproteins are not necessarily detected using phosphostains and/or MS. In this study, we report a comparative analysis of 2-DE phosphoproteome profiles using Pro-Q Diamond phosphoprotein stain (Pro-Q DPS) and chemical dephosphorylation of proteins with HF-P from longissimus thoracis (LT) muscle samples of the Rubia Gallega cattle breed. We found statistically significant differences in the number of identified phosphoproteins between methods. More specifically, we found a three-fold increase in phosphoprotein detection with the HF-P method. Unlike Pro-Q DPS, phosphoprotein spots with low volume and phosphorylation rate were identified by HF-P technique. This is the first approach to assess meat phosphoproteome maps using HF-P at a global scale. The results open a new window for 2-DE gel-based phosphoproteome analysis.

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.

Dual-Functional Nanocluster Probe-Based Single-Cell Analysis of RNA Splice Variants

Differential expression of RNA splice variants among individual cells accounts for cell heterogeneity of gene expression, which plays a key role in the regulation of the immune system. However, currently available techniques face difficulties in achieving single-cell analysis of RNA splice variants with high base resolution, high spatial resolution and accurate quantification. Herein, we constructed DNA-templated dual-functional nanocluster probes to achieve in situ imaging and accurate quantification of RNA splice variants at the single-cell level. By designing ultrasmall nanocluster labeled probes to directly target the splicing junction sequence of RNA splice variants, the base recognition resolution is significantly improved. Benefit from the controllable fluorescence of nanoclusters, in situ imaging and genotyping of RNA splice variants are achieved. Due to the atom-precise nanocluster, RNA splice variants can be accurately quantified by laser ablation inductively coupled plasma mass spectrometry at the single-cell level. We further applied the probes to explore the function of MyD88 splice variants in mononuclear macrophages under immune activation. This strategy provides a novel single-cell analysis tool for studying the functional diversity of the immune system and splicing-related immune diseases.

Zr4+-mediated hybrid chain reaction and its application for highly sensitive electrochemical detection of protein kinase A

An electrochemical platform has been developed to detect protein kinase activity through the combined actions of Zr⁴⁺ mediated signal transition and hybridization chain reaction (HCR)-stimulated DNAzymes nanowires. First of all, protein kinase A (PKA) phosphorylates substrate peptides immobilized on gold electrode surface. Thereafter, the DNA1 containing 5'-phosphoryl ends is linked to the phosphorylated substrate peptide via the robust phosphate-Zr⁴⁺-phosphate linkages. By the introduction of molecular beacons (MBs), the DNA1 can open the hairpin structures of MBs through toehold mediated strand displacement (TMSDR), leading to an autonomous stem-opening process and subsequent assembly of G-quadruplex-containing DNA chains by HCR. After the addition of hemin, the formed HRP-mimicking DNAzymes can catalyze the hydroquinone-H₂O₂ system to generate amplified electrochemical signals. As expected, this method can achieve ultrahigh analytical performance with a low detection limit of 0.02U/mL and exhibit high cost-savings potential without the need for antibody, protease and labeling. Therefore, this method can serve as a new tool for the assay of protein kinase A and its inhibitor screening in the future.

Electrochemical Evaluation of Laccase Activity in Must

As laccase (produced by Botrytis cinerea) can significantly alter the properties of wine, winemakers frequently use commercially available colorimetric kits and spectrophotometers to measure the activity of this enzyme in grapes, must and wine. Although the used kits are based on electrochemically active substrates (such as syringaldazine and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), ABTS), the electrochemical determination of laccase activity as an alternative to the colorimetric determination was not thoroughly investigated up to now. Therefore, in the present work, we explored the electrochemical determination of laccase activity. Laccase activity measurements were carried out using either carbon fiber microelectrodes or screen-printed electrodes as working electrodes, either syringaldazine or ABTS as the electrochemically active laccase substrate, and either cyclic voltammetry or constant potential amperometry as the electrochemical method. The best performing approach, which combines ABTS, screen-printed gold electrodes, and constant potential amperometry, allowed identifying laccase positive must sample (i.e., must samples with › 3U/mL laccase) in about 5 min.

Fluorescence Method for the Detection of Protein Kinase Activity by Using a Zirconium-Based Metal-Organic Framework as an Affinity Probe

In cell-signaling pathways, protein kinases are critical and ubiquitous regulators. Abnormal kinase activity leads to many major diseases; therefore, simple and efficient methods for detecting protein kinases are in high demand. This study proposed a simple, rapid fluorescence-based sensor for protein kinase activity analysis, using the zirconium-based metal organic framework UiO-66 as a highly efficient affinity probe. UiO-66 has a large specific surface area, good stability, and a large number of Zr defect sites, which can efficiently identify phosphorylation sites. UiO-66 is an ideal nanoreactor that can efficiently enrich phosphorylated peptides. Under optimal experimental conditions, the increased fluorescence intensity was directly proportional to the protein kinase activity. The lower limit of detection was 0.00005 U·μL^-1. The assay could also be used for the screening of protein kinase inhibitors, could determine the activity of other kinds of kinases, and was universally applicable. This method was used for protein kinase activity detection in drug-stimulated MCF-7 cell lysates and demonstrated its potential applicability in kinase-related research.

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.