Real-time monitoring of dephosphorylation process of phosphopeptide and rapid assay of PTP1B activity based on a 100 MHz QCM biosensing platform

The misregulation of protein phosphatases is a key factor in the development of many human diseases, notably cancers. Here, based on a 100 MHz quartz crystal microbalance (QCM) biosensing platform, the dephosphorylation process of phosphopeptide (P-peptide) caused by protein tyrosine phosphatase 1B (PTP1B) was monitored in real time for the first time and PTP1B activity was assayed rapidly and sensitively. The QCM chip, coated with a gold (Au) film, was used to immobilized thiol-labeled single-stranded 5'-phosphate-DNAs (P-DNA) through Au-S bond. The P-peptide, specific to PTP1B, was then connected to the P-DNA via chelation between Zr4+ and phosphate groups. When PTP1B was injected into the QCM flow cell where the P-peptide/Zr4+/MCH/P-DNA/Au chip was placed, the P-peptide was dephosphorylated and released from the Au chip surface, resulting in an increase in the frequency of the QCM Au chip. This allowed the real-time monitoring of the P-peptide dephosphorylation process and sensitive detection of PTP1B activity within 6 min with a linear detection range of 0.01-100 pM and a detection limit of 0.008 pM. In addition, the maximum inhibitory ratios of inhibitors were evaluated using this proposed 100 MHz QCM biosensor. The developed 100 MHz QCM biosensing platform shows immense potential for early diagnosis of diseases related to protein phosphatases and the development of drugs targeting protein phosphatases.

High-Frequency Quartz Crystal Microbalance and Dual-Signaling Electrochemical Ratiometric Assays of PTP1B Activity Based on COF@Au@Fc Hybrids

The abnormal expression of protein tyrosine phosphatase 1B (PTP1B) is highly related to several serious human diseases. Therefore, an accurate PTP1B activity assay is beneficial to the diagnosis and treatment of these diseases. In this study, a dual-mode biosensing platform that enabled the sensitive and accurate assay of PTP1B activity was constructed based on the high-frequency (100 MHz) quartz crystal microbalance (QCM) and dual-signaling electrochemical (EC) ratiometric strategy. Covalent-organic framework@gold nanoparticles@ferrocene@single-strand DNA (COF@Au@Fc-S0) was introduced onto the QCM Au chip via the chelation between Zr4+ and phosphate groups (phosphate group of the phosphopeptide (P-peptide) on the QCM Au chip and the phosphate group of thiol-labeled single-stranded DNA (S0) on COF@Au@Fc-S0) and used as a signal reporter. When PTP1B was present, the dephosphorylation of the P-peptide led to the release of COF@Au@Fc-S0 from the QCM Au chip, resulting in an increase in the frequency of the QCM. Meanwhile, the released COF@Au@Fc-S0 hybridized with thiol/methylene blue (MB)-labeled hairpin DNA (S1-MB) on the Au NPs-modified indium-tin oxide (ITO) electrode. This caused MB to be far away from the electrode surface and Fc to be close to the electrode, leading to a decrease in the oxidation peak current of MB and an increase in the oxidation peak current of Fc. Thus, PTP1B-induced dephosphorylation of the P-peptide was monitored in real time by QCM, and PTP1B activity was detected sensitively and reliably using this innovative QCM-EC dual-mode sensing platform with an ultralow detection limit. This platform is anticipated to serve as a robust tool for the analysis of protein phosphatase activity and the discovery of drugs targeting protein phosphatase.

Label-Free Multimetric Measurement of Molecular Binding Kinetics by Electrical Modulation of a Flexible Nanobiolayer

Most label-free techniques rely on measuring refractive index or mass change on the sensor surface. Thus, it is challenging for them to measure small molecules or enzymatic processes that only induce a minor mass change on the analyte molecules. Here, we have developed a technique by combining Surface Plasmon Resonance sensing with an Oscillating Biomolecule Layer approach (SPR-OBL) to enhance the sensitivity of traditional SPR. In addition to the inherent mass sensitivity, SPR-OBL is also sensitive to the charge and conformational change of the analyte; hence it overcomes the mass limit and is able to detect small molecules. We show that the multimetric SPR-OBL measurement allows for sensing any changes regarding mass, charge, and conformation, which expands the detection capability of SPR.

Novel fluorescence biosensor custom-made for protein tyrosine phosphatase 1B detection based on titanium dioxide-decorated single-walled carbon nanohorn nanocomposite

This paper presents a new fluorescent approach for the detection of protein tyrosine phosphatase 1B (PTP1B) based on titanium dioxide-decorated single-wall carbon nanohorns (TiO₂-SWCNHs). The novel TiO₂-SWCNHs nanocomposite was synthesized and characterized for the first time and the phosphorylated peptide as the substrate of PTP1B was designed. Properties of SWCNHs and TiO₂ were combined by growing nano-sized TiO₂ particles on SWCNHs, resulting in TiO₂-SWCNHs. TiO₂ provides SWCNHs a large adsorption surface area and can specifically bind to phosphopeptide substrate. TiO₂-SWCNHs effectively quenched the fluorescence of the phosphorylated peptide substrate labeled by the fluorophore, and the system had a low fluorescence background. In the presence of PTP1B, dephosphorylation of the peptide occurred owing to the reaction between PTP1B and the peptide, causing the separation of the dye-labeled peptide from TiO₂-SWCNHs, which resulted in fluorescence enhancement of the reaction system. Thus, a simple and rapid strategy for the detection of PTP1B activity was developed, with a detection limit of 0.01 ng/mL and linear range of 0-10 ng/mL. The system can be used to detect PTP1B in serum using the standard addition method. This system provides a new approach for screening PTP1B inhibitors.

Bifunctional Magnetic Fe3O4@Cu2O@TiO2 Nanosphere-Mediated Dual-Mode Assay of PTP1B Activity Based on Photocurrent Polarity Switching and Nanozyme-Engineered Biocatalytic Precipitation Strategies

Dysregulation of protein phosphatases is associated with the progression of various human diseases and cancers. Herein, a photoelectrochemical (PEC)-quartz crystal microbalance (QCM) dual-mode sensing platform was developed for protein tyrosine phosphatase 1B (PTP1B) activity assay based on bifunctional magnetic Fe₃O₄@Cu₂O@TiO₂ nanosphere-mediated PEC photocurrent polarity switching and QCM signal amplification strategies. The PTP1B-specific phosphopeptide (P-peptide) with a cysteine end was designed and immobilized onto the QCM Au chip via the Au-S bond. Subsequently, the Fe₃O₄@Cu₂O@TiO₂ nanosphere was connected to the P-peptide via the specific interaction between the phosphate group on the P-peptide and TiO₂. After incubation with PTP1B, the dephosphorylation of the P-peptide occurred, causing some Fe₃O₄@Cu₂O@TiO₂ nanospheres to be released from the chip surface. The released magnetic Fe₃O₄@Cu₂O@TiO₂ nanospheres (labeled as R-Fe₃O₄@Cu₂O@TiO₂) were quickly separated via magnetic separation technology and attached to the Bi₂S₃-decorated magnetic indium-tin oxide (Bi₂S₃/MITO) electrode by magnetic force, inducing the switch of the photocurrent polarity of the electrode from anodic current (the Bi₂S₃/MITO electrode) to cathodic current (the R-Fe₃O₄@Cu₂O@TiO₂/Bi₂S₃/MITO electrode). Also, the nondephosphorylated P-peptide linked Fe₃O₄@Cu₂O@TiO₂ nanospheres as nanozymes with horseradish peroxidase activity to catalyze the formation of precipitation on the surface of the Au chip, leading to a frequency change of the QCM. Thus, the proposed PEC-QCM dual-mode sensing platform achieved accurate and reliable assay of PTP1B activity because of the different mechanisms and independent signal transductions. In addition, this dual-mode sensing platform can be easily extended for other protein phosphatase activity analysis and shows great potential in the early diagnosis of the protein phosphatase-related diseases and the protein phosphatase-targeted drug discovery.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

Molecular dynamics simulation studies on the specific regulation of PTPN18 to the HER2 phospho-peptides

The specific regulation of PTPN18 protein to three HER2 phospho-peptides has been studied by molecular dynamics simulations and free energy calculations. The results revealed that the three HER2 phospho-peptides binding to the PTPN18 catalytic domain is energetically favorable due to substrate specificity of PTPN18, and moreover, the PTPN18 protein have significantly higher affinity to pY1248 peptide (-45.22 kcal/mol) than that of pY1112 (-25.3 kcal/mol) and pY1196 (-31.86 kcal/mol) peptides. Further, the binding of HER2 phospho-peptides to PTPN18 have also caused the closure of WPD-loop with the decrease of the centroid distances between the P-loop and the WPD loop. The WPD-loop closure of PTPN18 relates directly to the new hydrogen bond and hydrophobic interaction formations between the residues Tyr62, Asp64, Val65, Ala231, Arg235, and Ala273 in PTPN18 and Tyr(PO3) in the HER2 phospho-peptides, which suggests that these key residues would contribute to the specific regulation of PTPN18 to the substrates. The correlation analysis revealed the allosteric communication networks from the pY binding loop to the WPD loop through the structural change and the residue interactions in PTPN18. These results will be helpful to understand the specific regulation through the allosteric communication network in the PTPN18 catalytic domain.