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Jiang S, Geng YX, Liu WJ, Wang ZY, Zhang CY. Construction of a phos-tag-directed self-assembled fluorescent magnetobiosensor for the simultaneous detection of multiple protein kinases. J Mater Chem B 2022; 10:9992-10000. [PMID: 36449302 DOI: 10.1039/d2tb01820a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein kinases play important roles in regulating various cellular processes and may function as potential diagnostic and therapeutic targets for various diseases including cancers. Herein, we construct a phos-tag-directed self-assembled fluorescent magnetobiosensor to simultaneously detect multiple protein kinases with good selectivity and high sensitivity. In the presence of protein kinases (i.e., PKA and Akt1), their substrate peptides (i.e., a FITC-labeled substrate peptide and a Cy5-labeled substrate peptide) are phosphorylated, and are then specifically recognized and captured by a biotinylated phos-tag to generate biotinylated substrate peptides for the assembly of magnetic bead (MB)-peptides-FITC/Cy5 nanostructures. After magnetic separation, the phosphorylated substrate peptides are disassembled from the MB-peptides-FITC/Cy5 nanostructures using deionized water at 80 °C, releasing FITC and Cy5 molecules. The released FITC and Cy5 molecules are detected by steady-state fluorescence measurements, with FITC indicating PKA and Cy5 indicating Akt1. This magnetobiosensor only involves one phos-tag without the requirement of radiolabeling, antibody screening, carboxypeptidase Y (CPY) cleavage, and cumbersome chemical/enzyme reactions. The introduction of magnetic separation can effectively eliminate the interference from complex real samples, generating an extremely low background signal. Moreover, this magnetobiosensor can accurately measure cellular protein kinase activities and screen inhibitors, with great potential for kinase-related biomedical research and therapeutic applications.
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Affiliation(s)
- Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
| | - Yi-Xuan Geng
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
| | - Wen-Jing Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
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Jiang S, Wang P, Li CC, Cui L, Li YY, Zhang CY. Development of a phos-tag-based fluorescent biosensor for sensitive detection of protein kinase in cancer cells. J Mater Chem B 2022; 10:3260-3267. [DOI: 10.1039/d2tb00264g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein kinase can catalyze the phosphorylation of peptides/proteins, and it is closely associated with various human diseases such as cancer, immune deficiencies, and Alzheimer’s disease. Sensitive monitoring of protein kinase...
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Wang LJ, Yang Y, Zhang CY. Phosphorylation-Directed Assembly of a Single Quantum Dot Based Nanosensor for Protein Kinase Assay. Anal Chem 2015; 87:4696-703. [DOI: 10.1021/ac504358q] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Li-juan Wang
- Single-Molecule
Detection and Imaging
Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Guangdong 518055, China
| | - Yong Yang
- Single-Molecule
Detection and Imaging
Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Guangdong 518055, China
| | - Chun-yang Zhang
- Single-Molecule
Detection and Imaging
Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Guangdong 518055, China
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Ho HP, Rathod P, Louis M, Tada CK, Rahaman S, Mark KJ, Leng J, Dana D, Kumar S, Lichterfeld M, Chang EJ. Studies on quantitative phosphopeptide analysis by matrix-assisted laser desorption/ionization mass spectrometry without label, chromatography or calibration curves. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2681-9. [PMID: 25380489 PMCID: PMC4225566 DOI: 10.1002/rcm.7063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/23/2014] [Accepted: 09/23/2014] [Indexed: 05/12/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry combined with isotope labeling methods are effective for protein and peptide quantification, but limited in their multiplexing capacity, cost-effectiveness and dynamic range. This study investigates MALDI-MS-based quantification of peptide phosphorylation without labeling, and aims to overcome the shot-to-shot variability of MALDI using a mathematical transformation and extended data acquisition times. METHODS A linear relationship between the reciprocal of phosphopeptide mole fraction and the reciprocal of phosphorylated-to-unphosphorylated signal ratio is derived, and evaluated experimentally using three separate phosphopeptide systems containing phosphorylated serine, threonine and tyrosine residues: mixtures of phosphopeptide and its des-phospho-analog with known stoichiometry measured by vacuum MALDI-linear ion trap mass spectrometry and fit to the linear model. The model is validated for quantifying in vitro phosphorylation assays with inhibition studies on Cdk2/cyclinA. RESULTS Dynamic range of picomoles to femtomoles, good accuracy (deviations of 1.5-3.0% from expected values) and reproducibility (relative standard deviation (RSD) = 4.3-6.3%) are achieved. Inhibition of cyclin-dependent kinase phosphorylation by the classical inhibitors olomoucine and r-roscovitine was evaluated and IC50 values found to be in agreement with reported literature values. These results, achieved with single-point calibration, without isotope or chromatography, compare favorably to those arrived at using isotope dilution (p > 0.5 for accuracy). CONCLUSIONS The mathematical relationship derived here can be applied to a method that we term Double Reciprocal Isotope-free Phosphopeptide Quantification (DRIP-Q), as a strategy for quantification of in vitro phosphorylation assays, the first MALDI-based, isotope- and calibration curve-free method of its type. These results also pave the way for further systematic studies investigating the effect of peptide composition and experimental conditions on quantitative, label-free MALDI.
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Affiliation(s)
- Hsin-Pin Ho
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Pratikkumar Rathod
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Marissa Louis
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Christine K. Tada
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Sherida Rahaman
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
| | - Kevin J. Mark
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
- Department of Natural Sciences, LaGuardia Community College, The City University of New York, Long Island City, NY, USA
| | - Jin Leng
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA and Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Dibyendu Dana
- Department of Chemistry and Biochemistry, Queens College, The City University of New York, Queens, NY USA
| | - Sanjai Kumar
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, Queens College, The City University of New York, Queens, NY USA
- Department of Biochemistry, The Graduate Center, The City University of New York, New York, NY, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA and Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Emmanuel J. Chang
- Department of Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Department of Chemistry, York College, The City University of New York, Jamaica, NY, USA
- Department of Biochemistry, The Graduate Center, The City University of New York, New York, NY, USA
- Address reprint requests to Emmanuel Chang; York College, 94-20 Guy R. Brewer Blvd, Jamaica, NY 11451, 718-262-3778 (phone), 718-262-2652 (fax),
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Otsubo Y, Ikeda H, Kamimoto J, Niidome T, Mori T, Katayama Y. A Rapid and Quantitative Detection of Cellular Protein Kinase Activity Based on MALDI-TOF-MS. CHEM LETT 2014. [DOI: 10.1246/cl.131227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuki Otsubo
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
| | - Hiromu Ikeda
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
| | - Junpei Kamimoto
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
| | - Takuro Niidome
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
- Center for Future Chemistry, Kyushu University
| | - Takeshi Mori
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
- Center for Future Chemistry, Kyushu University
| | - Yoshiki Katayama
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University
- Center for Future Chemistry, Kyushu University
- International Research Center for Molecular System, Kyushu University
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Zhou G, Khan F, Dai Q, Sylvester JE, Kron SJ. Photocleavable peptide-oligonucleotide conjugates for protein kinase assays by MALDI-TOF MS. MOLECULAR BIOSYSTEMS 2012; 8:2395-404. [PMID: 22772337 DOI: 10.1039/c2mb25163a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Robust methods for highly parallel, quantitative analysis of cellular protein tyrosine kinase activities may provide tools critically needed to decipher oncogenic signaling, discover new targeted drugs, diagnose cancer and monitor patients. Here, we describe proof-of-principle for a novel protein kinase assay with the potential to help overcome these challenges. MALDI-TOF mass spectrometry provides an ideal tool for label-free multiplexed analysis of peptide phosphorylation, but is poorly matched to homogeneous assays and complex samples. Thus, we conjugated a common oligonucleotide tag to multiple peptide substrates, offering efficient capture from solution-phase kinase reactions by annealing to the complementary sequence tethered to PEG-passivated superparamagnetic microparticles. To enable reversible conjugation, we developed a novel bifunctional cross-linker allowing simple and efficient preparation of photocleavable peptide-oligonucleotide conjugates. After washing away contaminants and following photorelease, MALDI-TOF analysis yielded relative phosphorylation of each peptide with high sensitivity and specificity. Validating the hybridization-mediated multiplexed kinase assay, when three peptide substrate-oligonucleotide conjugates were mixed with the tyrosine kinase c-Abl and ATP, we readily observed their differential phosphorylation yet measured a common IC(50) for the Abl kinase inhibitor imatinib. This new assay enables analysis of protein kinase activities in a multiplexed format amenable to screening inhibitors against multiple kinases in parallel, an important capability for drug discovery and predictive diagnostics.
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Affiliation(s)
- Guangchang Zhou
- Department of Molecular Genetics and Cell Biology, Gordon Center for Integrative Sciences, W522A, The University of Chicago, Chicago, IL 60637, USA
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Zhou G, Yan X, Wu D, Kron SJ. Photocleavable peptide-conjugated magnetic beads for protein kinase assays by MALDI-TOF MS. Bioconjug Chem 2011; 21:1917-24. [PMID: 20860375 DOI: 10.1021/bc1003058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides were immobilized onto superparamagnetic beads via photocleavable linkers. This enabled simple, rapid, and label-free protein kinase assays via MALDI-TOF MS detection of substrate peptide phosphorylation. Abltide, a model substrate for the Abl protein tyrosine kinase model, was coupled onto amine-terminated beads, incubated with ATP and recombinant c-Abl kinase, and released and further detected to determine phosphorylation. Abltide phosphorylation was found to depend significantly on the length and composition of linkers to the bead surface. Inserting a diblock spacer of poly(glycine) and poly(ethylene glycol) segments markedly enhanced phosphorylation. To validate the assay, the activity of two small-molecule kinase inhibitors, imatinib and dasatinib, which target the oncogenic mutant tyrosine kinase Bcr-Abl to treat chronic myeloid leukemia (CML), was tested. Examining inhibition of the purified c-Abl or Bcr-Abl in K562 CML cell extracts, IC(50) values were determined to be consistent with the literature. This simple, label-free, MALDI-based protein kinase assay can be readily adapted to allow multiplexed assays of multiple peptide substrates and/or analysis of alternative post-translational modifications as a tool for drug discovery and clinical testing.
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Affiliation(s)
- Guangchang Zhou
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois 60637, USA
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Wu D, Sylvester JE, Parker LL, Zhou G, Kron SJ. Peptide reporters of kinase activity in whole cell lysates. Biopolymers 2010; 94:475-86. [PMID: 20593469 DOI: 10.1002/bip.21401] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Kinase assays are used to screen for small-molecule inhibitors that may show promise as targeted pharmaceutical therapies. Using cell lysates instead of purified kinases provides a more accurate estimate of inhibitor sensitivity and selectivity in a biological setting. This review summarizes the range of homogeneous (solution-phase) and heterogeneous (solid-supported) formats available for using peptide substrates to monitor kinase activities in cell lysates. With a focus on heterogeneous kinase assays, the peptide substrate Abltide is used as a model to optimize presentation geometries and the modular arrangement of short sequences for kinase recognition. We present results from peptides immobilized on two- and three-dimensional surfaces such as hydrogels on 96-well plates and glass slides, and fluorescent Luminex beads. We discuss methods to increase assay sensitivity using chemifluorescent ELISAs, antibody-based recognition, and label-free mass spectrometry. Monitoring the activity of specific kinases in cell lysates presents challenges that can be overcome by manipulating peptide substrates to optimize assay conditions. In particular, signal-to-background ratios were improved by (1) adding long branched hydrophilic linkers between the substrate and the surface, (2) changing the orientation of peptides relative to the surface, and (3) including peptide ligands in cis or in trans to recruit kinases to the surface. By improving the accessibility of immobilized peptide substrates to kinases in solution, the apparent rate of phosphorylation increased and assays were more sensitive to changes in endogenous kinase activities. These strategies can be generalized to improve the reactivity of most peptide substrates used in heterogeneous kinase assays with cell lysates.
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Affiliation(s)
- Ding Wu
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
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Zhou G, Sylvester JE, Wu D, Veach DR, Kron SJ. A magnetic bead-based protein kinase assay with dual detection techniques. Anal Biochem 2010; 408:5-11. [PMID: 20807497 DOI: 10.1016/j.ab.2010.08.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 08/17/2010] [Accepted: 08/26/2010] [Indexed: 01/08/2023]
Abstract
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.
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Affiliation(s)
- Guangchang Zhou
- Ludwig Center for Metastasis Research, The University of Chicago, IL 60637, USA
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Parker L, Engel-Hall A, Drew K, Steinhardt G, Helseth DL, Jabon D, McMurry T, Angulo DS, Kron SJ. Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:518-527. [PMID: 18064576 PMCID: PMC2874747 DOI: 10.1002/jms.1342] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Despite advances in methods and instrumentation for analysis of phosphopeptides using mass spectrometry, it is still difficult to quantify the extent of phosphorylation of a substrate because of physiochemical differences between unphosphorylated and phosphorylated peptides. Here we report experiments to investigate those differences using MALDI-TOF mass spectrometry for a set of synthetic peptides by creating calibration curves of known input ratios of peptides/phosphopeptides and analyzing their resulting signal intensity ratios. These calibration curves reveal subtleties in sequence-dependent differences for relative desorption/ionization efficiencies that cannot be seen from single-point calibrations. We found that the behaviors were reproducible with a variability of 5-10% for observed phosphopeptide signal. Although these data allow us to begin addressing the issues related to modeling these properties and predicting relative signal strengths for other peptide sequences, it is clear that this behavior is highly complex and needs to be further explored.
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Affiliation(s)
- Laurie Parker
- Ludwig Center for Metastasis Research, University of Chicago, Knapp R322, 924 E. 57th Street, Chicago, IL 60637, USA.
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Kang JH, Kuramoto M, Tsuchiya A, Toita R, Asai D, Sato YT, Mori T, Niidome T, Katayama Y. Letter: correlation between phosphorylation ratios by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis and enzyme kinetics. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2008; 14:261-265. [PMID: 18756024 DOI: 10.1255/ejms.916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
To identify the correlation between the phosphorylation ratios by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-ToF MS) analysis and enzyme kinetics (Km, Vmax, and Vmax/Km) is important to understand whether MALDI-TOF MS can be applied for monitoring the properties of peptides that are substrates of protein kinases. The correlation between phosphorylation ratios and enzyme kinetics was examined using peptides for protein kinase C (PKC) and for 60 kDa phosphoprotein, encoded by the cellular sarcoma gene (c-Src). Phosphorylation ratios, analyzed by MALDI-ToF MS, showed higher correlation coefficient (r = or > +0.7) for Vmax/Km compared with that (r = or < -/+0.6) for Km or Vmax. For ion modes, a higher correlation coefficient between phosphorylation ratios and Vmax/Km was identified in the positive mode (r = or > +0.7) compared to that in the negative mode (r = or < +0.5). These results suggest that MALDI-ToF MS is a useful tool to evaluate Vmax/Km of peptides for protein kinases.
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Affiliation(s)
- Jeong-Hun Kang
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Japan.
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