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Eskonen V, Tong-Ochoa N, Mattsson L, Miettinen M, Lastusaari M, Pulliainen AT, Kopra K, Härmä H. Single-Peptide TR-FRET Detection Platform for Cysteine-Specific Post-Translational Modifications. Anal Chem 2020; 92:13202-13210. [PMID: 32872778 PMCID: PMC7735653 DOI: 10.1021/acs.analchem.0c02370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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Post-translational
modifications (PTMs) are one of the most important
regulatory mechanisms in cells, and they play key roles in cell signaling
both in health and disease. PTM catalyzing enzymes have become significant
drug targets, and therefore, tremendous interest has been focused
on the development of broad-scale assays to monitor several different
PTMs with a single detection platform. Most of the current methodologies
suffer from low throughput or rely on antibody recognition, increasing
the assay costs, and decreasing the multifunctionality of the assay.
Thus, we have developed a sensitive time-resolved Förster resonance
energy transfer (TR-FRET) detection method for PTMs of cysteine residues
using a single-peptide approach performed in a 384-well format. In
the developed assay, the enzyme-specific biotinylated substrate peptide
is post-translationally modified at the cysteine residue, preventing
the subsequent thiol coupling with a reactive AlexaFluor 680 acceptor
dye. In the absence of enzymatic activity, increase in the TR-FRET
signal between the biotin-bound Eu(III)-labeled streptavidin donor
and the cysteine-coupled AlexaFluor 680 acceptor dye is observed.
We demonstrate the detection concept with cysteine modifying S-nitrosylation
and ADP-ribosylation reactions using a chemical nitric oxide donor
S-nitrosoglutathione and enzymatic ADP-ribosyltransferase PtxS1-subunit
of pertussis toxin, respectively. As a proof of concept, three peptide
substrates derived from the small GTPase K-Ras and the inhibitory
α-subunit of the heterotrimeric G-protein Gαi showed expected
functionality in both chemical and enzymatic assays. Measurements
yielded signal-to-background ratios of 28.7, 33.0, and 8.7 between
the modified and the nonmodified substrates for the three peptides
in the S-nitrosylation assay, 5.8 in the NAD+ hydrolysis
assay, and 6.8 in the enzymatic ADP-ribosyltransferase inhibitor dose–response
assay. The developed antibody-free assay for cysteine-modifying enzymes
provides a detection platform with low nanomolar peptide substrate
consumption, and the assay is potentially applicable to investigate
various cysteine-modifying enzymes in a high throughput compatible
format.
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Affiliation(s)
- Ville Eskonen
- Chemistry of Drug Development, Department of Chemistry, University of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Natalia Tong-Ochoa
- Chemistry of Drug Development, Department of Chemistry, University of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Leena Mattsson
- Chemistry of Drug Development, Department of Chemistry, University of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Moona Miettinen
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Mika Lastusaari
- Inorganic Materials Chemistry Research Group, Department of Chemistry, University of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Arto T Pulliainen
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Kari Kopra
- Chemistry of Drug Development, Department of Chemistry, University of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Harri Härmä
- Chemistry of Drug Development, Department of Chemistry, University of Turku, Vatselankatu 2, FI-20014 Turku, Finland
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Eskonen V, Tong-Ochoa N, Valtonen S, Kopra K, Härmä H. Thermal Dissociation Assay for Time-Resolved Fluorescence Detection of Protein Post-Translational Modifications. ACS OMEGA 2019; 4:16501-16507. [PMID: 31616828 PMCID: PMC6787904 DOI: 10.1021/acsomega.9b02134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Post-translational modifications (PTMs) of proteins provide an important mechanism for cell signal transduction control. Impaired PTM control is a key feature in multiple different disease states, and thus the enzyme-controlling PTMs have drawn attention as highly promising drug targets. Due to the importance of PTMs, various methods to monitor PTM enzyme activity have been developed, but universal high-throughput screening (HTS), a compatible method for different PTMs, remains elusive. Here, we present a homogeneous single-label thermal dissociation assay for the detection of enzymatic PTM removal. The developed method allows the use of micromolar concentration of substrate peptide, which is expected to be beneficial when monitoring enzymes with low activity and peptide binding affinity. We prove the thermal dissociation concept functionality using peptides for dephosphorylation, deacetylation, and demethylation and demonstrate the HTS-compatible flash isothermal method for PTM enzyme activity monitoring. Using specific inhibitors, we detected literature-comparable IC50 values and Z' factors from 0.61 to 0.72, proving the HTS compatibility of the thermal peptide-break technology.
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Affiliation(s)
- Ville Eskonen
- Materials Chemistry and Chemical
Analysis, Department of Chemistry, University
of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Natalia Tong-Ochoa
- Materials Chemistry and Chemical
Analysis, Department of Chemistry, University
of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Salla Valtonen
- Materials Chemistry and Chemical
Analysis, Department of Chemistry, University
of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Kari Kopra
- Materials Chemistry and Chemical
Analysis, Department of Chemistry, University
of Turku, Vatselankatu 2, FI-20014 Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical
Analysis, Department of Chemistry, University
of Turku, Vatselankatu 2, FI-20014 Turku, Finland
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Villafañez F, Gottifredi V, Soria G. Development and Optimization of a Miniaturized Western Blot-Based Screening Platform to Identify Regulators of Post-Translational Modifications. High Throughput 2019; 8:ht8020015. [PMID: 31163614 PMCID: PMC6631403 DOI: 10.3390/ht8020015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/15/2019] [Accepted: 05/28/2019] [Indexed: 12/28/2022] Open
Abstract
Post-translational modifications (PTMs) are fundamental traits of protein functionality and their study has been addressed using several approaches over the past years. However, screening methods developed to detect regulators of PTMs imply many challenges and are usually based on expensive techniques. Herein, we described the development and optimization of a western blot-based platform for identification of regulators of a specific PTM—mono-ubiquitylation of proliferating cell nuclear antigen (PCNA). This cell-based method does not require specific equipment, apart from the basic western blot (WB) devices and minor accessories, which are accessible for most research labs. The modifications introduced to the classical WB protocol allow the performance of PTM analysis from a single well of a 96-well plate with minimal sample manipulation and low intra- and inter-plate variability, making this method ideal to screen arrayed compound libraries in a 96-well format. As such, our experimental pipeline provides the proof of concept to design small screenings of PTM regulators by improving the quantitative accuracy and throughput capacity of classical western blots.
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Affiliation(s)
- Florencia Villafañez
- Centro de Investigaciones en Bioquímica Clínica e Inmunología, CIBICI-CONICET, Córdoba X5000, Argentina.
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000, Argentina.
| | - Vanesa Gottifredi
- Fundación Instituto Leloir_Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Buenos Aires C1405BWE, Argentina.
| | - Gastón Soria
- Centro de Investigaciones en Bioquímica Clínica e Inmunología, CIBICI-CONICET, Córdoba X5000, Argentina.
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000, Argentina.
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Kopra K, Tong-Ochoa N, Laine M, Eskonen V, Koskinen PJ, Härmä H. Homogeneous peptide-break assay for luminescent detection of enzymatic protein post-translational modification activity utilizing charged peptides. Anal Chim Acta 2019; 1055:126-132. [PMID: 30782363 DOI: 10.1016/j.aca.2018.12.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/18/2018] [Indexed: 11/18/2022]
Abstract
We have developed a rapid and sensitive universal peptide-based time-resolved luminescence assay for detection of enzymatic post-translational modifications (PTMs). PTMs play essential roles in intracellular signaling and cell regulation, thus providing functional protein diversity in cell. Due this, impaired PTM patterns have been linked to multiple disease states. Clear link between PTMs and pathological conditions have also driven assay development further, but still today most of the methodologies are based on single-specificity or group-specific PTM-recognition. We have previously introduced leuzine-zipper based peptide-break technology as a viable option for universal PTM detection. Here, we introduce peptide-break technology utilizing single-label homogeneous quenching resonance energy transfer (QRET) and charge-based peptide-peptide interaction. We demonstrate the functionality of the new assay concept in phosphorylation, deacetylation, and citrullination. In a comparable study between previously introduced leucine-zipper and the novel charge-based approach, we found equal PTM detection performance and sensitivity, but the peptide design for new targets is simplified with the charged peptides. The new concept allows the use of short <20 amino acid peptides without limitations rising from the leucine-zipper coiled-coil structure. Introduced methodology enables wash-free PTM detection in a 384-well plate format, using low nanomolar enzyme concentrations. Potentially, the peptide-break technique using charged peptides may be applicable for natural peptide sequences directly obtained from the target protein.
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Affiliation(s)
- Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland.
| | - Natalia Tong-Ochoa
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Mari Laine
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Ville Eskonen
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Päivi J Koskinen
- Section of Physiology and Genetics, Department of Biology, University of Turku, Vesilinnantie 5, Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
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Hewitt SH, Butler SJ. Application of lanthanide luminescence in probing enzyme activity. Chem Commun (Camb) 2018; 54:6635-6647. [PMID: 29790500 DOI: 10.1039/c8cc02824a] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Enzymes play critical roles in the regulation of cellular function and are implicated in numerous disease conditions. Reliable and practicable assays are required to study enzyme activity, to facilitate the discovery of inhibitors and activators of enzymes related to disease. In recent years, a variety of enzyme assays have been devised that utilise luminescent lanthanide(iii) complexes, taking advantage of their high detection sensitivities, long luminescence lifetimes, and line-like emission spectra that permit ratiometric and time-resolved analyses. In this Feature article, we focus on recent progress in the development of enzyme activity assays based on lanthanide(iii) luminescence, covering a variety of strategies including Ln(iii)-labelled antibodies and proteins, Ln(iii) ion encapsulation within defined peptide sequences, reactivity-based Ln(iii) probes, and discrete Ln(iii) complexes. Emerging approaches for monitoring enzyme activity are discussed, including the use of anion responsive lanthanide(iii) complexes, capable of molecular recognition and luminescence signalling of polyphosphate anions.
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Affiliation(s)
- Sarah H Hewitt
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK.
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