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Method Article

Fluorescence-based Monitoring of PAD4 Activity via a Pro-fluorescence Substrate Analog

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DOI:

10.3791/52114

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November 5th, 2014

 ,  , 
1Department of Chemistry, Lehigh University

In This Article

Summary

PAD4 is an enzyme responsible for the conversion of peptidyl-arginine to peptidyl-citrulline. Dysregulation of PAD4 has been implicated in a number of human diseases. A facile and high-throughput compatible fluorescence based PAD4 assay is described.

Abstract

Post-translational modifications may lead to altered protein functional states by increasing the covalent variations on the side chains of many protein substrates. The histone tails represent one of the most heavily modified stretches within all human proteins. Peptidyl-arginine deiminase 4 (PAD4) has been shown to convert arginine residues into the non-genetically encoded citrulline residue. Few assays described to date have been operationally facile with satisfactory sensitivity. Thus, the lack of adequate assays has likely contributed to the absence of potent non-covalent PAD4 inhibitors. Herein a novel fluorescence-based assay that allows for the monitoring of PAD4 activity is described. A pro-fluorescent substrate analog was designed to link PAD4 enzymatic activity to fluorescence liberation upon the addition of the protease trypsin. It was shown that the assay is compatible with high-throughput screening conditions and has a strong signal-to-noise ratio. Furthermore, the assay can also be performed with crude cell lysates containing over-expressed PAD4.

Introduction

A large number of mammalian proteins are heavily modified by the action of enzymes following the biosynthesis of proteins by the ribosome. These post-translational modifications (PTMs) can greatly increase the functional diversity of the proteome by changing the size, charge, structure, and oligomerization state (amongst other features) of proteins1-3. As a result, the change in protein structure can lead to physiological consequences, such as protein degradation, cellular differentiation, signaling, modulation in gene expression, and protein-protein interactions. While these modifications are prevalent in a large percentage of all human proteins, the terminal ends on histone proteins undergo an unusually high number of covalent modifications4. Histone proteins are a family of structural proteins that facilitate the condensation of genomic DNA. Covalent modifications of the unstructured histone tails are carried out and regulated by a series of enzymes that can catalyze the covalent modification of residues (writers), reverse the same modifications (erasers), and distinguish among the changes being imprinted onto the histone tails (readers)5-7. In fact, most of the known PTMs can be observed within this short segment of the histone including methylation, phosphorylation, acetylation, sumoylation, ubiquitination, and citrullination8.

Citrullination involves the conversion of peptidyl-arginine to the non-tRNA encoded peptidyl-citrulline (Figure 1A). The proteins, responsible for this side chain neutralization, are members of the PAD (peptide arginine deiminase) protein family, all of which are calcium-dependent enzymes.9,10. To date, five members of the PAD family have been described (PAD1, PAD2, PAD3, PAD4, and PAD6). Each member of this family appears to target distinct cellular proteins and also displays unique tissue distribution profiles. PAD4 is the only member of this protein family known to be localized within the nucleus via a nuclear localization sequence11. Accordingly, it has been shown to deiminate a number of nuclear targets, including arginine side chains on the N-terminal tails of histones H2A arginine residue 3 (H2R3), H3 (H3R2, H3R17, and H3R26) and H4 (H4R3)12,13. While each of the PAD isozymes have specific and critical physiological functions, PAD4 has received considerably more attention due to its role in a number of human processes in both diseased and healthy cells. Recently, PAD4 was shown to be a member of the pluripotency transcriptional network14. Both PAD4 expression levels and activity were shown to be elevated during reprogramming and ground-state pluripotent states in mice. By controlling the regulation of stem-cell genes, PAD4 may retain a pivotal role in cellular reprogramming efficiency. PAD4 has also been implicated in the formation of neutrophil extracellular traps, which upon binding of pathogens enable their system clearance. The hypercitrullination of histone proteins by PAD4 induces decondensation of the chromatin, which serves as the base material for the encapsulation of pathogenic bacteria by the extracellular trap, thus warding off bacterial infections15,16.

Additionally, PAD4 has been found to play an active role in a number of human diseases. It has been previously shown that aberrant expression of PAD4 is associated with the onset and severity of rheumatoid arthritis, Alzheimer’s, Parkinson’s disease, and multiple sclerosis17. In fact, the presence of anti-citrullinated protein antibodies is one of the most reliable and definitive diagnostic and prognostic biomarkers of rheumatoid arthritis18. Likewise, dysregulated PAD4 activity has recently been observed in a number of human cancers including ovarian, breast, lung, and esophageal cancers19-22. The link between PAD4 and cancer has been shown to be mediated through the ELK1 oncogene or via the p53 tumor suppressor protein22,23 and previous work has suggested that PAD4 could be a novel anti-cancer therapeutic target17,24,25. As a proof of principle study, the depletion of PAD4 via shRNA in the colorectal cancer cell line HCT116 was revealed to be sufficient for inducing apoptosis and cell cycle arrest26. A recently developed irreversible PAD4 inhibitor led to a seventy percent reduction in tumor mass in mice27. Quite remarkably, PAD4 inhibition appeared to act as a targeted therapy that resulted in selective killing of cancerous cells while sparing untransformed cells.

The use of small molecules to turn off the function of PAD4 may prove to be a powerful new strategy to target cancer cells or to augment existing cancer chemotherapeutics28. Unfortunately, a potent reversible PAD4 inhibitor has yet to be discovered. A number of covalent inhibitors have been developed using the chloro/fluoro imidine handle that mimics the arginine substrate27,29,30 and have proven to be practical tools in understanding the role of PAD4 in both healthy and diseased state cells. However, these molecules inhibit all of the active PADs with similar potency. Therefore, the need for a facile assay that reports on the activity of PAD4 is crucial. To date, PAD4 assays have been described that link the release of ammonia from the reaction to a colorimetric readout31, utilize a fluorescently labeled chloroamidine substrate analog for fluorescence polarization assay32, rely on the acid-assisted reaction between glyoxal and citrulline33, and couple the PAD4 activity to a fluorescence dequenching step34. Of these, only the covalent modifier haloacetamidine strategy has proven to be compatible with high-throughput screening platforms32,35,36. We describe a facile fluorescence based assay that reliably measures the activity of PAD4. The assay, which displays a strong signal-to-noise ratio, speed of analysis, and robustness of measurement, has the potential to discover a truly potent and selective PAD4 inhibitor.

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Protocol

1. PAD4 Transformation, Expression, and Purification

  1. For PAD4 Transformation, transform the pGEX plasmid containing PAD4 GST fusion into chemically competent E. Coli (BL21(DE3)) cells for protein expression using the following procedure. Prepare chemically competent (calcium chloride) E. Coli (BL21(DE3)) cells according to standard protocols.
    1. Thaw 50 μl of previously prepared chemically competent BL21(DE3) cells on ice and mix with 1 μl of the pGEX plasmid containing PAD4 gene in a 5 ml culture tube. Incubate the mixture on ice for 10 min while gently shaking every 2 min.
    2. Heat shock the cells by placing the mixture in a 42 °C water bath for 40 sec. Immediately place the cell-plasmid mixture back on ice for 2 min to allow the cells to recover. Add 1 ml of sterile LB broth to the mixture and place on ice for 1 min.
    3. Incubate the heat shocked cells at 37 °C, shaking at 250 rpm for 1 hr. Pipette 75 μl of the transformed cells onto an ampicillin resistant agar plate and incubate at 37 °C for 15 hr. Store plate at 4 °C.
  2. PAD4 Expression.
    1. Pick 1 colony of BL21(DE3) cells from the ampicillin agar plate and place in 5 ml of LB containing 1x ampicillin. Place in incubator and shake O/N at 37 °C.
    2. Transfer the 5 ml of LB (starter) into 1 L of sterile LB containing 1x ampicillin trihydrate (MW 403.45 g/mol). Place growth in a 37 °C shaking incubator. Monitor the OD600 of the growth. When growth reaches an OD600 of 0.3, move growth into 16 °C shaking incubator.
    3. Upon reaching an OD600 of 0.6, induce the cells with 0.3 mM isopropylthiagalactoside (IPTG, MW 238.30 g/mol). Allow cells to shake for 15 hr at 16 °C.
    4. Harvest cells by centrifugation at 4,000 x g for 20 min at 0 °C. Pour off supernatant and store pellet at -80 °C.
  3. PAD4 Purification
    1. Re-suspend the pellet containing the expressed PAD4 in BL21(DE3) cells in a buffer of 50 mM NaCl (MW 58.44 g/mol), 300 mM NaH2PO4 (MW 119.98 g/mol), 10 mM Imidazole (MW 68.077 g/mol), 0.1 mM phenylmethylsulfonyl fluoride (PMSF, MW 174.94 g/mol) and 1 mM dithiothreitol (DTT, 154.25 g/mol), pH = 8.0.
    2. Lyse the cells via sonication for 15 min at 4 °C. Following sonication, centrifuge the cell lysate at 20,000 x g for 20 min at 0 °C. Pour off and save supernatant. Batch the supernatant with glutathione (GSH) agarose beads for 30 min at RT.
    3. Drain supernatant from GST beads/column via gravity. Wash beads with 4 x 25 ml of 1x PBS (phosphate buffered saline, pH = 8.0) at RT.
    4. Elute PAD4 with 2 x 10 ml Elution buffer, 50 mM tris (hydroxymethyl) aminomethane (Tris Base, MW 121.14 g/mol), 10 mM glutathione (GSH, MW 307.32 g/mol), pH = 8.0.
    5. Concentrate PAD4 using 100k MW cut-off centrifuge tubes and centrifuge at 4,000 x g for 20 min at 4 °C. Aliquot protein into 200 μl volumes in 1.0 ml microcentrifuge tubes and store at -80 °C.

2. Preparing Stock Solutions for Buffers

  1. Weigh out sodium chloride (NaCl, MW 58.44 g/mol) and prepare a 2 M solution. Mix solution until clear.
  2. Weigh out Tris(hydroxymethyl)aminomethane (Tris Base, MW 121.14 g/mol) and prepare a 2 M solution, pH = 8.0. Mix solution until clear.
  3. Weigh out calcium chloride dihydrate (CaCl2 2H2O, MW 147.01 g/mol) and prepare a 500 mM solution. Mix solution until clear.
  4. Weigh out Tris(2-carboxyethyl)phosphine (TCEP, MW 250.19 g/mol) and prepare a 200 mM solution. Mix solution until clear and store at -20 °C.
  5. Weigh out dithiothreitol (DTT, MW 154.25 g/mol) and prepare a 1 M solution. Mix solution until clear and store at -20 °C.
  6. Prepare a 0.5% solution of Triton X-100.
  7. Weigh out ethylenediaminetetraacetic acid (EDTA, MW 292.24 g/mol) and prepare a 100 mM solution. Mix solution until clear.
  8. Weigh out Z-​Arg-​Arg-​7-​amido-​4-​methylcoumarin hydrochloride (ZRcoum, MW 621.69 g/mol) and prepare a 10 mM solution in dimethyl sulfoxide (DMSO).

3. PAD4 Assay at 37 °C

  1. From 10 mM ZRcoum stock, prepare a 125 μM solution of ZRcoum in water. This 125 μM ZRcoum solution will be Solution A.
  2. Prepare a buffer of 62.5 mM NaCl, 62.5 mM Tris, 12.5 mM CaCl2, 6.25 mM DTT, and 5 μM PAD4 (pH = 8.0). This will be Solution B.
  3. Prepare a buffer of 62.5 mM NaCl, 62.5 mM Tris, 12.5 mM CaCl2, and 6.25 mM DTT (pH = 8.0). This will be Solution C.
  4. Weigh out Trypsin, crystalline (from bovine pancreas) and prepare a 10 mg/ml in 100 mM EDTA. Mix solution until clear and store at -20 °C. This will be Solution D.
  5. Obtain a 96-well plate and designate a number of wells for controls (no PAD4) and test wells (+ PAD4).
  6. Pipette 160 μl of Solution B into test wells and pipette 160 μl of Solution C into control wells. Incubate for 15 min at 37 °C.
  7. Pipette 40 μl of Solution A into all wells and incubate at 37 °C for 45 min.
  8. Pipette 10 μl of dH2O to half of the control wells and half of the test wells. To the other half of control wells and test controls, pipette 10 μl of Solution D. Incubate for 10 min at 37 °C.
  9. Obtain a fluorescence reading on a multimodal reader with an excitation wavelength of 345 nm and an emission wavelength of 465 nm.

4. PAD4 Assay at RT

  1. From 10 mM ZRcoum stock, prepare a 50 μM solution of ZRcoum in water. This 50 μM ZRcoum solution will be Solution A.
  2. Prepare a buffer of 100 mM NaCl, 100 mM Tris, 20 mM CaCl2, 2 mM TCEP, 0.02% Triton X-100, and 8 μM PAD4 (pH = 8.0). This will be Solution B.
  3. Prepare a buffer of 100 mM NaCl, 100 mM Tris, 20 mM CaCl2, 2 mM TCEP, and 0.02% Triton X-100 (pH = 8.0). This will be Solution C.
  4. Weigh out Trypsin, crystalline (from bovine pancreas) and prepare a 10 mg/ml in 100 mM EDTA. Mix solution until clear and store at -20 °C. This will be Solution D.
  5. Obtain a 384-well plate and designate wells for controls (no PAD4) and test wells (+ PAD4).
  6. Pipette 25 μl of Solution B into test wells and pipette 25 μl of Solution C into control wells. Allow buffer with/without PAD4 to incubate in wells for 20 min at RT.
  7. Pipette 25 μl of Solution C into all wells and incubate for 45 min at RT.
  8. Pipette 10 μl of dH2O to half of the control wells and half of the test wells. To the other half of control wells and test controls, pipette 10 μl of Solution D. Incubate at RT for 10 min.
  9. Obtain a fluorescence reading on a multimodal reader with an excitation wavelength of 345 nm and an emission wavelength of 465 nm.

5. PAD4 Time Course Assays at 37 °C and RT

  1. From 10 mM ZRcoum stock, prepare a 125 μM solution of ZRcoum in water. This 125 μM ZRcoum solution will be Solution A.
  2. Prepare a buffer of 62.5 mM NaCl, 62.5 mM Tris, 12.5 mM CaCl2, 6.25 mM DTT, and 5 μM PAD4 (pH = 8.0). This will be Solution B.
  3. Weigh out Trypsin, crystalline (from bovine pancreas) and prepare a 10 mg/ml in 100 mM EDTA. Mix solution until clear and store at -20 °C. This will be Solution C.
  4. Obtain 2 96-well plates and pipet 160 μl of Solution B into # amount of wells (# of wells will depend on how many time points).
  5. Incubate one 96-well plate at 37 °C. Incubate the other 96 well plate at RT.
  6. Pipette 40 μl of Solution A into all wells in both 96-well plates and immediately pipette 10 μl of Solution C into the t = 0 min wells. Continue adding 10 μl of Solution C at specific time points until all wells have been quenched.
  7. Obtain a fluorescence reading on a multimodal reader with an excitation wavelength of 345 nm and an emission wavelength of 465 nm.

6. PAD4 Inhibition Assay at RT

  1. From 10 mM ZRcoum stock, prepare a 83 μM solution of ZRcoum in water. This 83 μM ZRcoum solution will be Solution A.
  2. Weigh out Cl-amidine (MW 424.8 g/mol) and prepare a 100 μM stock solution. This will be Solution B.
  3. Prepare a buffer of 100 mM NaCl, 100 mM Tris, 20 mM CaCl2, 2 mM TCEP, 0.02% Triton X-100, and 8 μM PAD4 (pH = 8.0). This will be Solution C.
  4. Prepare a buffer of 100 mM NaCl, 100 mM Tris, 20 mM CaCl2, 2 mM TCEP, and 0.02% Triton X-100 (pH = 8.0). This will be Solution D.
  5. Weigh out Trypsin, crystalline (from bovine pancreas) and prepare a 10 mg/ml in 100 mM EDTA. Mix solution until clear and store at -20 °C. This will be Solution E.
  6. Obtain a 384-well plate and designate wells for controls (no PAD4), test wells (+ PAD4), and inhibition wells (PAD4 + Cl-amidine).
  7. Pipette 25 μl of Solution C into test wells and pipette 25 μl of Solution D into control wells. Allow buffer with/without PAD4 to incubate in wells for 20 min at RT.
  8. Pipette 10 μl of Solution B into inhibition wells and incubate for 20 min at RTe.
  9. Pipette 15 μl of Solution A into all wells and incubate for 45 min at RT.
  10. Pipette 10 μl of Solution E to all wells. Incubate at RT for 10 min.
  11. Obtain a fluorescence reading on a multimodal reader with an excitation wavelength of 345 nm and an emission wavelength of 465 nm.

7. Crude Cell Lysate Assay at RT

  1. After harvesting cells from PAD4 1 L growth, resuspend cells in 10 ml of 50 mM Tris, 50 mM NaCl, 0.1 mM phenylmethylsulfonyl fluoride (PMSF, MW 174.94 g/mol) and 1 mM dithiothreitol (DTT, 154.25 g/mol), pH = 8.0.
  2. Lyse the cells via sonication for 15 min at 4 °C. Centrifuge the cell lysate at 20,000 x g for 20 min at 0 °C. Concentrate the clear supernatant to half the volume by centrifugation at 4,000 rpm at 4 °C using 100k MW cut-off centrifuge tubes.
  3. From 10 mM ZRcoum stock, prepare a 250 μM solution of ZRcoum in water. This 250 μM ZRcoum solution will be Solution A.
  4. Prepare a buffer of 100 mM NaCl, 100 mM Tris, 20 mM CaCl2, and 2 mM TCEP (pH = 8.0). This will be Solution B.
  5. Weigh out Trypsin, crystalline (from bovine pancreas) and prepare a 10 mg/ml in 100 mM EDTA. Mix solution until clear and store at -20 °C. This will be Solution C.
  6. Obtain a black 384-well plate and designate wells for controls (no cell lysate) and test wells (+ cell lysate).
  7. Pipette 100 μl of Solution B into all wells and pipette 60 μl of cell lysate into test wells. Incubate for 20 min at RT.
  8. Pipette 40 μl of Solution A into all wells and incubate for 45 min at RT.
  9. Pipette 10 μl of Solution C to all wells. Incubate at RT for 10 min.
  10. Obtain a fluorescence reading on multimodal reader with an excitation wavelength of 345 nm and an emission wavelength of 465 nm.

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Results

Initially, it was demonstrated that ZRcoum can report on the activity of PAD4 in a 96-well plate format. Wells were incubated with the substrate ZRcoum and in the presence/absence of PAD4. Following an incubation period of 45 min at 37 °C, the fluorescence was measured with a 340/40 – 475/15 nm filter (Figure 2A). As expected, the fluorescence levels remained low as the fluorophore within ZRcoum (or the citrullinated ZRcoum) remained in ...

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Discussion

Herein, a fluorescence based assay was successfully developed that monitors the activity of PAD4. The assay has proven to be incredibly robust in a number of high-throughput conditions and is also compatible with whole cell lysates37.

The affinity between the histone proteins and the DNA strands surrounding it loosens due the neutralization of the positive charge on the arginine side chain upon citrullination. It was envisioned that the neutralization of the arginine side-chain coul...

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Disclosures

The authors have nothing to disclose.

Acknowledgements

This work was supported by the Lehigh University Start-up Package. We thank Dr. Walter Fast for providing the GST-PAD4 plasmid for protein expression.

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Materials

List of materials used in this article
NameCompanyCatalog NumberComments
LB Broth, Miller (LURIA-BERTANI)AmrescoJ106-2KGhttp://www.amresco-inc.com
Ampicillin Trihydrate (Off-white Powder), Fisher BioReagentsFisher ScientificBP902-25 http://www.fishersci.com
Isopropylthiagalactonse (IPTG)Life Technogolies15529-019http://www.lifetechnologies.com
All Buffer Salts Fisher ScientificCan purchase from Fisher Scieintifc; VWR; Acros; Sigma-Aldrich; etc.
Protino Glutathione (GSH) agarose Machery-Nagel745500.10Store at 4 °C; http://www.mn-net.com/
Chloroamidine Cayman Chemical 10599Store at -20 °C; https://www.caymanchem.com/app/template/Home.vm
Triton X-100Sigma AldrichX100-100MLwww.sigmaaldrich.com
Corning/Nunclon MicroWell plates (96 and 384)Purchase from Corning; Sigma-Aldrich
Tecan Infinite 200 / Tecan i-control microplate reader softwarewww.tecan.com
Europium Ex. 340/40 Em. 475/15 filterhttp://www.perkinelmer.com

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Fluorescence based AssayPro fluorescent SubstrateTrypsin ActivationProtein ExpressionGST PurificationHigh throughput ScreeningFluorescence MeasurementEnzyme InhibitionCrude Lysate
Fluorescence-based Monitoring of PAD4 Activity via a Pro-fluorescence Substrate Analog
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