Evaluation of Protein–Protein Interactions using an On-Membrane Digestion Technique

* These authors contributed equally
Biochemistry

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Summary

Here, we present a protocol for an on-membrane digestion technique for the preparation of samples for mass spectrometry. This technique facilitates the convenient analysis of protein–protein interactions.

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Obama, T., Miyazaki, T., Aiuchi, T., Miyazaki, A., Itabe, H. Evaluation of Protein–Protein Interactions using an On-Membrane Digestion Technique. J. Vis. Exp. (149), e59733, doi:10.3791/59733 (2019).

Abstract

Numerous intracellular proteins physically interact in accordance with their intracellular and extracellular circumstances. Indeed, cellular functions largely depend on intracellular protein–protein interactions. Therefore, research regarding these interactions is indispensable to facilitating the understanding of physiologic processes. Co-precipitation of associated proteins, followed by mass spectrometry (MS) analysis, enables the identification of novel protein interactions. In this study, we have provided details of the novel technique of immunoprecipitation-liquid chromatography (LC)-MS/MS analysis combined with on-membrane digestion for the analysis of protein–protein interactions. This technique is suitable for crude immunoprecipitants and can improve the throughput of proteomic analyses. Tagged recombinant proteins were precipitated using specific antibodies; next, immunoprecipitants blotted onto polyvinylidene difluoride membrane pieces were subjected to reductive alkylation. Following trypsinization, the digested protein residues were analyzed using LC-MS/MS. Using this technique, we were able to identify several candidate associated proteins. Thus, this method is convenient and useful for the characterization of novel protein–protein interactions.

Introduction

Although proteins play constitutive roles in living organisms, they are continually synthesized, processed, and degraded in the intracellular environment. Furthermore, intracellular proteins frequently physically and biochemically interact, which affects the function of one or both1,2,3. For example, the direct binding of spliceosome-associated protein homolog CWC22 with eukaryotic translation initiation factor 4A3 (eIF4A3) is necessary for the assembly of the exon junction complex4. Consistent with this, an eIF4A3 mutant that lacks affinity for CWC22 fails to facilitate exon junction complex-driven mRNA splicing4. Thus, the study of protein interactions is crucial for the precise understanding of physiologic regulation as well as of cellular functions.

Recent advances in mass spectrometry (MS) have been applied to the comprehensive analysis of protein-protein interactions. For instance, the co-precipitation of endogenous proteins or exogenously introduced tagged proteins with their associated proteins, followed by MS analysis, enables the identification of novel protein interactions5. However, one major bottleneck of MS/MS analysis is poor recovery from tryptic digests of protein samples. For conducting proteomic analyses on cell lysates, in-gel and on-membrane digestion techniques are generally employed to prepare MS/MS samples. We have previously compared an in-gel digestion procedure with an on-membrane digestion technique6, and showed that the latter was associated with better sequence coverage. Polyvinylidene difluoride (PVDF) membrane may be suitable for this purpose because it is mechanically robust and resistant to high concentrations of organic solvents7,8, permitting the enzymatic digestion of immobilized proteins in the presence of 80% acetonitrile9. Furthermore, immobilization on a membrane can induce conformational changes in target proteins, leading to improvements in tryptic digestion efficiency10. Accordingly, in this article, we have described the use of immunoprecipitation-LC/MS/MS analysis of protein interactions using an on-membrane digestion technique. This simple method facilitates the convenient analysis of protein-protein interactions even in non-specialist laboratories.

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Protocol

1. Immunoprecipitation

NOTE: We used non-sodium dodecyl sulfate (SDS) lysis buffer and citrate elution, as described in the following sections. However, the use of an alternative in-house immunoprecipitation technique may be also applicable for preparing LC-MS/MS samples.

  1. Transfect cultured cells with vectors encoding an epitope tag alone or a fusion protein. For acquiring representative data, transfer J774 cells (1 x 106) with vectors encoding green fluorescent protein (GFP) alone or GFP-fused Capn6 (calpain-6 gene) using cationic liposomes.
  2. Conjugate antibody to magnetic beads.
    1. For this purpose, mix anti-GFP antibody (2 μL/reaction) with magnetic beads (25 μL/reaction) in 500 µL of citrate phosphate buffer (24.5 mM citric acid, 51.7 mM dibasic sodium phosphate; pH 5.0) in a 1.5 mL test tube.
    2. Rotate the mixture at 50 rpm for 1 h at room temperature. Then, wash the IgG-conjugated beads three times with citrate phosphate buffer containing 0.1% Polyoxyethylene (20) sorbitan monolaurate.
  3. Lyse the transfected cells using an appropriate lysis buffer. For acquiring representative data, lyse the transfected cells for 30 min on ice in 400 µL of lysis buffer (50 mM Tris-HCl; pH 7.5, 120 mM NaCl, 0.5% poly(oxyethelene) octylphenyl ether) containing 40 μmol/L phenylmethylsulfonyl fluoride, 50 μg/mL leupeptin, 50 μg/mL aprotinin, 200 μmol/L sodium orthovanadate, and 1 mM ethylene glycol tetraacetic acid (EGTA) in 1.5 mL test tubes 24 h after transfection.
  4. Clear the lysate by centrifuging at 15,000 x g for 5 min and collect the supernatant.
  5. Preclear the lysate. Add unlabeled magnetic beads (25 μL/reaction) in a 1.5 mL-test tube. Wash the beads three times with 500 µL of citrate phosphate buffer. After the removal of citrate phosphate buffer in final wash, add the cell lysate over the magnetic beads. Rotate the mixture using rotator at 50 rpm for 30 min at room temperature.
  6. Place the test tube on a magnetic stand for 5 min for magnetic separation, and collect the cell lysate. Use of the magnetic stand designated by the manufacturer is recommended.
  7. Bind the target proteins to the conjugated beads. Place the immunoglobulin (Ig)G-conjugated beads on a magnetic stand for 5 min for magnetic separation, discard the citrate buffer, and then add the cell lysate to the separated beads.
  8. Rotate the mixture at 50 rpm for 1 h at room temperature.
  9. Separate the target proteins from free non-target proteins. Wash the beads three times using 500 µL of citrate phosphate buffer containing 0.1% Polyoxyethylene (20) sorbitan monolaurate. After the final wash, add 30 µL of citrate buffer (pH 2–3), and incubate for 5 min at room temperature to elute the target proteins.
    NOTE: If recovery from the immunoprecipitation is insufficient, the use of alternative epitope tags, such as FLAG or HIS, may improve the efficiency. If the efficiency of the elution is insufficient, the use of other eluants, such as an SDS-based solution, may improve the efficiency.

2. On-membrane digestion of proteins

NOTE: Using protein-free materials and equipment is necessary to avoid contamination with exogenous proteins. In addition, it is recommended that the operator wear a surgical mask and gloves to avoid contamination by human proteins.

  1. Cut PVDF membranes into 3 mm x 3 mm pieces using surgical scissors that have been wiped with methanol and dried immediately prior to use.
  2. Add 2–5 µL of ethanol on the pieces of PVDF membrane on clean aluminum foil.
  3. Before they dry completely, add the eluant (2–5 µL each, 4–6 pieces per sample) onto the hydrophilic PVDF membranes, and then air-dry the membranes until the membrane surface becomes matte. Dried membranes can be stored at 4 °C.
  4. Transfer the all membranes into 1.5 mL plastic tubes, add 20–30 µL of ethanol to make the membranes hydrophilic, and then remove the ethanol using a pipette.
  5. Before the membrane dries out completely, add 200 µL of dithiothreitol (DTT)-based reaction solution (80 mM NH4HCO3, 10 mM DTT, and 20% acetonitrile) and incubate it at 56 °C for 1 h.
  6. Replace the reaction solution with 300 µL of iodoacetamide solution (80 mM NH4HCO3, 55 mM iodoacetamide, and 20% acetonitrile), and incubate for 45 min at room temperature in the dark.
  7. Wash the membranes twice with 1 mL of distilled water and once with 1 mL of 2% acetonitrile by vortex mixing for >10 s.
  8. Dissolve lyophilized MS-grade trypsin (Table of Materials) directly in the reaction solution (30 mM NH4HCO3 containing 70% acetonitrile). Add 100 µL of the reaction solution containing 1 μg of trypsin (Table of Materials) (30 mM NH4HCO3 containing 70% acetonitrile) and incubate at 37 °C overnight.
  9. Transfer the reaction solution containing the tryptic digests into a clean 1.5 mL test tube using a pipette.
  10. Add 100 µL of wash solution (70% acetonitrile/1% trifluoroacetic acid) to the membrane and incubate it at 60 °C for 2 h. Collect the wash solution and mix it with the reaction solution. Add another 100 μL of wash solution to the membrane and sonicate it for 10 min. Then collect the wash solution and mix with the reaction solution.
  11. Cover the test tube with a piece of laboratory film and make a couple of small holes with a needle. Dry the solution using a vacuum concentrator.
  12. Dissolve the residue in 10 µL of 0.2% formic acid. After centrifugation (12,000 × g, 3 min at room temperature), transfer the supernatant into a sample tube.
    NOTE: The washes are the critical steps of this section. During on-membrane protein digestion, the washing of the membranes containing the immobilized proteins after reduction and alkylation with distilled water, followed by 2% acetonitrile, for more than 10 sec each, is critical for the removal of the reagents.

3. LC–electrospray ionization (ESI)-MS/MS analysis

  1. Activate an ESI-MS/MS instrument (Table of Materials) coupled with a nano-LC HPLC system (Table of Materials). Link a pre-column (Table of Materials) and an analytical column (Table of Materials).
  2. Prior to the analysis, calibrate the mass spectrometer using tryptic digests of bovine serum albumin dissolved in 0.2% formic acid, which provides standard peptides.
  3. Analyze the samples using positive ion mode and a mass range of 400–1,250 m/z; then acquire up to 10 MS/MS spectra (100 ms each) with a mass range of 100–1,600 m/z and a linear gradient of 2%–80% acetonitrile and 0.2% formic acid for 80 min at a flow rate of 300 nL/min.
  4. Analyze the output data using software for protein identification (Table of Materials) to identify the candidate associated proteins. For the positive identification of a candidate protein, detection of at least one high-fidelity peptide fragment (> 95% fidelity) is required.
  5. Omit the proteins that are similarly precipitated in GFP-expressing lysates (transfection of vector expressing a GFP tag alone) from the list of candidate proteins.
    NOTE: If few proteins are identified in the database analysis, modification of the MS/MS acquisition conditions (e.g., changing the time from 100 ms each to 50 ms each) may increase the number of proteins identified.

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Representative Results

By means of the above-described procedure, immunoprecipitants were analyzed using LC-MS/MS (Figure 1). After the exclusion of exogenously derived proteins (proteins from other species and IgGs), 17 proteins were identified in calpain-6-associated immunoprecipitants (Table 1) and 15 proteins were identified in GFP-associated immunoprecipitants (Table 2). Of the calpain-6 and GFP-associated proteins, 11 were identified in both immunoprecipitants (Figure 2). Once these and calpain-6 itself were excluded, five candidate calpain-6-associated proteins remained: complement C1q subcomponent subunit C, keratin type II cytoskeletal 8, IgE-binding protein, ADP/ATP translocase 1, and ubiquitin.

Figure 1
Figure 1. Scheme for the on-membrane digestion technique
Cell lysates were precipitated using magnetic beads conjugated with specific antibodies. The eluant from the immunoprecipitation was blotted onto pieces of PVDF membrane. Subsequently, the membranes were treated with reagents for reductive alkylation, and then incubated with trypsin. The reaction solution was then analyzed using LC-MS/MS. Please click here to view a larger version of this figure.

Figure 2
Figure 2. Overview of the representative data
Seventeen proteins were identified in the calpain-6-associated immunoprecipitant and 15 proteins were detected in the GFP-associated immunoprecipitant. Of these, 11 proteins were identified in both immunoprecipitants. Please click here to view a larger version of this figure.

Name Accession Peptides(95%) %Cov
Actin, cytoplasmic 2 sp|P63260|ACTG 5 18.4
Actin, aortic smooth muscle sp|P62737|ACTA 5 18.57
Actin, cytoplasmic 1 sp|P60710|ACTB 5 18.41
Actin, alpha skeletal muscle sp|P68134|ACTS 5 13.53
Actin, alpha cardiac muscle 1 sp|P68033|ACTC 5 13.53
Actin, gamma-enteric smooth muscle sp|P63268|ACTH 5 13.56
Elongation factor 1-alpha 1 sp|P10126|EF1A1 3 33.33
Elongation factor 1-alpha 2 sp|P62631|EF1A2 3 16.2
Keratin, type II cytoskeletal 8 sp|P11679|K2C8 3 22.65
Complement C1q subcomponent subunit C sp|Q02105|C1QC 2 8.94
IgE-binding protein sp|P03975|IGEB 2 21.72
Calpain-6 sp|O35646|CAN6 1 15.91
ADP/ATP translocase 2 sp|P51881|ADT2 1 27.52
ADP/ATP translocase 1 sp|P48962|ADT1 1 19.13
Ubiquitin sp|P62991|UBIQ 1 40.79
Runt-related transcription factor 3 sp|Q64131|RUNX3 1 15.89
Isoform 2 of Runt-related transcription factor 3 sp|Q64131-2|RUNX3 1 13
“Peptides (95%)” indicates the number of peptides identified with a fidelity score > 95% in the MS/MS data. “%Cov” refers to the percentage of the amino acid residues identified in all the peptides (with > 95% fidelity) relative to the total number of amino acid residues constituting the corresponding protein. To improve clarity, exogenous proteins (proteins from other species and IgGs), ribosomal proteins, and histones are not shown.

Table 1. Calpain-6-associated proteins

Name Accession Peptides(95%) %Cov
Elongation factor 1-alpha 1 sp|P10126|EF1A1 3 24.24
Elongation factor 1-alpha 2 sp|P62631|EF1A2 3 24.41
Actin, alpha skeletal muscle sp|P68134|ACTS 3 13.53
Actin, alpha cardiac muscle 1 sp|P68033|ACTC 3 13.53
Actin, gamma-enteric smooth muscle sp|P63268|ACTH 3 13.56
Actin, cytoplasmic 2 sp|P63260|ACTG 3 13.6
Actin, aortic smooth muscle sp|P62737|ACTA 3 13.53
Actin, cytoplasmic 1 sp|P60710|ACTB 3 13.6
ADP/ATP translocase 2 sp|P51881|ADT2 2 25.5
rRNA 2'-O-methyltransferase fibrillarin sp|P35550|FBRL 2 14.37
Prohibitin sp|P67778|PHB 1 9.19
Heterogeneous nuclear ribonucleoprotein U sp|Q8VEK3|HNRPU 1 10.63
Runt-related transcription factor 3 sp|Q64131|RUNX3 1 39.12
Isoform 2 of Runt-related transcription factor 3 sp|Q64131-2|RUNX3 1 26
Elongation factor 1-gamma sp|Q9D8N0|EF1G 1 12.36
“Peptides (95%)” indicates the number of peptides identified with a fidelity score > 95% in the MS/MS data. “%Cov” refers to the percentage of the amino acid residues identified in all the peptides (with > 95% fidelity) relative to the total number of amino acid residues constituting the corresponding protein. To improve clarity, exogenous proteins (proteins from other species and IgGs), ribosomal proteins, and histones are not shown.

Table 2. GFP-associated proteins

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Discussion

We have previously described an analysis of the oxidative modifications of apolipoprotein B-100 in oxidized low-density lipoprotein using LC-MS/MS preceded by an on-membrane digestion technique6. In the present study, we combined this technique with immunoprecipitation and have identified several calpain-6-associated proteins. This novel technique represents a convenient method of screening for candidate associated proteins. Calpain-6 is a non-proteolytic member of the calpain proteolytic family11 that has reportedly modify cellular functions through its protein-protein interactions12,13. Using an on-membrane digestion technique, we have previously identified other calpain-6-associated proteins employing a different MS set-up12. Therefore, we recommend testing several MS conditions for maximizing the number of candidates identified. For the same reason, the evaluation of the immunoprecipitation conditions, such as the types of epitope tag, detergent, and elution solution used, is important for obtaining optimal outputs.

In the present study, we identified 11 proteins in both calpain-6- and GFP-associated immunoprecipitants. The majority of the overlapping proteins were actin isotypes, and contamination with actin cytoskeletal proteins is common in the analyses of cellular protein-protein interactions because the expression levels of these proteins are very high. These candidates should therefore be omitted from further analysis. In addition, elongation factors were detected in both immunoprecipitants. They regulate the speed and fidelity of protein synthesis and affect protein-folding14, and, therefore, the co-immunoprecipitation of elongation factors is not surprising. These proteins should also be omitted from further evaluation.

Immunoprecipitants can be subjected to reductive alkylation and enzymatic digestion directly in the elution solution15, and this in-solution digestion method may also be applied for the preparation of samples for MS/MS. However, we consider the use of on-membrane digestion to have considerable advantages over in-solution digestion. PVDF membrane serves as a scaffold for the subsequent reductive alkylation and enzymatic digestion, meaning that the solvents required for these processes can be replaced easily. Consequently, it is possible to use a variety of elution solutions for immunoprecipitation. Conversely, for in-solution digestion, it may be challenging to use SDS-based or low pH elution solutions because protease activity may be limited under such conditions. Furthermore, immobilization of the target proteins can make the subsequent washing procedure easier. Hence, on-membrane digestion is highly suitable for the preparation of immunoprecipitants for MS/MS analysis. A limited number of proteases may be appropriate for this protocol. Thus far, only Lysyl-C, other than trypsin, is reportedly active in the presence of up to 80% acetonitrile6,9,10,15.

Our on-membrane digestion technique is suitable for the identification of proteins in a small quantity of immunoprecipitant with a highly sensitive detection limit. However, it should be remembered that the detection efficiency for a target protein depends on the amount present. Proteins that are present in larger quantities are preferentially detected and they may prevent other proteins present in smaller amounts being detected by MS. Nevertheless, under normal circumstances numerous proteins are detected using LC-MS/MS analysis, and other assays must be used for clarify which of the candidate proteins are of appropriate biologic significance.

In this study, we have evaluated an on-membrane digestion technique for the analysis of immunoprecipitants. Such a convenient and comprehensive method for the analysis of protein-protein interactions should be widely applicable to improve the throughput of future proteomic analyses.

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Disclosures

The authors have nothing to disclose.

Acknowledgments

This study was supported in part by Japan Society for the Promotion of Science KAKENHI Grant Number 17K09869 (to AM), Japan Society for the Promotion of Science KAKENHI Grant Number 15K09418 (to TM), a research grant from Kanehara Ichiro Medical Science Foundation and a research grant from Suzuken Memorial Foundation (all to TM).

Materials

Name Company Catalog Number Comments
Acetonitrile Wako 014-00386
Citric acid Wako 030-05525
DiNA KYA Tech Co. nanoflow high-performance liquid chromatography
DiNa AI KYA Tech Co. nanoflow high-performance liquid chromatography equipped with autosampler
DTT Nacalai tesque 14112-94
Dynabeads protein G Thermo Fisher Scientific 10003D
Formic acid Wako 066-00461
HiQ Sil C18W-3 KYA Tech Co. E03-100-100 0.10mmID * 100mmL
Iodoacetamide Wako 095-02151
Lipofectamine 3000 Thermo Fisher Scientific L3000008
Living Colors A.v. Monoclonal Antibody (JL-8) Clontech 632380
NaCl Wako 191-01665
NH4HCO3 Wako 018-21742
Nonidet P-40 Sigma N6507 poly(oxyethelene) octylphenyl ether (n=9)
peptide standard KYA Tech Co. tBSA-04 tryptic digests of bovine serum albumin
PP vial KYA Tech Co. 03100S plastic sample tube
Protease inhibitor cooctail Sigma P8465
ProteinPilot software Sciex 5034057 software for protein identification
Sequencing Grade Modified Trypsin Promega V5111 trypsin
Sodium orthovanadate Sigma S6508
Sodium phosphate dibasic dihydrate Sigma 71643
TFA Wako 206-10731
trap column KYA Tech Co. A03-05-001 0.5mmID * 1mmL
TripleTOF 5600 system Sciex 4466015 Hybrid quadrupole time-of-flight tandem mass spectrometer
Tris Wako 207-06275
Tween-20 Wako 160-21211

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References

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  2. Miyazaki, T., Miyazaki, A. Defective protein catabolism in atherosclerotic vascular inflammation. Frontiers in Cardiovascular Medicine. 4, 79 (2017).
  3. Miyazaki, T., Miyazaki, A. Dysregulation of calpain proteolytic systems underlies degenerative vascular disorders. Journal of Atherosclerosis and Thrombosis. 25, (1), 1-15 (2018).
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  5. Turriziani, B., von Kriegsheim, A., Pennington, S. R. Protein-protein interaction detection via mass spectrometry-based proteomics. Advances in Experimental Medicine and Biology. 919, 383-396 (2016).
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  7. Matsudaira, P. Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. The Journal of Biological Chemistry. 262, (21), 10035-10038 (1987).
  8. Yamaguchi, M., et al. High-throughput method for N-terminal sequencing of proteins by MALDI mass spectrometry. Analytical Chemistry. 77, (2), 645-651 (2005).
  9. Iwamatsu, A. S-carboxymethylation of proteins transferred onto polyvinylidene difluoride membranes followed by in situ protease digestion and amino acid microsequencing. Electrophoresis. 13, (3), 142-147 (1992).
  10. Strader, M. B., Tabb, D. L., Hervey, W. J., Pan, C., Hurst, G. B. Efficient and specific trypsin digestion of microgram to nanogram quantities of proteins in organic-aqueous solvent systems. Analytical Chemistry. 78, (1), 125-134 (2006).
  11. Miyazaki, T., Miyazaki, A. Emerging roles of calpain proteolytic systems in macrophage cholesterol handling. Cellular and Molecular Life Sciences. 74, (16), 3011-3021 (2017).
  12. Miyazaki, T., et al. Calpain-6 confers atherogenicity to macrophages by dysregulating pre-mRNA splicing. Journal of Clinical Investigation. 126, (9), 3417-3432 (2016).
  13. Tonami, K., et al. Calpain-6, a microtubule-stabilizing protein, regulates Rac1 activity and cell motility through interaction with GEF-H1. Journal of Cell Science. 124, (Pt 8), 1214-1223 (2011).
  14. Rodnina, M. V., Wintermeyer, W. Protein elongation, co-translational folding and targeting. Journal of Molecular Biology. 428, (10 Pt B), 2165-2185 (2016).
  15. Bunai, K., et al. Proteomic analysis of acrylamide gel separated proteins immobilized on polyvinylidene difluoride membranes following proteolytic digestion in the presence of 80% acetonitrile. Proteomics. 3, (9), 1738-1749 (2003).

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