Pierce qIP Assay: A Novel, HTS-compatible Protein-Protein Interaction Assay System

A cell-based, quantitative co-immunoprecipitation method for protein interaction analysis involving a sensitive luciferase assay strategy

by Jae Choi, Ph.D.; Kate Wolf, B.S.1; Janaki Narahari, Ph.D.; Georgyi Los, Ph.D.; Atul Deshpande, Ph.D.; Brian Webb, Ph.D.; Peter Bell, Ph.D. - 05/02/14

The study of protein interaction networks is an important approach to understanding cell biology and represents a growing interest in drug discovery. However, developing sensitive, quantitative, and high-throughput screening (HTS) methods that permit direct measurements of protein-protein interactions has proven challenging. The traditional co-immunoprecipitation approach is not practical for HTS as it requires time-consuming sample processing and detection, including Western blotting.

We have developed the Thermo Scientific™ Pierce™ Quantitative Immunoprecipitation (qIP) System to measure interactions between pairs of recombinant proteins expressed in mammalian cells. The highly sensitive luciferase assay method eliminates the need for gel electrophoresis and Western blotting; furthermore, the technique is amenable to HTS. Here we briefly describe the Pierce qIP Assay System and then demonstrate its utility by presenting results from several example experiments, including  one performed as an HTS compatible assay in 384-well plates which yielded high signal-to-noise ratios and Z’ values.

The Pierce qIP assay depends upon a small, bright luciferase, Thermo Scientific™ TurboLuc™ (Tluc) Luciferase, which is fused to a protein of interest and transiently co-expressed with an epitope-tagged (e.g., HA or Myc tag) protein in mammalian cells. Cells expressing both proteins are lysed, and the interaction (HA-protein X with Tluc-protein Y) is captured onto a solid support, typically either anti-tag agarose or magnetic beads. (In this study, we also demonstrate the method using anti-tag coated microplate wells.) The protein interaction (between X and Y proteins) is quantified by measuring the Tluc luciferase activity of the pull-down product.

To test the interaction of two proteins of interest (X and Y) in this assay system, genes for X and Y must be cloned into two separate expression vectors; gene X into an epitope-tagged vector (HA- or Myc-tag), and gene Y into Tluc-fusion vector. Upon co-transfection into mammalian cells, the vectors express the X and Y proteins, which then interact based on treatment conditions. Next, the cells are lysed, and the target protein-complex is immunoprecipitated using anti-epitope-tag beads. Finally, the co-IP product (protein Y) is quantified by measuring Tluc luciferase activity (Figure 1).

A. Bead-based qIP assays

B. Plate-based qIP assays

The Pierce quantitative immunoprecipitation (qIP) system depends on TurboLuc luciferase enzyme (Tluc) to accurately and precisely reflect the abundance of a specific co-IP product without time-consuming Western blot and band densitometry steps. Tluc luciferase is a small (18kDa) intracellular luciferase expressed by a synthetic gene designed based on the luciferase from Metridinidae copepods. Tluc luciferase uses coelenterazine as substrate and has been engineered to provide bioluminescence that is much brighter than commonly used firefly and Renilla luciferases. The intense bioluminescence greatly enhances sensitivity of Tluc luciferase-based assays, enabling detection of very minute amounts of luciferase (signal) in qIP assays. In addition, the Tluc luciferase gene is codon optimized for mammalian cell expression.

To demonstrate the excellent sensitivity of Tluc luciferase as a reporter for the qIP protein interaction assay, we benchmarked Tluc against three conventional luciferases, WT Renilla, Green Renilla, and intracellular Gaussia (icGaussia) in the qIP assay system (Figure 3). We cloned two genes (p53 and Bcl-xL) into equivalent expression vectors with each luciferase. Then, we performed qIP assays using each luciferase vector with the respective HA-tagged interactors (p53 and BAD) of p53 and Bcl-xL. Tluc activity in qIP assay with p53-p53 pair was 2.3 million RLU, which is 15 times greater than the intracellular Gaussia (0.15 million RLU). Tluc activity in qIP assay with BAD/Bcl-xL pair was 15.6 million RLU, which is 5 times greater than the intracellular Gaussia (3.19 million RLU).

To demonstrate the wide dynamic range of the Pierce qIP assay, we measured three very different known protein-protein interaction pairs (IRF3/HPV16 E6, p53/p53, and BAD/Bcl-xL) with the system (Figure 4). The RLU value ranged from 5,000 to 15 million (5-orders of magnitude), showing an excellent dynamic range to quantify protein-protein interaction pairs.

A simple experiment with SMAD2 and SMAD4 demonstrates the ability of the Pierce qIP assay to accurately measure protein interactions that are dependent upon known treatment conditions affecting post-translational modification (Figure 5).

Finally, we demonstrate that Pierce qIP assays can be performed using plate-based IP, i.e., capturing the expressed protein interaction directly to wells of anti-tag antibody-coated 96-well or 384-well plate instead of agarose or magnetic beads (Figure 6). We used our positive (BAD/Bcl-xL) and negative (RFP/Bcl-xL) controls to test the plate-based implementation of the Pierce qIP assay.  The normalized QIR value (approx. 300) for BAD/Bcl-xL from the microplate-based assay is close to the value (approx. 500) from the resin-based assay, indicating that the sensitivity of both methods is compatible although the absolute RLU values are different due to the reaction volume.

• Tluc luciferase activity in the qIP protein interaction assay generated much higher signal output than three other luciferases (wt Renilla, Green Renilla, and intracellular Gaussia).
• The quantitative immunoprecipitation (qIP) system depends on Tluc luciferase enzyme to accurately and precisely reflect the abundance of a specific co-IP product without time-consuming gel electrophoresis, Western blot and band densitometry steps.
• The signal output (RLU) of the qIP protein interaction assay has a wide dynamic range (180-fold; 2.25 orders of magnitude), enabling detection of a wide range of affinities of protein-protein interaction pairs.
• The qIP assay is capable of detecting post-translational modification (PTM)-dependent protein-protein interactions.
• The microplate-based qIP assay, in which the pull-down (capture) step of the co-IP is performed directly in coated 384-well plates, results in a robust assay that is amenable for HTS.

Bead-based qIP assay

Assay reagents used in this procedure are identical to those supplied in the Pierce Agarose qIP Protein Interaction Kit, Tluc and HA Tags (Part No. 82032). 293T cells were plated at a concentration of 1.6 million cells/2mL into each well of a 6-well plate. DNA constructs (1.5μg each) were transfected to each well in a total volume of 200μL serum free media. After 24 hours, cells were lysed with vortexing and the clear lysates were added to microspin columns for pull-down. After approx. 3 hours, the resins were washed with the qIP assay reagents and resuspended in 160µL (see Figure 2). Finally, 20µL of the resuspended resins were transferred to wells of a black 96-well microplate, and the bioluminescence was measured after adding 60μL of prepared Tluc luciferase assay reagent (Part No. 82015).

Microplate-based qIP assay

293T cells, 1.6 x 10^6, were plated in 6-well culture plate and incubated overnight at 37°C. Transfection reaction mixture was prepared with 1.5μg of each DNA construct, HA-tagged BAD and Tluc-tagged Bcl-xL, and 6μL of TurboFect Transfection Reagents in a total volume of 200μL serum free media. The transfection mixture was added to each well. The control transfection mixture was prepared with HA-tagged RFP and Tluc-tagged Bcl-xL. After 24 hours of post-transfection, the cells were harvested by trypsin treatment and lysed with 160μL of the qIP lysis buffer. The total lysates were diluted with 360μL of the dilution buffer (1:3 ratio of the qIP lysis buffer: dilution buffer).

A black 386-well microplate was coated overnight at 4°C with 5μg/mL anti-HA monoclonal antibody in carbonate/nicarbonate coating buffer. The microplate was incubated with cell lysate by rocking for 2 hours. Plates were then washed three times in Thermo Scientific Multidrop Combi (#5840320) with washing buffer, which is a 1:3 mixture of qIP assay lysis buffer (Part No. 82013) and dilution buffer (Part No. 82014). Finally, the bioluminescence (RLU) was measured after adding 60μL of Tluc luciferase assay reagent (Part No. 82015).

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2. Roberts, A.W., et al. (2012) Substantial susceptibility of chronic lymphocytic leukemia to BCL2 inhibition: results of a phase I study of navitoclax in patients with relapsed or refractory disease. Journal of Clinical Oncology. J. Clin. 30(5):488-96.

Some contents of this article were first presented as a poster:

Bell, P., et al. (2014). Quantitative immunoprecipitation (qIP) assay: a novel and high-throughput-compatible protein-protein interaction assay. Poster ID#051. Third Annual Conference of the Society for Laboratory Automation & Screening.