The authors thank the staff of the department of Pharmaceutical Biotechnology and Molecular Biology and especially Monique De Pelsmacker for the preparation of the radioactive labeled virus. We are grateful to Ellen Merckx and Hadewych Halewyck for their interesting remarks and discussions and to Gerrit De Bleeser for his help in the lab. This work was financially supported by an OZR grant of the Vrije Universiteit Brussel (OZR1807), the Fonds voor Wetenschappelijk Onderzoek Vlaanderen (G.0168.10N) and the World Health Organization (TSA 200410791). Lise Schotte is a predoctoral fellow of the Fonds voor Wetenschappelijk Onderzoek Vlaanderen (FWO).

The principle (A) and an overview of the method (B) are depicted in Figure 1.
1. Preparation of the Buffer
<ol>
	<li>Prepare Binding/Wash buffer by dissolving sodium dihydrogen phosphate (50 mM) and sodium chloride (300 mM) in water and adjust the pH to 8.0. Additionally add Tween 20 (0.01% (m/v) final concentration), methionine (2% (m/v) final concentration) and albumin (0.1% (m/v) final concentration) and adjust to the required volume.</li>
</ol>
2. Preparation of the Magnetic Beads
Prepare the magnetic beads according to the instruction manual. Briefly:
<ol>
	<li>Resuspend the magnetic beads using a vortex.</li>
	<li>Transfer, for each sample, 10 &mu;l of the resuspended magnetic beads (40 mg/ml) into a tube.</li>
	<li>Collect the magnetic beads using a magnet, until the supernatant is clear (+/- 30 sec) and remove the supernatant carefully.</li>
	<li>Wash the magnetic beads two times: resuspend the beads in 150 &mu;l of Binding/Wash buffer. Migrate the magnetic beads to one side of the tube using a magnet until the supernatant is clear and carefully remove the supernatant.</li>
	<li>Use 40 &mu;l of Binding/Wash buffer, for each sample, to resuspend the beads (10 mg/ml).</li>
</ol>
3. Affinity Capture Assay
Note: To measure the (cosmic) background radioactivity (0% radioactivity), no radiolabeled virus is added to a control sample 1. Instead, the same volume Binding/Wash buffer is added.
Note: 100% radioactivity is defined by a control sample 2 to which all components are added except the nanobody. Instead, the same volume Binding/Wash buffer is added.
<ol>
	<li>Bring 2000 cpm of 35S labeled (&beta;-radiation) poliovirus Sabin strain type 19, diluted with Binding/Wash buffer to 80 &mu;l into a 96-well microtiter plate.</li>
	<li>Add 10 &mu;l of nanobody dilution to the wells.</li>
	<li>Mix for about 10 seconds using a shaker.</li>
	<li>Allow the samples to incubate for 1 hour at room temperature.</li>
	<li>Add 40 &mu;l of the washed magnetic beads suspension and incubate for 10 minutes at room temperature, under continuously shaking.</li>
	<li>Separate the beads and the supernatant using a magnet and transfer the cleared supernatant into a tube.</li>
</ol>
4. Measurement of the Radioactivity
<ol>
	<li>Transfer 50 &mu;l of the supernatant from step 3.6 into a counting flask.</li>
	<li>Add 3 ml of scintillation fluid and mix. Measure the radioactivity in a &beta;-scintillation counter.</li>
</ol>
5. Recycling the Beads
<ol>
	<li>Collect the used magnetic beads in a tube and centrifuge at 500 x g for 2 minutes or until a clear supernatant is obtained.</li>
	<li>Remove the supernatant and resuspend the beads in 6 ml 0.5 M NaOH.</li>
	<li>Transfer the suspension to multiple tubes and incubate in an ultrasonic bath for 5 minutes.</li>
	<li>Use the magnets to collect the magnetic beads and remove the supernatant.</li>
	<li>Add 1 ml 2% SDS-solution to each tube and resuspend using a vortex. Boil during 5 minutes.</li>
	<li>Collect the beads and remove the supernatant. Resuspend the beads in 1 ml 0.2 M EDTA (pH=7).</li>
	<li>Incubate the tubes in an ultrasonic bath for 5 minutes and once more, remove the supernatant.</li>
	<li>Add 1 ml of water to each tube and resuspend the beads. Collect the beads and remove the supernatant. Repeat this wash step twice.</li>
	<li>Remove the supernatant and resuspend the beads in 1 ml 10 mM CoCl2 solution. Put on a shaker for 10 minutes.</li>
	<li>Remove the supernatant using a magnet to collect the beads and resuspend in 1 ml of Binding/Wash buffer.</li>
	<li>Remove the supernatant and wash the beads two times using 1 ml of 20% (v/v) ethanol</li>
	<li>Resuspend the beads in their original volume of 20% (v/v) ethanol to obtain regenerated beads in a concentration of 40 mg/ml.</li>
</ol>
6. Interpretation of the Results
<ol>
	<li>Control sample 1, in which no radiolabeled virus was added, will be used to correct for the background radioactivity and to set the 0% radioactivity value. Control sample 2, which does not contain nanobody and where consequently all radiolabeled virus remains in the supernatant, is set as the 100% radioactivity value.</li>
	<li>The percentage of radioactivity in the supernatant (= a %) is a measure of the overall precipitation (= 100 - a %) of the radiolabeled virus by the nanobody.</li>
</ol>
7. Representative Results
Representative results for this affinity capture assay are shown in Figures 2, 3 and 4. In Figure 2, the affinity of PVSS38C, a nanobody specific for poliovirus, is shown. The affinity of PVSS38C was tested for three different antigens of poliovirus: Native-antigen (N-antigen), Heated-antigen (H-antigen) and 14S subunits. N-antigen is the intact virus that is infectious. When the virus is heated (20 minutes at 56 &deg;C) or attached to a solid surface (unpublished results), the conformation of the capsid changes, resulting in a (partial) loss of the viral RNA and the capsid protein VP4, and empty capsids are formed which are then called H-antigens. 14S subunits are assembly intermediates. These antigens are recognized by different sets of antibodies after immunization10 and possess therefore different epitopes and antigenic sites. In the figure the percentage of radioactivity found in the supernatant is represented as a function of the concentration of nanobody. It can be seen that the radioactivity in the supernatant of the samples containing radiolabeled 14S subunits decreases with increasing concentrations of the nanobody PVSS38C. This can be translated as an increase in the amount of poliovirus 14S subunits connected to the nanobody PVSS38C and indirectly to the magnetic beads. The capturing titer (= the concentration of nanobody necessary to capture 50% of radiolabeled virus) can be graphically calculated as 0.099 nM. No affinity of PVSS38C for the N-antigenic and H-antigenic form of poliovirus is observed. From these data it is interpreted that PVSS38C is interacting with an epitope that is exclusively present on the 14S subunit and not on the two other antigenic forms of poliovirus.
To demonstrate that the loss of radioactivity from the supernatant is only due to the specific affinity of the nanobody towards its antigens, the same assay was performed with Nb1, a nanobody generated against the lrpB transcriptional regulator of Sulfolobus sulfataricus and known to have no interaction with any poliovirus antigen. The result of this assay is shown in Figure 3. All radiolabeled virus remains in the supernatants showing that there is no reactivity of Nb1 against the three antigenic forms of poliovirus.
Reproducibility of the results was tested by repeating the experiment for a total of eight times for one given nanobody (i.e., PVSP29F) at different days and by different persons. The results are shown in Figure 4. The mean value of percentage radioactivity in the supernatant was calculated for each nanobody concentration and is represented in correspondence with its standard deviation.
<img alt="Figure 1." src="/files/ftp_upload/3937/3937fig1.jpg" /> 
Figure 1. An overview of the principle (A) and the method (B) of the assay. A. His-tagged nanobodies that specifically recognize a certain poliovirus antigen will be able to interact with the cobalt-coated magnetic beads and will precipitate the radioactively labeled virus. B. His-tagged nanobodies are added to radioactively labeled poliovirus and incubated. Cobalt-coated magnetic beads are added and magnetic separation of the bound/unbound antigen is performed. The radioactivity of the supernatant is measured and the amount of captured antigen can be derived.
<img alt="Figure 2" src="/files/ftp_upload/3937/3937fig2.jpg" /> 
Figure 2. Magnetic beads affinity capture of different poliovirus antigens by nanobody PVSS38C. The percentage of radioactivity found in the supernatant is represented as a function of the concentration of PVSS38C. For 14S a concentration-response relationship can be found, showing the interaction of PVSS38C with an epitope exclusively present on 14S. No significant interaction with N- , nor H-antigen can be detected, although a negligible non-specific capturing at very high concentrations is noticed.
<img alt="Figure 3" src="/files/ftp_upload/3937/3937fig3.jpg" /> 
Figure 3. Magnetic beads affinity capture of different poliovirus antigens by nanobody Nb1. The percentage of radioactivity found in the supernatant is represented as a function of the concentration of Nb1. Nb1 is known to have no interaction with any poliovirus-antigen or -subunit. Since 100 % of the radioactivity is found in the supernatant, no virus was non-specifically bound to Nb1. The loss of radioactivity in figure 2 is therefore only due to the specific affinity of the nanobody towards its antigens.
<img alt="Figure 4." src="/files/ftp_upload/3937/3937fig4.jpg" /> 
Figure 4. Reproducibility of the assay. The mean value of percentage radioactivity in the supernatant is represented as a function of the concentration of nanobody. The experiment was repeated eight times at different days and by different persons. The standard deviation is represented as vertical bars.

<ol>
	<li>Thys, B., Schotte, L., Muyldermans, S., Wernery, U., Hassanzadeh-Ghassabeh, G., Rombaut, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vitro+antiviral+activity+of+single+domain+antibody+fragments+against+poliovirus.">In vitro antiviral activity of single domain antibody fragments against poliovirus.</a> Antiviral Res. 87, 257-264 (2010).</li><li>Meloen, R. H., Briaire, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+study+of+the+cross-reacting+antigens+on+the+intact+foot-and-mouth+disease+virus+and+its+12S+subunits+with+antisera+against+the+structural+proteins.">A study of the cross-reacting antigens on the intact foot-and-mouth disease virus and its 12S subunits with antisera against the structural proteins.</a> J. Gen. Virol. 51, 107-116 (1980).</li><li>Vrijsen, R., Rombaut, B., Boeye, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+simple+quantitative+protein+A+micro-immunoprecipitation+method:+assay+of+antibodies+to+the+N+and+H+antigens+of+poliovirus.">A simple quantitative protein A micro-immunoprecipitation method: assay of antibodies to the N and H antigens of poliovirus.</a> J. Immunol. Methods. 59, 217-220 (1983).</li><li>Rombaut, B., Jore, J., Boeye, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+competition+immunoprecipitation+assay+of+unlabeled+poliovirus+antigens.">A competition immunoprecipitation assay of unlabeled poliovirus antigens.</a> J. Virol. Methods. 48, 73-80 (1994).</li><li>Kessler, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+isolation+of+antigens+from+cells+with+a+staphylococcal+protein+A-antibody+adsorbent:+parameters+of+the+interaction+of+antibody-antigen+complexes+with+protein+A.">Rapid isolation of antigens from cells with a staphylococcal protein A-antibody adsorbent: parameters of the interaction of antibody-antigen complexes with protein A.</a> J. Immunol. 115, 1617-1624 (1975).</li><li>Hamers-Casterman, C., Atarhouch, T., Muyldermans, S., Robinson, G., Hamers, C., Songa, B. a. j. y. a. n. a., Bendahman, E., N, ., Hamers, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Naturally+occurring+antibodies+devoid+of+light+chains.">Naturally occurring antibodies devoid of light chains.</a> Nature. 363, 446-448 (1993).</li><li>Arbabi Ghahroudi, M., Desmyter, A., Wyns, L., Hamers, R., Muyldermans, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selection+and+identification+of+single+domain+antibody+fragments+from+camel+heavy-chain+antibodies.">Selection and identification of single domain antibody fragments from camel heavy-chain antibodies.</a> FEBS Lett. 414, 521-526 (1997).</li><li>Muyldermans, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+domain+camel+antibodies:+current+status.">Single domain camel antibodies: current status.</a> Rev. Mol. Biotechnol. 74, 277-302 (2001).</li><li>Rombaut, B., Vrijsen, R., Boeye, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epitope+evolution+in+poliovirus+maturation.">Epitope evolution in poliovirus maturation.</a> Arch. Virol. 76, 289-298 (1983).</li><li>Brioen, P., Sijens, R. J., Vrijsen, R., Rombaut, B., Thomas, A. A., Jackers, A., Boeye, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hybridoma+antibodies+to+poliovirus+N+and+H+antigen.">Hybridoma antibodies to poliovirus N and H antigen.</a> Arch. Virol. 74, 325-330 (1982).</li><li>Thys, B., Saerens, D., Schotte, L., De Bleeser, G., Muyldermans, S., Hassanzadeh-Ghassabeh, G., Rombaut, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+simple+quantitative+affinity+capturing+assay+of+poliovirus+antigens+and+subviral+particles+by+single-domain+antibodies+using+magnetic+beads.">A simple quantitative affinity capturing assay of poliovirus antigens and subviral particles by single-domain antibodies using magnetic beads.</a> J. Virol. Methods. 173, 300-305 (2011).</li><li>Wild, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The Immunoassay Handbook. , (2005).</li><li>Kremser, L., Konecsni, T., Blaas, D., Kenndler, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence+labeling+of+human+rhinovirus+capsid+and+analysis+by+capillary+electrophoresis.">Fluorescence labeling of human rhinovirus capsid and analysis by capillary electrophoresis.</a> Anal. Chem. 76, 4175-4181 (2004).</li><li>Pelkmans, L., Kartenbeck, J., Helenius, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Caveolar+endocytosis+of+simian+virus+40+reveals+a+new+two-step+vesicular-transport+pathway+to+the+ER.">Caveolar endocytosis of simian virus 40 reveals a new two-step vesicular-transport pathway to the ER.</a> Nat. Cell Biol. 3, 473-483 (2001).</li></ol>

We have nothing to disclose.

In the protocol, the radioactivity of the antigen interacting with the nanobody is defined as the loss of radiolabeled virus from the supernatant. Therefore the amount of precipitated radioactivity (=100 - a %) (bound to the magnetic beads) can be estimated in an indirect way by the radioactivity in the supernatant (= a %). On the other hand, it is also possible to measure the radioactivity of the precipitated bound fraction of antigen in a direct way by eluting the immunocomplexes from the magnetic beads with 500 mM imi...

<table border="1">
 <tbody>
 <tr>
 <td>Name of the reagent</td>
 <td>Company</td>
 <td>Catalogue number</td>
 <td>Comments </td>
 </tr>
 <tr>
 <td>Dynabeads His-Tag Isolation and Pulldown </td>
 <td>Invitrogen</td>
 <td>101.03D</td>
 <td>Magnetic beads</td>
 </tr>
 <tr>
 <td>Optiphase 'HiSafe' 2</td>
 <td>Perkin Elmer</td>
 <td>1200 - 436</td>
 <td>Scintillation fluid</td>
 </tr>
 </tbody>
 </table>

a liquid phase affinity capture assay using magnetic beads to study protein-protein interaction: the poliovirus-nanobody example

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. Provided that one protein can be tagged and another protein labeled, this method can be implemented for the investigation of protein-protein interactions. It is based on one hand on the recognition of the tagged protein by cobalt coated magnetic beads and on the other hand on the interaction between the tagged protein and a second specific protein that is labeled. First, the labeled and tagged proteins are mixed and incubated at room temperature. The magnetic beads, that recognize the tag, are added and the bound fraction of labeled protein is separated from the unbound fraction using magnets. The amount of labeled protein that is captured can be determined in an indirect way by measuring the signal of the labeled protein remained in the unbound fraction. The described liquid phase affinity assay is extremely useful when conformational conversion sensitive proteins are assayed. The development and application of the assay is demonstrated for the interaction between poliovirus and poliovirus recognizing nanobodies1. Since poliovirus is sensitive to conformational conversion2 when attached to a solid surface (unpublished results), the use of ELISA is limited and a liquid phase based system should therefore be preferred. An example of a liquid phase based system often used in polioresearch3,4 is the micro protein A-immunoprecipitation test5. Even though this test has proven its applicability, it requires an Fc-structure, which is absent in the nanobodies6,7. However, as another opportunity, these interesting and stable single-domain antibodies8 can be easily engineered with different tags. The widely used (His)6-tag shows affinity for bivalent ions such as nickel or cobalt, which can on their turn be easily coated on magnetic beads. We therefore developed this simple quantitative affinity capture assay based on cobalt coated magnetic beads. Poliovirus was labeled with 35S to enable unhindered interaction with the nanobodies and to make a quantitative detection feasible. The method is easy to perform and can be established with a low cost, which is further supported by the possibility of effectively regenerating the magnetic beads.

Watch this Scientific Journal Video about A Liquid Phase Affinity Capture Assay Using Magnetic Beads to Study Protein-Protein Interaction: The Poliovirus-Nanobody Example at JoVE.com

A Liquid Phase Affinity Capture Assay Using Magnetic Beads to Study Protein-Protein Interaction: The Poliovirus-Nanobody Example

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. It is a reliable technique based on the interaction between magnetic beads and tagged proteins (e.g. nanobodies) on one hand and the affinity between the tagged protein and a second, labeled protein (e.g. poliovirus) on the other.

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. Provided that one protein can be tagged and another protein ...

a-liquid-phase-affinity-capture-assay-using-magnetic-beads-to-study

Research

JoVE Journal

Biology

11.8K Views.  Vrije Universiteit Brussel. In this article, a simple, quantitative, liquid phase affinity capture assay is presented. It is a reliable technique based on the interaction between magnetic beads and tagged proteins (e.g. nanobodies) on one hand and the affinity between the tagged protein and a second, labeled protein (e.g. poliovirus) on the other.

Video: A Liquid Phase Affinity Capture Assay Using Magnetic Beads to Study Protein-Protein Interaction: The Poliovirus-Nanobody Example

Using the GELFREE 8100 Fractionation System for Molecular Weight-Based Fractionation with Liquid Phase Recovery

The GELFREE 8100 Fractionation System is a novel protein fractionation system designed to maximize protein recovery during molecular weight based fractionation. The system is comprised of single-use, 8-sample capacity cartridges and a benchtop GELFREE Fractionation Instrument. During separation, a constant voltage is applied between the anode and cathode reservoirs, and each protein mixture is electrophoretically driven from a loading chamber into a specially designed gel column gel. Proteins are concentrated into a tight band in a stacking gel, and separated based on their respective electrophoretic mobilities in a resolving gel. As proteins elute from the column, they are trapped and concentrated in liquid phase in the collection chamber, free of the gel. The instrument is then paused at specific time intervals, and fractions are collected using a pipette. This process is repeated until all desired fractions have been collected. If fewer than 8 samples are run on a cartridge, any unused chambers can be used in subsequent separations.
This novel technology facilitates the quick and simple separation of up to 8 complex protein mixtures simultaneously, and offers several advantages when compared to previously available fractionation methods. This system is capable of fractionating up to 1mg of total protein per channel, for a total of 8mg per cartridge. Intact proteins over a broad mass range are separated on the basis of molecular weight, retaining important physiochemical properties of the analyte. The liquid phase entrapment provides for high recovery while eliminating the need for band or spot cutting, making the fractionation process highly reproducible1.

The accompanying video describes the use of the GELFREE 8100 Fractionation System, which partitions complex protein samples on the basis of molecular weight and recovers the fractions in liquid phase. The video describes how the technology works, how it is used, and provides resultant data, with polyacrylamide gel electrophoresis analysis of fractionated bovine liver homogenate.

The GELFREE 8100 Fractionation System is a novel protein fractionation system designed to maximize protein recovery during molecular weight based ...

Bimolecular Fluorescence Complementation (BiFC) Assay for Protein-Protein Interaction in Onion Cells Using the Helios Gene Gun

Investigation of gene function in diverse organisms relies on knowledge of how the gene products interact with each other in their normal cellular environment. The Bimolecular Fluorescence Complementation (BiFC) Assay1 allows researchers to visualize protein-protein interactions in living cells and has become an essential research tool. This assay is based on the facilitated association of two fragments of a fluorescent protein (GFP) that are each fused to a potential interacting protein partner. The interaction of the two protein partners would facilitate the association of the N-terminal and C-terminal fragment of GFP, leading to fluorescence. For plant researchers, onion epidermal cells are an ideal experimental system for conducting the BiFC assay because of the ease in obtaining and preparing onion tissues and the direct visualization of fluorescence with minimal background fluorescence. The Helios Gene Gun (BioRad) is commonly used for bombarding plasmid DNA into onion cells. We demonstrate the use of Helios Gene Gun to introduce plasmid constructs for two interacting Arabidopsis thaliana transcription factors, SEUSS (SEU) and LEUNIG HOMOLOG (LUH)2 and the visualization of their interactions mediated by BiFC in onion epidermal cells.

Bimolecular Fluorescence Complementation BiFC Assay for Protein-Protein Interaction in Onion Cells Using the Helios Gene Gun

This article illustrates how to properly use the BioRad Helios Gene Gun to introduce plasmid DNA into onion epidermal cells and how to test for protein-protein interactions in onion cells based on the principle of Bimolecular Fluorescence Complementation (BiFC)

Investigation of gene function in diverse organisms relies on knowledge of how the gene products interact with each other in their normal cellular ...

Lipid Vesicle-mediated Affinity Chromatography using Magnetic Activated Cell Sorting (LIMACS): a Novel Method to Analyze Protein-lipid Interaction

The analysis of lipid protein interaction is difficult because lipids are embedded in cell membranes and therefore, inaccessible to most purification procedures. As an alternative, lipids can be coated on flat surfaces as used for lipid ELISA and Plasmon resonance spectroscopy. However, surface coating lipids do not form microdomain structures, which may be important for the lipid binding properties. Further, these methods do not allow for the purification of larger amounts of proteins binding to their target lipids.
 To overcome these limitations of testing lipid protein interaction and to purify lipid binding proteins we developed a novel method termed lipid vesicle-mediated affinity chromatography using magnetic-activated cell sorting (LIMACS). In this method, lipid vesicles are prepared with the target lipid and phosphatidylserine as the anchor lipid for Annexin V MACS. Phosphatidylserine is a ubiquitous cell membrane phospholipid that shows high affinity to the protein Annexin V. Using magnetic beads conjugated to Annexin V the phosphatidylserine-containing lipid vesicles will bind to the magnetic beads. When the lipid vesicles are incubated with a cell lysate the protein binding to the target lipid will also be bound to the beads and can be co-purified using MACS. This method can also be used to test if recombinant proteins reconstitute a protein complex binding to the target lipid. 
 We have used this method to show the interaction of atypical PKC (aPKC) with the sphingolipid ceramide and to co-purify prostate apoptosis response 4 (PAR-4), a protein binding to ceramide-associated aPKC. We have also used this method for the reconstitution of a ceramide-associated complex of recombinant aPKC with the cell polarity-related proteins Par6 and Cdc42. Since lipid vesicles can be prepared with a variety of sphingo- or phospholipids, LIMACS offers a versatile test for lipid-protein interaction in a lipid environment that resembles closely that of the cell membrane. Additional lipid protein complexes can be identified using proteomics analysis of lipid binding protein co-purified with the lipid vesicles.

Lipid Vesicle-mediated Affinity Chromatography using Magnetic Activated Cell Sorting LIMACS: a Novel Method to Analyze Protein-lipid Interaction

To test the interaction of a protein with its target lipid we used MACS and Annexin V-conjugated magnetic beads and lipid vesicles synthesized from the target lipid and Annexin V-binding phosphatidylserine. Proteins bound to the target lipid are co-purified and analyzed after elution from the beads.

The analysis of lipid protein interaction is difficult because lipids are embedded in cell membranes and therefore, inaccessible to most purification ...

Conversion of a Capture ELISA to a Luminex xMAP Assay using a Multiplex Antibody Screening Method

The enzyme-linked immunosorbent assay (ELISA) has long been the primary tool for detection of analytes of interest in biological samples for both life science research and clinical diagnostics. However, ELISA has limitations. It is typically performed in a 96-well microplate, and the wells are coated with capture antibody, requiring a relatively large amount of sample to capture an antigen of interest . The large surface area of the wells and the hydrophobic binding of capture antibody can also lead to non-specific binding and increased background. Additionally, most ELISAs rely upon enzyme-mediated amplification of signal in order to achieve reasonable sensitivity. Such amplification is not always linear and can thus skew results.
In the past 15 years, a new technology has emerged that offers the benefits of the ELISA, but also enables higher throughput, increased flexibility, reduced sample volume, and lower cost, with a similar workflow 1, 2. Luminex xMAP Technology is a microsphere (bead) array platform enabling both monoplex and multiplex assays that can be applied to both protein and nucleic acid applications 3-5. The beads have the capture antibody covalently immobilized on a smaller surface area, requiring less capture antibody and smaller sample volumes, compared to ELISA, and non-specific binding is significantly reduced. Smaller sample volumes are important when working with limiting samples such as cerebrospinal fluid, synovial fluid, etc. 6. Multiplexing the assay further reduces sample volume requirements, enabling multiple results from a single sample.
Recent improvements by Luminex include: the new MAGPIX system, a smaller, less expensive, easier-to-use analyzer; Low-Concentration Magnetic MagPlex Microspheres which eliminate the need for expensive filter plates and come in a working concentration better suited for assay development and low-throughput applications; and the xMAP Antibody Coupling (AbC) Kit, which includes a protocol, reagents, and consumables necessary for coupling beads to the capture antibody of interest. (See Materials section for a detailed list of kit contents.)
In this experiment, we convert a pre-optimized ELISA assay for TNF-alpha cytokine to the xMAP platform and compare the performance of the two methods 7-11. TNF-alpha is a biomarker used in the measurement of inflammatory responses in patients with autoimmune disorders.
We begin by coupling four candidate capture antibodies to four different microsphere sets or regions. When mixed together, these four sets allow for the simultaneous testing of all four candidates with four separate detection antibodies to determine the best antibody pair, saving reagents, sample and time. Two xMAP assays are then constructed with the two most optimal antibody pairs and their performance is compared to that of the original ELISA assay in regards to signal strength, dynamic range, and sensitivity.

An ELISA can be easily converted to a Luminex xMAP assay and, through the benefits of multiplexing, several antibodies can be screened simultaneously to identify an optimum antibody pair, resulting in increased sensitivity and dynamic range, while reducing assay cost.

The enzyme-linked immunosorbent assay (ELISA) has long been the primary tool for detection of analytes of interest in biological samples for both life ...

Flow Cytometric Analysis of Bimolecular Fluorescence Complementation: A High Throughput Quantitative Method to Study Protein-protein Interaction

Among methods to study protein-protein interaction inside cells, Bimolecular Fluorescence Complementation (BiFC) is relatively simple and sensitive. BiFC is based on the production of fluorescence using two non-fluorescent fragments of a fluorescent protein (Venus, a Yellow Fluorescent Protein variant, is used here). Non-fluorescent Venus fragments (VN and VC) are fused to two interacting proteins (in this case, AKAP-Lbc and PDE4D3), yielding fluorescence due to VN-AKAP-Lbc-VC-PDE4D3 interaction and the formation of a functional fluorescent protein inside cells.
BiFC provides information on the subcellular localization of protein complexes and the strength of protein interactions based on fluorescence intensity. However, BiFC analysis using microscopy to quantify the strength of protein-protein interaction is time-consuming and somewhat subjective due to heterogeneity in protein expression and interaction. By coupling flow cytometric analysis with BiFC methodology, the fluorescent BiFC protein-protein interaction signal can be accurately measured for a large quantity of cells in a short time. Here, we demonstrate an application of this methodology to map regions in PDE4D3 that are required for the interaction with AKAP-Lbc. This high throughput methodology can be applied to screening factors that regulate protein-protein interaction.

Flow cytometric analysis of Bimolecular Fluorescence Complementation provides a high throughput quantitative method to study protein-protein interaction. This methodology can be applied to mapping protein binding sites and for screening factors that regulate protein-protein interaction.

Among methods to study protein-protein interaction inside cells, Bimolecular Fluorescence Complementation (BiFC) is relatively simple and sensitive. BiFC ...

Identifying Protein-protein Interaction in Drosophila Adult Heads by Tandem Affinity Purification (TAP)

Genetic screens conducted using Drosophila melanogaster (fruit fly) have made numerous milestone discoveries in the advance of biological sciences. However, the use of biochemical screens aimed at extending the knowledge gained from genetic analysis was explored only recently. Here we describe a method to purify the protein complex that associates with any protein of interest from adult fly heads. This method takes advantage of the Drosophila GAL4/UAS system to express a bait protein fused with a Tandem Affinity Purification (TAP) tag in fly neurons in vivo, and then implements two rounds of purification using a TAP procedure similar to the one originally established in yeast1 to purify the interacting protein complex. At the end of this procedure, a mixture of multiple protein complexes is obtained whose molecular identities can be determined by mass spectrometry. Validation of the candidate proteins will benefit from the resource and ease of performing loss-of-function studies in flies. Similar approaches can be applied to other fly tissues. We believe that the combination of genetic manipulations and this proteomic approach in the fly model system holds tremendous potential for tackling fundamental problems in the field of neurobiology and beyond.

Identifying Protein-protein Interaction in Drosophila Adult Heads by Tandem Affinity Purification TAP

Drosophila is famous for its powerful genetic manipulation, but not for its suitability of in-depth biochemical analysis. Here we present a TAP-based procedure to identify interacting partners of any protein of interest from the fly brain. This procedure can potentially lead to new avenues of research.

Genetic screens conducted using Drosophila melanogaster (fruit fly) have made numerous milestone discoveries in the advance of biological sciences. ...

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Protein-protein interactions mediate most of the processes in the living cell and control homeostasis of the organism. Impaired protein interactions may result in disease, making protein interactions important drug targets. It is thus highly important to understand these interactions at the molecular level. Protein interactions are studied using a variety of techniques ranging from cellular and biochemical assays to quantitative biophysical assays, and these may be performed either with full-length proteins, with protein domains or with peptides. Peptides serve as excellent tools to study protein interactions since peptides can be easily synthesized and allow the focusing on specific interaction sites. Peptide arrays enable the identification of the interaction sites between two proteins as well as screening for peptides that bind the target protein for therapeutic purposes. They also allow high throughput SAR studies. For identification of binding sites, a typical peptide array usually contains partly overlapping 10-20 residues peptides derived from the full sequences of one or more partner proteins of the desired target protein. Screening the array for binding the target protein reveals the binding peptides, corresponding to the binding sites in the partner proteins, in an easy and fast method using only small amount of protein.
In this article we describe a protocol for screening peptide arrays for mapping the interaction sites between a target protein and its partners. The peptide array is designed based on the sequences of the partner proteins taking into account their secondary structures. The arrays used in this protocol were Celluspots arrays prepared by INTAVIS Bioanalytical Instruments. The array is blocked to prevent unspecific binding and then incubated with the studied protein. Detection using an antibody reveals the binding peptides corresponding to the specific interaction sites between the proteins.

Peptide array screening is a high throughput assay for identifying protein-protein interaction sites. This allows mapping multiple interactions of a target protein and can serve as a method for identifying sites for inhibitors that target a protein. Here we describe a protocol for screening and analyzing peptide arrays.

Protein-protein interactions mediate most of the processes in the living cell and control homeostasis of the organism. Impaired protein interactions may ...

Electrophoretic Mobility Shift Assay (EMSA) for the Study of RNA-Protein Interactions: The IRE/IRP Example

RNA/protein interactions are critical for post-transcriptional regulatory pathways. Among the best-characterized cytosolic RNA-binding proteins are iron regulatory proteins, IRP1 and IRP2. They bind to iron responsive elements (IREs) within the untranslated regions (UTRs) of several target mRNAs, thereby controlling the mRNAs translation or stability. IRE/IRP interactions have been widely studied by EMSA. Here, we describe the EMSA protocol for analyzing the IRE-binding activity of IRP1 and IRP2, which can be generalized to assess the activity of other RNA-binding proteins as well. A crude protein lysate containing an RNA-binding protein, or a purified preparation of this protein, is incubated with an excess of32 P-labeled RNA probe, allowing for complex formation. Heparin is added to preclude non-specific protein to probe binding. Subsequently, the mixture is analyzed by non-denaturing electrophoresis on a polyacrylamide gel. The free probe migrates fast, while the RNA/protein complex exhibits retarded mobility; hence, the procedure is also called &#8220;gel retardation&#8221; or &#8220;bandshift&#8221; assay. After completion of the electrophoresis, the gel is dried and RNA/protein complexes, as well as free probe, are detected by autoradiography. The overall goal of the protocol is to detect and quantify IRE/IRP and other RNA/protein interactions. Moreover, EMSA can also be used to determine specificity, binding affinity, and stoichiometry of the RNA/protein interaction under investigation.

Electrophoretic Mobility Shift Assay EMSA for the Study of RNA-Protein Interactions: The IRE/IRP Example

Here we present a protocol to analyze RNA/protein interactions. The electrophoretic mobility shift assay (EMSA) is based on the differential migration of RNA/protein complexes and free RNA during native gel electrophoresis. By using a radiolabeled RNA probe, RNA/protein complexes can be visualized by autoradiography.

RNA/protein interactions are critical for post-transcriptional regulatory pathways. Among the best-characterized cytosolic RNA-binding proteins are iron ...

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Proteins are the building blocks, effectors and signal mediators of cellular processes. A protein&#8217;s function, regulation and localization often depend on its interactions with other proteins. Here, we describe a protocol for the yeast protein-fragment complementation assay (PCA), a powerful method to detect direct and proximal associations between proteins in living cells. The interaction between two proteins, each fused to a dihydrofolate reductase (DHFR) protein fragment, translates into growth of yeast strains in presence of the drug methotrexate (MTX). Differential fitness, resulting from different amounts of reconstituted DHFR enzyme, can be quantified on high-density colony arrays, allowing to differentiate interacting from non-interacting bait-prey pairs. The high-throughput protocol presented here is performed using a robotic platform that parallelizes mating of bait and prey strains carrying complementary DHFR-fragment fusion proteins and the survival assay on MTX. This protocol allows to systematically test for thousands of protein-protein interactions (PPIs) involving bait proteins of interest and offers several advantages over other PPI detection assays, including the study of proteins expressed from their endogenous promoters without the need for modifying protein localization and for the assembly of complex reporter constructs.

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Proteins interact with each other and these interactions determine in a large part their functions. Protein interaction partners can be identified at high-throughput in vivo using a yeast fitness assay based on the dihydrofolate reductase protein-fragment complementation assay (DHFR-PCA).

Proteins are the building blocks, effectors and signal mediators of cellular processes. A protein&#8217;s function, regulation and localization often ...

In Vivo Study of Human Endothelial-Pericyte Interaction Using the Matrix Gel Plug Assay in Mouse

Angiogenesis is the process by which new blood vessels are formed from existing vessels. New vessel growth requires coordinated endothelial cell proliferation, migration, and alignment to form tubular structures followed by recruitment of pericytes to provide mural support and facilitate vessel maturation. Current in vitro cell culture approaches cannot fully reproduce the complex biological environment where endothelial cells and pericytes interact to produce functional vessels. We present a novel application of the in vivo matrix gel plug assay to study endothelial-pericyte interactions and formation of functional blood vessels using severe combined immune deficiency mutation (SCID) mice. Briefly, matrix gel is mixed with a solution containing endothelial cells with or without pericytes followed by injection into the back of anesthetized SCID mice. After 14 days, the matrix gel plugs are removed, fixed and sectioned for histological analysis. The length, number, size and extent of pericyte coverage of mature vessels (defined by the presence of red blood cells in the lumen) can be quantified and compared between experimental groups using commercial statistical platforms. Beyond its use as an angiogenesis assay, this matrix gel plug assay can be used to conduct genetic studies and as a platform for drug discovery. In conclusion, this protocol will allow researchers to complement available in vitro assays for the study of endothelial-pericyte interactions and their relevance to either systemic or pulmonary angiogenesis.

In Vivo Study of Human Endothelial-Pericyte Interaction Using the Matrix Gel Plug Assay in Mouse

We present a protocol to study human endothelial-pericyte interactions in mouse using a variation of the matrix gel plug angiogenesis assay.