This work was supported by the Max Planck Society.

1. Creation of Plasmids
<ol>
	<li>Subclone the cDNAs for each protein of interest into both the pLuc and pYFP vectors, using standard molecular biology techniques (Figure 1). For detailed protocols see Green&#160;et al13.</li>
	<li>Sequence all constructs to verify that the proteins of interest are in frame with the Luc/YFP sequence with no intervening stop codons.</li>
	<li>Perform functional assays as desired to confirm that the fusion proteins retain biological activity. In the case presented here the subcellular localization of YFP fusion proteins was ascertained by fluorescence microscopy.</li>
	<li>Make expression plasmids for appropriate Luc and YFP control proteins by engineering the relevant targeting signals into the pLuc and pYFP expression vectors. In the case presented here, generate nuclear-targeted Luc and YFP constructs by inserting a nuclear localization signal into the pLuc and pYFP vectors.</li>
	<li>Make a positive control construct in which Luc and YFP are fused into a single polypeptide. In the case presented here, generate a positive control in which the YFP coding sequence is inserted into the pLuc vector.</li>
	<li>Select a neutral filler plasmid to be used to equalize the mass of DNA in transfection mixes. Use a plasmid that has no eukaryotic promoter and will therefore be transcriptionally inactive in mammalian cells, such as a bacterial cloning vector.</li>
</ol>
2. Preparation of DNA Mixes
<ol>
	<li>Estimate the concentration of all the plasmids described in Section 1 based on absorbance at 260 nm (1 absorbance unit is equivalent to 50 &#181;g/ml of DNA). Determine the molecular mass of each plasmid by multiplying the number of base pairs by 650 Da. Use the concentration and molecular mass to calculate the molar concentration of each plasmid preparation. Dilute the plasmid DNA preparations to a concentration of 36 nM. These will be the working stocks that will be used to prepare the DNA mixes for transfection.</li>
	<li>Prepare a control DNA mix containing 1,800 ng of filler plasmid in a final volume of 20 &#181;l of water.</li>
	<li>Prepare a control DNA mix containing 5 &#181;l of the pLuc-control construct. Add filler plasmid to bring the total DNA mass to 1,800 ng. Add water to bring the final volume to 20 &#181;l.</li>
	<li>Prepare a control DNA mix containing 5 &#181;l of pLuc-control construct and 5 &#181;l of pYFP-control construct. Add filler plasmid to bring the total DNA mass to 1,800 ng. Add water to bring the final volume to 20 &#181;l.</li>
	<li>Prepare a control DNA mix containing 5 &#181;l of positive control construct. Add filler plasmid to bring the total DNA mass to 1,800 ng. Add water to bring the final volume to 20 &#181;l.</li>
	<li>Prepare the following DNA mixes to test for homodimerization of a protein of interest, X. For each DNA mix combine 5 &#181;l of the relevant pLuc construct and 5 &#181;l of the pYFP construct. Add filler plasmid to bring the total DNA mass to 1,800 ng. Add water to bring the final volume to 20 &#181;l. 
	A) pLuc-control and pYFP-X 
	B) pLuc-X and pYFP-control 
	C) pLuc-X and pYFP-X</li>
	<li>Prepare the following DNA mixes to test for an interaction between a pair of proteins of interest, X and Y. For each DNA mix combine 5 &#181;l of the relevant pLuc construct and 5 &#181;l of the pYFP construct. Add filler plasmid to bring the total DNA mass to 1,800 ng. Add water to bring the final volume to 20 &#181;l. 
	A) pLuc-control and pYFP-X 
	B) pLuc-X and pYFP-control 
	C) pLuc-control and pYFP-Y 
	D) pLuc-Y and pYFP-control 
	E) pLuc-X and pYFP-Y 
	F) pLuc-Y and pYFP-X</li>
</ol>
3. Transfection
<ol>
	<li>Harvest subconfluent HEK293 cells from a 75 cm2 flask. Dilute 10% of the total cells into 13 ml of culture medium. Dispense 130 &#181;l of cell suspension into each well of a white clear bottomed 96-well tissue culture plate. Culture cells for 24 hr.</li>
	<li>Calculate the number of wells to be transfected by multiplying the number of DNA mixes by 3. Bring serum-free culture medium to room temperature. Prepare a master mix containing 6.3 &#181;l of serum-free medium and 0.18 &#181;l transfection reagent per well. Mix by vortexing and incubate at room temperature for 5 min.</li>
	<li>Prepare transfection mixes by adding 2 &#181;l of DNA mix to 20 &#181;l of serum-free medium/transfection reagent master mix. Do not vortex. Incubate at room temperature for 10 min.</li>
	<li>Transfect three wells with each transfection mix dispensing 6.5 &#181;l of transfection mix per well. Culture the cells for a further 36-48 hr.</li>
</ol>
4. Measurement of BRET Signal
<ol>
	<li>Dissolve live-cell luciferase substrate at 34 mg/ml in DMSO by vortexing.</li>
	<li>Dilute reconstituted live-cell luciferase substrate at 1:1,000 in substrate dilution medium pre-warmed to 37 &#176;C. Allow 50 &#181;l of substrate dilution medium per well. Vortex to mix. A precipitate may form, but will not interfere with the assay.</li>
	<li>Aspirate the culture medium from the 96-well plate. Dispense 50 &#181;l of diluted live-cell luciferase substrate into each well. Culture cells for at least 2 hr (up to 24 hr).</li>
	<li>Remove the lid from the 96-well plate and incubate the plate for 10 min at room temperature inside the luminometer.</li>
	<li>Measure emission from Luc and YFP one well at a time. Measure emission from Luc using a filter blocking wavelengths longer than 470 nm. Measure emission from YFP using a 500-600 nm band-pass filter. Integrate emission signals over 10 sec.&#160;</li>
</ol>
5. Data Analysis
<ol>
	<li>Average the Luc emission readings from the 3&#160;wells that received only the filler plasmid. Subtract this value from all other Luc emission readings to produce the background-subtracted Luc emission values.</li>
	<li>Average the YFP emission readings from the 3 wells that received only the filler plasmid. Subtract this value from all other YFP emission readings to produce the background-subtracted YFP emission values.</li>
	<li>For each well, divide the background-subtracted YFP emission value by the background-subtracted Luc emission value to give the uncorrected BRET ratio.</li>
	<li>Average the uncorrected BRET ratios from the three wells that were transfected with only the pLuc-control plasmid. Subtract this value from all the other uncorrected BRET ratios to give the corrected BRET ratios.</li>
	<li>For each of the remaining sets of corrected BRET ratios, average the values from the three transfected wells to obtain a final BRET ratio.</li>
</ol>

<ol>
	<li>Suter, B., Kittanakom, S., Stagljar, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two-hybrid+technologies+in+proteomics+research.">Two-hybrid technologies in proteomics research.</a> Curr Opin Biotechnol. 19, 316-323 (2008).</li><li>Gingras, A. C., Gstaiger, M., Raught, B., Aebersold, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+protein+complexes+using+mass+spectrometry.">Analysis of protein complexes using mass spectrometry.</a> Nat Rev Mol Cell Biol. 8, 645-654 (2007).</li><li>Berggard, T., Linse, S., James, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methods+for+the+detection+and+analysis+of+protein-protein+interactions.">Methods for the detection and analysis of protein-protein interactions.</a> Proteomics. 7, 2833-2842 (2007).</li><li>Ciruela, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescence-based+methods+in+the+study+of+protein-protein+interactions+in+living+cells.">Fluorescence-based methods in the study of protein-protein interactions in living cells.</a> Curr Opin Biotechnol. 19, 338-343 (2008).</li><li>Pfleger, K. 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D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extended+bioluminescence+resonance+energy+transfer+(eBRET)+for+monitoring+prolonged+protein-protein+interactions+in+live+cells.">Extended bioluminescence resonance energy transfer (eBRET) for monitoring prolonged protein-protein interactions in live cells.</a> Cell Signal. 18, 1664-1670 (2006).</li><li>Kocan, M., Dalrymple, M., Seeber, R., Feldman, B., Pfleger, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhanced+BRET+technology+for+the+monitoring+of+agonist-induced+and+agonist-independent+interactions+between+GPCRs+and+&#946;-arrestins.">Enhanced BRET technology for the monitoring of agonist-induced and agonist-independent interactions between GPCRs and &#946;-arrestins.</a> Frontiers in Endocrinology. 1, (2011).</li><li>Boute, N., Pernet, K., Issad, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monitoring+the+activation+state+of+the+insulin+receptor+using+bioluminescence+resonance+energy+transfer.">Monitoring the activation state of the insulin receptor using bioluminescence resonance energy transfer.</a> Mol Pharmacol. 60, 640-645 (2001).</li><li>Perroy, J., Pontier, S., Charest, P. G., Aubry, M., Bouvier, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+monitoring+of+ubiquitination+in+living+cells+by+BRET.">Real-time monitoring of ubiquitination in living cells by BRET.</a> Nat Methods. 1, 203-208 (2004).</li><li>Roduit, R., Escher, P., Schorderet, D. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mutations+in+the+DNA-binding+domain+of+NR2E3+affect+in+vivo+dimerization+and+interaction+with+CRX.">Mutations in the DNA-binding domain of NR2E3 affect in vivo dimerization and interaction with CRX.</a> PLoS One. 4, (2009).</li><li>Deriziotis, P., Fisher, S. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neurogenomics+of+speech+and+language+disorders:+the+road+ahead.">Neurogenomics of speech and language disorders: the road ahead.</a> Genome Biol. 14, 204 (2013).</li><li>Green, M. R., Sambrook, 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> Molecular Cloning: A Laboratory Manual. , (2012).</li><li>Lai, C. S., Fisher, S. E., Hurst, J. A., Vargha-Khadem, F., Monaco, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+forkhead-domain+gene+is+mutated+in+a+severe+speech+and+language+disorder.">A forkhead-domain gene is mutated in a severe speech and language disorder.</a> Nature. 413, 519-523 (2001).</li><li>Fisher, S. E., Scharff, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FOXP2+as+a+molecular+window+into+speech+and+language.">FOXP2 as a molecular window into speech and language.</a> Trends Genet. 25, 166-177 (2009).</li><li>Graham, S. A., Fisher, S. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Decoding+the+genetics+of+speech+and+language.">Decoding the genetics of speech and language.</a> Curr Opin Neurobiol. 23, 43-51 (2013).</li><li>O'Roak, B. 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F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=De+novo+mutations+in+FOXP1+in+cases+with+intellectual+disability,+autism,+and+language+impairment.">De novo mutations in FOXP1 in cases with intellectual disability, autism, and language impairment.</a> Am J Hum Genet. 87, 671-678 (2010).</li><li>Talkowski, M. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sequencing+chromosomal+abnormalities+reveals+neurodevelopmental+loci+that+confer+risk+across+diagnostic+boundaries.">Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries.</a> Cell. 149, 525-537 (2012).</li><li>Li, S., Weidenfeld, J., Morrisey, E. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcriptional+and+DNA+binding+activity+of+the+Foxp1/2/4+family+is+modulated+by+heterotypic+and+homotypic+protein+interactions.">Transcriptional and DNA binding activity of the Foxp1/2/4 family is modulated by heterotypic and homotypic protein interactions.</a> Mol Cell Biol. 24, 809-822 (2004).</li><li>MacDermot, K. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+FOXP2+truncation+as+a+novel+cause+of+developmental+speech+and+language+deficits.">Identification of FOXP2 truncation as a novel cause of developmental speech and language deficits.</a> Am J Hum Genet. 76, 1074-1080 (2005).</li><li>Vernes, S. 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The authors declare that they have no competing financial interests.

The design of the fusion protein expression constructs is a critical step in setting up the BRET assay. In the experiments presented here, the proteins of interest were fused to the C-terminus of luciferase or YFP. It is also possible, and may be necessary, to fuse proteins to the N-terminus of luciferase/YFP. For some proteins, fusions may only be accepted at either the N- or C-terminus in order to avoid disruption of protein structure and function. Furthermore, for transmembrane proteins in which the N and C termini re...

Both classical linkage and next-generation sequencing analyses of human disorders are revealing the clinical relevance of proteins involved in a range of biological pathways. It is often the case that, prior to their identification in such studies, there has been little or no investigation of the biological role of these proteins. One fruitful avenue to begin exploring the biological function of a protein of interest is to identify which other proteins it interacts with in its physiological context. Characterizing molecular networks in this fashion provides insights into the biological pathways underlying the human phenotype.
The most frequently used large-scale screening approaches for identifying candidate interaction partners for proteins of interest are yeast two-hybrid screening1 and mass spectrometry-based proteomics2. These methods can be very successful in suggesting potential interacting proteins, but are vulnerable to false positive results. Therefore, confirmation of an interaction identified by yeast two-hybrid or mass spectrometry screening requires validation of the interaction using a second technique. Typically a co-immunoprecipitation or pull-down assay is used for this purpose3. One disadvantage of using such techniques for validation is the requirement for cell lysis, which destroys the intracellular conditions that may be essential for maintaining certain protein interactions. A second disadvantage is that weak or transient protein interactions may be disrupted during washing steps. Furthermore, these assays demand significant hands-on time, are limited in the number of samples that can be processed simultaneously, and often require time-consuming optimization of reagents and protocols.
To overcome some of the problems associated with co-immunoprecipitation experiments, several assays have been developed based on fluorescent and bioluminescent proteins that can be used in live cells. The first such assays were based on Fluorescence (or F&#246;rster) Resonance Energy Transfer (FRET), the non-radiative transfer of energy between two fluorescent proteins with overlapping emission and excitation spectra4. The efficiency of energy transfer is strongly distance-dependent, therefore observation of the FRET phenomenon requires that the donor and acceptor fluorophores be in close proximity. To test for an interaction between two proteins of interest, one protein is expressed as a fusion with the donor fluorophore (commonly cyan fluorescent protein; CFP) and the second as a fusion with the acceptor fluorophore (commonly yellow fluorescent protein; YFP). An interaction between the two proteins of interest may bring the donor and acceptor fluorophores sufficiently close for energy transfer to occur, which will result in a measurable increase in the emission of light from the YFP acceptor relative to the CFP donor. FRET has been successful in detecting protein-protein interactions in live cells4. The main drawback of using FRET for detecting protein-protein interactions is the requirement for external illumination for excitation of the donor fluorophore. External illumination results in high background in the emission signal, unwanted excitation of the acceptor, and photobleaching of both donor and acceptor fluorophores. These effects reduce the sensitivity of the assay for detecting protein-protein interactions.
A modification of the FRET assay which overcomes the problem of high background from external illumination is the Bioluminescence Resonance Energy Transfer (BRET) assay5,6. In the BRET system the donor fluorophore is replaced by a luciferase enzyme. Thus the energy for the excitation of the acceptor fluorophore is generated within the system by the oxidation of a luciferase substrate, rendering external illumination unnecessary. In the most common configuration of this assay, the donor is Renilla reniformis luciferase and the acceptor is YFP (for a discussion of alternative donor and acceptor proteins see Pfleger&#160;et al.5). Accordingly, in this system, a protein of interest is fused to luciferase and a potentially-interacting protein to YFP, or vice versa. The BRET assay requires the addition of coelenterazine as a substrate for luciferase. Because coelenterazine is cell-permeable, it is possible to perform BRET assays in live cells. However, native coelenterazine is unstable in aqueous solution, and the enzyme-independent breakdown of coelenterazine both reduces the concentration of substrate available for the assay and generates autoluminescence, which reduces the sensitivity of measurements of luciferase activity. The use of BRET in live cells has been facilitated by the development of protected coelenterazines, which are stable in aqueous solution but are cleaved by cytosolic esterases after diffusion across the cell membrane to generate active coelenterazine inside the cell7.
Following addition of substrate to cells expressing luciferase- and YFP-fusion proteins, energy transfer resulting from protein-protein interactions is quantified by monitoring emission from luciferase and YFP. Because protein interactions can be monitored directly in live cells in multi-well plates, the BRET assay constitutes a simple, scalable method for validating putative interactions that is cost- and time-efficient.
In addition to validating putative interactors identified in proteomic screening studies, the BRET system can also be used to test candidate interactors arising from prior biochemical and structural studies on the protein of interest. Once the existence of a protein-protein interaction has been established (either by using the BRET assay or by other techniques), there is potential for the BRET assay to be employed further to characterize the interaction. For example, the interacting regions can be mapped by generating truncated versions of the proteins, and the involvement of specific residues in the interaction can be demonstrated by creating point mutations. Furthermore, the modulatory effect of posttranslational modifications or small molecules (such as drugs or ligands) on protein-protein interactions can be investigated8-10.
The BRET assay also has great potential for investigating mutations identified in patient DNA. In cases where a causative role for a mutation has been established, studying the effect of the mutation on protein-protein interactions using BRET may reveal more about the molecular etiology of the phenotype11. Since the advent of next-generation sequencing methodologies, it is increasingly common for several potentially-damaging mutations to be identified within an individual, in which case it is unclear which are relevant to the phenotype12. In this situation the BRET assay may be valuable in evaluating the impact of mutations on protein function and hence their relevance to the disorder.

<table border="0" cellpadding="0" cellspacing="0" width="1333">
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:276px;">Nanodrop 8000</td>
			<td style="width:123px;">Nanodrop</td>
			<td style="width:155px;"></td>
			<td style="width:780px;">Any spectrophotometer capable of reading absorbances at 260 nm will be suitable. Determining the molecular mass of the plasmid is crucial for calculating DNA quantities to be used in transfection mixes.</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;">96 microwell plates, flat bottom, white</td>
			<td>Greiner Bio One</td>
			<td>655098</td>
			<td style="width:780px;">White plates reduce the crosstalk between wells and maximize the sensitivity of luminescence detection. Clear-bottomed wells allow monitoring of cell density. Plates must be suitable for cell culture. If using a top-reading luminometer the plate lid should be taken off.</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:276px;">Infinite F200Pro plate reader with control software</td>
			<td>TECAN</td>
			<td></td>
			<td style="width:780px;">Use the &#39;Blue 1&#39; and &#39;Green 1&#39; filters for luminescence measurement and the filter sets and dichoic mirror for GFP for fluorescence measurement. Any top-reading plate reader with capability of measuring dual-color luminescence and fluorescence is suitable.&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pLuc, pYFP, positive control plasmid</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Plasmids available from the authors upon request.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pGEM-3Zf(+)</td>
			<td>Promega</td>
			<td>P2271</td>
			<td>Filler plasmid for equilization of DNA mass in transfection mixes. Any plasmid lacking a eukaryotic promoter would be suitable.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HEK293 cells</td>
			<td>ECACC</td>
			<td>85120602</td>
			<td>Other cell lines that transfect with reasonable efficiency may be suitable.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">DMEM, high glucose, with phenol red</td>
			<td>Gibco</td>
			<td>41966</td>
			<td style="width:780px;">This is the medium used for culturing HEK293 cells. Warm in 37 &#176;C waterbath before use. If using a different cell line, replace the growth medium described here with cell-line specific medium.</td>
		</tr>
		<tr height="67">
			<td height="67" style="height:67px;">DMEM, high glucose, no phenol red (substrate dilution medium)</td>
			<td>Gibco</td>
			<td>21063</td>
			<td style="width:780px;">This is the substrate dilution medium used for dilution of the luciferase substrate (EnduRen) as it does not contain phenol red, which reduces the sensitivity of the assay. Contains HEPES to maintain correct pH during luminescence measurements while cells are out of the CO2 incubator. Warm in 37 &#176;C waterbath before use.</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">OptiMEM</td>
			<td>Gibco</td>
			<td>31985</td>
			<td style="width:780px;">OptiMEM is used for dilution of GeneJuice transfection reagent. Other serum-free media would also be suitable. Warm to room temperature before use.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fetal bovine serum</td>
			<td>Gibco</td>
			<td>10270</td>
			<td>For supplementation of cell culture media at a concentration of 10% v/v.</td>
		</tr>
		<tr height="84">
			<td height="84" style="height:84px;">GeneJuice transfection reagent</td>
			<td>Novagen</td>
			<td>70967</td>
			<td style="width:780px;">If using a cell line other than HEK293, it may be necessary to adjust the ratio of Genejuice transfection reagent to DNA in the transfection mixes. Other transfection reagents may be used. If using an alternative transfection reagent, it may be necessary to optimize the amount of DNA used in the transfection mixes based on manufacturer&#39;s instructions.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DMSO</td>
			<td>Sigma</td>
			<td>D2650</td>
			<td style="width:780px;">Use sterile DMSO that is suitable for tissue culture.&#160;</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;">EnduRen live-cell substrate</td>
			<td>Promega</td>
			<td>E6481</td>
			<td style="width:780px;">Reconstitute EnduRen at 34 mg/ml in DMSO. Upon dilution of EnduRen in culture medium a precipitate may form. This will not interfere with the assay. Store reconstituted EnduRen at -20 &#176;C, and avoid multiple freeze-thaw cycles. Ensure that reconstituted EnduRen is completely thawed before diluting it in culture medium.</td>
		</tr>
	</tbody>
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investigating protein-protein interactions in live cells using bioluminescence resonance energy transfer

Assays based on Bioluminescence Resonance Energy Transfer (BRET) provide a sensitive and reliable means to monitor protein-protein interactions in live cells. BRET is the non-radiative transfer of energy from a 'donor' luciferase enzyme to an 'acceptor' fluorescent protein. In the most common configuration of this assay, the donor is Renilla reniformis luciferase and the acceptor is Yellow Fluorescent Protein (YFP). Because the efficiency of energy transfer is strongly distance-dependent, observation of the BRET phenomenon requires that the donor and acceptor be in close proximity. To test for an interaction between two proteins of interest in cultured mammalian cells, one protein is expressed as a fusion with luciferase and the second as a fusion with YFP. An interaction between the two proteins of interest may bring the donor and acceptor sufficiently close for energy transfer to occur. Compared to other techniques for investigating protein-protein interactions, the BRET assay is sensitive, requires little hands-on time and few reagents, and is able to detect interactions which are weak, transient, or dependent on the biochemical environment found within a live cell. It is therefore an ideal approach for confirming putative interactions suggested by yeast two-hybrid or mass spectrometry proteomics studies, and in addition it is well-suited for mapping interacting regions, assessing the effect of post-translational modifications on protein-protein interactions, and evaluating the impact of mutations identified in patient DNA.

The principle of the BRET assay is illustrated in Figure 2. The assay setup used throughout the experiments presented here is depicted in Figure 3. The detection of a strong BRET signal from cells transfected with a luciferase-YFP fusion protein confirmed that energy transfer was observable in this experimental setup (Figure 4).
Our research focuses on the role of the FOXP family of transcriptional repressors in brain development. Heterozygous...

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Investigating Protein-protein Interactions in Live Cells Using Bioluminescence Resonance Energy Transfer

Interactions between proteins are fundamental to all cellular processes. Using Bioluminescence Resonance Energy Transfer, the interaction between a pair of proteins can be monitored in live cells and in real time. Furthermore, the effects of potentially pathogenic mutations can be assessed.

Assays based on Bioluminescence Resonance Energy Transfer (BRET) provide a sensitive and reliable means to monitor protein-protein interactions in live ...

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22.8K Views.  Max Planck Institute for Psycholinguistics. Interactions between proteins are fundamental to all cellular processes. Using Bioluminescence Resonance Energy Transfer, the interaction between a pair of proteins can be monitored in live cells and in real time. Furthermore, the effects of potentially pathogenic mutations can be assessed.

Video: Investigating Protein-protein Interactions in Live Cells Using Bioluminescence Resonance Energy Transfer

Microfluidic Co-culture of Epithelial Cells and Bacteria for Investigating Soluble Signal-mediated Interactions

The human gastrointestinal (GI) tract is a unique environment in which intestinal epithelial cells and non-pathogenic (commensal) bacteria coexist. It has been proposed that the microenvironment that the pathogen encounters in the commensal layer is important in determining the extent of colonization. Current culture methods for investigating pathogen colonization are not well suited for investigating this hypothesis as they do not enable co-culture of bacteria and epithelial cells in a manner that mimics the GI tract microenvironment. Here we describe a microfluidic co-culture model that enables independent culture of eukaryotic cells and bacteria, and testing the effect of the commensal microenvironment on pathogen colonization. The co-culture model is demonstrated by developing a commensal Escherichia coli biofilm among HeLa cells, followed by introduction of enterohemorrhagic E. coli (EHEC) into the commensal island, in a sequence that mimics the sequence of events in GI tract infection.

This protocol describes a microfluidic co-culture model for simultaneous and localized culture of epithelial cells and bacteria. This model can be used for investigating the role of different soluble molecular signals on pathogenesis as well as screen the effectiveness of putative probiotic bacterial strains.

The human gastrointestinal (GI) tract is a unique environment in which intestinal epithelial cells and non-pathogenic (commensal) bacteria coexist. It has ...

Investigating Tissue- and Organ-specific Phytochrome Responses using FACS-assisted Cell-type Specific Expression Profiling in Arabidopsis thaliana

Light mediates an array of developmental and adaptive processes throughout the life cycle of a plant. Plants utilize light-absorbing molecules called photoreceptors to sense and adapt to light. The red/far-red light-absorbing phytochrome photoreceptors have been studied extensively. Phytochromes exist as a family of proteins with distinct and overlapping functions in all higher plant systems in which they have been studied1. Phytochrome-mediated light responses, which range from seed germination through flowering and senescence, are often localized to specific plant tissues or organs2. Despite the discovery and elucidation of individual and redundant phytochrome functions through mutational analyses, conclusive reports on distinct sites of photoperception and the molecular mechanisms of localized pools of phytochromes that mediate spatial-specific phytochrome responses are limited. We designed experiments based on the hypotheses that specific sites of phytochrome photoperception regulate tissue- and organ-specific aspects of photomorphogenesis, and that localized phytochrome pools engage distinct subsets of downstream target genes in cell-to-cell signaling. We developed a biochemical approach to selectively reduce functional phytochromes in an organ- or tissue-specific manner within transgenic plants. Our studies are based on a bipartite enhancer-trap approach that results in transactivation of the expression of a gene under control of the Upstream Activation Sequence (UAS) element by the transcriptional activator GAL43. The biliverdin reductase (BVR) gene under the control of the UAS is silently maintained in the absence of GAL4 transactivation in the UAS-BVR parent4. Genetic crosses between a UAS-BVR transgenic line and a GAL4-GFP enhancer trap line result in specific expression of the BVR gene in cells marked by GFP expression4. BVR accumulation in Arabidopsis plants results in phytochrome chromophore deficiency in planta5-7. Thus, transgenic plants that we have produced exhibit GAL4-dependent activation of the BVR gene, resulting in the biochemical inactivation of phytochrome, as well as GAL4-dependent GFP expression. Photobiological and molecular genetic analyses of BVR transgenic lines are yielding insight into tissue- and organ-specific phytochrome-mediated responses that have been associated with corresponding sites of photoperception4, 7, 8. Fluorescence Activated Cell Sorting (FACS) of GFP-positive, enhancer-trap-induced BVR-expressing plant protoplasts coupled with cell-type-specific gene expression profiling through microarray analysis is being used to identify putative downstream target genes involved in mediating spatial-specific phytochrome responses. This research is expanding our understanding of sites of light perception, the mechanisms through which various tissues or organs cooperate in light-regulated plant growth and development, and advancing the molecular dissection of complex phytochrome-mediated cell-to-cell signaling cascades.

Investigating Tissue- and Organ-specific Phytochrome Responses using FACS-assisted Cell-type Specific Expression Profiling in Arabidopsis thaliana

The molecular basis of spatial-specific phytochrome responses is being investigated using transgenic plants that exhibit tissue- and organ-specific phytochrome deficiencies. The isolation of specific cells exhibiting induced phytochrome chromophore depletion by Fluorescence-Activated Cell Sorting followed by microarray analyses is being utilized to identify genes involved in spatial-specific phytochrome responses.

Light mediates an array of developmental and adaptive processes throughout the life cycle of a plant. Plants utilize light-absorbing molecules called ...

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

Unraveling the interaction network of molecules in-vivo is key to understanding the mechanisms that regulate cell function and metabolism. A multitude of methodological options for addressing molecular interactions in cells have been developed, but most of these methods suffer from being rather indirect and therefore hardly quantitative. On the contrary, a few high-end quantitative approaches were introduced, which however are difficult to extend to high throughput. To combine high throughput capabilities with the possibility to extract quantitative information, we recently developed a new concept for identifying protein-protein interactions (Schwarzenbacher et al., 2008). Here, we describe a detailed protocol for the design and the construction of this system which allows for analyzing interactions between a fluorophore-labeled protein ("prey") and a membrane protein ("bait") in-vivo. Cells are plated on micropatterned surfaces functionalized with antibodies against the bait exoplasmic domain. Bait-prey interactions are assayed via the redistribution of the fluorescent prey. The method is characterized by high sensitivity down to the level of single molecules, the capability to detect weak interactions, and high throughput capability, making it applicable as screening tool.

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

This video shows experiments with subsequent analysis of protein-protein interactions by the use of micro-patterned surfaces. The approach offers the possibility to detect protein interactions in living cells and combines high throughput capabilities with the possibility to extract quantitative information.

Unraveling the interaction network of molecules in-vivo is key to understanding the mechanisms that regulate cell function and metabolism. A multitude of ...

Imaging Protein-protein Interactions in vivo

Protein-protein interactions are a hallmark of all essential cellular processes. However, many of these interactions are transient, or energetically weak, preventing their identification and analysis through traditional biochemical methods such as co-immunoprecipitation. In this regard, the genetically encodable fluorescent proteins (GFP, RFP, etc.) and their associated overlapping fluorescence spectrum have revolutionized our ability to monitor weak interactions in vivo using F&ouml;rster resonance energy transfer (FRET)1-3. Here, we detail our use of a FRET-based proximity assay for monitoring receptor-receptor interactions on the endothelial cell surface.

Imaging Protein-protein Interactions in vivo

This protocol describes how to image protein-protein interactions using a FRET-based proximity assay.

Protein-protein interactions are a hallmark of all essential cellular processes. However, many of these interactions are transient, or energetically weak, ...

Real-time Monitoring of Ligand-receptor Interactions with Fluorescence Resonance Energy Transfer

FRET is a process whereby energy is non-radiatively transferred from an excited donor molecule to a ground-state acceptor molecule through long-range dipole-dipole interactions1. In the present sensing assay, we utilize an interesting property of PDA: blue-shift in the UV-Vis electronic absorption spectrum of PDA (Figure 1) after an analyte interacts with receptors attached to PDA2,3,4,7. This shift in the PDA absorption spectrum provides changes in the spectral overlap (J) between PDA (acceptor) and rhodamine (donor) that leads to changes in the FRET efficiency. Thus, the interactions between analyte (ligand) and receptors are detected through FRET between donor fluorophores and PDA. In particular, we show the sensing of a model protein molecule streptavidin. We also demonstrate the covalent-binding of bovine serum albumin (BSA) to the liposome surface with FRET mechanism. These interactions between the bilayer liposomes and protein molecules can be sensed in real-time. The proposed method is a general method for sensing small chemical and large biochemical molecules. Since fluorescence is intrinsically more sensitive than colorimetry, the detection limit of the assay can be in sub-nanomolar range or lower8. Further, PDA can act as a universal acceptor in FRET, which means that multiple sensors can be developed with PDA (acceptor) functionalized with donors and different receptors attached on the surface of PDA liposomes.

We demonstrate FRET between conjugated polymer polydiacetylene (PDA) and fluorophore attached to the surface of PDA liposomes for the sensing of biomolecules. PDA liposomes also contained receptor molecules on their surfaces for biomolecules to be used as probes. Ligand-receptor interactions lead to changes in the FRET efficiency between the fluorophore and PDA which is the basis of the sensing mechanism.

FRET is a process  whereby energy is non-radiatively transferred from an excited donor molecule to  a ground-state acceptor molecule through long-range ...

Protein-protein Interactions Visualized by Bimolecular Fluorescence Complementation in Tobacco Protoplasts and Leaves

Many proteins interact transiently with other proteins or are integrated into multi-protein complexes to perform their biological function. Bimolecular fluorescence complementation (BiFC) is an in vivo method to monitor such interactions in plant cells. In the presented protocol the investigated candidate proteins are fused to complementary halves of fluorescent proteins and the respective constructs are introduced into plant cells via agrobacterium-mediated transformation. Subsequently, the proteins are transiently expressed in tobacco leaves and the restored fluorescent signals can be detected with a confocal laser scanning microscope in the intact cells. This allows not only visualization of the interaction itself, but also the subcellular localization of the protein complexes can be determined. For this purpose, marker genes containing a fluorescent tag can be coexpressed along with the BiFC constructs, thus visualizing cellular structures such as the endoplasmic reticulum, mitochondria, the Golgi apparatus or the plasma membrane. The fluorescent signal can be monitored either directly in epidermal leaf cells or in single protoplasts, which can be easily isolated from the transformed tobacco leaves. BiFC is ideally suited to study protein-protein interactions in their natural surroundings within the living cell. However, it has to be considered that the expression has to be driven by strong promoters and that the interaction partners are modified due to fusion of the relatively large fluorescence tags, which might interfere with the interaction mechanism. Nevertheless, BiFC is an excellent complementary approach to other commonly applied methods investigating protein-protein interactions, such as coimmunoprecipitation, in vitro pull-down assays or yeast-two-hybrid experiments.

Formation of protein complexes in vivo can be visualized by bimolecular fluorescence complementation. Interaction partners are fused to complementary parts of fluorescent tags and transiently expressed in tobacco leaves, resulting in a reconstituted fluorescent signal upon close proximity of the two proteins.

Many proteins interact transiently with other proteins or are integrated into multi-protein complexes to perform their biological function. Bimolecular ...

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

High-density functional protein microarrays containing ~4,200 recombinant yeast proteins are examined for kinase protein-protein interactions using an affinity purified yeast kinase fusion protein containing a V5-epitope tag for read-out. Purified kinase is obtained through culture of a yeast strain optimized for high copy protein production harboring a plasmid containing a Kinase-V5 fusion construct under a GAL inducible promoter. The yeast is grown in restrictive media with a neutral carbon source for 6 hr followed by induction with 2% galactose. Next, the culture is harvested and kinase is purified using standard affinity chromatographic techniques to obtain a highly purified protein kinase for use in the assay. The purified kinase is diluted with kinase buffer to an appropriate range for the assay and the protein microarrays are blocked prior to hybridization with the protein microarray. After the hybridization, the arrays are probed with monoclonal V5 antibody to identify proteins bound by the kinase-V5 protein. Finally, the arrays are scanned using a standard microarray scanner, and data is extracted for downstream informatics analysis1,2 to determine a high confidence set of protein interactions for downstream validation in vivo.

Using protein microarrays containing nearly the entire S. cerevisiae proteome is probed for rapid unbiased interrogation of thousands of protein-protein interactions in parallel. This method can be utilized for protein-small molecule, posttranslational modification, and other assays in high-throughput.

High-density functional protein microarrays containing ~4,200 recombinant yeast proteins are examined for kinase protein-protein interactions using an ...

Real Time Measurements of Membrane Protein:Receptor Interactions Using Surface Plasmon Resonance (SPR)

Protein-protein interactions are pivotal to most, if not all, physiological processes, and understanding the nature of such interactions is a central step in biological research. Surface Plasmon Resonance (SPR) is a sensitive detection technique for label-free study of bio-molecular interactions in real time. In a typical SPR experiment, one component (usually a protein, termed 'ligand') is immobilized onto a sensor chip surface, while the other (the 'analyte') is free in solution and is injected over the surface. Association and dissociation of the analyte from the ligand are measured and plotted in real time on a graph called a sensogram, from which pre-equilibrium and equilibrium data is derived. Being label-free, consuming low amounts of material, and providing pre-equilibrium kinetic data, often makes SPR the method of choice when studying dynamics of protein interactions. However, one has to keep in mind that due to the method's high sensitivity, the data obtained needs to be carefully analyzed, and supported by other biochemical methods. 
SPR is particularly suitable for studying membrane proteins since it consumes small amounts of purified material, and is compatible with lipids and detergents. This protocol describes an SPR experiment characterizing the kinetic properties of the interaction between a membrane protein (an ABC transporter) and a soluble protein (the transporter's cognate substrate binding protein).

Real Time Measurements of Membrane Protein:Receptor Interactions Using Surface Plasmon Resonance SPR

Surface Plasmon Resonance (SPR) is a label-free method for detecting bio-molecular interactions in real time. Herein, a protocol for a membrane protein:receptor interaction experiment is described, while discussing the pros and cons of the technique.

Protein-protein interactions are pivotal to most, if not all, physiological processes, and  understanding the nature of such interactions is a central ...

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 ...

A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.

We present a software solution for semi-automated tracking of relative protein concentration along the length of dynamic cellular protrusions.

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex ...

Investigating Protein-protein Interactions in Live Cells Using Bioluminescence Resonance Energy Transfer

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Microfluidic Co-culture of Epithelial Cells and Bacteria for Investigating Soluble Signal-mediated Interactions

Investigating Tissue- and Organ-specific Phytochrome Responses using FACS-assisted Cell-type Specific Expression Profiling in Arabidopsis thaliana

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

Imaging Protein-protein Interactions in vivo

Real-time Monitoring of Ligand-receptor Interactions with Fluorescence Resonance Energy Transfer

Protein-protein Interactions Visualized by Bimolecular Fluorescence Complementation in Tobacco Protoplasts and Leaves

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Real Time Measurements of Membrane Protein:Receptor Interactions Using Surface Plasmon Resonance (SPR)

Identifying Protein-protein Interaction Sites Using Peptide Arrays

A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions