We thank the generous support of several foundations and philanthropic donors (see SakmarLab.org).

1. Site-specific Genetic Incorporation of Unnatural Amino Acids into GPCRs
<ol>
	<li>Maintain HEK293T cells in DMEM (4.5 g/L of glucose, 2 mM glutamine) supplemented with 10% fetal bovine serum (FBS) at 37 &#176;C in a 5% CO2 atmosphere.</li>
	<li>Transfect the cells grown to 60-80% confluence in a 10-cm plate using Lipofectamine Plus reagent.
	<ol>
		<li>To 750 &#956;l DMEM, add 10 &#956;l Plus reagent, 3.5 &#956;g of GPCR cDNA (pMT4. Rho or pcDNA 3.1. CCR5) containing the amber stop codon at a desired position, 3.5 &#956;g of suppressor tRNA cDNA (pSVB.Yam) and 0.35 &#956;g of mutant amino-acyl tRNA synthetase cDNA for p-azido-L-phenylalanine (pcDNA.RS). Incubate at room temperature for 15 min. Also perform a similar transfection using the wt GPCR cDNA (not containing an amber stop codon) to serve as a control. Add this mixture to 750 &#956;l of DMEM with 17 &#956;l Lipofectamine. After equilibrating 15 min at room temperature, bring the total volume to 4 ml.</li>
		<li>Aspirate media on 10-cm plate, apply transfection mixture to cells, and return to 37 &#176;C in 5% CO2 atmosphere. After 4-6 hr, supplement cells with 4 ml DMEM containing 20% FBS and 1 mM azF.</li>
	</ol>
	</li>
	<li>The next day, replace the growth media with DMEM containing 10% FBS and 0.5 mM azF.</li>
	<li>Harvest cells 48 hr post-transfection, to analyze expression or proceed to photocrosslinking or labeling procedures described in the following sections.
	<ol>
		<li>Confirm expression of the GPCR amber mutant in the presence of the UAA in the growth media. We do this by Western immunoblot detection. Lyse the cell pellet in 1% (w/v) dodecyl-&#946;-D-maltoside (DDM) in 20 mM Tris-HCl, pH 7.5, 100 mM NaCl for 1 hr at 4 &#176;C. Centrifuge the lysate at 16,000 x g and resolve the supernatant under reducing conditions by SDS-PAGE. Transfer to a PVDF membrane and carry out immunoblot analysis to detect full-length receptor expression using the 1D4 mAb (National Cell Culture Center), which recognizes an engineered epitope at the C-terminus of the receptor.31</li>
	</ol>
	</li>
</ol>
2. Mapping a Ligand Binding Site Using Targeted Photocrosslinking
<ol>
	<li>48 hr post-transfection, aspirate media from cells and replace with 4 ml 1x Phosphate Buffered Saline (PBS). Return to 37 &#176;C for 15 min.</li>
	<li>Resuspend the cells with 1x PBS and transfer to a Falcon tube. Centrifuge at 1,500 rpm for 2 min to pellet the cells and aspirate the supernatant.</li>
	<li>Resuspend the cell pellet in 1x Hank&#39;s Buffered Salt Solution containing 20 mM HEPES, pH 7.5, 0.2% BSA and the tritiated ligand at saturating binding concentration for the required length of time and temperature to ensure receptor-ligand complex formation.</li>
	<li>Transfer the cell suspension to a 24-well or 96-well plate for photoactivation of the azF at 365 nm (e.g. use a UV-A lamp) for 15 min at 4 &#176;C. Maintain the plate on ice to avoid sample heating and cell lysis.</li>
	<li>Transfer the cells to an Eppendorf tube, centrifuge to pellet the cells, remove the supernatant and proceed to analysis. The pellets can be stored at -20 &#176;C for future use.</li>
	<li>Resuspend the cell pellets in lysis buffer containing 1% (w/v) DDM, 20 mM Tris-HCl, pH 7.5 and protease inhibitors. After 1-hr incubation at 4 &#176;C, centrifuge the cell lysate for 10 min at 16,000 x g, and transfer the supernatant to a new tube.</li>
	<li>Add 1D4 mAb-sepharose 2B resin to the supernatant and incubate overnight at 4 &#176;C to immunopurify the GPCR using the engineered C-terminus 1D4 mAb epitope. Next day wash the beads several times with lysis buffer. Elute samples with 1% SDS at 37 &#176;C for 1 hr with shaking.</li>
	<li>Transfer a portion of the eluent to a 15 ml vial containing scintillation fluid and count on a beta scintillation counter to quantify the amount of specific binding of the tritiated ligand to the receptor.</li>
	<li>Resolve the remaining 1D4 mAb purified eluent by standard gel electrophoresis. We use a 4-12% SDS-PAGE gel and then semi-dry transfer to a PVDF membrane for immunoblotting. We also include a lane with standard protein ladder to guide visual approximation of molecular weight.
	<ol>
		<li>Block the PVDF membrane with 5% milk in TBS buffer containing 0.05% Tween-20. Probe the membrane to confirm full-length receptor expression with 1D4 mAb followed by HRP-conjugated anti-mouse IgG secondary antibody.</li>
		<li>Treat with enhanced chemiluminescence (ECL) reagent and expose membrane to autoradiography film to visualize bands.</li>
	</ol>
	</li>
	<li>Cut the membrane with a razor blade to separate each sample lane, followed by cutting at specific molecular weight markers. Transfer membrane segments to vials containing scintillation fluid. Quantify the amount of tritium in each membrane segment by counting on a beta-scintillation counter.</li>
	<li>Identify the positive photocrosslink with the detection of tritium at the apparent molecular mass equal to the sum of that of the GPCR and the ligand.</li>
</ol>
3. Targeted Epitope Tagging and Cell Surface Enzyme-linked Immunosorbent Assay (ELISA)
<ol>
	<li>24 hr post-transfection, wash cells with 1 ml 1x PBS and trypsinize with 1 ml 0.25% trypsin for 3 min. Supplement with 9 ml DMEM containing 10% FBS and 0.5 mM azF. Resuspend cells and count the cell density. We use a standard hemocytometer.</li>
	<li>Pre-treat a high-binding, clear-bottom 96-well plate with 100 ml of 0.01 mg/ml poly-D-lysine per well. Incubate for 30 min at room temperature, wash repeatedly with 1x PBS and air-dry.</li>
	<li>Plate 200 &#956;l of the transfected cells at a density of 6 x 104 - 8 x 104 cells/well to the 96-well plate and return to 37 &#176;C in 5% CO2 atmosphere.</li>
	<li>Next day prepare cells for labeling. Gently wash three times with 100 &#956;l/well 1x PBS to remove any azF containing growth media. Ensure cells remain adhered, for example, by using PBS containing Ca2+ and Mg2+.</li>
	<li>Prepare 50-200 &#956;M FLAG-triarylphosphine labeling reagent in 1x HBSS/PBS from a stock maintained at 5-20 mM in PBS. Apply 60 ml to each well (in triplicate for each amber mutant) and return to 37 &#176;C for 30 min to 4 hr. Maintain a set of wells without label treatment in 1x HBSS/PBS. Also include a wt GPCR control to compare with azF-GPCR variants.</li>
	<li>Wash cells 3 times with 100 &#956;l/well of blocking buffer, BB (1x PBS, 0.5% BSA), to remove unreacted label completely.</li>
	<li>Apply 100 &#956;l/well of 4% paraformaldehyde (prepared from a 16% stock in 1x PBS) to the cells. Incubate for 20 min at room temperature. Wash three times with BB.</li>
	<li>Perform standard cell surface ELISA protocol to detect labeled receptor and receptor expression. Incubate with primary antibody for 1.5 hr on ice followed by secondary antibody incubation at room temperature for 1 hr.
	<ol>
		<li>Add 100 &#956;l of anti-FLAG M2 antibody (e.g. 1:2,000 dilution of antibody made in BB) to detect FLAG peptide epitope of the FLAG-triarylphosphine labeling reagent. Also probe non-label treated wells as a negative control. Add anti-CCR5 2D7 (we use a 1:500 dilution) antibody to a separate set of wells to determine wt or azF-GPCR cell surface expression.</li>
		<li>Wash cells three times with BB, and incubate with 100 &#956;l of HRP-conjugated anti-mouse IgG secondary antibody (1:2,000 dilution).</li>
		<li>Carefully wash cells five times with BB. Add 50 &#956;l detection buffer: Amplex Red, 20 mM H2O2, 1x PBS (1:10:90 ratio) and incubate 15 min at room temperature. Collect spectral data on a fluorescence multi-well plate reader at &#955;ex=530 and &#955;em=590.</li>
	</ol>
	</li>
</ol>
4. Bioorthogonal Fluorescent Labeling of a GPCR
<ol>
	<li>Lyse 107 harvested cells expressing wt or azF-Rhodopsin variants in 1 ml solubilization buffer containing 1% (w/v) DM, 50 mM HEPES or Tris-HCl, pH 6.8, 100 mM NaCl, 1 mM CaCl2 and protease inhibitors for 1 hr at 4 &#176;C. Centrifuge the cell lysate at 15,000 x g for 10 min and collect the supernatant fraction.</li>
	<li>Add 100 &#956;l 1D4-mAb sepharose 2B resin to capture receptor using the engineered C terminus 1D4 epitope. Incubate for 12 hr at 4 &#176;C. Wash the resin three times with 0.1% (w/v) DDM in 0.1 M sodium phosphate buffer, pH 7.3.</li>
	<li>Add 0.1 mM Fluorescein-phosphine in a total volume of 0.3 - 0.5 ml to label receptor immobilized on the immunoaffinity matrix (1D4-mAb sepharose 2B). Incubate for 12 hr at room temperature. Centrifuge and remove supernatant. Wash the resin to remove unreacted label.</li>
	<li>Elute the labeled receptor with 100 ml elution buffer containing 0.1% (w/v) DDM and 0.33 mg/ml nonapeptide (C9 peptide against the 1D4 epitope) in 2 mM phosphate buffer, pH 6.0 by incubation on ice for 1 hr.</li>
	<li>Resolve labeled samples by SDS-PAGE under reducing conditions. Wash gels briefly in PBS and then visualize labeling of azF-GPCR by in-gel fluorescence. For example, use a confocal fluorescence scanner with a 488-nm wavelength laser to detect receptor modified with fluorescein.</li>
</ol>

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Ed. 45, 7581-7584 (2006).</li><li>Yanagisawa, T., 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=Multistep+engineering+of+pyrrolysyl-tRNA+synthetase+to+genetically+encode+N(epsilon)-(o-azidobenzyloxycarbonyl)+lysine+for+site-specific+protein+modification.">Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification.</a> Chemistry &amp; biology. 15, 1187-1197 (2008).</li></ol>

Authors have nothing to disclose.

We describe here a robust methodology for site-specific incorporation of a reactive probe, azF, into GPCRs and demonstrate three useful applications of this tool to study the structure and dynamics of GPCRs. Our method to site-specifically incorporate UAAs circumvents a fundamental problem with an alternative strategy based on chemically labeling32, 33 or attaching photocrosslinkers34 to a single accessible cysteine mutant. Although, chemistries that target cysteine thiol groups have been used to at...

Heptahelical G protein-coupled receptors (GPCRs) comprise a superfamily of highly dynamic membrane proteins that mediate important and diverse extracellular signals. In the classical paradigm, receptor activation is coupled with ligand-induced conformational changes.1, 2 Recent advancements in structural biology of GPCRs have provided significant insight on the molecular mechanisms of transmembrane signaling.3-5 However, to understand with greater chemical precision the functional mechanism and structural dynamics of GPCR signaling, a toolkit of approaches is required to incorporate informative molecular and chemical probes to interrogate active signaling complexes.
To this end, we adapted a method to site-specifically introduce non- or minimally perturbing probes into expressed receptors based on unnatural amino acid (UAA) mutagenesis using amber codon suppression technology previously pioneered by Schultz and coworkers.6 We optimized the UAA mutagenesis methodology to achieve a high-yield expression and mutagenesis system for proteins such as GPCRs, which are difficult to express in most heterologous systems other than mammalian cells. Using an orthogonal engineered suppressor tRNA and evolved aminoacyl-tRNA synthetase pair for a specific UAA, we site-specifically introduced UAAs in expressed target GPCRs. The successful incorporation of UAAs, p-acetyl-L-phenylalanine (AcF), p-benzoyl-L-phenylalanine (BzF), and p-azido-L-phenylalanine (azF) has been demonstrated in our model GPCRs - rhodopsin and human C-C chemokine receptor, CCR5.7, 8
In principle, an UAA can be genetically encoded at any position within the protein sequence and this property is an invaluable biochemical tool as it enables single-codon scanning of a target GPCR. We focus here specifically on the versatility of the UAA, azF, which has a reactive azido moiety. In addition to serving as a unique infrared (IR) probe,8, 9 azF can also serve as a photoactivatable cross-linker by reacting with neighboring primary amines or aliphatic hydrogens. Additionally, the biologically inert azido group can participate as a selective chemical handle in bioorthogonal labeling reactions. Here we present examples illustrating the useful applications of site-specific incorporation of azF into GPCRs, such as targeted photocrosslinking to trap a receptor-ligand complex, and modification of GPCRs by bioorthogonal epitope tagging and fluorescent labeling strategies.
Photoactivatable reagents have been used to study biological systems since the 1960s.10 In this period, an abundance of receptor-ligand crosslinking experiments have been reported to study GPCR complexes, most of which involved the use of photoaffinity ligands.11, 12 However, these applications are technically limited, as they require synthesis of ligands bearing a crosslinking group.13-15 Moreover, with the crosslinker moiety in the ligand, it is challenging to identify the location of the crosslink on the GPCR. Site-specifically introducing photocrosslinking groups as UAAs into proteins using the amber codon suppression technology is a valuable advancement. 16, 17 We developed a photocrosslinking technique to identify the binding interface on a receptor that is involved in the formation of a receptor-ligand complex in live cells by introducing photolabile groups into GPCRs.18, 19 Here we describe the experimental protocol and method of data analysis for applying this targeted photocrosslinking technology to identify the binding site of a small-molecule ligand, tritiated maraviroc, on CCR5. This method capitalizes on the precise quantification of the radioactive handle on the ligand, in addition to retaining the native chemical structure of the ligand.
Fluorescence-based techniques support the precise understanding of the structural basis of receptor activation by directly probing the conformational state of the receptor.20, 21 However, techniques possessing the flexibility to introduce fluorescent labels into GPCRs site-specifically are limited. We are interested in employing bioorthogonal chemical modification strategies to facilitate single-molecule detection (SMD) of GPCR signaling complexes.22 The azido group can participate in bioorthogonal chemistries such as Staudinger-Bertozzi ligation,23, 24 copper-free strain-promoted azide-alkyne cycloaddition (SpAAC)25 and copper-catalyzed azide-alkyne cycloaddition (CuAAC).26 We focus here on the Staudinger-Bertozzi ligation reaction that involves the specific reaction between an azide and a phosphine. We demonstrate the use of two different phosphine derivatives, conjugated to a peptide epitope (FLAG peptide) or a fluorescent label (fluorescein) to achieve site-specific modification of GPCRs.
We previously optimized the conditions for site-specific labeling of rhodopsin azF variants using the X-ray crystal structure and dynamic simulations to choose target sites that are solvent exposed. 27, 28 We also illustrated the feasibility to achieve background-free labeling by Staudinger-Bertozzi ligation.29 We demonstrate here the general procedure employed to achieve fluorescent labeling of a detergent-solubilized receptor that is immobilized on an immunoaffinity matrix and subsequently visualized by in-gel fluorescence. Additionally, we demonstrate a useful extension on this labeling strategy to identify positions amenable to labeling on a receptor of unknown structure, CCR5. This is carried out using a targeted peptide-epitope tagging strategy that relies on bioorthogonal modification of azF-GPCR variants in a cell-based semi-high throughput format.30 This method exploits the multi-step detection properties of a cell-surface ELISA to monitor labeling events.
The methodologies we discuss here are general and in principle can be applied to any GPCR incorporated with azF using the amber codon suppression technology. In the protocols presented here we detail the steps involved in mammalian cell expression of receptors incorporated with UAAs such as azF using the unnatural amino acid mutagenesis method and their subsequent applications to facilitate structural and dynamic studies of GPCRs.

<table border="1">
	<tbody>
		<tr>
			<td>Name of Reagent/Material</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Plasmid pSVB. Yam</td>
			<td></td>
			<td></td>
			<td>(Ye et al., 2008)</td>
		</tr>
		<tr>
			<td>Plasmid pcDNA.RS for azF</td>
			<td></td>
			<td></td>
			<td>(Ye et al., 2009)</td>
		</tr>
		<tr>
			<td>Plasmids pMT4.Rho and pcDNA 3.1.CCR5</td>
			<td></td>
			<td></td>
			<td>Optionally contain the amber stop codon (TAG) at a desired position</td>
		</tr>
		<tr>
			<td>HEK 293T cells</td>
			<td></td>
			<td></td>
			<td>Adherent cells</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle&#39;s Medium (DMEM)</td>
			<td>Gibco</td>
			<td>10566</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline</td>
			<td>Gibco</td>
			<td>14200</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Gemini Bio-products</td>
			<td>100-106</td>
			<td></td>
		</tr>
		<tr>
			<td>Lipofectamine Plus</td>
			<td>Invitrogen</td>
			<td>Lipofectamine: 18324-012 
			Plus: 11514-015</td>
			<td></td>
		</tr>
		<tr>
			<td>p-azido-L-phenylalanine</td>
			<td>Chem-Impex International</td>
			<td>6162</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>Table 1. Site-specific genetic incorporation of unnatural amino acids into GPCRs materials</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>[header]</td>
		</tr>
		<tr>
			<td>Maxima ML-3500S UV-A lamp</td>
			<td>Spectronics Corporation</td>
			<td></td>
			<td>azF is activated by 365-nm light</td>
		</tr>
		<tr>
			<td>Hank&#39;s Buffered Salt Solution (HBSS)</td>
			<td>Gibco</td>
			<td>14065</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Irvine Scientific</td>
			<td>9319</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine serum albumin</td>
			<td>Roche</td>
			<td>3117405001</td>
			<td></td>
		</tr>
		<tr>
			<td>Tritium-labeled ligand</td>
			<td></td>
			<td></td>
			<td>From collaborator (Grunbeck et al., 2012)</td>
		</tr>
		<tr>
			<td>1% (w/v) n-dodecyl-&#946;-D-maltoside</td>
			<td>Anatrace</td>
			<td>D310LA</td>
			<td></td>
		</tr>
		<tr>
			<td>1D4-sepharose resin</td>
			<td></td>
			<td></td>
			<td>1D4 mAb immobilized on CNBr-activated sepharose 2B resin</td>
		</tr>
		<tr>
			<td>1% (w/v) sodium dodecyl sulfate (SDS)</td>
			<td>Fisher Scientific</td>
			<td>BP166</td>
			<td></td>
		</tr>
		<tr>
			<td>NuPAGE Novex 4 - 12% SDS gels</td>
			<td>Invitrogen</td>
			<td>NP0322BOX</td>
			<td>SDS-PAGE performed on NuPAGE apparatus</td>
		</tr>
		<tr>
			<td>Trans-Blot SD apparatus</td>
			<td>Biorad</td>
			<td></td>
			<td>Apparatus for semi-dry transfer</td>
		</tr>
		<tr>
			<td>Immobilon polyvinylidene difluoride (PVDF) membrane</td>
			<td>Millipore</td>
			<td>IPVH00010</td>
			<td></td>
		</tr>
		<tr>
			<td>Non-fat powered milk</td>
			<td>Fisher Scientific</td>
			<td>NC9934262</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Aldrich</td>
			<td>274348</td>
			<td></td>
		</tr>
		<tr>
			<td>Ecoscint A</td>
			<td>National Diagnostics</td>
			<td>LS-273</td>
			<td>Scintillation fluid</td>
		</tr>
		<tr>
			<td>Scintillation vials</td>
			<td>Fisher Scientific</td>
			<td>333726</td>
			<td></td>
		</tr>
		<tr>
			<td>LKB Wallac 1209 Rackbeta Liquid Scintillation Counter</td>
			<td>Perkin Elmer</td>
			<td></td>
			<td>Beta-Scintillation counter</td>
		</tr>
		<tr>
			<td>Anti-rhodopsin 1D4 mAb</td>
			<td>National Cell Culture Center</td>
			<td>custom</td>
			<td></td>
		</tr>
		<tr>
			<td>Horseradish peroxidase (HRP)-conjugated anti-mouse IgG</td>
			<td>KPL, Inc.</td>
			<td>474-1806</td>
			<td></td>
		</tr>
		<tr>
			<td>SuperSignal West Pico Chemiluminescent Substrate</td>
			<td>Thermo Scientific</td>
			<td>34080</td>
			<td></td>
		</tr>
		<tr>
			<td>Hyblot CL AR film</td>
			<td>Denville</td>
			<td>E3018</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>Table 2. Targeted photocrosslinking materials</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>[header]</td>
		</tr>
		<tr>
			<td>0.25% Trypsin</td>
			<td>Invitrogen</td>
			<td>15050065</td>
			<td></td>
		</tr>
		<tr>
			<td>FLAG-triarylphosphine</td>
			<td>Sigma</td>
			<td>GPHOS1</td>
			<td></td>
		</tr>
		<tr>
			<td>M2 FLAG mAb</td>
			<td>Sigma</td>
			<td>F1804</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-CCR5 2D7 mAb</td>
			<td>BD Biosciences</td>
			<td>555990</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly-D-lysine</td>
			<td>Sigma</td>
			<td>P6407</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well plate</td>
			<td>Costar</td>
			<td>3601</td>
			<td>Clear bottom, high binding EIA/RIA</td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline (Calcium, Magnesium)</td>
			<td>Gibco</td>
			<td>14040</td>
			<td></td>
		</tr>
		<tr>
			<td>16% Paraformaldehyde</td>
			<td>EMS</td>
			<td>28908</td>
			<td></td>
		</tr>
		<tr>
			<td>HRP-conjugated</td>
			<td>KPL, Inc.</td>
			<td>474-1516</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-rabbit IgG</td>
			<td>KPL, Inc.</td>
			<td>474-1516</td>
			<td></td>
		</tr>
		<tr>
			<td>Amplex Red</td>
			<td>Invitrogen</td>
			<td>A12222</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrogen peroxide</td>
			<td>DE Healthcare Products</td>
			<td>97-93399</td>
			<td></td>
		</tr>
		<tr>
			<td>CytoFluor II fluorescence multi-well plate reader</td>
			<td>Perseptive Biosystems</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>Table 3. Targeted peptide-epitope tagging and cell surface ELISA materials</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>[header]</td>
		</tr>
		<tr>
			<td>Fluorescein-phosphine</td>
			<td></td>
			<td></td>
			<td>(Huber et al., submitted 2012)</td>
		</tr>
		<tr>
			<td>Nonapeptide (C9 peptide)</td>
			<td>AnaSpec</td>
			<td>62190</td>
			<td>Peptide mimicking the 1D4-epitope NH2-TETSQVAPA-COOH</td>
		</tr>
		<tr>
			<td>1% (w/v) n-dodecyl-&#946;-D-maltoside</td>
			<td>Anatrace</td>
			<td>D310LA</td>
			<td></td>
		</tr>
		<tr>
			<td>1D4-sepharose resin</td>
			<td></td>
			<td></td>
			<td>1D4 mAb immobilized on CNBr-activated sepharose 2B resin</td>
		</tr>
		<tr>
			<td>NuPAGE Novex 4 - 12% SDS gels</td>
			<td>Invitrogen</td>
			<td>NP0322BOX</td>
			<td>SDS-PAGE performed on NuPAGE apparatus</td>
		</tr>
		<tr>
			<td>Confocal Typhoon 9400 fluorescence scanner</td>
			<td>GE Healthcare</td>
			<td>discontinued</td>
			<td>Scanner with 488-nm wavelength laser</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td>Table 4. Fluorescent labeling materials</td>
		</tr>
	</tbody>
</table>

genetically-encoded molecular probes to study g protein-coupled receptors

To facilitate structural and dynamic studies of G protein-coupled receptor (GPCR) signaling complexes, new approaches are required to introduce informative probes or labels into expressed receptors that do not perturb receptor function. We used amber codon suppression technology to genetically-encode the unnatural amino acid, p-azido-L-phenylalanine (azF) at various targeted positions in GPCRs heterologously expressed in mammalian cells. The versatility of the azido group is illustrated here in different applications to study GPCRs in their native cellular environment or under detergent solubilized conditions. First, we demonstrate a cell-based targeted photocrosslinking technology to identify the residues in the ligand-binding pocket of GPCR where a tritium-labeled small-molecule ligand is crosslinked to a genetically-encoded azido amino acid. We then demonstrate site-specific modification of GPCRs by the bioorthogonal Staudinger-Bertozzi ligation reaction that targets the azido group using phosphine derivatives. We discuss a general strategy for targeted peptide-epitope tagging of expressed membrane proteins in-culture and its detection using a whole-cell-based ELISA approach. Finally, we show that azF-GPCRs can be selectively tagged with fluorescent probes. The methodologies discussed are general, in that they can in principle be applied to any amino acid position in any expressed GPCR to interrogate active signaling complexes.

We employed the unnatural amino acid mutagenesis methodology to site-specifically introduce molecular probes into a GPCR using the amber codon suppression technology. The scheme in Figure 1 outlines the salient steps of the methodology and the various applications of incorporating the versatile UAA, p-azido-L-phenylalanine (azF), into GPCRs. Expression of azF-GPCRs in mammalian cells enables targeted photocrosslinking to ligands, and targeted peptide-epitope tagging or fluorescent modifications ...

Watch this Scientific Journal Video about Genetically-encoded Molecular Probes to Study G Protein-coupled Receptors at JoVE.com

Genetically-encoded Molecular Probes to Study G Protein-coupled Receptors

We genetically-encode the unnatural amino acid, p-azido-L-phenylalanine at various targeted positions in GPCRs and show the versatility of the azido group in different applications. These include a targeted photocrosslinking technology to identify residues in the ligand-binding pocket of a GPCR, and site-specific bioorthogonal modification of GPCRs with a peptide-epitope tag or fluorescent probe.

To facilitate structural and dynamic studies of G protein-coupled receptor (GPCR) signaling complexes, new approaches are required to introduce ...

genetically-encoded-molecular-probes-to-study-g-protein-coupled

Research

JoVE Journal

Biology

15.1K Views.  The Rockefeller University. We genetically-encode the unnatural amino acid, p-azido-L-phenylalanine at various targeted positions in GPCRs and show the versatility of the azido group in different applications. These include a targeted photocrosslinking technology to identify residues in the ligand-binding pocket of a GPCR, and site-specific bioorthogonal modification of GPCRs with a peptide-epitope tag or fluorescent probe.

Video: Genetically-encoded Molecular Probes to Study G Protein-coupled Receptors

Testing Visual Sensitivity to the Speed and Direction of Motion in Lizards

Testing visual sensitivity in any species provides basic information regarding behaviour, evolution, and ecology. However, testing specific features of the visual system provide more empirical evidence for functional applications. Investigation into the sensory system provides information about the sensory capacity, learning and memory ability, and establishes known baseline behaviour in which to gauge deviations (Burghardt, 1977). However, unlike mammalian or avian systems, testing for learning and memory in a reptile species is difficult. Furthermore, using an operant paradigm as a psychophysical measure of sensory ability is likewise as difficult. Historically, reptilian species have responded poorly to conditioning trials because of issues related to motivation, physiology, metabolism, and basic biological characteristics. Here, I demonstrate an operant paradigm used a novel model lizard species, the Jacky dragon (Amphibolurus muricatus) and describe how to test peripheral sensitivity to salient speed and motion characteristics. This method uses an innovative approach to assessing learning and sensory capacity in lizards. I employ the use of random-dot kinematograms (RDKs) to measure sensitivity to speed, and manipulate the level of signal strength by changing the proportion of dots moving in a coherent direction. RDKs do not represent a biologically meaningful stimulus, engages the visual system, and is a classic psychophysical tool used to measure sensitivity in humans and other animals. Here, RDKs are displayed to lizards using three video playback systems. Lizards are to select the direction (left or right) in which they perceive dots to be moving. Selection of the appropriate direction is reinforced by biologically important prey stimuli, simulated by computer-animated invertebrates.

Testing visual sensitivity in lizards using an operant conditioning paradigm that employs video playback of random-dot kinematograms and computer-generated invertebrates.

Testing visual sensitivity in any species provides basic information regarding behaviour, evolution, and ecology. However, testing specific features of ...

Isolation and Purification of Drosophila Peripheral Neurons by Magnetic Bead Sorting

The Drosophila peripheral nervous system (PNS) is a powerful model for investigating the complex processes of neuronal development and dendrite morphogenesis at the functional and molecular levels. To aid in these analyses, we have developed a strategy for the isolation of a subclass of PNS neurons called dendritic arborization (da) neurons that have been widely used for studying dendrite morphogenesis1,2. These neurons are very difficult to isolate as a pure population, due in part to their extremely low occurrence and their difficult-to-reach location below the tough chitinous larval cuticle. Our newly developed method overcomes these challenges, and is based on a fast and specific cell enrichment using antibody-coated magnetic beads. For our magnetic bead sorting studies, we have used age-matched third instar larvae expressing a mouse CD8 tagged GFP fusion protein (UAS-mCD8-GFP)3 under the control of either the class IV dendritic arborization (da) neuron-specific pickpocket (ppk)-GAL4 driver4 or the control of the pan-da neuron-specific GAL421-7 driver5. Although this protocol has been optimized for isolating PNS cells which are attached to the inner wall of the larval cuticle, by varying a few parameters, the same protocol could be used to isolate many different cell types attached to the cuticle at larval or pupal stages of development (e.g. epithelia, muscle, oenocytes etc.), or other cell types from larval organs depending upon the GAL4-specific driver expression pattern. The RNA isolated by this method is of high quality and can be readily used for downstream genomic analyses such as microarray gene expression profiling studies. This approach offers a powerful new tool to perform studies on isolated Drosophila dendritic arborization (da) neurons thereby providing novel insights into the molecular mechanisms underlying dendrite morphogenesis.

Isolation and Purification of Drosophila Peripheral Neurons by Magnetic Bead Sorting

In this video-article we present a method for the isolation and purification of Drosophila peripheral neurons using a fast magnetic bead assisted cell sorting strategy. RNA obtained from the isolated cells can be readily used for downstream applications including microarray analyses.

The Drosophila peripheral nervous system (PNS) is a powerful model for investigating the complex processes of neuronal development and dendrite ...

In vivo Quantification of G Protein Coupled Receptor Interactions using Spectrally Resolved Two-photon Microscopy

The study of protein interactions in living cells is an important area of research because the information accumulated both benefits industrial applications as well as increases basic fundamental biological knowledge. F&ouml;rster (Fluorescence) Resonance Energy Transfer (FRET) between a donor molecule in an electronically excited state and a nearby acceptor molecule has been frequently utilized for studies of protein-protein interactions in living cells. The proteins of interest are tagged with two different types of fluorescent probes and expressed in biological cells. The fluorescent probes are then excited, typically using laser light, and the spectral properties of the fluorescence emission emanating from the fluorescent probes is collected and analyzed. Information regarding the degree of the protein interactions is embedded in the spectral emission data. Typically, the cell must be scanned a number of times in order to accumulate enough spectral information to accurately quantify the extent of the protein interactions for each region of interest within the cell. However, the molecular composition of these regions may change during the course of the acquisition process, limiting the spatial determination of the quantitative values of the apparent FRET efficiencies to an average over entire cells. By means of a spectrally resolved two-photon microscope, we are able to obtain a full set of spectrally resolved images after only one complete excitation scan of the sample of interest. From this pixel-level spectral data, a map of FRET efficiencies throughout the cell is calculated. By applying a simple theory of FRET in oligomeric complexes to the experimentally obtained distribution of FRET efficiencies throughout the cell, a single spectrally resolved scan reveals stoichiometric and structural information about the oligomer complex under study. Here we describe the procedure of preparing biological cells (the yeast Saccharomyces cerevisiae) expressing membrane receptors (sterile 2 &alpha;-factor receptors) tagged with two different types of fluorescent probes. Furthermore, we illustrate critical factors involved in collecting fluorescence data using the spectrally resolved two-photon microscopy imaging system. The use of this protocol may be extended to study any type of protein which can be expressed in a living cell with a fluorescent marker attached to it.

In vivo Quantification of G Protein Coupled Receptor Interactions using Spectrally Resolved Two-photon Microscopy

By employing a spectrally resolved two-photon microscopy imaging system, pixel-level maps of F&ouml;rster Resonance Energy Transfer (FRET) efficiencies are obtained for cells expressing membrane receptors hypothesized to form homo-oligomeric complexes. From the FRET efficiency maps, we are able to estimate stoichiometric information about the oligomer complex under study.

The study of protein interactions in living cells is an important area of research because the information accumulated both benefits industrial ...

Monitoring Dynamic Changes In Mitochondrial Calcium Levels During Apoptosis Using A Genetically Encoded Calcium Sensor

Dynamic changes in intracellular calcium concentration in response to various stimuli regulates many cellular processes such as proliferation, differentiation, and apoptosis1. During apoptosis, calcium accumulation in mitochondria promotes the release of pro-apoptotic factors from the mitochondria into the cytosol2. It is therefore of interest to directly measure mitochondrial calcium in living cells in situ during apoptosis. High-resolution fluorescent imaging of cells loaded with dual-excitation ratiometric and non-ratiometric synthetic calcium indicator dyes has been proven to be a reliable and versatile tool to study various aspects of intracellular calcium signaling. Measuring cytosolic calcium fluxes using these techniques is relatively straightforward. However, measuring intramitochondrial calcium levels in intact cells using synthetic calcium indicators such as rhod-2 and rhod-FF is more challenging. Synthetic indicators targeted to mitochondria have blunted responses to repetitive increases in mitochondrial calcium, and disrupt mitochondrial morphology3. Additionally, synthetic indicators tend to leak out of mitochondria over several hours which makes them unsuitable for long-term experiments. Thus, genetically encoded calcium indicators based upon green fluorescent protein (GFP)4 or aequorin5 targeted to mitochondria have greatly facilitated measurement of mitochondrial calcium dynamics. Here, we describe a simple method for real-time measurement of mitochondrial calcium fluxes in response to different stimuli. The method is based on fluorescence microscopy of 'ratiometric-pericam' which is selectively targeted to mitochondria. Ratiometric pericam is a calcium indicator based on a fusion of circularly permuted yellow fluorescent protein and calmodulin4. Binding of calcium to ratiometric pericam causes a shift of its excitation peak from 415 nm to 494 nm, while the emission spectrum, which peaks around 515 nm, remains unchanged. Ratiometric pericam binds a single calcium ion with a dissociation constant in vitro of ~1.7 &mu;M4. These properties of ratiometric pericam allow the quantification of rapid and long-term changes in mitochondrial calcium concentration. Furthermore, we describe adaptation of this methodology to a standard wide-field calcium imaging microscope with commonly available filter sets. Using two distinct agonists, the purinergic agonist ATP and apoptosis-inducing drug staurosporine, we demonstrate that this method is appropriate for monitoring changes in mitochondrial calcium concentration with a temporal resolution of seconds to hours. Furthermore, we also demonstrate that ratiometric pericam is also useful for measuring mitochondrial fission/fragmentation during apoptosis. Thus, ratiometric pericam is particularly well suited for continuous long-term measurement of mitochondrial calcium dynamics during apoptosis.

This protocol describes a method for real-time measurement of mitochondrial calcium fluxes by fluorescent imaging. The method takes advantage of a circularly permutated YFP-based dual-excitation ratiometric calcium sensor (ratiometric pericam-mt) selectively expressed in mitochondria.

Dynamic changes in intracellular calcium concentration in response to various stimuli regulates many cellular processes such as proliferation, ...

Imaging G-protein Coupled Receptor (GPCR)-mediated Signaling Events that Control Chemotaxis of Dictyostelium Discoideum

Many eukaryotic cells can detect gradients of chemical signals in their environments and migrate accordingly 1. This guided cell migration is referred as chemotaxis, which is essential for various cells to carry out their functions such as trafficking of immune cells and patterning of neuronal cells 2, 3. A large family of G-protein coupled receptors (GPCRs) detects variable small peptides, known as chemokines, to direct cell migration in vivo 4. The final goal of chemotaxis research is to understand how a GPCR machinery senses chemokine gradients and controls signaling events leading to chemotaxis. To this end, we use imaging techniques to monitor, in real time, spatiotemporal concentrations of chemoattractants, cell movement in a gradient of chemoattractant, GPCR mediated activation of heterotrimeric G-protein, and intracellular signaling events involved in chemotaxis of eukaryotic cells 5-8. The simple eukaryotic organism, Dictyostelium discoideum, displays chemotaxic behaviors that are similar to those of leukocytes, and D. discoideum is a key model system for studying eukaryotic chemotaxis. As free-living amoebae, D. discoideum cells divide in rich medium. Upon starvation, cells enter a developmental program in which they aggregate through cAMP-mediated chemotaxis to form multicullular structures. Many components involved in chemotaxis to cAMP have been identified in D. discoideum. The binding of cAMP to a GPCR (cAR1) induces dissociation of heterotrimeric G-proteins into G&gamma; and G&beta;&gamma; subunits 7, 9, 10. G&beta;&gamma; subunits activate Ras, which in turn activates PI3K, converting PIP2 into PIP3 on the cell membrane 11-13. PIP3 serve as binding sites for proteins with pleckstrin Homology (PH) domains, thus recruiting these proteins to the membrane 14, 15. Activation of cAR1 receptors also controls the membrane associations of PTEN, which dephosphorylates PIP3 to PIP2 16, 17. The molecular mechanisms are evolutionarily conserved in chemokine GPCR-mediated chemotaxis of human cells such as neutrophils 18. We present following methods for studying chemotaxis of D. discoideum cells. 1. Preparation of chemotactic component cells. 2. Imaging chemotaxis of cells in a cAMP gradient. 3. Monitoring a GPCR induced activation of heterotrimeric G-protein in single live cells. 4. Imaging chemoattractant-triggered dynamic PIP3 responses in single live cells in real time. Our developed imaging methods can be applied to study chemotaxis of human leukocytes.

Imaging G-protein Coupled Receptor GPCR-mediated Signaling Events that Control Chemotaxis of Dictyostelium Discoideum

Here, we describe detailed live cell imaging methods for investigating chemotaxis. We present fluorescence microscopic methods to monitor spatiotemporal dynamics of signaling events in migrating cells. Measurement of signaling events permits us to further understand how a GPCR-signaling network achieves gradient sensing of chemoattractants and controls directional migration of eukaryotic cells.

Many eukaryotic cells can detect gradients of chemical signals in their environments and migrate accordingly 1.  This guided cell migration is referred as ...

Quantifying Agonist Activity at G Protein-coupled Receptors

When an agonist activates a population of G protein-coupled receptors (GPCRs), it elicits a signaling pathway that culminates in the response of the cell or tissue. This process can be analyzed at the level of a single receptor, a population of receptors, or a downstream response. Here we describe how to analyze the downstream response to obtain an estimate of the agonist affinity constant for the active state of single receptors.
Receptors behave as quantal switches that alternate between active and inactive states (Figure 1). The active state interacts with specific G proteins or other signaling partners. In the absence of ligands, the inactive state predominates. The binding of agonist increases the probability that the receptor will switch into the active state because its affinity constant for the active state (Kb) is much greater than that for the inactive state (Ka). The summation of the random outputs of all of the receptors in the population yields a constant level of receptor activation in time. The reciprocal of the concentration of agonist eliciting half-maximal receptor activation is equivalent to the observed affinity constant (Kobs), and the fraction of agonist-receptor complexes in the active state is defined as efficacy (&#949;) (Figure 2).
Methods for analyzing the downstream responses of GPCRs have been developed that enable the estimation of the Kobs and relative efficacy of an agonist 1,2. In this report, we show how to modify this analysis to estimate the agonist Kb value relative to that of another agonist. For assays that exhibit constitutive activity, we show how to estimate Kb in absolute units of M-1.
Our method of analyzing agonist concentration-response curves 3,4 consists of global nonlinear regression using the operational model 5. We describe a procedure using the software application, Prism (GraphPad Software, Inc., San Diego, CA). The analysis yields an estimate of the product of Kobs and a parameter proportional to efficacy (&tau;). The estimate of &tau;Kobs of one agonist, divided by that of another, is a relative measure of Kb (RAi) 6. For any receptor exhibiting constitutive activity, it is possible to estimate a parameter proportional to the efficacy of the free receptor complex (&tau;sys). In this case, the Kb value of an agonist is equivalent to &tau;Kobs/&tau;sys 3.
Our method is useful for determining the selectivity of an agonist for receptor subtypes and for quantifying agonist-receptor signaling through different G proteins.

A method for estimating the affinity constant of an agonist for the active state (Kb) of a G protein-coupled receptor is described. The analysis provides absolute or relative measures of Kb depending on whether constitutive receptor activation is measurable. Our method applies to various responses downstream from receptor activation.

When an agonist activates a population of G protein-coupled receptors (GPCRs), it elicits a signaling pathway that culminates in the response of the cell ...

Characterization of G Protein-coupled Receptors by a Fluorescence-based Calcium Mobilization Assay

For more than 20 years, reverse pharmacology has been the preeminent strategy to discover the activating ligands of orphan G protein-coupled receptors (GPCRs). The onset of a reverse pharmacology assay is the cloning and subsequent transfection of a GPCR of interest in a cellular expression system. The heterologous expressed receptor is then challenged with a compound library of candidate ligands to identify the receptor-activating ligand(s). Receptor activation can be assessed by measuring changes in concentration of second messenger reporter molecules, like calcium or cAMP. The fluorescence-based calcium mobilization assay described here is a frequently used medium-throughput reverse pharmacology assay. The orphan GPCR is transiently expressed in human embryonic kidney 293T (HEK293T) cells and a promiscuous G&#945;16 construct is co-transfected. Following ligand binding, activation of the G&#945;16 subunit induces the release of calcium from the endoplasmic reticulum. Prior to ligand screening, the receptor-expressing cells are loaded with a fluorescent calcium indicator, Fluo-4 acetoxymethyl. The fluorescent signal of Fluo-4 is negligible in cells under resting conditions, but can be amplified more than a 100-fold upon the interaction with calcium ions that are released after receptor activation. The described technique does not require the time-consuming establishment of stably transfected cell lines in which the transfected genetic material is integrated into the host cell genome. Instead, a transient transfection, generating temporary expression of the target gene, is sufficient to perform the screening assay. The setup allows medium-throughput screening of hundreds of compounds. Co-transfection of the promiscuous G&#945;16, which couples to most GPCRs, allows the intracellular signaling pathway to be redirected towards the release of calcium, regardless of the native signaling pathway in endogenous settings. The HEK293T cells are easy to handle and have proven their efficacy throughout the years in receptor deorphanization assays. However, optimization of the assay for specific receptors may remain necessary.

The here described fluorescence-based calcium mobilization assay is a medium-throughput reverse pharmacology screening system for the identification of functionally activating ligand(s) of orphan G protein-coupled receptors (GPCRs).

For more than 20 years, reverse pharmacology has been the preeminent strategy to discover the activating ligands of orphan G protein-coupled receptors ...

Visualizing Clathrin-mediated Endocytosis of G Protein-coupled Receptors at Single-event Resolution via TIRF Microscopy

Many important signaling receptors are internalized through the well-studied process of clathrin-mediated endocytosis (CME). Traditional cell biological assays, measuring global changes in endocytosis, have identified over 30 known components participating in CME, and biochemical studies have generated an interaction map of many of these components. It is becoming increasingly clear, however, that CME is a highly dynamic process whose regulation is complex and delicate. In this manuscript, we describe the use of Total Internal Reflection Fluorescence (TIRF) microscopy to directly visualize the dynamics of components of the clathrin-mediated endocytic machinery, in real time in living cells, at the level of individual events that mediate this process. This approach is essential to elucidate the subtle changes that can alter endocytosis without globally blocking it, as is seen with physiological regulation. We will focus on using this technique to analyze an area of emerging interest, the role of cargo composition in modulating the dynamics of distinct clathrin-coated pits (CCPs). This protocol is compatible with a variety of widely available fluorescence probes, and may be applied to visualizing the dynamics of many cargo molecules that are internalized from the cell surface.

Clathrin-mediated endocytosis, a rapid and highly dynamic process internalizes many proteins, including signaling receptors. The protocol described here directly visualizes the kinetics of individual endocytic events. This is essential for understanding how core members of the endocytic machinery coordinate with each other, and how protein cargo influence this process.

Many important signaling receptors are internalized through the well-studied process of clathrin-mediated endocytosis (CME). Traditional cell biological ...

Hydroponics: A Versatile System to Study Nutrient Allocation and Plant Responses to Nutrient Availability and Exposure to Toxic Elements

Hydroponic systems have been utilized as one of the standard methods for plant biology research and are also used in commercial production for several crops, including lettuce and tomato. Within the plant research community, numerous hydroponic systems have been designed to study plant responses to biotic and abiotic stresses. Here we present a hydroponic protocol that can be easily implemented in laboratories interested in pursuing studies on plant mineral nutrition.
This protocol describes the hydroponic system set up in detail and the preparation of plant material for successful experiments. Most of the materials described in this protocol can be found outside scientific supply companies, making the set up for hydroponic experiments less expensive and convenient.
The use of a hydroponic growth system is most advantageous in situations where the nutrient media need to be well controlled and when intact roots need to be harvested for downstream applications. We also demonstrate how nutrient concentrations can be modified to induce plant responses to both essential nutrients and toxic non-essential elements.

Here, we present an easy-to-follow protocol to establish a successful hydroponic system for plant nutrition studies. This protocol has been extensively tested in Arabidopsis and can easily be adapted to other plant species to study specific nutritional requirements or the effect of non-essential elements on plant growth and development.

Hydroponic systems have been utilized as one of the standard methods for plant biology research and are also used in commercial production for several ...

Imaging G Protein-coupled Receptor-mediated Chemotaxis and its Signaling Events in Neutrophil-like HL60 Cells

Eukaryotic cells sense and move towards a chemoattractant gradient, a cellular process referred as chemotaxis. Chemotaxis plays critical roles in many physiological processes, such as embryogenesis, neuron patterning, metastasis of cancer cells, recruitment of neutrophils to sites of inflammation, and the development of the model organism Dictyostelium discoideum. Eukaryotic cells sense chemo-attractants using G protein-coupled receptors. Visual chemotaxis assays are essential for a better understanding of how eukaryotic cells control chemoattractant-mediated directional cell migration. Here, we describe detailed methods for: 1) real-time, high-resolution monitoring of multiple chemotaxis assays, and 2) simultaneously visualizing the chemoattractant gradient and the spatiotemporal dynamics of signaling events in neutrophil-like HL60 cells.

Visual chemotaxis assays are essential for a better understanding of how eukaryotic cells control chemoattractant-mediated directional cell migration. Here, we describe detailed methods for: 1) real-time, high-resolution monitoring of multiple chemotaxis assays, and 2) simultaneously visualizing the chemoattractant gradient and the spatiotemporal dynamics of signaling events in neutrophil-like HL60 cells.

Eukaryotic cells sense and move towards a chemoattractant gradient, a cellular process referred as chemotaxis. Chemotaxis plays critical roles in many ...