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

Summary

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.

Abstract

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.

Introduction

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.

Protocol

1. Site-specific Genetic Incorporation of Unnatural Amino Acids into GPCRs

1. Maintain HEK293T cells in DMEM (4.5 g/L of glucose, 2 mM glutamine) supplemented with 10% fetal bovine serum (FBS) at 37 °C in a 5% CO₂ atmosphere.
2. Transfect the cells grown to 60-80% confluence in a 10-cm plate using Lipofectamine Plus reagent.
   1. To 750 μl DMEM, add 10 μl Plus reagent, 3.5 μg of GPCR cDNA (pMT4. Rho or pcDNA 3.1. CCR5) containing the amber stop codon at a desired position, 3.5 μg of suppressor tRNA cDNA (pSVB.Yam) and 0.35 μg 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 μl of DMEM with 17 μl Lipofectamine. After equilibrating 15 min at room temperature, bring the total volume to 4 ml.
   2. Aspirate media on 10-cm plate, apply transfection mixture to cells, and return to 37 °C in 5% CO₂ atmosphere. After 4-6 hr, supplement cells with 4 ml DMEM containing 20% FBS and 1 mM azF.
3. The next day, replace the growth media with DMEM containing 10% FBS and 0.5 mM azF.
4. Harvest cells 48 hr post-transfection, to analyze expression or proceed to photocrosslinking or labeling procedures described in the following sections.
   1. 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-β-D-maltoside (DDM) in 20 mM Tris-HCl, pH 7.5, 100 mM NaCl for 1 hr at 4 °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

2. Mapping a Ligand Binding Site Using Targeted Photocrosslinking

1. 48 hr post-transfection, aspirate media from cells and replace with 4 ml 1x Phosphate Buffered Saline (PBS). Return to 37 °C for 15 min.
2. 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.
3. Resuspend the cell pellet in 1x Hank'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.
4. 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 °C. Maintain the plate on ice to avoid sample heating and cell lysis.
5. 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 °C for future use.
6. 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 °C, centrifuge the cell lysate for 10 min at 16,000 x g, and transfer the supernatant to a new tube.
7. Add 1D4 mAb-sepharose 2B resin to the supernatant and incubate overnight at 4 °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 °C for 1 hr with shaking.
8. 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.
9. 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.
   1. 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.
   2. Treat with enhanced chemiluminescence (ECL) reagent and expose membrane to autoradiography film to visualize bands.
10. 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.
11. 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.

3. Targeted Epitope Tagging and Cell Surface Enzyme-linked Immunosorbent Assay (ELISA)

1. 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.
2. 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.
3. Plate 200 μl 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 °C in 5% CO₂ atmosphere.
4. Next day prepare cells for labeling. Gently wash three times with 100 μl/well 1x PBS to remove any azF containing growth media. Ensure cells remain adhered, for example, by using PBS containing Ca²⁺ and Mg²⁺.
5. Prepare 50-200 μM 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 °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.
6. Wash cells 3 times with 100 μl/well of blocking buffer, BB (1x PBS, 0.5% BSA), to remove unreacted label completely.
7. Apply 100 μl/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.
8. 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.
   1. Add 100 μl 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.
   2. Wash cells three times with BB, and incubate with 100 μl of HRP-conjugated anti-mouse IgG secondary antibody (1:2,000 dilution).
   3. Carefully wash cells five times with BB. Add 50 μl 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 λ_ex=530 and λ_em=590.

4. Bioorthogonal Fluorescent Labeling of a GPCR

1. 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 °C. Centrifuge the cell lysate at 15,000 x g for 10 min and collect the supernatant fraction.
2. Add 100 μl 1D4-mAb sepharose 2B resin to capture receptor using the engineered C terminus 1D4 epitope. Incubate for 12 hr at 4 °C. Wash the resin three times with 0.1% (w/v) DDM in 0.1 M sodium phosphate buffer, pH 7.3.
3. 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.
4. 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.
5. 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.

Results

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 ...

Discussion

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 labeling^{32, 33} or attaching photocrosslinkers³⁴ to a single accessible cysteine mutant. Although, chemistries that target cysteine thiol groups have been used to at...

Materials

Name	Company	Catalog Number	Comments
Name of Reagent/Material	Company	Catalog Number	Comments
Plasmid pSVB. Yam			(Ye et al., 2008)
Plasmid pcDNA.RS for azF			(Ye et al., 2009)
Plasmids pMT4.Rho and pcDNA 3.1.CCR5			Optionally contain the amber stop codon (TAG) at a desired position
HEK 293T cells			Adherent cells
Dulbecco's Modified Eagle's Medium (DMEM)	Gibco	10566
Phosphate Buffered Saline	Gibco	14200
Fetal Bovine Serum	Gemini Bio-products	100-106
Lipofectamine Plus	Invitrogen	Lipofectamine: 18324-012 Plus: 11514-015
p-azido-L-phenylalanine	Chem-Impex International	6162
			Table 1. Site-specific genetic incorporation of unnatural amino acids into GPCRs materials
			[header]
Maxima ML-3500S UV-A lamp	Spectronics Corporation		azF is activated by 365-nm light
Hank's Buffered Salt Solution (HBSS)	Gibco	14065
HEPES	Irvine Scientific	9319
Bovine serum albumin	Roche	3117405001
Tritium-labeled ligand			From collaborator (Grunbeck et al., 2012)
1% (w/v) n-dodecyl-β-D-maltoside	Anatrace	D310LA
1D4-sepharose resin			1D4 mAb immobilized on CNBr-activated sepharose 2B resin
1% (w/v) sodium dodecyl sulfate (SDS)	Fisher Scientific	BP166
NuPAGE Novex 4 - 12% SDS gels	Invitrogen	NP0322BOX	SDS-PAGE performed on NuPAGE apparatus
Trans-Blot SD apparatus	Biorad		Apparatus for semi-dry transfer
Immobilon polyvinylidene difluoride (PVDF) membrane	Millipore	IPVH00010
Non-fat powered milk	Fisher Scientific	NC9934262
Tween-20	Aldrich	274348
Ecoscint A	National Diagnostics	LS-273	Scintillation fluid
Scintillation vials	Fisher Scientific	333726
LKB Wallac 1209 Rackbeta Liquid Scintillation Counter	Perkin Elmer		Beta-Scintillation counter
Anti-rhodopsin 1D4 mAb	National Cell Culture Center	custom
Horseradish peroxidase (HRP)-conjugated anti-mouse IgG	KPL, Inc.	474-1806
SuperSignal West Pico Chemiluminescent Substrate	Thermo Scientific	34080
Hyblot CL AR film	Denville	E3018
			Table 2. Targeted photocrosslinking materials
			[header]
0.25% Trypsin	Invitrogen	15050065
FLAG-triarylphosphine	Sigma	GPHOS1
M2 FLAG mAb	Sigma	F1804
anti-CCR5 2D7 mAb	BD Biosciences	555990
Poly-D-lysine	Sigma	P6407
96-well plate	Costar	3601	Clear bottom, high binding EIA/RIA
Phosphate Buffered Saline (Calcium, Magnesium)	Gibco	14040
16% Paraformaldehyde	EMS	28908
HRP-conjugated	KPL, Inc.	474-1516
anti-rabbit IgG	KPL, Inc.	474-1516
Amplex Red	Invitrogen	A12222
Hydrogen peroxide	DE Healthcare Products	97-93399
CytoFluor II fluorescence multi-well plate reader	Perseptive Biosystems
			Table 3. Targeted peptide-epitope tagging and cell surface ELISA materials
			[header]
Fluorescein-phosphine			(Huber et al., submitted 2012)
Nonapeptide (C9 peptide)	AnaSpec	62190	Peptide mimicking the 1D4-epitope NH2-TETSQVAPA-COOH
1% (w/v) n-dodecyl-β-D-maltoside	Anatrace	D310LA
1D4-sepharose resin			1D4 mAb immobilized on CNBr-activated sepharose 2B resin
NuPAGE Novex 4 - 12% SDS gels	Invitrogen	NP0322BOX	SDS-PAGE performed on NuPAGE apparatus
Confocal Typhoon 9400 fluorescence scanner	GE Healthcare	discontinued	Scanner with 488-nm wavelength laser
			Table 4. Fluorescent labeling materials