PURIFICATION OF THE G PROTEIN-COUPLED RECEPTOR RHODOPSIN

FOR STRUCTURAL STUDIES

David Salom4, Ning Li4, Li Zhu1,3, Izabela Sokal1, and Krzysztof Palczewski1,2,3

Departments of Ophthalmology1, Pharmacology2, and Chemistry3, University of

Washington, Seattle, WA 98195, USA 4Novasite Pharmaceuticals Inc., San Diego, CA 92121, USA

Key Words: G protein-coupled receptors, membrane proteins, photoreceptor cells,

rhodopsin, purification of membrane proteins

Correspondence to:

Krzysztof Palczewski, Ph.D.

University of Washington, Department of Ophthalmology

Box 356485, Seattle, WA 98195-6485, USA

Phone: +206-543-9074; Fax: +206-221-6784; E-mail: palczews@u.washington.edu

and

David Salom, Ph.D.

Novasite Pharmaceuticals, Inc.

11095 Flintkote Ave.

San Diego, CA 92121, USA

Phone: +858-638-8671; Fax: +858-597-4943; E-mail: dsalom@novasite.com

Abbreviations used: BTP, 1,3-bis[tris(hydroxymethyl)methylamino]propane; DM, n-dodecyl-β-

D-maltoside; DTT, 1,4-dithio-DL-threitol; GPCR, G protein-coupled receptor, mAb, monoclonal

antibody, NG, nonyl-β-D-glucoside; PAGE, polyacrylamide gel electrophoresis; PBS, phosphate

buffered saline; ROS, rod outer segment(s); SDS, sodium dodecyl sulphate; THM,

transmembrane helix..

1

1. INTRODUCTION

2. RHODOPSIN AND OTHER GPCRs

3. WORKING WITH RHODOPSIN

4. ROD OUTER SEGMENT ISOLATION

A. Materials

B. Stock solutions

C. Sucrose gradient procedure

5. IMMUNOAFFINITY CHROMATOGRAPHY

A. Coupling of antibody to solid support

a. Purification of monoclonal antibodies

b. Materials and solutions

c. Coupling procedure

B. Chromatographic purification from ROS extract

a. Materials and solutions

b. Chromatographic procedure

C. Chromatographic purification from the whole retinal extract

a. Buffers

b. Purification

6. NON-CHROMATOGRAPHIC PURIFICATION OF RHODOPSIN

A. Stock solutions

B. Precipitation of contaminant proteins

C. DEAE-Sepharose chromatography

7. CONCLUSIONS

2

1. INTRODUCTION

Rhodopsin, the visual pigment expressed in rod photoreceptor cells of the vertebrate

retina (Fig. 1A), consists of the apoprotein opsin and the chromophore 11-cis-retinal

(Ebrey and Koutalos 2001; Hargrave 2001; Filipek et al. 2003b). The chromophore is

bound to opsin via the protonated Schiff base linkage (Wang et al. 1980; Hubbard and

Wald 1999). In vertebrates, rhodopsin is synthesized in the rod inner segment and

vectorially transported to the rod outer segments (ROS) (Molday 1998; Papermaster

2002). Perception of light starts with the photoisomerization of the chromophore 11-cis-

retinal to all-trans-retinal and the formation of signaling metarhodopsin II (Meta II)

(Okada et al. 2001). Catalytic activation of the G protein, transducin (Gt), by Meta II

leads to a cascade of biochemical reactions termed phototransduction, resulting in a

hyperpolarization of the plasma membrane of the rod cell (Polans et al. 1996; Fain et al.

2001). Ultimately, these events within the rod cell lead to the reduced rate of the

neurotransmitter release at the synaptic terminal, resulting in changes in the signaling

state to the secondary retinal neurons.

The cellular signaling upon binding of extracellular ligands to rhodopsin-like

receptors and activation of G proteins by ligand-occupied receptor, termed G protein-

coupled receptors (GPCRs), is a common mechanism in biology of signal transduction

across the plasma membranes (Gether 2000; Ballesteros et al. 2001). More than a

thousand GPCR genes, including sensory receptors, were identified in human genome,

and today ~50% of all pharmaceutical targets are directed toward modulating the

physiological responses of these receptors (Drews 2000; Ballesteros and Palczewski

2001; Klabunde and Hessler 2002). Among this signaling superfamily of transmembrane

receptors, rhodopsin is the best-studied prototypical member (Menon et al. 2001). Many

useful methods to study rhodopsin have been developed that could be adapted to other

GPCRs due to their structural, biochemical and functional similarities (Hargrave and

McDowell 1992; Filipek et al. 2003a). Here, we describe several protocols for the

purification of rhodopsin that will enable structural studies. These methods that have

been adapted and refined in this study are based on previously described procedures first

developed in the 70’s (Hargrave 1976; Papermaster 1982; Oprian et al. 1987; Okada et al.

1998).

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2. RHODOPSIN AND OTHER GPCRs

Vertebrate rhodopsin is one of the best-studied GPCRs because of its important role

in vision, its high expression in the eye, the technical accessibility of its visual system for

electrophysiological manipulations, and the fast and quantitative conversion of the

chromophore ligand from inverse agonist to agonist by light (Ebrey and Koutalos 2001;

Hargrave 2001; Okada et al. 2001; Okada and Palczewski 2001; Filipek et al. 2003b).

Many of the methods used to study GPCR’s structure and function were first developed

to investigate rhodopsin. Structural studies on rhodopsin have also led the GPCR field,

beginning with the understanding of the general topology of the receptor by electron

microscopy of two-dimensional crystals of bovine and frog rhodopsin (Schertler et al.

1993; Unger and Schertler 1995). The recent elucidation of the high-resolution three-

dimensional structure of bovine rhodopsin further paved the way for our current

understanding of the organization of the polypeptide chain of rhodopsin and its interplay

with the chromophore (Palczewski et al. 2000; Okada et al. 2001; Okada and Palczewski

2001; Teller et al. 2001). The structural core of GPCRs is characterized by a heptahelical

bundle of transmembrane segments (TM) with an additional helix 8 running parallel to

the membrane (reviewed in (Filipek et al. 2003b)).

GPCRs contain an extracellular N-terminus, three extracellular loops (ECL), seven

transmembrane helices (TMH), three intracellular loops (ICL), and an intracellular C-

terminus. On the basis of the conservation pattern of the primary amino acid sequence,

GPCRs have been grouped into three subfamilies (for review see Ref. (Ghanouni et al.

2000)) (Table I). The majority of GPCRs belong to Family 1, which is defined by

receptors whose sequences are related to rhodopsin (Mirzadegan et al. 2003). The overall

sequence identity within GPCR Family 1 is relatively low (in many cases, <35%

compared with rhodopsin) (Mirzadegan et al. 2003), but the existence of conserved

structural “microdomains” within the 7-TM clearly supports the evolutionary relationship

between rhodopsin and other GPCRs (Ballesteros et al. 2001). Family 2 includes GPCRs

similar in sequence to the secretin receptor and Family 3 includes GPCRs related in

sequence to the GABAB receptor. Beyond the seven TMH topology and a conserved

disulfide bridge between ECL2 and TMH3, there is little identifiable sequence identity

4

between these three families, although it is believed that these receptors share similar

polypeptide fold (Filipek et al. 2003a; Malherbe et al. 2003).

In general, GPCRs are activated as a result of the binding of extracellular, receptor-

specific ligands to extracellular and/or transmembrane domains. Conformational changes

of the receptor induced by the ligand are relayed to the cytoplasmic surface, allowing

productive coupling of the receptor with a heterotrimeric G protein. In this context,

rhodopsin, as well as other visual pigments, is unique in that its intrinsic ligand, 11-cis-

retinal, is coupled via a protonated Schiff base (PSB) with the side-chain of

transmembrane Lys296 residue. The 11-cis-retinylidene moiety acts as an inverse agonist,

suppressing the activity of the receptor to an undetectable level. This feature is especially

important for the function of rod cells, which contain ~108 molecules of rhodopsin per

cell and specialize in detecting light at low intensities. Any spontaneous activation of

rhodopsin present at such a high concentration would trigger phototransduction, lowering

the overall light sensitivity (Ebrey and Koutalos 2001). The ground state of rhodopsin

with its intrinsic ligand and its rigid extracellular structure appears to be specifically

suited for maintaining the receptor in the inactive state.

Rhodopsin has been described as a prototypical GPCR and the structural similarities

between all GPCRs may suggest a common mechanism by which GPCRs activate G

proteins (Mirzadegan et al. 2003) and how these receptors may self-organize within

native membranes (Fotiadis et al. 2003; Liang et al. 2003).

3. WORKING WITH RHODOPSIN

Rhodopsin is a photosensitive membrane protein. Therefore, to avoid denaturing

and/or photobleaching, there are several precautions that need to be taken when working

with this receptor (see Fig. 5B). The following recommendations apply for any

manipulation of rhodopsin (sections 4 through 6).

Experiments with rhodopsin must be performed in a dark room with dim red light,

using a Kodak 2-way Safelamp with Kodak 1A Safelight Filter (or a Kodak Adjustable

Safelight Lamp with Kodak Safelight Filter No 2) and 15 W bulb. Although rhodopsin is

stable for a short exposure up to ~55oC; experiments that take several hours should be

carried out in a cold room to prevent bleaching and denaturation. To measure rhodopsin

5

concentration in a sample, an aliquot of suspended membranes is solubilized in the

detergent-containing buffer (1-10 mM n-dodecyl-β-D-maltoside (DM) or other

alkylglucoside, 20 mM 1,3-bis[tris(hydroxymethyl)methylamino]-propane (BTP), 5-50

mM hydroxylamine, pH 7.5) and absorbance is measured at 500 nm (ε498 = 40,600 M-1·

cm-1 (Wald and Brown 1953). The absorbance ratio A280/A500 provides an indication of

the rhodopsin purity, and the value of 1.56 is the theoretical minimum for pure bovine

rhodopsin (Fig. 1B). In general, samples with absorbance ratios of 1.56-1.8 are suitable

for structural studies. If an appropriate blank is not available, a difference spectrum can

be obtained. In this case, an aliquot of suspended membranes is solubilized in the

detergent-containing buffer and used as a blank. Then, the sample in the cuvette is

photobleached for a few min (e.g. under a 50 W bulb of white light) and spectrum is

recorded. The negative peak at 500 nm in this difference spectrum is proportional to the

concentration of rhodopsin. When the difference spectrum is recorded, the absorbance

ratio at A280/A500 cannot be directly obtained.

The retinylidene-Schiff base is not accessible to hydroxylamine bleaching in ground-

state rhodopsin. Therefore, absorbance at 500 nm in presence of hydroxylamine is a

measure of the concentration of the protein-retinal complex in the native conformation.

Hydroxylamine hydrolyzes accessible to the aqueous environment retinylidene-Schiff

base linkage. Photoproducts, mainly metarhodopsin II, which forms upon illumination,

absorb in the visible region. Hydroxylamine forms retinal oxime with these

photoproducts and absorbs maximally at shorter wavelengths (363 nm).

The detergent-containing buffer for measurements of rhodopsin concentration, and

any other stock solution containing detergents, should be stored in 10-50 ml frozen

aliquots to avoid hydroxylamine and/or detergent breakdown. To assess rhodopsin

concentration, the protein in the cuvette should be below 0.3 mg/ml. To minimize

oligomerization of rhodopsin, samples should not be boiled for SDS polyacrylamide gels,

and the electrophoresis should be run without overheating (Fig.1C and 5A).

4. ROD OUTER SEGMENT ISOLATION

6

Rhodopsin is the main protein component of the stacked disks found in the outer

segments of rod cells (ROS) in the vertebrate retina (Fig.1). ROS are easily separated

from the remaining part of the rod cells by mechanical disruption, since they attach to the

cell body through a thin cilium (Fig. 1A). Rhodopsin comprises about 70% of the total

protein in osmotically intact frog ROS (Hamm and Bownds 1986), and this percentage

increases to about 90-95% when soluble and membrane-associated peripheral proteins are

washed away.

A method for ROS isolation from total retina samples was developed after the

observation that ROS, in the presence of divalent cations, floated at a lower buoyant

density than other ER and mitochondrial membranes (Papermaster and Dreyer 1974). The

following procedure has been adapted from Papermaster (Papermaster 1982).

4.A. Materials

Specific Gravity Hydrometers with ranges 1.060–1.130 and 1.120–1.190 g/ml (one

each, Fisher)

Fresh or frozen, dark-adapted bovine retinas (100) (Schenk Packing Company,

Stanwood, WA; or W. L. Lawson Co., Lincoln, NE)

Sorvall AH-629 swinging-bucket rotor with 36 ml buckets (or Beckman JS-13.1

Swinging Bucket Rotor with 50 ml buckets)

16 high-speed transparent (e.g. polycarbonate) centrifuge tubes with round bottom.

250 ml graduated cylinder (2)

10 ml syringe with luer lock (3)

Popper Laboratory Pipetting Needle (i.e., canula), 14G x 6”

Funnel

Gauze Sponges, 12-ply, 4” x 4”

4.B. Stock solutions

3 liters of the phosphate buffer: 67 mM potassium phosphate, pH 7.0, 1 mM magnesium

acetate, 0.1 mM EDTA, 1 mM DTT.

1 liter of 45% sucrose (w/v) in the phosphate buffer

7

To make 250 ml of each gradient solution, 45% solution of sucrose and the phosphate

buffer should be mixed:

Approximate volumes are:

density (g/ml) 45% sucrose (ml) phosphate buffer (ml)

1.10 145.9 104.1

1.11 159.5 90.5

1.13 190.0 60.0

1.15 216.6 33.4

After mixing, the density must be fine tuned by adjusting the density with either sucrose

solution or phosphate buffer and measuring the density with hydrometer.

4.C. Sucrose gradient procedure

1. Thaw 100 bovine retinas and collect them into a graduated bottle (with TFE-lined

closure) on wet ice. Add 1 volume (about 65 ml) of 45% sucrose solution. Shake

vigorously by hand for 1 min. Collect suspension to four 36 ml centrifuge tubes and

centrifuge for 5 min at 3,300g (4°C).

2. Pour the supernatant through a gauze-lined funnel into a 250 ml cylinder and add 1

volume (about 90 ml) of the phosphate buffer. Mix the suspension gently by wrapping

the end of the cylinder with Parafilm and rocking back and forth slowly by hand. Collect

the suspension into six 36 ml centrifuge tubes and centrifuge for 10 min at 13,000g (4°C).

3. During centrifugation step, prepare a three-step sucrose gradient (1.11, 1.13, and 1.15

g/ml sucrose solutions, respectively) on six transparent 36 ml centrifuge tubes using a

canula with a 10 ml syringe. Start with 10 ml of 1.11 g/ml sucrose, next add 16 ml of

1.13 g/ml sucrose underneath the 1.11 g/ml layer. Finally, add 10 ml of density 1.15 g/ml

sucrose underneath the 1.13 g/ml layer. Avoid air bubbles.

4. After the centrifugation step, pour off the supernatant, and resuspend each pellet in 1

ml of 1.10 g/ml sucrose plus 0.5 ml of the phosphate buffer. Carefully load this

suspension on the step gradients and centrifuge for 20 min at 22,000g (4°C), with brakes

off.

8

5. Collect the 1.11-1.13 g/ml interface, which contains intact ROS, into a 250 ml

cylinder. Add 1 volume of the phosphate buffer to the cylinder and mix the suspension

gently by wrapping the end of the cylinder with Parafilm and rocking back and forth

slowly by hand. Collect suspension into six 36 ml centrifuge tubes and centrifuge for 7

min at 6,500g (4°C).

6. Discard the supernatant and wrap the tubes containing the pelleted ROS with

aluminum foil and store them at -80°C until use.

Comments: All solutions, material and equipment in this procedure should be cold before

use.

In step 5, after collecting the ROS from the first centrifuge tube take the remaining

gradient solution to light to check how efficient the collection has been. If any rhodopsin

is left, it will be visible as a red band, and harvesting needs to be improved for the next

tubes. If rhodopsin will be further purified by immunochromatography, the top part of the

1.13-1.15 g/ml interface (formed mainly by disrupted ROS) can be collected since it

contains a significant amount of rhodopsin, especially when frozen retinas are used.

Typical yields are 0.5-0.8 mg of rhodopsin per bovine retina. The ROS can be washed

several times with a low ionic strength buffer at neutral pH with 1 mM DTT and 0.5 mM

EDTA to remove soluble and membrane-associated proteins.

5. IMMUNOAFFINITY CHROMATOGRAPHY

5.A. Coupling of antibody to solid support

5.A.a.Purification of monoclonal antibodies

Several monoclonal antibodies (mAb) to rhodopsin have been obtained by different

laboratories. Molday’s 1D4 mAb (Molday and MacKenzie 1983) is highly efficient in the

immunoaffinity purification of rhodopsin (Oprian et al. 1987) and other proteins tagged

with rhodopsin’s C-terminus, including several GPCRs such as the human parathyroid

hormone (PTH)/PTH-related protein receptor PTH1R (Shimada et al. 2002), the human

chemokine receptor CCR5 (Mirzabekov et al. 2000), and the human retinal metabotropic

9

glutamate receptor mGluR6 (Weng et al. 1997). This mAb can be obtained from

Chemicon International (Temecula, CA, USA), although production in the laboratory

from hybridoma cells, if available, is more economical.

For the immunopurification of rhodopsin, anti- C-terminus antibodies are more

efficient (for two examples see Table II). The use of anti-N-terminal mAb is more limited

due to poor accessibility of rhodopsin’s N-terminus. Most important application of

antibodies against the extracellular domain is to separate misfolded receptor from the

native form. For example, the misfolded rhodopsin can be separated from native

conformation by immobilized antibodies against its N-terminus (Ridge et al. 1995).

Several hybridoma cell lines producing different anti-rhodopsin antibodies have been

grown in our laboratory in SIGMA hybridoma medium supplemented with 1% low IgG

fetal bovine serum plus 2 mM glutamine. For the purification of the 1D4 and B6-30 (an

mAb against rhodopsin’s N-terminal (Adamus et al. 1991)) antibodies from the

hybridoma supernatant two-step chromatography is used. The first chromatography is

carried out on the DEAE-cellulose column using the hybridoma supernatant that was

dialyzed against 10 mM Tris-HCl, pH 8.2. The antibody is eluted with a 0-0.5 M NaCl

gradient. The chromatography of partially purified mAbs on immobilized Protein-A or

Protein-G is used in the second step of purification. Highly purified mAbs are eluted

from the column at acidic conditions. The typical yield was ~35 mg mAbs per liter of the

hybridoma supernatant.

We have recently switched the growth of hybridoma cells to GIBCO chemically

defined (CD) hybridoma medium supplemented with 1:400 (v/v) of GIBCO CD lipid

concentrate, 8 mM glutamine, and GIBCO’s OptiMAb (the latest, 3 days before

collection). Hybridoma supernatant obtained with gentle orbital shaking in this protein-

free medium contains less protein contaminants so that the mAb can be sufficiently

purified only on the ion exchange cellulose chromatography. Using this method, the yield

increased to >200 mg of purified mAb per liter of hybridoma supernatant.

For the coupling of the mAb to a cyanogen bromide (CNBr)-activated agarose gel the

solution must be free of primary amines. Therefore, the elution of the mAb from the

cellulose column is performed with an amine-free buffer.

10

5.A.b. Materials and solutions

60-180 mg of 1D4 mAb, at 5-20 mg/ml, in PBS buffer.

12 ml of cyanogen bromide-activated agarose gel (i.e. Aminolink PlusTM, from

Pierce)

Stock of the coupling buffer: 0.67 M sodium citrate, 0.335 M sodium carbonate, pH

10.0

Coupling buffer: 0.1 M sodium citrate, 0.05 M sodium carbonate, pH 10.0

PBS buffer: 0.1 M sodium phosphate, 0.15 M NaCl, pH 7.2

Quenching Buffer: 1 M Tris-HCl, pH 7.4

1 M NaCl

5.0 M sodium cyanoborohydride (NaBH3CN) in 10 mM NaOH

Column 2.5 cm x 10 cm with caps

5.A.c. Coupling Procedure

Ligand Immobilization

1. Equilibrate 12 ml of CNBr-activated agarose gel in the column with 30 ml of the

coupling buffer, pH 10.0. Place the bottom cap on the column.

2. Adjust the pH of the mAb solution to 10.0, by adding 0.2 volumes of stock coupling

buffer and load the solution onto the column.

3. Place the top cap on the column and mix the reaction slurry by gentle end-over-end

rocking for 4 hr at room temperature.

4. Drain the column and then wash the gel with 30 ml of PBS buffer.

5. Replace the bottom cap and add 10 ml of PBS buffer and 200 µl of 5 M NaBH3CN.

6. Replace the top cap and rock for 4 hr at room temperature.

Blocking of Remaining Active Sites

1. Drain liquid coupling solution into a tube and wash with 20 ml of Quenching Buffer

(be careful when removing the top cap because some hydrogen gas pressure may have

built up during the reduction reaction). Place the bottom cap on the column.

2. Add 10 ml of the Quenching Buffer and 200 µl of 5 M NaBH3CN.

3. Replace the top cap and mix for 30 min by gentle end-over-end rocking.

11

Final Wash

1. Allow the column to drain, and wash the column with 100 ml of 1 M NaCl (be careful

when removing the top cap because some hydrogen gas pressure may have built up

during the reduction reaction)

2. Wash the gel with 30 ml of PBS buffer (0.1% sodium azide).

3. Load the gel in a 30 cm x 0.7 cm column.

4. Cap and store the column in an upright position at 4°C protected from light.

Comments: This protocol can be scaled up or down. Perform all steps involving highly

toxic NaBH3CN in a fume hood. Collect flow-through and washes to assess coupling

efficiency. To estimate the amount of ligand coupled to the Sepharose gel, load about

1:5,000 parts of mAb sample and each collected wash and flow-through in a

polyacrylamide gel and run a SDS-PAGE. Coupling efficiency is usually >95%.

5.B. Chromatographic purification from ROS extract

5.B.a. Materials and solutions

11.5 ml of 1D4-agarose gel packed in a column of dimensions 30 cm x 0.7 cm

Peristaltic pump

Fraction collector

Microfuge tubes

Solubilization buffer: 20 mM BTP, 250 mM NaCl, pH 7.4

10 mM DM in solubilization buffer

100 mM n-nonyl-β-D-glucoside (NG) in solubilization buffer

1D4 competing peptide (TETSQVAPA >90% purity) 15 mg/ml in water

0.6 mM 1D4 competing peptide in solubilization buffer plus 100 mM NG

2 mM DM in 0.1 M glycine, pH 3.0

2 mM DM in 0.1 M Tris-HCl, pH 8.0

5.B.b. Chromatographic procedure

12

Dissolve the ROS membranes containing ~10 mg of rhodopsin in the solubilization

buffer containing 10 mM DM to a rhodopsin concentration of 1-3 mg/ml. Remove

insoluble particles by centrifugation.

1. Equilibrate the column with 20 ml of 10 mM DM in solubilization buffer (0.5 ml/min).

2. Load sample (up to 10 mg of rhodopsin) at 0.5 ml/min. Wrap the column with

aluminum foil.

3. Wash with 30 ml of 10 mM DM in solubilization buffer (0.5 ml/min).

4. Wash with 20 ml of 100 mM NG in solubilization buffer (0.5 ml/min).

5. Elute with 20 ml of 0.6 mM 1D4 competing peptide in solubilization buffer containing

100 mM NG. Collect 200-300 µl fractions at a flow rate 8 ml/hr.

6. Regenerate the column with 2 mM DM in 0.1 M glycine, pH 3.0 and 2 mM DM in 0.1

M Tris-HCl pH 8.0, at a flow rate 1 ml/min (10 min each wash). This wash should be

repeated 3 times.

7. Finally, wash the column with 20 ml of solubilization or PBS buffer (with 0.1%

sodium azide) at a flow rate 0.3 ml/min.

8. Measure spectra of fractions to determine concentration and ratio A280/A500.

Comments: The binding capacity of this column was up to ~0.7 mg rhodopsin per ml of

1D4-agarose gel. With increased length of the column, higher concentrations of

rhodopsin are obtained in the eluting fractions (see Fig. 2). Highest concentrations up to

3.5 mg/ml were obtained in our laboratories. Other factors that can affect rhodopsin

concentration during the elution are: the type and concentration of detergent used,

competing peptide concentration (see Fig. 3), the flow rate of the column development,

pH, temperature, and other parameters. The binding capacity of the column decreased

after each use, mainly due to the washing of the 1D4 column at pH 3.0 to eliminate the

bound peptide.

The competing peptide can be bought as a crude product from solid-phase synthesis

and the small molecular weight impurities can be eliminated by size-exclusion

chromatography on a 1 meter-long Sephadex G-10 (Pharmacia) column.

13

5.C. Chromatographic purification from the whole retinal extract

It is possible to obtain purified rhodopsin directly from total retina extract from an

immobilized-mAb column, without the ROS isolation. This procedure is especially useful

for rhodopsin purification for a small-scale assay and/or from animals for which a ROS

isolation protocol is not available. Next, we describe the purification of rhodopsin using

mouse and rat eyes.

5.C.a. Buffers

Buffer A: 10 mM BTP, 150 mM NaCl (Sigma), Protease Inhibitor Cocktail (Sigma), pH

7.5

Buffer B: 10 mM BTP, 500 mM NaCl, 20 mM DM, pH 7.5

Buffer C: 10 mM BTP, 500 mM NaCl, 2 mM DM, pH 7.5

Buffer D: 800 µM 1D4 peptide (TETSQVAPA), 10 mM BTP, 500 mM NaCl, 2 mM

DM, pH 7.5

5.C.b. Purification

1D4 mAb is coupled to CNBr-activated Sepharose 4B (Amersham Biosciences) at a

density of 2 mg of mAb per ml of gel. Two whole mouse or rat eyes are homogenized

with a glass-glass homogenizer in 1 ml of Buffer A. After centrifugation (16,000g for 2

min), the pellet is solubilized in buffer B for 15 min at room temperature. Insoluble

material is removed by ultracentrifugation (540,000g for 20 min) and the supernatant is

incubated with 0.2 ml of 1D4-Sepharose gel on an end-over-end shaker for 2 hr at room

temperature and then packed into a column. The column is washed with 20 ml of Buffer

C at a flow rate of 0.2 ml/min. Finally, rhodopsin is eluted with 1.5-2 ml Buffer D (Fig.

4). Note that the ratio A280/A500 of purified rhodopsin can vary for different species.

6. NON-CHROMATOGRAPHIC PURIFICATION OF RHODOPSIN

It has been shown that rhodopsin can be selectively solubilized from bovine ROS

membranes by using a combination of alkyl(thio)glucosides and divalent cations in the

extraction buffer (Okada et al. 1998). The samples obtained by this procedure are highly

14

purified and concentrated, sufficient so as to allow formation of 3D crystals of rhodopsin

(Okada et al. 2000).

6.A. Stock solutions

1 M zinc acetate

1 M sodium acetate

0.5 M MES pH 6.3-6.4

10% (v/w) n-octyl-β-D-glucoside (OG)

6.B. Precipitation of contaminant proteins

ROS obtained from 25 bovine retinas are homogenized in 10 ml of water and

membranes are centrifuged at 100,000g for 20 min. Washing is repeated once with 10 ml

of water and twice with 10 ml of 10 mM BTP, pH 7.5, containing 1 M NH4Cl. Washed

ROS membranes are solubilized by mixing with stock solutions of the detergent and

buffers, to the final concentrations of 28.6 mM OG, 30-50 mM MES, pH 6.4, and 90-120

mM zinc acetate. The final concentration of rhodopsin is 0.16 mM. After 5-7 hr of

incubation at room temperature, the sample is centrifuged again for 5 min. Some

additional precipitate from the sample, which is occasionally observed within about a

week at 4°C, was removed by centrifugation (100,000g for 20 min) before use. Typically,

a ratio at A280/A500 of 1.56-1.8 is obtained.

6.C. DEAE-Sepharose chromatography.

To remove phospholipids from the rhodopsin solution, ion exchange chromatography

is used (Fig. 5). Rhodopsin (1 mg) in the buffer solution, as described above, is loaded

onto 1 ml DEAE-Sepharose column (Amersham, HiTrapTM DEAE FF) equilibrated with

10 mM BTP, pH 7.5, containing 0.5 mM DM. After extensive washing with the same

buffer, rhodopsin is eluted with 0-0.5 M NaCl gradient during 30 min. The concentration

of rhodopsin in the eluted fractions is monitored spectrophotometrically.

7. CONCLUSIONS

15

We have described well-developed, reproducible methods of rhodopsin

purification. These refined methods derived from the published original contributions can

be further adopted for studies of photo-bleaching intermediates of rhodopsin, complexes

of rhodopsin with interacting proteins, and other GPCR receptors for the structural

studies.

Acknowledgements:

We would like to thank Dr. Juan Ballesteros for his help during the course of this work.

This research was supported by NIH grants EY09339 and EY13385, a grant from

Research to Prevent Blindness, Inc. (RPB) to the Department of Ophthalmology at the

University of Washington, and a grant from the E.K. Bishop Foundation. KP is a RPB

Senior Investigator.

8. REFERENCES

Adamus G., Zam Z. S., Arendt A., Palczewski K., McDowell J. H. and Hargrave P. A. (1991) Anti-rhodopsin monoclonal antibodies of defined specificity: characterization and application. Vision Res 31, 17-31. Ballesteros J. and Palczewski K. (2001) G-protein-coupled receptor drug discovery: implications from the crystal structure of rhodopsin. Current Opinion in Drug Discovery and Development 4, 561-574. Ballesteros J. A., Shi L. and Javitch J. A. (2001) Structural mimicry in G protein-coupled receptors: implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors. Mol Pharmacol 60, 1-19. Drews J. (2000) Drug discovery: a historical perspective. Science 287, 1960-1964. Ebrey T. and Koutalos Y. (2001) Vertebrate photoreceptors. Prog Retin Eye Res 20, 49-94. Fain G. L., Matthews H. R., Cornwall M. C. and Koutalos Y. (2001) Adaptation in vertebrate photoreceptors. Physiol Rev 81, 117-151. Filipek S., Teller D. C., Palczewski K. and Stenkamp R. (2003a) The Crystallographic Model of Rhodopsin and Its Use in Studies of Other G Protein-Coupled Receptors. Annu Rev Biophys Biomol Struct. Filipek S., Stenkamp R. E., Teller D. C. and Palczewski K. (2003b) G PROTEIN-COUPLED RECEPTOR RHODOPSIN: A Prospectus. Annu Rev Physiol 65, 851-879. Fotiadis D., Liang Y., Filipek S., Saperstein D. A., Engel A. and Palczewski K. (2003) Atomic-force microscopy: Rhodopsin dimers in native disc membranes. Nature 421, 127-128. Gether U. (2000) Uncovering molecular mechanisms involved in activation of G protein-coupled receptors. Endocr Rev 21, 90-113.

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Ghanouni P., Schambye H., Seifert R., Lee T. W., Rasmussen S. G., Gether U. and Kobilka B. K. (2000) The effect of pH on beta(2) adrenoceptor function. Evidence for protonation-dependent activation. J Biol Chem 275, 3121-3127. Hamm H. E. and Bownds M. D. (1986) Protein complement of rod outer segments of frog retina. Biochemistry 25, 4512-4523. Hargrave P. A. (1976) The large scale preparation of rhodopsin. Vision Res 16, 1013-1014. Hargrave P. A. (2001) Rhodopsin structure, function, and topography the Friedenwald lecture. Invest Ophthalmol Vis Sci 42, 3-9. Hargrave P. A. and McDowell J. H. (1992) Rhodopsin and phototransduction: a model system for G protein-linked receptors. Faseb J 6, 2323-2331. Hubbard R. and Wald E. (1999) George Wald memorial talk. Novartis Found Symp 224, 5-18; discussion 18-20. Klabunde T. and Hessler G. (2002) Drug design strategies for targeting G-protein-coupled receptors. Chembiochem 3, 928-944. Liang Y., Fotiadis D., Filipek S., Saperstein D. A., Palczewski K. and Engel A. (2003) Organization of the G Protein-coupled Receptors Rhodopsin and Opsin in Native Membranes. J Biol Chem. MacKenzie D., Arendt A., Hargrave P., McDowell J. H. and Molday R. S. (1984) Localization of binding sites for carboxyl terminal specific anti-rhodopsin monoclonal antibodies using synthetic peptides. Biochemistry 23, 6544-6549. Malherbe P., Kratochwil N., Knoflach F., Zenner M. T., Kew J. N., Kratzeisen C., Maerki H. P., Adam G. and Mutel V. (2003) Mutational analysis and molecular modeling of the allosteric binding site of a novel, selective, noncompetitive antagonist of the metabotropic glutamate 1 receptor. J Biol Chem 278, 8340-8347. Menon S. T., Han M. and Sakmar T. P. (2001) Rhodopsin: structural basis of molecular physiology. Physiol Rev 81, 1659-1688. Mirzabekov T., Kontos H., Farzan M., Marasco W. and Sodroski J. (2000) Paramagnetic proteoliposomes containing a pure, native, and oriented seven-transmembrane segment protein, CCR5. Nat Biotechnol 18, 649-654. Mirzadegan T., Benko G., Filipek S. and Palczewski K. (2003) Sequence Analyses of G-Protein-Coupled Receptors: Similarities to Rhodopsin. Biochemistry 42, 2759-2767. Molday R. S. (1998) Photoreceptor membrane proteins, phototransduction, and retinal degenerative diseases. The Friedenwald Lecture. Invest Ophthalmol Vis Sci 39, 2491-2513. Molday R. S. and MacKenzie D. (1983) Monoclonal antibodies to rhodopsin: characterization, cross-reactivity, and application as structural probes. Biochemistry 22, 653-660. Okada T. and Palczewski K. (2001) Crystal structure of rhodopsin: implications for vision and beyond. Curr Opin Struct Biol 11, 420-426. Okada T., Takeda K. and Kouyama T. (1998) Highly selective separation of rhodopsin from bovine rod outer segment membranes using combination of divalent cation and alkyl(thio)glucoside. Photochem Photobiol 67, 495-499. Okada T., Ernst O. P., Palczewski K. and Hofmann K. P. (2001) Activation of rhodopsin: new insights from structural and biochemical studies. Trends Biochem Sci 26, 318-324.

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Okada T., Le Trong I., Fox B. A., Behnke C. A., Stenkamp R. E. and Palczewski K. (2000) X-Ray diffraction analysis of three-dimensional crystals of bovine rhodopsin obtained from mixed micelles. J Struct Biol 130, 73-80. Oprian D. D., Molday R. S., Kaufman R. J. and Khorana H. G. (1987) Expression of a synthetic bovine rhodopsin gene in monkey kidney cells. Proc Natl Acad Sci U S A 84, 8874-8878. Palczewski K., Kumasaka T., Hori T., Behnke C. A., Motoshima H., Fox B. A., Le Trong I., Teller D. C., Okada T., Stenkamp R. E., Yamamoto M. and Miyano M. (2000) Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289, 739-745. Papermaster D. S. (1982) Preparation of retinal rod outer segments. Methods Enzymol 81, 48-52. Papermaster D. S. (2002) The birth and death of photoreceptors: the Friedenwald Lecture. Invest Ophthalmol Vis Sci 43, 1300-1309. Papermaster D. S. and Dreyer W. J. (1974) Rhodopsin content in the outer segment membranes of bovine and frog retinal rods. Biochemistry 13, 2438-2444. Polans A., Baehr W. and Palczewski K. (1996) Turned on by Ca2+! The physiology and pathology of Ca(2+)-binding proteins in the retina. Trends Neurosci 19, 547-554. Ridge K. D., Lu Z., Liu X. and Khorana H. G. (1995) Structure and function in rhodopsin. Separation and characterization of the correctly folded and misfolded opsins produced on expression of an opsin mutant gene containing only the native intradiscal cysteine codons. Biochemistry 34, 3261-3267. Schertler G. F., Villa C. and Henderson R. (1993) Projection structure of rhodopsin. Nature 362, 770-772. Shimada M., Chen X., Cvrk T., Hilfiker H., Parfenova M. and Segre G. V. (2002) Purification and characterization of a receptor for human parathyroid hormone and parathyroid hormone-related peptide. J Biol Chem 277, 31774-31780. Teller D. C., Okada T., Behnke C. A., Palczewski K. and Stenkamp R. E. (2001) Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs). Biochemistry 40, 7761-7772. Unger V. M. and Schertler G. F. (1995) Low resolution structure of bovine rhodopsin determined by electron cryo-microscopy. Biophys J 68, 1776-1786. Wald G. and Brown P. K. (1953) The molecular excitation of rhodopsin. J. Gen. Physiol. 37, 189-200. Wang J. K., McDowell J. H. and Hargrave P. A. (1980) Site of attachment of 11-cis-retinal in bovine rhodopsin. Biochemistry 19, 5111-5117. Weng K., Lu C., Daggett L. P., Kuhn R., Flor P. J., Johnson E. C. and Robinson P. R. (1997) Functional coupling of a human retinal metabotropic glutamate receptor (hmGluR6) to bovine rod transducin and rat Go in an in vitro reconstitution system. J Biol Chem 272, 33100-33104.

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Table I. Mammalian GPCR families.

Family Examples Family characteristics 1

rhodopsin; β2-adrenergic receptor; cannabinoid receptors; olfactory receptors

DRY motif in TMH3, palmytoilated Cys in C-terminus, relatively short N-terminus, at least one conserved residue per TMH

2

secretin receptor; glucagon receptor; calcitonin receptor; vasoactive intestinal peptide receptor

long N-terminus (~100 residues) with 6 conserved Cys, several extracellular disulfide bridges, five conserved TMH residues, extracellular binding sites for peptide ligands

3

calcium receptors; metabotropic GABA receptors; metabotropic glutamate receptors; taste receptors

long N-terminus (>500 residues), short conserved ICL3, more conserved residues in ICLs than in TMHs

Table II. Specificity of Antibodies Used in Purification. Nomenclature Type Class Epitope Reference

1D4 mAb IgG1 ETSQVAPA Rhodopsin (aa 341-348)

(MacKenzie et al. 1984)

C7 mAb IgG3 SKTETSQVAP Rhodopsin (aa 338-347)

Palczewski, unpublished

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FIGURE LEGENDS

Figure 1. Vertebrate rhodopsin and rod outer segments. A. Schematic representation

of the rod cell. B. Normalized spectra of detergent-solubilized rhodopsin from ROS

extract (thin line) and purified rhodopsin by immuno-affinity chromatography (thick

line). C. SDS-PAGE of a retina extract (lane 1), ROS extract (lane 2), and purified

rhodopsin (lane 3). Rho and (Rho)2 refer to the monomer and dimer of rhodopsin,

respectively.

Figure 2. Influence of column length on rhodopsin purification. A 10-cm x 0.7-cm

column (white squares) or a 20-cm x 0.5-cm column (black squares) packed with 1D4-

agarose gel was overloaded with a ROS extract solubilized in DM-containing buffer.

Then, the column was washed with several column volumes of 20 mM BTP, 50 mM

NaCl, 10 mM DM, pH 7.4. Elution was carried out with 100 µM 1D4 competing peptide,

20 mM BTP, 150 mM NaCl, 20 mM DM, pH 7.4, at a flow rate of 4 ml/hr.

Figure 3. Influence of the chromatography conditions on rhodopsin purification. In

both cases, a 30-cm long column packed with 1D4-agarose gel was overloaded with the

ROS detergent extract contaning rhodopsin. Elution was carried out with 100 µM 1D4

competing peptide (white squares), 20 mM BTP, 150 mM NaCl, 12 mM NG, pH 7.4, at a

flow rate of 4 ml/hr or with 200 µM 1D4 competing peptide, 20 mM BTP, 150 mM

NaCl, 100 mM NG, pH 7.4, at a flow rate of 7 ml/hr (black squares).

Figure 4. Purification of rhodopsin from the mouse (A) and rat (B) eye extract on

the 1D4-agarose gel column. A. Purification of rhodopsin from 2 mouse eyes. B.

Purification of rhodopsin from 2 rat eyes. The volume of each chromatographic fractions

was 0.5 ml. The vertical arrows indicate the starting of eluting conditions. Insets:

Immunoblots of selected fractions using the 1D4 mAb as a primary antibody. “Insol” is

the insoluble material after DM solubilization; “sol” is the supernatant from DM

solubilization; “ft” is the flow-through after loading the gel in a column; “fn” refers to

20

21

fraction number n. Rho and (Rho)2 refer to the monomer and dimer of rhodopsin,

respectively.

Fig. 5. Purification of rhodopsin on ion-exchanger. A. Ion exchange chromatography

on DEAE-Sepharose of purified rhodopsin in OG micelles (see text for details). Inset,

SDS-PAGE (15% polyacrylamide gel) of the highest concentrated fraction of rhodopsin.

Left lane: purified rhodopsin; right lane: molecular weight marker. B. Absorption spectra

of rhodopsin in the most concentrated fraction. Absorbance was measured before (thick

line) and after (thin line) illumination.

Figure 1

250 350 450 550 650

Wavelenght (nm)

Abs

orba

nce

(AU

) BRodoutersegment(ROS)

Inner segment

Nucleus

Synapse

Cilium

A

Rho

(Rho)2

1 2 3 C

Figure 2

0.0

0.5

1.0

1.5

2.0

0 2 4 6

Elution volume (ml)

[Rho

dops

in] (

mg/

ml)

Figure 3

0.0

0.5

1.0

1.5

2.0

2.5

0 5 10 15 20

Elution volume (ml)

[Rho

dops

in] (

mg/

ml)

Figure 4

4 8 12 16 20

Abso

rban

ce

0.00

0.05

0.10

0.15

0.20280 nm500 nm

4 8 12 16 20

0.00

0.05

0.10

0.15

0.20280 nm500 nmA

peptide

Bpeptide

Rho

(Rho)281.0 kDa

38.5 kDa31.3 kDa

18.8 kDa

Rho

(Rho)2

insol sol ft f20 f21 f22 f23 f24 insol sol ft f1 f20 f21 f22 f23

Abs

orba

nce

81.0 kDa

38.5 kDa31.3 kDa

18.8 kDa

Fraction Number Fraction Number

Figure 5

113 kDa93 kDa

50 kDa

35 kDa

29 kDa

21 kDa

A

B

A280

Time (min)

0.05

5

300 400 500 600

0.07

0.14

0.21

before bleachingafter bleaching

Abs

orba

nce

Wavelenght (nm)