THE JOURNAL OF BIOI.OGICAL CHEMISTRY

Vol. 252, No. 22, issue of November 25, pp. 8092-8100, 1917 Prmted in U.S.A.

Hydrogen Exchange Study of Membrane-bound Rhodopsin I. PROTEIN STRUCTURE*

(Received for publication, February 11, 1977)

NANCY W. DOWNERS AND S. WALTER ENGLANDER

From the Department of Biochemistry and Biophysics, University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania 19104

Structural parameters of rhodopsin in disc membrane preparations from frog and cattle were studied by hydrogen exchange methods. The method measures the exchange of protein amide hydrogens with water and can distinguish protons which are internally bonded from those which are hydrogen-bonded to water. The results show that about 70% of rhodopsin’s peptide group protons are exposed to water. The identification of these groups as free peptides was made initially on the usual basis of the identity of their exchange rate with the well characterized free peptide rate; other experiments specifically excluded contributions from lipids, protein side chains, adventitious mucopolysaccha- rides, and intradisc water. In contrast to rhodopsin, other proteins generally have only 20 to 40% free peptide groups. Apparently rhodopsin has some unusual structural feature. Our results together with available information on rhodop- sin suggest that a considerable length of its polypeptide chain is arranged at the surface of a channel of water penetrating into the membrane. Physicochemical consider- ations indicate that such a channel would have to be quite wide, 10 to 12 w or more, to explain the hydrogen exchange results.

Rhodopsin plays a central role in the excitation of photore-

ceptor cells but its exact mode of action is unknown. A clue is

given by the microanatomy of rod cells. Virtually all of the

rhodopsin in rod photoreceptor cells is embedded in disc

membranes which do not contact the cell’s outer plasma

membrane, yet photon absorption by rhodopsin in the discs

leads to hyperpolarization of the plasma membrane. This

hyperpolarization then modulates the receptor’s synaptic

activity. Thus it seems that a diffusible transmitter substance,

moving from disc membrane to plasma membrane, must

intervene in the phototransduction process (1). Analysis of

photoreceptor responses to light led earlier to a similar sugges-

tion (2). One probable function of rhodopsin then is to trigger

the release of some intracellular transmitter.

* This work was supported by Research Grant AM 11295 from the National Institutes of Health. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “aduertisement” in accordance with 18 U.S.C. Sectlon 1734 solely to indicate this fact.

$ Part of thesis submitted to University of Pennsylvania for Ph.D. This has been briefly reported in (1975) Biophys. J. 15, 274a and (1976) Nature 254, 625-627.

Our results point to certain aspects of rhodopsin structure

and structure change that may adapt this membrane protein

for releasing a diffusible transmitter substance from within

the disc membrane. We have studied rhodopsin in situ by

applying hydrogen exchange methods to preparations of disc

membranes from vertebrate photoreceptor cells. In this paper

we discuss the structure of rhodopsin in disc membranes from

frog and cattle retinas. Structure changes following illumina-

tion are considered in an accompanying paper.

A serious obstacle to structure analysis of rhodopsin is the

apolar nature of this protein which renders it soluble only in

detergent solutions. Measurements on rhodopsin in detergent

may reflect neither its native conformation nor structure

changes that occur in uiuo (3, 4) while the study of rhodopsin

in its native membrane environment has not been feasible by

most of the methods commonly used to obtain specific infor-

mation on protein structure. The hydrogen exchange method

is not subject to these difficulties; suspensions of disc mem-

branes can be examined directly by most of the tritium-

Sephadex techniques developed for soluble proteins. With

these techniques, one can use an innocuous probe, exchange-

able tritium label present in trace amounts, to uniformly

monitor structural parameters of all polypeptide chains pres-

ent in the membrane and to detect possible changes in

structure. Since rhodopsin makes up close to 85% of the

membrane protein, it will dominate the exchange measured

for disc membranes, and narrow limits can be set on contri-

butions of the other proteins present.

It has previously been established that hydrogen exchange

techniques can be used to distinguish and to count free and

internally bonded peptide groups in water-soluble proteins.

Free peptides can be recognized unequivocally because they

exchange their protons with water at precisely predictable

rates; structurally involved peptides are much slower. This

has been demonstrated in small molecules, oligopeptides, a

random chain polypeptide (oxidized ribonuclease), a globular

protein (myoglobin), and a fibrous protein (collagen). The

present work applies this kind of analysis to membrane-bound

rhodopsin. Not surprisingly, rhodopsin exchanges its free

peptide hydrogens with water at the usual free peptide rate.

The unusual finding is that rhodopsin has a very large

fraction of its peptide group protons freely exposed to solvent

water.

EXPERIMENTAL PROCEDURES

Materzals- Cattle eyes were collected at the abattoir within about

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R hodopsin Structure

10 min of decapitation. They were maintained for 1 h at room temperature in the dark before being placed on ice for 3 to 6 h until dissection. Adult frogs (Ram p&ens) were obtained from West Jersey Biological Supply, Wenonah, N. J. During the summer months they were dark adapted at room temperature for several hours, then kept at 4” for up to 24 h before dissection. In winter the frogs were maintained at room temperature for 1 week on a diet of carrot-fed live crickets (Selph’s Cricket Ranch, Memphis, Term.) before being dark adapted, chilled, and dissected.

Preparation of Disc Membranes - All procedures were carried out under dim red light at O-4”. Disc membranes were purified using a discontinous sucrose gradient method (5, 6). All sucrose solutions were prepared in a Ringer buffer appropriate for either cattle (140 mM NaCl, 3.5 rnM KCl, 1.8 rnM CaCl,, 0.5 rnM MgCl,, 10 rnM Tris base, pH 7.4) or frog (115 rnM NaCl, 2.5 rnM KCl, 1.8 mM CaCl,, 3 rnrvr PO,, pH 7.0). The percentage of sucrose (w/w) was adjusted at 25” using a refractometer.

In order to measure the amount of tritium still bound to mem- brane protein after any given exchange-out time, tritiated water newly formed during the exchange-out period must be removed. These second separations were accomplished by use of a Sephadex column, rapid dialysis (101, or centrifugation (11). For each ex- change-out time point, several drops of column eluant or a small volume of membrane suspension from inside the dialysis bag was diluted with distilled water or dilute buffer for analysis. If samples were separated by centrifugation, the tip of the small centrifuge tube containing the membrane pellet was cut off, excess buffer was quickly wicked off the pellet with a Kimwipe, and the pellet was resuspended in 0.06% Ammonyx LO.

Dissected cattle retinas were first equilibrated with 31.5% sucrose and collected by sedimentation. A crude rod outer segment prepara- tion was made by homogenization of the sedimented material in 33.5% sucrose using a 15.gauge syringe needle and subsequent flotation of rod outer segment to a sucrose-Ringer interface. The crude rod outer segment preparation in 19% sucrose was run on a discontinuous sucrose gradient with steps at 52, 32.5, 31.1, 30.6, and 29.5% sucrose. Bands which floated on 29.5% and 30.6% sucrose were collected separateiy. Material with an absorbance ratio of

&,JA 500 5 2.8 was washed by twice recentrifuging in Ringer solution to remove material absorbing at 280 nm. Membranes with a ratio >2.8 were repurified on a second gradient.

Frog disc membranes were prepared similarly except that flota- tion employed 39.5% sucrose and the discont,inuous gradient was composed of layers of 52, 39.5, 32.6, 30.6, and 29.5% sucrose. Material with A,,,IA 500 5 2.6 was washed as above. Preparations were stored under argon at 0”.

The number of hydrogens remaining unexchanged per peptide group was calculated from the ratio of tritium counts to protein concentration in each sample. A factor of 1.19 (121 was used to compensate for the hydrogen-tritium equilibrium isotope effect. The concentration of total protein was determined using a scaled-down Lowry assay (13) with bovine serum albumin as working standard. Quantitative amino acid analyses of several disc membrane prepa- rations were performed in order to calibrate protein values, mea- sured by the Lowry method, in terms of total weight of amino acid residues in the preparation. Lowry absorbance/g for disc membrane proteins was found to be 1.3 times that of bovine serum albumin. Tritium assays were performed by pipetting 0.2-ml aqueous samples into 10 ml of liquid scintillation counting mixture and counting in an Intertechnique SL30 spectrometer. These operations measure, on an absolute scale, the moles of amino acid residues in experimen- tal samples and the moles of protons not yet exchanged. Thus the computed parameter, hydrogens per peptide group not yet ex- changed, is also obtained on an absolute scale and is independent of such factors as assumed molecular size of rhodopsin, relative purity of the preparation, relative completeness of exchange-in (141, etc.

Spectrophotometry- Absorption spectra were obtained on a Pye- Unicam SP 1800 ultraviolet recording spectrophotometer with sam- ple and reference cells in the secondary position (wider angle detection by photomultiplier) for turbid samples. Membrane suspen- sions were diluted into 2% lauryl dimethylamine oxide (Ammonyx LO, a gift from Onyx Chemical Co., Jersey City, N. J.) containing neutralized 0.1 M hydroxylamine. To determine A,,/A,,,, the ratio was corrected for the contribution at 280 nm due to scattering. This was estimated by extrapolation of a plot of log (optical density) versus log (wavelength) from the nonabsorbing region of the bleached spectrum (7).

DLSC Membrane Preparations

Sodium Dodecyl Sulfate-Gel Electrophoresis - Disc membranes were solubilized in 1% sodium dodecyl sulfate containing 40 rnM dithiothreitol. Electrophoresis on 5.6% gels and staining with Coo- massie brilliant blue were carried out according to Fairbanks et al. (8). Gels were scanned at 550 nm and the recorded peaks were cut out and weighed to determine the percentage of absorbance ac- counted for by opsin. Gels were calibrated using myoglobin, pepsin, and bovine serum abumin.

Hydrogen Exchange- Tritium-Sephadex methods described most recently by Englander and Englander (9) were used. All exchange experiments were carried out at 0” under dim red light unless otherwise indicated.

Exchangeable hydrogen sites were labeled with tritium (ex- change-in) by incubating 0.5 to 5.0 ml of disc membrane suspension (5 to 10 mgiml total protein) for at least 50 h in the appropriate Ringer buffer at pH 8.2 and 0” with tritiated water added to a level of 10 to 30 mCi/ml. To initiate exchange-out of membrane-bound tritium, samples of tritiated membranes (0.2 to 1.0 ml) were passed through a Sephadex column 1 cm in diameter and 4 to 8 cm high in order to separate disc membranes from free tritiated water. For short exchange-out times, the sample was allowed to spend the entire exchange-out period within the column. For exchange-out times longer than about 200 s, the excluded volume peak containing disc membranes was collected in a test tube where exchange contin- ued. Most experiments utilized negatively charged SP-Sephadex (C- 25) which gave consistently better separations than did G grade Sephadex. Positively charged DEAE-Sephadex was used at pH 4.5 where disc membranes, apparently carrying more positive charges, bind to SP-Sephadex. Before initiating exchange-out, 2% solid su- crose was added to the equilibrated disc membrane suspension to facilitate layering on the Sephadex column. Also, the pH of the exchange-in suspension was adjusted to the intended exchange-out pH by addition of a very small volume of concentrated buffer.

In order to interpret hydrogen exchange results on disc

membranes in terms of rhodopsin structure, it is necessary to

know how much of the total membrane protein is rhodopsin.

The absorbance ratio A,,,,/A,,,,, calculated from the spectrum

of solubilized disc membranes can be used as a relative index

of purity, but especially in the case of bovine disc membranes

where some fraction of the photopigment is bleached, it does

not allow one to calculate the fraction of the total protein that

is present as rhodopsin and the apoprotein opsin. In order to

determine the protein composition of membranes isolated by

the procedure described above, several disc membrane prepa-

rations from cattle and frog retinas were analyzed by poly-

acrylamide gel electrophoresis in sodium dodecyl sulfate. Disc

membranes from both sources showed a major protein compo-

nent (opsin) with apparent molecular weight of 36,000 ?

4,000 and from four to six minor bands. An optical density

scan of a stained gel from a preparation of frog disc mem-

branes is shown in Fig. la. Fig. lb is the spectrum of the

same preparation solubilized in detergent.

For washed preparations of frog disc membranes with

absorbance ratio A,,,,/A,,,,, of 2.2 to 2.3, opsin accounted for 85

t 10% of the total Coomassie blue staining. Similarly, opsin

accounted for 83 +- 10% of the staining on gels of bovine disc

membranes, although the ratio A,,,/A,,,,, for these prepara-

tions varied in the slightly higher range 2.3 to 2.5. Bickle and

Traut (15) have shown that the intensity of Coomassie blue

staining is roughly proportional to the weight of protein

present and that different proteins have similar proportional-

ity constants with a standard deviation in color yield on the

order of 15%. Since the disc membranes contain such a high

proportion of a single protein, the maximum uncertainty in

its estimation introduced by differences in Coomassie blue

binding is 5%. In determining the total protein staining, a

fast component (5% of total, mobility 0.95 relative to dye)

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RESULTS

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8094 Rhodopsin Structure

which appeared in almost all the gels was included although

it probably represents phospholipid rather than protein (16).

We conclude that opsin accounts for 84 2 10% of the total

protein in our preparations from both cattle and frog.

All preparations used for hydrogen exchange studies had

final ratios A,,,/A 50,, of less than 2.4 for frog and 2.6 for

bovine disc membranes. The consistently higher absorbance

ratios observed for the bovine preparations are probably a

consequence of incomplete dark adaptation of the cattle eyes.

Several experiments in which samples were incubated with

ll-cis-retinaldehyde in order to regenerate rhodopsin (17)

indicated that the cattle eyes used here were only 80 to 90%

dark adapted.

Electron micrographs of a disc membrane preparation from

cattle retinas showed mostly rather uniform flattened mem-

brane vesicles with diameter about 1.5 p. That these represent

intact disc membranes was suggested by their apparent size

and also by comparison with broken outer segments occasion-

ally seen in the micrographs. Preparations from frog retinas

yielded smaller membrane vesicles, presumably owing to

fragmentation of the lobulated frog disc membranes.

Slow Hydrogens -The exchange-out data in Fig. 2 for disc

membranes at relatively high pH focus on the most slowly

exchanging hydrogens of disc membranes. The semiloga-

rithmic plot indicates that the slowest class of hydrogens,

which accounts for less than 10% of the total peptide hydro-

gens, has a half-time of about 31 h at pH 7.7 and 0”. Labeling

in TrisiRinger buffer at pH 8.2 and O”, where exchange rate is

about three times greater than at pH 7.7, appeared to be

essentially complete after 50 to 60 h, since incubation of disc

membranes with tritiated water for as long as 7 days led to

no detectable increase in labeling. An exchange-in period of

50 to 60 h was then used routinely to fully label disc membrane

protein. Subsequent developments indicate that some very

TOP

300 400 500 600

WAVELENGTH (nm)

FIG. 1. Characterization of frog disc membrane preparation. a, densitometric scan of sodium dodecyl sulfate-gel electrophoresis of reduced and dissociated disc membrane protein. b, spectra of prepa- ration solubilized in 20/o Ammonyx LO, 0.1 M hydroxylamine, pH 7. F, dark adapted; - - -, bleached; ‘, extrapolation of light scattering contribution (7).

slow sites were still not labeled by this procedure (see “Discus-

sion”).

Fast Hydrogens -In order to study the exchange behavior

of the faster protons of disc membranes, exchange-out condi-

tions were adjusted so that even free peptides would have

rates measurable on a time scale of minutes. The free peptide

rate is the maximum rate at which peptide protons can

exchange in aqueous solution. A pH of 5.3 was initially

chosen for these studies because it is within the pH stability

range observed for digitonin solutions of rhodopsin at 4” by

Matthews et al. (181, and the expected half-time for free

peptides at this pH, just under a minute, is still measurable

by our techniques. Results for cattle and frog disc membranes

exchanged out at pH 5.3 are shown in Fig. 3, a, b, and c.

An obvious discrepancy appears (Fig. 3~) between data

from one column runs in SP-Sephadex and data at longer

times collected by the centrifuge technique. For one column

runs, the disc membranes were in suspension within the

Sephadex column for the entire exchange-out period. In the

column plus centrifuge technique, the time in the column

was only that required for separation, less than 40 s, after

which exchange-out continued in a test tube at the buffer pH.

The slower exchange rate observed inside the column suggests

that the effective pH within the Sephadex bed was lower than

5.3. This can be accounted for by a Donnan equilibrium in

which the high density of negative charge bound to the SP-

Sephadex causes a compensating increase in concentration of

positive ions in the surrounding solution. Hence the pH

within the column bed was lower than the buffer with which

the column was equilibrated (19). That there was an effect in

this direction could be demonstrated directly by letting a

slurry of SP-Sephadex in buffer settle around a glass pH

electrode. The pH-meter reading was about 0.2 unit below

that of the equilibrating buffer.

Since subsequent considerations depended critically on

knowing the effective column pH, it was necessary to have a

more reliable estimate of this quantity. This was obtained by

measuring the first-order exchange rate of poly(nL-alanine)

in these same columns. A half-time of 1.95 2 0.10 min was

TIME (hr)

FIG. 2. Exchange-out of the slowest hydrogens at pH 7.7 in 0.1 M phosphate buffer. Bovine (0) and frog (A) disc membranes were initially exchanged-in for periods between 2l/z and 7 days in Trisl Ringer buffer at pH 8.2, 0°C. The kinetic data are plotted as unexchanged hydrogensitotal peptide groups in the membrane.

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R hodopsin Structure

measured. Since the rate-pH dependence of poly(Ala) is known

to high accuracy (201, the column pH could then be deter-

mined, it was 0.35 unit lower than that of the equilibrating

buffer. Therefore, early time data from one column runs were

corrected to pH 5.3 by decreasing the time scale by a factor

10Jp”, equal to 2.2. Data corrected in this way are shown in

Fig. 3b to be consistent with exchange measured by the

column plus centrifuge technique.

Fig. 3 shows data from cattle and frog disc membranes,

both dark adapted and after bleaching. The exchange curves

for all these cases are very similar (only the slowest exchang-

ing hydrogens, not shown here, are affected on bleaching).

The curves display a distinct break between a faster and a

slower phase. The slower phase, when extrapolated to zero

time accounts for 0.38 hydrogempeptide group. For the fast

phase, better consistency is found when the cattle and frog

data are plotted separately (Fig. 4, a and b 1, although extrap-

olation of the faster phase to zero time indicates that a total

of 1.05 ? 0.10 hydrogensipeptide group were labeled for both

species under our conditions of exchange-in. We find 0.67

hydrogempeptide group exchanging with a half-time of just

less than a minute.

This is the rate expected for free peptides under these

conditions. In order to test this identification, the measured

exchange behavior was compared with an exchange curve

predicted for free peptides on the basis of the known depend-

ence of peptide hydrogen exchange rate on temperature, pH,

and primary sequence (21). Since the amino acid sequence of

rhodopsin is not known, the prediction was generated for an

averaged sequence based on amino acid composition data for

purified disc membranes from bovine and frog rod outer

segments (22, 23). Amino acid compositions of proteins from

the two sources do not differ in any significant respect (24)

and essentially the same free peptide exchange rate may be

expected for membranes from both species. The predicted

exchange curve for disc membrane free peptides was normal-

ized to 0.67 hydrogempeptide and added onto the measured

amplitude of the slow phase to obtain the dashed line in Fig.

4, a and b. We do not know whether the slightly faster

exchange measured in the frog disc membrane is significant.

Exchange of Free Peptide Hydrogens under More Favorable

Conditions -Further experiments were carried out under con-

ditions designed to optimize the comparison of measured

exchange to predicted free peptide exchange. Reduction of the

experimental pH from 5.3 to 4.5 slowed the free peptide

exchange rate and made measurement easier. Also the column

pH artifact was thereby minimized since the -3 min hydrogen

exchange half-time was quite long relative to the -30 s

column separation time and disc membranes spent most of

the exchange-out time in a test tube at fully controlled pH.

Data points were then taken by the centrifuge technique.

Although pH 4.5 is more auspicious for hydrogen exchange

measurements, the disc membranes found it less so, and

tended to be trapped on the SP-Sephadex column by charge

effects and aggregation. However, when short columns of

positively charged DEAE-Sephadex were used instead of SP-

Sephadex, and disc membrane suspensions were passed

through a 26-gauge syringe needle just before exchange-out,

nearly 100% of the disc membranes could be recovered from

the first separation. The use of DEAE-Sephadex further

reduced any residual column pH artifact since the ApH effect

measured in slurries was half that of SP-Sephadex.

TIME (min )

FIG. 3. Exchange-out results for fully labeled disc membranes at pH 5.3 in 0.1 M citrate buffer. Column separations were made using SP-Sephadex. a, comparison of data from one column runs (filled symbols) and column plus centrifuge experiments (open symbols) demonstrating the column pH artifact. b, same data as in a but with the exchange-out time for one column runs divided by a factor of 2.2 to compensate for the column pH artifact. c, data at longer times showing break between faster and slower phases. Open sym- bols indicate exchange of fully bleached membranes. 0, 0, bovine; A, A, frog.

FIG. 4. Fast phase data through the free peptide time region. Results are shown for dark adapted (filled sym- bols) and fully bleached (open symbols) preparations at pH 5.3 for bovine (a) and frog (6) membranes, and at pH 4.5 (c) for bovine membranes. 0, 0, A, one column SP-Sephadex results; q , n , l , column plus centrifuge results; -, extrapolated level of slower phase (see Fig. 3~); - - -, predicted curve for 0.67 free peptide hydrogenlpeptide.

8095

In Fig. 4c, exchange-out data measured at pH 4.5 are

compared to the curve predicted for free peptides at this pH.

The predicted free peptide curve was generated as above and

added to the slow phase background measured at pH 4.5.

Absence of Nonpeptide Hydrogens

In addition to their peptide group protons, disc membrane

components also carry exchangeable hydrogens on phospho-

lipid head groups, on protein side chains, and perhaps on

adventitious mucopolysaccharides (see Table II). In principle,

TIME (min)

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8096 Rhodopsin Structure

these might contribute to our hydrogen exchange curves.

The possible presence in hydrogen exchange curves of

protons from hydroxyl and amino groups can be probed by

studying the effect of catalysts that would speed their ex-

change rate. Fig. 4 shows that increasing hydrogen ion con-

centration, which would catalyze hydroxyl group proton ex-

change below pH 7, results instead in a slowing of the

exchange as expected for peptide protons. Fig. 5a shows that

varying citrate concentration over a loo-fold range does not

alter disc membrane hydrogen exchange even though, under

these conditions, the exchange rate of amino group hydrogens

would be determined by transfer to citrate, and thus would be

proportional to citrate concentration. In these experiments

expected exchange rates are 1 s-’ due to OH- catalysis alone,

100 s ’ due to catalysis by 1 mM citrate, and 5 and 100 times

faster yet at the higher citrate concentrations. Thus, even if

citrate catalysis should be considerably slower (up to about

lo-l-fold slower) than is expected in aqueous solution, the

failure to observe increased catalysis by 0.1 M citrate indicates

the fast hydrogens do not come from amino groups. For the

slower disc membrane hydrogens, Fig. 5b shows that exchange

at pH 7.7 is insensitive to the substitution of 0.01 M Tris for

0.1 M phosphate which would be expected to slow amino

group proton exchange by s-fold. More telling is the fact that

amino group protons would have to be structurally slowed by

a factor of at least lo7 to appear among the slower hydrogens.

Mucopolysaccharide material might contaminate our prep-

arations and contribute exchangeable amide protons from its

acetylated amino groups. Reports in the literature suggest

that contaminating mucopolysaccharides can be removed from

disc membrane preparations by aqueous extraction (25). Wa-

ter-washed bovine disc membranes were prepared by dialysis

against distilled water overnight at 0”. They were then pel-

leted and resuspended in Tris-Ringer buffer for hydrogen

exchange experiments. Fig. 5c shows that the exchange of

water-washed preparations is indistinguishable from the un-

treated membranes. Independently, the level of mucopolysac-

charide contamination was assayed chemically. The glucosa-

mine and galactosamine content of preparations before and

after the water dialysis was measured by column chromatog-

raphy (Technicon amino acid analyzer) on samples hydrolyzed

in 6 N HCl for 24 h at 110”. Amino sugars appear as an early

peak on the short amino acid analysis column. The hydrolysis

conditions used degrade a maximum of 50% of the amino

sugars. On this basis, disc membranes isolated by our proce-

dure carried at most 16 amino sugar residues/rhodopsin mole-

cules corresponding to only 0.04 exchangeable amide hydro-

genipeptide. Water washing removed all but three or four of

the amino sugars.

pH Stability of Rhodopsin

It is possible, in principle, that the large number of free

peptides measured in our experiments arise as an artifact of

rhodopsin instability at the moderately low pH required to

make these measurements. A previous study has shown

rhodopsin in cold digitonin solutions to be stable to pH 5.3

and probably lower (18). Stability of rhodopsin in disc mem-

branes is expected to be even greater.

In order to test the stability, over the pH range studied, of

structural segments bearing exchangeable hydrogens, hydro-

gen exchange data collected at different pH can be plotted

against the function log (OH- x time), rather than against

time (26). This test is based on the very general observation

that protein hydrogen exchange proceeds via a so-called EX,

mechanism (27) for which measured exchange rate constants

(k,,) have the form shown in Equation 1.

k,x = Kkc, (1)

Here K is the equilibrium constant for “opening” of a given

protein segment and kch is the chemical exchange rate con-

stant of an exposed peptide group. The point is that if the

structural stability governing K remains constant with pH,

then measured exchange rates, k,,, will show the same linear

dependence on OH- concentration as k,, does. Therefore, in a

plot of hydrogens remaining unexchanged versus log (OH- x

time), data taken at different pH will fall on the same curve

throughout the OH--catalyzed region. Hydrogen exchange

data for a number of soluble proteins have been examined in

this way by Willumsen (26) and others. Protein exchange

rates typically are found to increase by factors of 10”.X”‘-‘/pH

unit in the region over which the protein appears perfectly

stable by the usual criteria. The tendency of internally bonded

0 5 IO 0 lb 0 2 4 6

min hr min

TIME

FIG. 5. Tests for contributions from nonpeptide sources. a, results for a bovine disc membrane preparation with varying citrate concen- tration at pH 5.3. 0, 100 0, 5 0, 1 curve from mu; IKX; mu; p, Fig. 4. b, slower phase results in different buffers at pH 7.7. 0, 10 rn~ Tris; q , 100 mu phosphate. c, water-washed bovine disc mem- brane preparation fully labeled and then exchanged-out in 0.1 M citrate at pH 5.3. curve from Fig. 4. -,

a, 0 'a 0.4, FL

1

02.

L I I I I -10 -6 -6 -4

Log [OH- x min ]

FIG. 6. Willumsen plot of exchange data from frog and cattle disc membranes at several pH values. Open and closed symbols

represent bleached and dark adapted samples, respectively. El, q , pH 7.7; A, A, pH 5.3; 0, 0, pH 4.5.

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R hodopsin

protein peptides to exhibit a rate dependence somewhat

weaker than the theoretically expected lo-fold change/pH

unit has been variously interpreted as a general effect of

protein charge on the OH--catalyzed exchange reaction (k,,,

in Equation 1) or on particular opening equilibrium constants

(K in Equation 1) (28). When structure changes do occur with

change in pH, they are reflected in much more striking

deviations from the expected pH dependence (29, 30).

Structure 8097

The majority of hydrogens exchange at rates corresponding

to values expected for freely exposed peptide groups (class 1).

The slowest hydrogens (classes 3 and 4 in Table I) are slower

than the expected free peptide rate by factors ranging up to

10”. A diffuse group of hydrogens (class 2) with rates interme-

diate between class 1 and class 3 presumably includes primary

amide hydrogens which are known to have half-times of 2 to

8 min at pH 5.3 (21).

Fig. 6 shows data for frog and cattle disc membranes plotted

as a function of log (OH- x time). Above 0.4 hydrogen/

peptide, the change from pH 4.5 to 5.3 (actually to pH 4.95 for

one column data) alters the exchange rate by the theoretical

factor, as expected for free peptides. On going from pH 5.3 to

pH 7.7, the rate of the slower hydrogens changes by lo’.“,

that is by a factor of 10”.“7/pH unit. The pa-rate dependence

of the slowly exchanging hydrogens therefore falls within the

normal limits observed for other stable proteins, and this

argues against gross conformational alterations in rhodopsin

in the pH range of this study.

Kinetic Classes in Disc Membrane Protein

Protons Measured Represent Amide Groups -The exchang-

ing protons measured in this work can be attributed to protein

amide groups. This result is expected on the basis of proton

transfer theory and previous experience with protein hydrogen

exchange. In the studies reported here for intact disc mem-

branes this conclusion is supported by direct evidence of two

kinds: the protons measured have just the number and ex-

change character expected for amide hydrogens, and addi-

tional results specifically exclude protons from other sources,

namely lipids, protein side chains, and adventitious mucopoly-

saccharides.

The hydrogen exchange data from disc membranes can be

analyzed into fairly distinct kinetic classes for which approxi-

mate exchange half-times can be recorded (Table I). Data

from cattle and frog were taken to be experimentally identical

and were combined for this analysis.

TABLE II

Half-time Slowing factor*

1 0.67 260 5.3 30 s 1

4.5 3 min 1

2’ 0.18 70 5.3 3-30 min 6-60

3 0.11 45 5.3 10 h 103

4” &OR 35 7.1 31 h 106

a Based on 382 amino acid residues present in the disc membrane/ rhodopsin molecule.

b Relative to free peptide rate. c May include primary amides. d Osborne (14) has uncovered a set of most slowly exchanging

hydrogens, amounting to 0.1 hydrogen/peptide, which can be labeled

with tritium in the presence of 0.15 M phosphate.

The number and source of exchangeable hydrogens in disc

membranes are tabulated in Table II. On the basis of past

experience, which leads one to expect only amide hydrogens

to be measurable in these experiments, about 440 hydrogens

are expected per rhodopsin molecule present, and all but -15

of these represent protein amides. This corresponds to 1.15 t

0.17 hydrogens/peptide group present in the disc membrane.

The number we observed, 1.05 t 0.10, is close to this, but

may be a bit low. Osborne (14) has now shown that under our

exchange-in conditions, the most slowly exchanging protons

of rhodopsin fail to become labeled and his data account for

an additional O.l+ hydrogempeptide group (14). Thus, as in

all other protein systems studied by these methods, the

number of hydrogens measured is close to the number of

amide hydrogens present. The measured exchange rates are

also consistent with those expected for protein amides. A

majority of the protons measured exchange at just the free

peptide rate. The slower protons span the region from about

one to six decades slower than the free peptide rate (Table I).

Results brought together by Willumsen (261 show that in

other proteins for which data is available, peptide exchange

TABLE I

Kinetic classes in disc membranes

Hydrogen/pep- Number/rho- pH tide dopsin”

DISCUSSION

TYPO

Number and source of exchangeable hydrogens m disc membranes

Source Hydrogensirhodopsin Hydrogensipeptide

1. Measurably slow hydrogens

Secondary amide Peptides 358 (382-24 proline) 0.94

Carbohydrate moietya 3 0.01

Sphingomyelin 1

Mucopolysaccharide <13 co.03

Primary amide Amide side chains

2. Intrinsically fast hydrogens

Amino hydrogens

Hydroxyl hydrogens

Phosphatidylethanolamine

Phosphatidylserine

Lysine

Phosphatidylinositol

Carbohydrate moiety

Protein side chains

Mucopolysaccharide

Other protein side chains

a Heller and Lawrence (31).

b Values measured for bovine disc membranes by deGrip et al. (23).

’ Calculated from Borggreven et al. (32) on basis of 82 Piretinaldehyde.

810 0.21

27b 0.07

48b 0.13

<25’ 0.07

-15 0.04

71 0.18

Cl30 co.34

70 0.18

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8098 Rhodopsin Structure

covers the range out to 7 r 1 decades slower than the free

peptide rate.

In the following we consider the possibility that other

nonamide groups could account for some of these exchanging

hydrogens. mhe polar head groups of phospholipids in the disc

membranes carry 0.35 exchangeable protons/peptide group

present (Table II). About the same number again are found

on protein side chains. The great majority of these are ac-

counted for by -NH,+ and -OH groups. The absence of any

significant contribution to measured protein hydrogen ex-

change curves from side chain amino and hydroxyl groups is

a general result well documented in the literature (27, 33).

Direct evidence that these groups were not measured in our

experiments was obtained by applying to our experimental

results some considerations stemming from proton transfer

theory. These considerations rest principally on the sound

presumption that the exchange rates of amino and hydroxyl

group protons will depend in a predictable way on the differ-

ence between the pK values of the exchanging group and the

exchange catalyst (34) (for a discussion of the application to

protein hydrogen exchange see Ref. 33).

Amino groups with pK about 10 would, if freely exposed to

solvent, experience exchange rates around 10’ s-l in the

presence of the 0.1 M citrate buffer concentration used here.

To just appear in the early region of our exchange curves

then, they would have to be slowed by a factor of more than

lo”. Perhaps this could occur through some structural mecha-

nism like hydrogen bonding. However, even the most slowly

exchanging (peptide) hydrogens measured in disc membranes

are slowed by only 10”. For phospholipid amino protons one

can additionally note that, just as for polar groups at the

surface of proteins, extreme structural slowing seems quite

unlikely for the polar groups which are at the aqueous surface

of the bilayer. In fact, the observation that phospholipid

amino groups in disc membranes are easily accessible to

several amino group reagents (23, 25) means they cannot be

much protected from the small molecules which function here

as the hydrogen exchange catalyst. Thus exchange of amino

protons will very probably be immeasurably fast in our

experiments.

Regardless of whether they are freely exposed or structur-

ally protected, the exchange rate of amino protons will be

proportional to the concentration of the dominant exchange

catalyst (Equation 1). On this basis, we attempt to detect a

contribution of amino protons to our data. At pH 5.3 in the

presence of citrate buffer above 0.1 mM, amino group exchange

will be dominated by transfer to citrate base, thus will vary

with citrate concentration. However, the disc membrane hy-

drogen exchange curve was unaffected by variation of citrate

buffer concentration in the range from 1 to 100 mM. It seems

evident that amino groups do not contribute to the data at

early exchange times. Again, to appear among our slower

hydrogens, amino protons must be slowed by the unlikely

factor of lo’+.

Significant contributions to our exchange curves from pro-

tein and lipid hydroxyl groups can also be unambiguously

excluded. Exchange of the hydroxyl group proton is H,O+-

catalyzed below neutral pH, but when the pH was lowered in

our experiments, no significant fraction of the exchange curve

was accelerated. On the contrary, the exchange of the hydro-

gens measured is OH--catalyzed down through pH 4.5.

In contrast to the behavior of hydroxyl and amino groups,

the observed response to pH and the lack of response to

general base catalysts is expected for the peptide group. The

extreme acid and base pK values of the peptide group cause

its exchange to be OH--catalyzed down to pH 3 and render it

immune to catalysis by general acids and bases such as the

buffers we used. This behavior of the peptide group is well

known (20, 27, 33).

It can be noted that amide hydrogens of mucopolysaccha-

rides have exchange characteristics quite similar to peptide

hydrogens and would not be distinguished by the tests just

mentioned. However, as indicated under “Results,” two kinds

of observation ruled out a contribution from the amides of

contaminating mucopolysaccharides. Water washing of the

disc membranes, which is expected to remove mucopolysac-

charide, left the hydrogen exchange curves unaltered, and

direct analysis showed our preparations not to contain amino

sugars in amounts sufficient to contribute importantly to the

exchange data.

Finally it should be noted that diffusion of tritiated water

out of disc membranes would be too fast to appear in our

exchange curves (35) and can also be excluded by our data

insofar as water efflux rate would be pH independent.

These considerations lead us to conclude that our exchange

data measure essentially protein amide groups.

On Recognrtion of Free and Hydrogen-bonded Peptides-

X-ray diffraction results for protein molecules have revealed

that peptide groups are always found in one of two hydrogen-

bonded states. They are either exposed and hydrogen-bonded

to solvent water or else form a hydrogen bond to some group

within the protein. This result is expected on thermodynamic

grounds since, in folding a protein, the cost in free energy of

breaking a hydrogen bond to water and failing to reform a

compensating, internal bond is about 4 kcal (36). By compari-

son native proteins are stabilized relative to their fully dena-

tured form by a net free energy of only 15 kcal or so (28). It is

obvious then that essentially all peptide protons must exist in

one or the other of these hydrogen bonded states.

These two states of the peptide group can now be distin-

guished by hydrogen exchange measurements. The precise

calibration of all the factors controlling peptide group hydro-

gen-tritium exchange rates has been accomplished in studies

with small molecule amide models (21) and oligopeptides (20).

Temperature and especially pH affect exchange rates in a

major way. A secondary influence, which speeds exchange

rates by 2- to 3-fold on the average, involves inductive effects

of neighboring side chains. There has been considerable dis-

cussion of other factors that might complicate the hydrogen

exchange analysis of protein structure, for example, the local

structuring of water by apolar groups, catalysis by protein

polar groups, and local charge effects (37). However, it now

seems clear that the exchange of peptide hydrogens in contact

with water is not influenced by these factors but very gener-

ally proceeds at the ideally expected rate as defined by Molday

et al. (21); that is, with calibrations of the effective parameters

in hand, the accurate predictability of free peptide exchange

rates has been demonstrated not only in random chain oligo-

and polypeptides (21) but also in the structured proteins,

myoglobin (38) and collagen (19). The present results now

indicate that even for membrane-embedded protein, free pep-

tide protons may be expected to exchange at just the same

predictable rates.

The distinction originally considered in early protein hydro-

gen exchange studies between “instantaneously” exchanging

free peptides and slowly exchanging a-helical peptides has

long been realized to be an oversimplification (27). It can now

be replaced by the more realistic distinction between free

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Rhodopsin Structure 8099

peptide hydrogens, which exchange at predictable and experi-

mentally recognizable rates, and much slower hydrogens,

which represent essentially protons from internally hydrogen-

bonded peptide groups, those in (1 helix, /3 structure, etc.

Free Peptides in Rhodopsin and Other Proteins -The fast-

est amide group protons measured in both bovine and frog

disc membranes form a distinct kinetic class with exchange

rate very close to that expected for free peptides. In view of

the considerations cited above, it is difficult to avoid the

conclusion that these represent essentially amide hydrogens

that are exposed and hydrogen-bonded to solvent water.

The fast protons measured, equal in number to 67% of the

total peptides present, are distributed among the different

disc membrane proteins. What fraction of rhodopsin’s peptides

are free? A low estimate (60%) would be obtained if the 16%

of nonrhodopsin peptides are assumed to be totally unbonded

and exposed to water, but this seems most unlikely. A more

reasonable estimate of the proportion of free peptides in

rhodopsin is 70%. This estimate assumes that the nonrhodop-

sin proteins in the disc membranes (16% of the total protein)

have a normal complement of 30% free peptides. Also, it is

reduced by a number of asparagine side chain protons and by

a small number of sugar amide protons (Table II) which may

be expected to overlap kinetically with free peptide exchange,

and it adds in the content of proline residues (6%) which are

necessarily non-hydrogen-bonded but do not contribute pro-

tons to the free amide measurements. This computation takes

the following form: 0.67 (free amide protons) - 0.07 (aspara-

gine amides) - 0.02 (sugar amides) = 0.16 x 0.30 + 0.84 P.

Here P, computed to be 0.63, represents the fraction of free

peptide protons in rhodopsin. Addition of proline content then

yields the rounded estimate of 70% free peptides.

A large uncertainty in this value is the size of the contribu-

tion due to asparagine amide protons. When freely exposed,

these are expected to exchange with a half-time (pH 5,o”l of 4

min, which is only 2-fold slower than the slowest of free

peptide rates (21), and therefore may well be kinetically

indistinguishable from free peptides at this pH. (Glutamine

protons are expected to be three times slower still, thus seem

not to be a problem.) For present purposes we assume that

half the Asx residues are amidated and therefore contribute

0.07 hydrogenipeptide to the fast exchanging, free amide

class. The maximum uncertainty in this value is kO.07. When

the uncertainty in the measured number itself is taken into

account, these results and considerations place the content of

free peptides in rhodopsin at 70 + 15% (outer limits).

Recently Osborne (14) has found conditions which led to the

labeling and measurement of the slowest of rhodopsin’s pro-

tons. His results appear to account for the extra 0.1 hydrogen/

peptide or so which our labeling conditions missed and this

would increase the number of slow hydrogens from the 0.381

peptide we measured to 0.48. Taken together with the 0.67

fast hydrogenipeptide we measured, this yields a total value

of 1.15 as expected for amide protons (Table II). It should be

stressed that Osborne’s result in no way alters our estimate

of the number of free amide protons since these were measured

on an absolute scale and not as a fraction of just those protons

that happened to be detected. Clearly, the measured size of

the free peptide class is independent of the degree of labeling

of much slower classes.

The presence of such a high proportion of freely exposed

groups is strikingly in contrast with the quite general obser-

vation in other proteins that only 20 to 40% of the peptide

protons are free. In the best studied case, both x-ray diffraction

results (39) and hydrogen exchange measurements (38) on

myoglobin count just the same number of free peptides, 20%

of the total. In collagen 30% of the peptide protons are free

(19, 40). A survey (41) of protein structures known from x-ray

diffraction results indicates that soluble proteins are on the

average 60% internally hydrogen bonded (LY helix, /3 sheet, /s’

turn) and this may be taken as a minimum estimate since

hydrogen bonding in disordered sections of polypeptide chain

is hard to define by x-ray methods. In the few cases where

hydrogen exchange estimates of secondary structure differ

from x-ray results, e.g. lysozyme (42), the hydrogen exchange

measurements detect more slow hydrogens, z.e. fewer free

peptide hydrogens, than are suggested by the x-ray structures.

Finally hydrogen-tritium exchange results on other mem-

brane systems, vesicles of sarcoplasmic reticulum (43) and

most pertinently, the bacteriorhodopsin-bearing purple mem-

branes of Halobacterium halobium (44) show that their mem-

brane proteins also have a much smaller proportion of free

peptides than does rhodopsin.

The apparent conclusion from these results is that rhodopsin

has an unusual structure. Other proteins quite generally

tend to maximize their internal hydrogen bonding, often by

using LY helices and b fo!ds as major structural elements.

Evidently, rhodopsin incorporates in addition to these some

alternative unbonded folding as a major structural element.

On Structure of Rhodopsin -Available information on rho-

dopsin structure bears on the disposition of this protein in the

disc membrane. The amino acid composition of rhodopsin

places it among the most apolar of membrane proteins (45).

This and the fact that rhodopsin is an intrinsic membrane

protein and can be solubilized only in detergent solutions

implies that it is held in the membrane by hydrophobic

interactions. Presumably there is considerable contact be-

tween hydrocarbons of the phospholipid bilayer and the many

apolar side chains of the protein. The accumulated evidence

from fluorescence transfer measurements, freeze-fracture

studies, and antibody labeling of rhodopsin in the disc mem-

brane (461, strongly suggests that rhodopsin is an asymmetric

molecule which penetrates into and perhaps traverses the

lipid bilayer of the disc membrane. Most recently x-ray (47,

48) and neutron (49) diffraction results have been interpreted

as indicating that a major fraction of rhodopsin is placed in

the hydrocarbon region and penetrates both halves of the

bilayer. The relative resistance of rhodopsin t,o attack by

externally applied proteolytic enzymes (50-541 also argues for

considerable burial of the protein in the hydrocarbon phase.

The hydrogen exchange results described in this paper now

show that about 200 of rhodopsin’s 300 peptide group protons

are exposed to aqueous solvent. Thus rhodopsin’s structure

and its placement in the membrane must not only allow for

extensive interaction of apolar side chains with the hydropho-

bic core of the bilayer but also must expose a majority of its

peptide groups to aqueous solvent. Resolution of these appar-

ently contradictory demands seems to require that considera-

ble portions of the polypeptide backbone be arranged at an

aqueous-apolar interface. It seems unlikely that the aqueous

surface of the membrane could carry large segments of loosely

laid out polypeptide chain. Especially telling here is the

limited availability of membrane-bound rhodopsin to proteo-

lytic attack. Also against an exposed and unfolded polypeptide

model is the consideration that such an arrangement seems

to have little potential for explaining rhodopsin function.

An alternative possibility would place the aqueous interface

at the surface of a water-filled channel penetrating into the

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8100 R hodopsin

membrane. This could allow for extensive contact of poly-

peptide chains with both lipid core and aqueous solvent and

is consistent with all available information on the shape and

disposition of rhodopsin within the disc membrane. If such a

channel exists, it would have to be quite large. The pertinent

observation here is the fairly precise agreement between the

exchange rate of rhodopsin’s fast peptides and the rate ex-

pected for peptides in free solution. This requires that aqueous

chemistry at the internal channel surface be perfectly normal,

that the exposed peptide groups see the same activity of

hydroxyl ion, the effective exchange catalyst, as is indicated

for the bulk solvent by a glass pH electrode. To contain

normally hydrated hydroxyl ion the channel must be larger

than the 6 A diameter of the first hydration sphere and

perhaps larger than the -10 A diameter of the second layer.

Indeed, it may be necessary for the channel to be wide enough

to accommodate the normally hydrated buffer ions we used,

but this is not clear to us. It does seem clear that the channel

must be able to contain at least 1 water molecule/exposed

peptide group in order to satisfy their hydrogen bonding

requirements. To solvate 40% of rhodopsin’s peptides, which

seems a reasonable guess at this time, a channel must

accommodate about 130 water molecules. It would then be 10

A wide if it just spans the 50 A thickness of the bilayer. In

this respect, the kind of channel considered here must differ

from the much narrower pores that are thought to govern

selective transmembrane ion transport (55). Also it is clear

that the channel could not be formed by a single hydrogen-

bonded helix (56).

One is mindful of the precarious nature of structural infer-

ences based on indirect data. The inference proposed above

seems worth considering because the wide, preformed aqueous

channel suggested by the experimental results appears partic-

ularly interesting with respect to rhodopsin’s probable func-

tion. Ion-specific pores in other membrane proteins are be-

lieved to function by stripping the hydration shells from ions,

thereby gaining selectivity at the expense of permeability

(57). On the other hand, for maximal efflux rate of an ionic

transmitter from within the disc membrane, an escape chan-

nel in rhodopsin would have to be large enough to accommo-

date the transmitter with its hydration shells and perhaps

the hydration layer of the channel walls besides. In such a

model, the specificity for the transmitter substance must then

be based elsewhere, most probably in the energy-dependent

transmitter accumulation system.

Access of transmitter to such a channel must be controlled

by changes in protein structure resulting from light-mediated

isomerization of the retinal chromophore. The accompanying

paper demonstrates the existence of light-induced changes in

rhodopsin structure.

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