Rhodopsin and bacteriorhodopsin: structure-function relationships

Molecular genetics of human color vision: the genes encoding blue, green, and red pigments

Human color vision is based on three light-sensitive pigments. The isolation and sequencing of genomic and complementary DNA clones that encode the apoproteins of these three pigments are described. The deduced amino acid sequences show 41 +/- 1 percent identity with rhodopsin. The red and green pigments show 96 percent mutual identity but only 43 percent identity with the blue pigment. Green pigment genes vary in number among color-normal individuals and, together with a single red pigment gene, are proposed to reside in a head-to-tail tandem array within the X chromosome.

Photoenergetics of octopus rhodopsin. Convergent evolution of biological photon counters?

The enthalpy changes associated with each of the major steps in the photoconversion of octopus rhodopsin have been measured by direct photocalorimetry. Formation of the primary photoproduct (bathorhodopsin) involves energy uptake of about 130 kJ/mol, corresponding to storage of over 50% of the exciting photon energy, and is comparable to the energy storage previously observed in bovine rhodopsin. Subsequent intermediates involve the step-wise dissipation of this energy to give the physiological end-product (acid metarhodopsin) at a level only slightly above the parent rhodopsin. No significant differences in energetics are observed between rhodopsin in microvilli membrane suspensions or detergent dispersions. Use of different buffer systems in the calorimetric experiments shows that conversion of rhodopsin to acid metarhodopsin involves no light-induced protonation change, whereas alkali metarhodopsin photoproduction occurs with the release of one proton per molecule and an additional enthalpy increase of about 50 kJ/mol. Van't Hoff analysis of the effect of temperature on the reversible metarhodopsin equilibrium gives an enthalpy for the acid----alkali transition consistent with this calorimetric result, and the proton release is confirmed by direct observation of light-induced pH changes. Acid-base titration of metarhodopsin yields an apparent pK of 9.5 for this transition, though the pH profile deviates slightly from ideal titration behaviour. We suggest that a high energy primary photoproduct is an obligatory feature of efficient biological photo-detectors, as opposed to photon energy transducers, and that the similarity at this stage between cephalopod and vertebrate rhodopsins represents either convergent evolution at the molecular level or strong conservation of a crucial functional characteristic.

An opsin gene expressed in only one photoreceptor cell type of the Drosophila eye

We have isolated an opsin gene from D. melanogaster that is expressed specifically in photoreceptor cell 8 of the Drosophila compound eye. This opsin is 381 amino acid residues long and is 67% homologous to the ninaE opsin, which is expressed in photoreceptor cells 1-6. The gene is divided into four exons; only one of the intron positions is conserved with that of the ninaE gene.

Modification of ovine opsin with the photosensitive hydrophobic probe 1-azido-4-[125I]iodobenzene. Labelling of the chromophore-attachment domain

The hydrophobic photosensitive probe 1-azido-4-[125I]iodobenzene (AIB) partitioned preferentially into photoreceptor disc membranes and, upon u.v. irradiation, became covalently bound to opsin and phospholipid. The labelling of both protein and phospholipid was linearly related to AIB concentration. The amount of probe incorporated into protein was not significantly different when membranes were irradiated at -100 degrees, 4 degrees or 25 degrees C, but irreversible aggregation of monomeric opsin was dramatically reduced by performing the photolysis at -100 degrees C. Labelling of opsin after irradiation at -100 degrees or 4 degrees was not significantly reduced by the presence of lysine in the aqueous buffer, indicating that significant amounts of reactive species did not enter the aqueous phase. The incorporation into phospholipid, unlike that into opsin, decreased as the temperature of irradiation increased. Some labelling of opsin occurred on incubation with pre-photoactivated AIB, indicating that reaction may also occur with reactive species of longer lifetimes than the nitrene. Proteolysis of labelled opsin with Staphylococcus aureus V8 proteinase yielded two radiolabelled membrane-bound fragments. The location of the modified sites (cysteine, tryptophan, tyrosine, lysine and histidine residues: all nucleophiles) in the smaller fragment was entirely consistent with putative models for the protein derived from other studies.

Two-dimensional crystallization of bovine rhodopsin

Bovine rhodopsin has been clustered into two-dimensional crystals in highly purified native rod disk membranes and studied with negative staining and transmission electron microscopy. The lattice is P2(1) with dimensions of 8.3 X 7.9 nm and interaxis angles of 86 +/- 3 degrees. 110 images of ordered areas were digitized and aligned with computer-correlation methods to calculate an average image with diffraction to the fourth order. The images were computer-filtered and reconstructed to approx. 2 nm resolution. When crystals appeared they covered 20-40% of the surface of the preparation and, since rhodopsin is at least 95% of the protein, there is no doubt that the crystals were due to rhodopsin. There appear to be two rhodopsin dimers per unit cell. Each rhodopsin molecules takes up about 7.5 nm2 of membrane area and is estimated to be associated with about 12 lipids on each side of the membrane. The membrane area found for bovine rhodopsin supports the rhodopsin origin of rarely seen but more highly ordered two-dimensional crystals found in detergent-treated frog rod membranes (Corless, J.M., McCaslin, D.R. and Scott, B.L. (1982) Proc. Natl. Acad. Sci. USA 79, 1116-1120). Furthermore, the rhodopsin membrane area is close to that of bacteriorhodopsin and is consistent with a seven transmembrane helix structure proposed for rhodopsin (for references see Dratz, E.A. and Hargrave, D.A. (1983) Trends Biochem. Sci. 8, 128-131). Crystallization was accomplished by lowering the pH to 5.5 near the isoelectric point of rhodopsin, raising the salt concentration of 2 M (NH4)2SO4, adding 5% glucose and 0.02% Hibitane (Ayerst), a cationic amphipathic antiseptic that favored crystal growth.

The yeast alpha-factor receptor: structural properties deduced from the sequence of the STE2 gene

The STE2 gene of the yeast Saccharomyces cerevisiae encodes a component of the receptor for the oligopeptide pheromone alpha-factor. We have cloned and determined the nucleotide sequence of the STE2 gene. A sequence involved in the control of cell-type expression of the STE2 gene was found 5' of an open reading frame that could encode a protein of 431 amino acids. The predicted STE2 protein contains seven hydrophobic segments, suggesting that the alpha-factor receptor is an integral membrane protein. No extensive homology at the primary sequence level was detected between the predicted STE2 protein and other available protein sequences.

The rhodopsin-like pigments of halobacteria: light-energy and signal transducers in an archaebacterium

Three similar, small retinylidene proteins, which resemble the visual pigments of animals, are found in halobacteria: two functions as light-driven ion pumps; the third is the receptor for phototaxis and allows color discrimination.

Ca2+ buffer sites in intact bovine rod outer segments: introduction to a novel optical probe to measure ionic permeabilities in suspensions of small particles

The nature of the Ca2+ buffer sites in intact rod outer segments isolated from bovine retinas (ROS) was investigated. The predominant Ca2+ buffer in intact ROS was found to be negatively charged groups confined to the surface of the disk membranes. Accordingly, Ca2+ buffering in ROS was strongly influenced by the electrostatic surface potential. The concentration of Ca2+ buffer sites was about 30 mM, 80% of which were located at the membrane surface in the intradiskal space. A comparison with observations in model systems suggests that phosphatidylserine is the major Ca2+ buffer site in ROS. Protons and alkali cations could replace Ca2+ as mobile counterions for the fixed negatively charged groups. At physiological ionic strength, the total number of these diffusible, but osmotically inactive, counterions was as large as the number of osmotically active cations in ROS. The surface potential is dependent on the concentration of cations in ROS and can be measured with the optical dye neutral red. Addition of cations to the external solution led to the release of the internally bound dye as the cations crossed the outer membrane. The chemical and spectral properties of the dye enable its use as a real-time indicator of cation transport across the outer envelope of small particles in suspension. In this study, the dye method is illustrated by the use of well-defined ionophores in intact ROS and in liposomes. In the companion paper this method is used to describe the cation permeabilities native to ROS.

Carboxyl group involvement in the meta I and meta II stages in rhodopsin bleaching. A Fourier transform infrared spectroscopic study

Structural changes due to photoreceptor membrane bleaching can be studied by Fourier transform infrared difference spectroscopy [1,2]. In this paper we focus on the differences between rhodopsin and metarhodopsin I or II. Peaks in the 1700-1770 cm-1 region are observed, which may be produced by carbonyl groups in either carboxyl (COOH) or ester carbonyl (COOC) groups, the latter being found exclusively in membrane lipids. In order to distinguish between these two types of carbonyl groups, we have studied reconstituted membranes of rhodopsin in a synthetic phosphatidylcholine that lacks ester carbonyl groups. On this basis, we conclude that the major changes in this region are due to rhodopsin carboxyls which undergo either a change in local environment or a protonation/deprotonation reaction. Additional small changes in this region may reflect a direct involvement of phospholipids in the metarhodopsin I-to-II transition. One or more groups responsible for peaks near 1727 and 1702 cm-1 are inaccessible to the outside medium according to hydrogen/deuterium exchange. In contrast, carboxyl group(s) producing peaks near 1710, 1745 and 1768 cm-1 exchange freely with the outside medium and are therefore likely to be located near the membrane surface. Removal of a portion of the C-terminal tail region using proteinase K demonstrates that the carboxyl groups in the C-terminal sequence 248-348 are not involved directly in the rhodopsin to metarhodopsin II transition. At the meta I stage, only carboxyl peaks associated with buried groups appear, suggesting that the initial bleaching events, leading to the formation of this intermediate, produce structural rearrangements in the interior region of rhodopsin. These changes then spread to the peripheral surface regions during the metarhodopsin I-to-II transition.

A statistical technique for predicting membrane protein structure

A statistical technique has been developed for predicting the transmembrane segments of membrane proteins from their amino acid sequences. A protein's amino acid sequence is represented by a sequence of membrane propensity values derived from the frequency of occurrence of the amino acids in a number of putative transmembrane segments. A running average over this numeric sequence yields a membrane propensity profile from which transmembrane segments may be chosen. When this method is applied to a pool of ten putative membrane proteins, the predicted intra- and extramembrane regions agree 93.6% on a residue-by-residue basis with previously suggested structures. Predictions of transmembrane segments in cytochrome c oxidase subunits I, II and III and cytochrome b from several species are given, and structural homology between species is examined using membrane propensity profiles. Conclusions are then made about the functionality of several regions in these proteins.

Isolation and structure of a rhodopsin gene from D. melanogaster

Using a novel method for detecting cross-homologous nucleic acid sequences we have isolated the gene coding for the major rhodopsin of Drosophila melanogaster and mapped it to chromosomal region 92B8-11. Comparison of cDNA and genomic DNA sequences indicates that the gene is divided into five exons. The amino acid sequence deduced from the nucleotide sequence is 373 residues long, and the polypeptide chain contains seven hydrophobic segments that appear to correspond to the seven transmembrane segments characteristic of other rhodopsins. Three regions of Drosophila rhodopsin are highly conserved with the corresponding domains of bovine rhodopsin, suggesting an important role for these polypeptide regions.

Light-induced conformational changes in the extradiscal regions of bovine rhodopsin

Light-induced conformational changes occurring at the cytosolic surface of rhodopsin were investigated by performing limited digestions of native and illuminated visual pigment with thermolysin, Arg-C endoproteinase, papain and proteinase K. A higher susceptibility of the extradiscal regions of the bleached pigment to the proteases were observed together with altered capacities of the digested bleached rhodopsins to activate the cGMP phosphodiesterase. The overall results strongly suggest that light induces conformational changes not only in the C-terminal end but also in the second and the third extradiscal loop of rhodopsin.

Localization of light-induced conformational changes in bovine rhodopsin

Conformational changes in the extradiscal regions of rhodopsin induced by illumination were investigated by modifying the visual pigment by mild treatment with cyanogen bromide prior to and after light exposure. Light induced an increased yield of cleavage of the Met bond 253-254 and a new cleavage at the Met bond 155-156 of the rhodopsin polypeptide chain. These residues, located at the beginnings of the membrane-buried helices 6 and 4, respectively, were concluded to become extradiscally exposed upon illumination.

Rhodopsin-egg phosphatidylcholine reconstitution by an octyl glucoside dilution procedure

The transmembrane protein bovine rhodopsin was reconstituted with egg phosphatidylcholine (PC) by using a modified detergent dilution technique employing the nonionic detergent octyl-beta-D-glucoside (octyl glucoside). Using this technique, reconstituted membranes having molar phospholipid/protein ratios between 60:1 and 255:1 were prepared. This is in contrast to the results obtained when an octyl glucoside dialysis technique was employed (Jackson, M.L. and Litman, B.J. (1982) Biochemistry 21, 5601-5608). In the latter case, the highest molar phospholipid/protein ratio that could be obtained when reconstituting rhodopsin with egg PC was approximately 50:1. Reconstituted vesicles prepared by the octyl glucoside dilution technique were examined by negative stain and freeze-fracture electron microscopy, and it was found that the vesicles were unilamellar providing the molar PC/protein ratio was below about 200:1, whereas in preparations having ratios higher than this, a significant number of the vesicles were multilamellar. The mean vesicle diameter showed no trend based on the molar PC/protein ratio within the range of 82:1 to 186:1. The mean diameters of the preparations were between 520 and 850 A. Approximately equal numbers of protein particles were observed on the concave and convex fracture faces of the freeze-fracture micrographs of the reconstituted membranes which is indicative of a symmetric distribution of the protein across the bilayer.

Complete amino acid sequence of gamma-subunit of the GTP-binding protein from cattle retina

The complete amino acid sequence of the gamma-subunit of the GTP-binding protein from cattle retina has been established. The polypeptide chain of the gamma-subunit consists of 69 amino acid residues and contains the unusual sequence Cys35-Cys36. The Mr of the gamma-subunit is 8008.7.

Stability of "salt bridges" in membrane proteins

We estimate the free energies of transfer of ionized amino acid side chains in water to both their ion-paired and neutral hydrogen-bonded states in low-dielectric media. The difference between the two free energies corresponds to the proton transfer free energy in a "salt bridge" formed between acidic and basic groups (i.e., lysine and glutamic acid residues). Our approach is to use gas phase proton transfer data, pK values, and experimentally determined solvation energies to estimate the standard state free energy changes involved in transferring amino acid side chains, in both ionized and neutral form, from water (dielectric constant epsilon = 80) to vacuum (epsilon = 1). The familiar expressions for the charging energy of a sphere and dipole are used to interpolate between epsilon = 1 and epsilon = 80. Our results suggest that it costs approximately 10-16 kcal/mol to transfer a salt bridge from water to a medium of epsilon = 2-4, in ionized or neutral form within the resolution of our estimates. The proton transfer energy is thus approximately 0. The tendency of salt bridges to form additional hydrogen bonds in real proteins suggests that the ion pair will be present in most biological systems.

Proteinase-treated photoreceptor discs. Photoelectric activity of the partially-digested rhodopsin and membrane orientation

Photoreceptor discs from rod outer segments of cattle retina were treated with (a) papain, (b) thermolysin or (c) trypsin, the procedures resulting in the cleavage of the rhodopsin polypeptide chain between (a) 323 and 324, 236 and 237, 241 and 242, (b) 327 and 328, 240 and 241, or (c) 339 and 340 amino acid residues, respectively. In all the cases, partially digested rhodopsins proved to be competent in generating photoelectric potential and increasing membrane conductance of the discs adsorbed onto phospholipid-impregnated collodion film. The kinetics of generation and dissipation of photopotential as well as of formation of metarhodopsin II and of the light-induced rhodopsin protonation were found to be the same in the partially digested preparations and in the intact one. Incubation of papain-treated or thermolysin-treated discs at pH 6.0 induced formation of inside-out vesicles which, when incorporated into the collodion film, generated an oppositely directed photopotential. Treatment of such vesicles with papain gave rise to further cleavages of the polypeptide localized between 30 and 31, 186 and 187 amino acid residues. One more proteinase-sensitive site, localized between 104 and 105 residues, has been discovered in the inside-out vesicles treated with thermolysin. This fact consistent with the scheme of the 'seven column' arrangement of the visual rhodopsin [Ovchinnikov, Yu. A. (1982) FEBS Lett. 148, 179-191]. Rhodopsin, when treated with papain on both sides, was deprived of sixty amino acid residues being split in two sites in the middle part of the polypeptide, but was still active as a photoelectric energy transducer. The main specific feature inherent in the photoelectric response of the papain-treated or thermolysin-treated rhodopsin and absent from the native protein is that the former survives addition of long trains of saturating flashes when the response of the intact preparation becomes negligible. This effect was shown to be due to conversion of partially digested rhodopsin to a photolytic product that at room temperature lived for minutes even in the presence of NH2OH. A 532-nm laser flash effectively converted this product back to rhodopsin.

Purification of bovine rhodopsin by high-performance size-exclusion chromatography

Bovine rhodopsin was purified from n-octylglucoside-solubilized retinas by high-performance size-exclusion chromatography. In one chromatographic step, six protein fractions were separated with baseline resolution. The major fraction was identified as monomeric rhodopsin by absorption spectroscopy. Amino acid analysis of this fraction further supported the assignment. A comparison of the elution profiles of rhodopsin purified by this method with that purified by Concanavalin A-Sepharose 4B affinity chromatography suggested that rhodopsin from high-performance chromatography was slightly purer than the conventionally purified rhodopsin.

Dynamic structure of membranes by deuterium NMR

Progress in our understanding of the dynamic structure of membrane lipids and proteins has recently been made possible by the advent of high-field "solid-state" nuclear magnetic resonance spectroscopic studies of specifically deuterium-labeled systems. Major features of lipid and protein dynamics have been deduced.

Target size analysis of rhodopsin in retinal rod disk membranes

Radiation inactivation of rhodopsin in situ using high-energy electrons gave a value for Mr of 20,200 by spectral assay, but 47,100 by assay of rhodopsin regeneration from opsin and 11-cis-retinal (sequence Mr = 38,840). No light/dark differences were seen. We conclude: (a) radiation inactivation measures the size of the functional unit, and the single hit hypothesis does not hold in our experiments; (b) 500 nm absorbance requires only about half the rhodopsin molecule to be intact, but reconstitution of rhodopsin from opsin requires the whole molecule; (c) we find no evidence for functional interactions between rhodopsin monomers in darkness or light.

Labelling of the cytoplasmic domains of ovine rhodopsin with hydrophilic chemical probes

The disposition of polypeptide chain of ovine rhodopsin in the photoreceptor disc membrane was investigated by using two hydrophilic reagents, 3,5-di-[125I]iodo-4-diazobenzenesulphonate [( 125I]DDISA) and [14C]succinic anhydride. Both reagents were used to modify rhodopsin in intact disc membranes under conditions where no loss of A500 occurred. Reaction of [125I]DDISA with rhodopsin approached completion after 30 min. Binding was saturated at a 75-fold molar excess of reagent, which gave binding ratios of up to 2 mol/mol of rhodopsin. Proteolysis of rhodopsin, using Staphylococcus aureus V8 proteinase, yielded two membrane-bound fragments, both of which contained bound radioactive probe. Subsequent CNBr cleavage of these fragments produced five radiolabelled peptides which corresponded to the C-terminal region and cytoplasmic loops of rhodopsin. Similar studies with [14C]-succinic anhydride also gave binding ratios of up to 2 mol/mol of rhodopsin. Sequencing of the [14C]succinylated peptides identified the location of the reactive sites as lysine residues 66, 67, 141, 245, 248, 311, 325 and 339 in the polypeptide chain. Non-permeability of both probes was demonstrated by the absence of any radioactivity associated with the intradiscal N-terminal glycopeptide. Sonication of membranes in the presence of [125I]DDISA led to the incorporation of label in this peptide.

Retinal migration during dark reduction of bacteriorhodopsin

When the retinal Schiff base in chymotryptically cleaved bacteriorhodopsin is reduced to a secondary retinylamine by prolonged exposure to 10% (wt/vol) sodium cyanoborohydride, at pH 10, in the absence of light, approximately 45% of the retinal is found linked to Lys-41 and 22% to Lys-40, and the remainder is scattered over various sites on the large chymotryptic fragment, including the physiological site at Lys-216. The retinal-binding site is destroyed or blocked by the reduction conditions, but the bacteriorhodopsin lattice remains intact. The results demonstrate that artifactual linkage to Lys-40/41 is possible under special conditions. Under these conditions, the epsilon-amino groups of Lys-40/41 show an enhanced ability to form retinylidene linkages with the retinal released by the physiological linkage site at Lys-216, due to some combination of close proximity to the normal linkage site, and increased reactivity with respect to other lysine epsilon-amino groups. The results are of interest for the characterization of the two newly discovered rhodopsin-like proteins, halorhodopsin and slow rhodopsin.

Sulfhydryl group modification of photoreceptor G-protein prevents its light-induced binding to rhodopsin

The effect of sulfhydryl modification on the light-induced interaction between rhodopsin and the peripheral GTP-binding protein of the photoreceptor membrane (G-protein) has been investigated by time-resolved near-infrared light-scattering and polyacrylamide gel electrophoresis. It has been found that the modification of rhodopsin with the alkylating agent N-ethylmaleimide (NEM) does not affect its light-induced interaction with the G-protein. Modification of G-protein with NEM or other sulfhydryl agents prevents any light-induced binding to rhodopsin. Dark-association of G to the membrane as well as the light-induced complex with rhodopsin (once formed) is insensitive to NEM.

Surface dynamics of the integral membrane protein bacteriorhodopsin

Recently, there has been great interest in determining the three-dimensional structures of membrane proteins, particularly bacteriorhodopsin, for which a variety of possible folding arrangements have been suggested. In this paper we present nuclear magnetic resonance (NMR) spectra of deuterated bacteriorhodopsin, and use the data to help interpret the various suggested bacteriorhodopsin folding patterns. The results strongly indicate that (1) a membrane surface (+/- 1 residue) may be defined by NMR in bacteriorhodopsin; (2) all amino acids inside the surface are essentially crystalline; (3) all amino acids outside the surface (surface residues) in bacteriorhodopsin are highly mobile on the time scale of the 2H NMR experiments; (4) NMR data may be used to help evaluate the various structural models that have been proposed; (5) aggregation of purple membrane sheets may lead to an immobilization of the surface residues.

The structure of mammalian rod opsins

Ovine rhodopsin is organised in disc membranes as a monomer. The determination of its amino acid sequence has permitted the utilisation of structure prediction programmes which indicate the probable disposition of the polypeptide chain in the bilayer. This putative model is consistent with labelling data using the chemical probes, [14C]succinic anhydride, [125I]diazodiido sulphanilic acid and [125I]iodophenyl azide, and with the cleavage points for several proteases. More surprisingly the predicted structure points to the occurrence of breaks/distortions in the transmembrane helical segments. These distorted regions may be of primary functional importance to the protein and at least one is associated with the attachment point of the chromophore. This particular part of the structure is also identified as a "mutational hot spot", for bovine, equine, ovine and porcine opsins exhibit different sequences (but conserved molecular volumes) in the four residues following the retinyllysine. In an otherwise highly conserved protein with no obvious functional differences between the four species, the high substitution rate in this region is unexplained.

Primary intermediates of rhodopsin studied by low temperature spectrophotometry and laser photolysis. Bathorhodopsin, hypsorhodopsin and photorhodopsin

The primary photochemical processes of rhodopsin studied by low temperature spectrophotometry and picosecond laser spectroscopy in our group was summarized. Low temperature spectroscopic experiments demonstrated that the retinylidene chromophores of hypso- and bathorhodopsins are in a twisted all-trans forms. Excitation of rhodopsin with 532 nm laser pulse (width: 25 psec) yielded a new bathochromic photoproduct "photorhodopsin"; its spectrum was located at longer wavelengths than that of bathorhodopsin. Photorhodopsin decays to bathorhodopsin with time constants of about 200 psec in squid and 40 psec in cattle. Squid and octopus hypsorhodopsins were produced within 25 psec by high energy pulse, but not by low energy pulse. Thus hypsorhodopsin is produced by two photon reactions (sequential two photochemical reactions) and decayed to bathorhodopsin with time constant of 125 psec.