A structural model for ovine rhodopsin

Anti-bovine rhodopsin monoclonal antibody recognizing light-dependent structural change

The antigenic structure of the bovine rhodopsin molecule was investigated by using a bovine rhodopsin-specific monoclonal antibody designated Rh 29. Competition assay with sealed intact disks and broken disks indicated that the antibody-binding region was localized in the intradiscal surface. An antigenic peptide obtained by a cyanogene bromide cleavage of rhodopsin was purified and determined as residues 2-39 in the amino acid sequence. Further analysis suggested that the antigenic determinant included at least residues 21-25. These results were consistent with the structural model for membrane topology of rhodopsin. The antigenicity of the rhodopsin was compared among several states. The antibody bound to both ammonyx LO-solubilized unbleached and bleached rhodopsin. In contrast, upon membrane-embedded rhodopsin, unbleached one was 100-times less antigenic than bleached one. The results suggested that the segment around the determinant of membrane-embedded rhodopsin should undergo a structural change upon absorption of light. Rh 29 detected a band corresponding to bovine, porcine and octopus opsins in immunoblotting. Protein blot of crayfish rhabdome did not show any reactive band. These bands except for crayfish reacted with concanavalin A as well. The N-terminal structure may, therefore, conserved between mammal and erthropoda and diverge between them and cepharopoda.

A simple method for classifying genes and a bootstrap test for classifications

A new simple method for classifying genes is proposed based on Klastorin's method. This method classifies genes into monophyletic groups which are made distinct from each other by evolutionary changes. The method is applicable as long as the phylogenetic tree of genes is obtained. There is a fast algorithm for obtaining the classification. A bootstrap test of a classification is also presented. As an example, we classified opsin genes. The classification obtained by this method is the same as the previous classification based on the function of opsins.

Nucleotide sequence of the canine rod-opsin-encoding gene

The major parts of two canine rod-specific opsin (Ops) transcripts have been cloned by polymerase chain reaction from retinal mRNA. Both transcripts are derived from the same gene. The 5' leader sequence of the transcripts was cloned from canine peripheral blood DNA. The transcripts code for a protein of 348 amino acids (aa), M(r) 38,962 (prior to any protein modification). The aa sequence suggests that in common with other sequenced Ops, canine rod Ops contains seven transmembrane domains, and residues believed essential for retinal pigment binding and for palmitate binding are conserved in the canine protein. Northern blotting using the central part of the ops gene as probe suggested that mature transcripts of three different sizes (about 1900, 2600 and 5500 bases) were found in retina. Of these, the 2600-base transcript was the most abundant. RACE cloning of the 3' end of ops showed that at least two of these size classes originate from differential transcript termination.

Knowledge-based protein modeling

Knowledge, both from the three-dimensional structures of homologous proteins and from the general analysis of protein structure, is of value in modeling a protein of known sequence but unknown structure. While many models are still constructed at least in part by manual methods on graphics devices, automated procedures have come into greater use. These procedures include those that assemble fragments of structure from other known structures and those that derive coordinates for the model from the satisfaction of restraints placed on atomic positions.

Early opsin expression in Xenopus embryos precedes photoreceptor differentiation

The visual pigment which serves as the first step in the phototransduction cycle in vertebrate rod cells consists of a retinal chromophore which is linked to the transmembrane protein, opsin. Opsin genes have been isolated from a number of different organisms and studies have shown opsin to be developmentally regulated with both mRNA and protein expression associated with the morphological differentiation of photoreceptor cells. Due to its potential utility as a marker for rod photoreceptor determination in studies of retinal tissue interactions, and because no amphibian opsin genes have as yet been cloned, we isolated cDNA clones of the Xenopus laevis opsin gene. Sequence analysis shows that within the coding region Xenopus opsin shares a high degree of identity with other rod opsin genes, except at the C-terminal where it more closely resembles the mammalian color opsins. A developmental analysis, on the other hand, reveals that Xenopus opsin transcripts are detectable in a retina-specific fashion early in retinal development. Using in situ hybridization we find that Xenopus opsin mRNA is initially restricted to a few isolated cells in the presumptive photoreceptor layer which express the gene at relatively high levels. This suggests that rod photoreceptor determination occurs in single cells, and that the mechanisms controlling opsin expression in Xenopus are initiated well before any evidence of morphological differentiation.

Modeling rhodopsin, a member of G-protein coupled receptors, by computer graphics. Interpretation of chemical shifts of fluorinated rhodopsins

An attempt has been made to construct a 3-D model of rhodopsin, a member of G-protein coupled receptors. Sequence homology of rhodopsin with the latter was a factor considered in the modeling procedure. The constructed model has been used to compare currently available specific protein/substrate interaction information, the shape of the binding cavity derived from shape of binding retinal isomers and analogs and challenged to explain recently available results from a series of fluorinated rhodopsins.

Molecular analysis of a human interferon-inducible gene family

Three functional members of the 1-8 gene family have been isolated on a single human genomic DNA fragment of less than 18 kb. The 1-8U and 1-8D genes are extremely similar; each is contained within a less than 2-kb fragment, has in its 5'flanking region two adjacent 14-base-pair sequences showing high similarity to interferon-stimulable response elements (ISREs) and has two highly related exons. The third gene (9-27) has a similar overall structure, shows substantial similarity to the 1-8s but has only one ISRE which is 3' of two CCAAT boxes not present in the 1-8U and D genes. The cDNA corresponding to the three genes share 120 nucleotides of identical sequence and show greater than 90% identity over 70% of the coding sequence. For the 1-8U and D genes the high similarity extends into the 5' non-coding and flanking regions. The open reading frames encode polypeptides that are likely to be of very similar structure. Antiserum to a conserved peptide detects a polypeptide(s) of about 14 kDa on PAGE which separates into three components on isoelectric focussing. The 9-27 and 1-8U genes are highly interferon-inducible the 1-8D gene is much less so. These differences are mimicked by the activities of the corresponding ISREs placed 5' of a marker gene in expression constructs. They presumably reflect differences in the interaction of the ISREs with the various interferon-inducible and constitutive factors that govern the interferon response.

Anti-rhodopsin monoclonal antibodies of defined specificity: characterization and application

A panel of anti-bovine rhodopsin monoclonal antibodies (MAbs) of defined site-specificity has been prepared and used for functional and topographic studies of rhodopsins. In order to select these antibodies, hybridoma supernatants that contained anti-rhodopsin antibodies have been screened by enzyme-linked immunosorbent assay (ELISA) in the presence of synthetic peptides from rhodopsin's cytoplasmic regions. We selected for antibodies against predominantly linear determinants (as distinct from complex assembled determinants) and have isolated antibodies that recognize rhodopsin's amino terminus, its carboxyl terminus, as well as the hydrophilic helix-connecting regions 61-75, 96-115, 118-203, 230-252 and 310-321. Detailed specificities have been further determined by using a series of overlapping peptides and chemically modified rhodopsins as competitors. A group of seven antibodies with epitopes clustered within the amino terminal region of rhodopsin and a group of 15 antibodies with epitopes within the carboxyl terminal region are described. These MAbs have high affinities for rhodopsin with Kas in the range of 10(8)-10(10) M-1. Some MAbs specific for the carboxyl and amino terminal regions were used to compare these bovine rhodopsin sequences to those of different vertebrates. The MAbs cross-reacted with the different species tested to different extents indicating that there is some similarity in the sequences of these regions. However, some differences in the sequences were indicated by a reduced or absent cross-reactivity with some MAbs. In membrane topographic studies the MAbs showed both the presence and the accessibility of rhodopsin sequences 330-348, 310-321 and 230-252 on the cytoplasmic surface of the disk membrane. Similarly, sequences 1-20 and 188-203 were shown to reside on the lumenal surface of the disk and to be accessible to a macromolecular (antibody) probe. Antibodies directed against rhodopsin's carboxyl terminal sequence did not bind well to highly phosphorylated rhodopsin. Similarly, these antibodies as well as those against the V-VI loop inhibited phosphorylation of rhodopsin. Antibody A11-82P, specific for phosphorylated rhodopsin, recognized rhodopsin containing two or more phosphates and inhibited its further phosphorylation.

Mutations within the rhodopsin gene in patients with autosomal dominant retinitis pigmentosa

BACKGROUND

Night blindness is an early symptom of retinitis pigmentosa. The rod photoreceptors are responsible for night vision and use rhodopsin as the photosensitive pigment.

METHODS AND RESULTS

We found three mutations in the human rhodopsin gene; each occurred exclusively in the affected members of some families with autosomal dominant retinitis pigmentosa. Two mutations were C-to-T transitions involving separate nucleotides of codon 347; the third was a C-to-G transversion in codon 58. Each mutation corresponded to a change in one amino acid residue in the rhodopsin molecule. None of these mutations were found in 106 unrelated normal subjects who served as controls. When the incidence of these three mutations was added to that of a previously reported mutation involving codon 23, 27 of 150 unrelated patients with autosomal dominant retinitis pigmentosa (18 percent) were found to carry one of these four defects in the rhodopsin gene. All 27 patients had abnormal rod function on monitoring of their electroretinograms. It appears that patients with the mutation involving codon 23 probably descend from a single ancestor.

CONCLUSIONS

In some patients with autosomal dominant retinitis pigmentosa, the disease is caused by one of a variety of mutations of the rhodopsin gene.

A molecular modelling study of the interaction of noradrenaline with the beta 2-adrenergic receptor

A model of the beta 2-adrenergic receptor binding site is built from the primary structure of the receptor, experimental evidence for key binding residues and analogy with a homologous protein of partially determined structure. It is suggested that residues Trp-109, Thr-110 and Asp-113 are involved in ligand binding. Noradrenaline is successfully docked into this model, and the results of an INDO molecular orbital calculation on the complex indicate that a charge transfer interaction between Trp-109 and noradrenaline is possible.

An analysis of the periodicity of conserved residues in sequence alignments of G-protein coupled receptors. Implications for the three-dimensional structure

Twenty-three sequences from the family of G-protein coupled receptors have been aligned according to the 'historical alignment' procedure of Feng and Doolittle. Fourier transform analysis of this reveals that parts of five of the seven putative membrane-spanning regions exhibit a periodicity of conserved/nonconserved residues which is compatible with the periodicity of the alpha-helix. This would place the conserved residues on one side of the helix, which may face the inside of the proposed seven membered helical bundle.

Consensus residues at the acetylcholine binding site of cholinergic proteins

The nicotinic (nAcChR) and muscarinic (mAcCh) acetylcholine receptors and acetylcholinesterase (AcChEase) are structurally unrelated but share a common functional property: interaction with acetylcholine (AcCh). Alignment of the probable AcCh binding site regions of the nAcChR and mAcChR protein sequences revealed the presence of ten nearly identically spaced consensus residues, six of which contain potentially ligand-interactive side chains. Important elements of the consensus residues also were found in one unique sequence region of the AcChEases. Alignments among the two receptors and AcChEase outside the apparent binding region were rare, and the consensus AcCh binding residues were largely substituted in the homologous proteins, which do not bind AcCh. The consensus residues include two possible anionic subsite Asp residues and a Ser that may hydrogen bond to the AcCh carbonyl in the receptors. These residues correspond to positions Asp-166, Ser-173, and Asp-200 in the neuromuscular nAcChR; Asp-71, Ser-78, and Asp-105 in the M1 mAcChR; and Asp-93 and Asp-128 in Torpedo AcChEase. No corresponding consensus Ser is found in the AcChEase sequence; this is expected because of a downstream esterase active-site Ser-200 (Torpedo). A receptor-conserved and disulfide-linked Cys corresponding to neuromuscular nAcChR residue 193 and M1 mAcChR residue 97 may be important in energy transduction associated with agonist-mediated events. The presence of additional binding-site aromatic residues that may form a hydrophobic environment near the anionic subsite are aligned within, but not between, the three cholinergic protein groups. These observations target specific regions and residues within these proteins for structure-function studies of the cholinergic binding domain.

Transglutaminase modification of rhodopsin in retinal rod outer segment disk membranes

Rhodopsin in rod outer segment disk membranes was enzymatically modified by erythrocyte transglutaminase, which linked small primary amines to glutamine residues. In order to avoid formation of protein crosslinks, rhodopsin was first reductively methylated to modify its lysines. From 1.9 to 2.5 mol of putrescine, ethanolamine, or dinitrophenylcadaverine were incorporated into rhodopsin by transglutaminase during 16 h reaction time. A maximum of 3.5 mol of [14C]putrescine was incorporated per mole of rhodopsin during 48 h. Essentially all of the rhodopsin sequence containing the putrescine could be removed by limited proteolysis of the membranes by thermolysin. Glutamine residues in positions 236, 237, 238, and 344 were modified to approximately equal extents, as determined by isolation of the cyanogen bromide peptides of modified rhodopsin followed by further subdigestion of the peptides. The modified glutamine residues are located in the helix V-VI (or F1-F2) connecting loop and in the carboxyl-terminal region of rhodopsin.

31P-NMR investigation of magnetically oriented rod outer segments. Spectral analysis and identification of individual phospholipids

A 31P-NMR study of magnetically oriented bovine rod outer segments is presented. We demonstrate that carefully isolated bovine rod outer segments retain the capacity to orient in a magnetic field. Maximal orientation (85-90%) is achieved at field strengths over 4.7 T in the NMR spectrometer. The lineshape of the 'oriented spectra' is totally different from the 'bilayer lineshape' of randomly oriented photoreceptor membranes. The oriented spectra consist of two phospholipid peaks, a major low-field peak (75-80% of the total intensity) near 30 ppm, and a minor high-field peak near - 14 ppm as well as two sharp metabolite peaks around 0 ppm. The phospholipid peaks are a composite of three narrower partially resolved resonances assigned to the individual phospholipid classes phosphatidylserine, phosphatidylcholine and phosphatidylethanolamine. Based on the morphology and magnetic anisotropy of the rod outer segment, the major phospholipid peak is attributed to the flat part of the disk membranes while the phospholipids of the plasma membrane are thought to contribute only to the minor peak. Disk rim phospholipids and non-oriented material contribute to the minor peak and, in addition, contribute some intensity to the middle part of the spectrum. The phospholipid class composition of the major peak is estimated by spectral simulation and is consistent with the phospholipid class composition of rod outer segment membranes. Hence, 31P analysis of oriented rod outer segments resolves the main phospholipids in at least two different membrane pools in the rod outer segment and allows the differential investigation of these pools. Most of the mobile phosphate metabolite intensity resides in the Pi peak at 3.5 ppm. A slight shift in the Pi resonance position indicates a 0.2 pH unit acidification upon illumination of rhodopsin. The absence of detectable nucleotide resonances, when compared with chemical analysis, indicates that the majority of the nucleotide population present is rather immobile and probably bound to the membranes.

Molecular biology of the visual pigments

With the identification and structural characterization of several visual pigments has come a new era of investigation. The above comparisons of amino acids sequences predict specific functional domains that may be tested to tell us how visual pigments function to absorb light and transform this "signal" to trigger a neural response. The details of how rod and cone pigments differ are now known for human pigments. The striking similarities between vertebrate and invertebrate pigments are remarkable for pigments that have been subject to divergence for over 500 million years. There are yet challenges ahead of us. The true tertiary structure of visual pigments must be obtained from a 3-dimensional crystal structure. The predictions for functional domains of interaction with the GTP binding protein must be confirmed or redefined. A rigorous definition of the chromophore environment and the properties that control the wavelength of absorption of 11-cis retinal chromophore are certainly still on the drawing boards. Specific genetic alteration through in vitro mutagenesis promises much insight, but the technology for expressing these membrane proteins in functional form has yet to be achieved. We may expect, however, these problems will be addressed and in the next few years facts should replace what are now speculations. Finally, it is a delightful observation that nature has capitalized on a general biochemical mechanism for control of second messengers in the cytoplasm of cells. Protein structural data deduced from genetic information now document the hypothesis that the structure and function of receptors for the catecholamines and that of visual pigments are similar. The receptors for serotonin, leukotrienes, prostaglandins, histamine and acetylcholine (muscarinic) are expected to belong to this same family. The lessons learned about visual pigments can be applied broadly to a general set of membrane receptors.

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.

The Drosophila ninaE gene encodes an opsin

The Drosophila ninaE gene was isolated by a multistep protocol on the basis of its homology to bovine opsin cDNA. The gene encodes the major visual pigment protein (opsin) contained in Drosophila photoreceptor cells R1-R6. The coding sequence is interrupted by four short introns. The positions of three introns are conserved with respect to positions in mammalian opsin genes. The nucleotide sequence has intermittent regions of homology to bovine opsin coding sequences. The deduced amino acid sequence reveals significant homology to vertebrate opsins; there is strong conservation of the retinal binding site and two other regions. The predicted protein secondary structure strikingly resembles that of mammalian opsins. We conclude the Drosophila and vertebrate opsin genes are derived from a common ancestor.

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.