Rhodopsin and bacteriorhodopsin: structure-function relationships

2-Hydroxy-5-nitrobenzyl bromide as a specific reagent for tryptophan residues in membrane proteins: bacteriorhodopsin as an example

The use of 2-hydroxy-5-nitrobenzyl bromide for the modification of tryptophan residues in integral membrane proteins is exemplified by its application to bacteriorhodopsin from Halobacterium halobium. Complete elimination of the unreacted reagent requires delipidation of the sample with detergents and posterior chromatography. This method also allows separation of the modified from the unmodified bacteriorhodopsin molecules. Modified molecules have lost the retinal, and are thus bleached, whereas the unmodified molecules appear to retain all the characteristics of solubilized native bacteriorhodopsin.

Topogenic signals in integral membrane proteins

Integral membrane proteins are characterized by long apolar segments that cross the lipid bilayer. Polar domains flanking these apolar segments have a more balanced amino acid composition, typical for soluble proteins. We show that the apolar segments from three different kinds of membrane-assembly signals do not differ significantly in amino acid content, but that the inside/outside location of the polar domains correlates strongly with their content of arginyl and lysyl residues, not only for bacterial inner-membrane proteins, but also for eukaryotic.proteins from the endoplasmic reticulum, the plasma membrane, the inner mitochondrial membrane, and the chloroplast thylakoid membrane. A positive-inside rule thus seems to apply universally to all integral membrane proteins, with apolar regions targeting for membrane integration and charged residues providing the topological information.

Octopus rhodopsin. Amino acid sequence deduced from cDNA

The primary structure of rhodopsin from the octopus Paroctopus defleini has been determined by parallel analysis of the protein and corresponding cDNA. The amino acid sequence is most similar to the recently cloned Drosophila opsins. Similarities to bovine and human opsins are also evident. The transmembrane topology of octopus rhodopsin is discussed.

Denaturation of bacteriorhodopsin by organic solvents

The denaturation of bacteriorhodopsin by various organic solvents was studied using absorption, circular dichroism (CD) and fluorescence measurements. Organic solvents with a hydrogen-bonding group caused the release of retinal. The CD measurements showed that the helical structure was maintained even in the denatured state, whereas its tertiary structure was destroyed. The change in fluorescence intensity of tryptophan and fluorescent retinal also confirmed that the tertiary structure was destroyed. Comparison of the denaturation efficiency of various organic solvents showed that the concentration at denaturation was inversely proportional to the partition coefficient of the denaturant. This inverse proportionality clearly indicated that denaturation was determined by the concentration of denaturants which partitioned into the hydrophobic region of the membrane. It was discussed from the experimental results that the tertiary structure of bacteriorhodopsin was stabilized by the hydrogen-bonding networks between side chains of the helices. The results obtained from analysis of the amino acid sequence were also consistent with the hydrogen-bonding mechanism for the formation of the tertiary structure.

Proline utilization in Saccharomyces cerevisiae: sequence, regulation, and mitochondrial localization of the PUT1 gene product

The PUT1 gene of Saccharomyces cerevisiae, believed to encode proline oxidase, has been completely sequenced and contains an open reading frame capable of encoding a polypeptide of 476 amino acids in length. The amino terminus of the protein deduced from the DNA sequence has a characteristic mitochondrial import signal; two PUT1-lacZ gene fusions were constructed that produced mitochondrially localized beta-galactosidase in vivo. The transcription initiation and termination sites of the PUT1 mRNA were determined. By using a PUT1-lacZ gene fusion that makes a cytoplasmic beta-galactosidase, the regulation of the PUT1 gene was studied. PUT1 is inducible by proline, responds only slightly to carbon catabolite repression, and is not regulated by the cytochrome activator proteins HAP1 and HAP2. The PUT1 gene is under oxygen regulation; expression in anaerobically grown cells is 10-fold lower than in aerobically grown cells. Oxygen regulation is abolished when cells are respiratory deficient. PUT1 expression in a [rho-] strain grown either aerobically or anaerobically is as high as that seen in a [rho+] strain grown aerobically. Studies on PUT1 promoter deletions define a region between positions -458 and -293 from the translation initiation site that is important for full expression of the PUT1 gene and required for oxygen regulation.

Two adjacent cysteine residues in the C-terminal cytoplasmic fragment of bovine rhodopsin are palmitylated

Covalent coupling of bovine rhodopsin to CPG-thiol glass was used for separation of CNBr peptides. It is shown that cysteine residues 322 and 323 in the C-terminal cytoplasmic fragment of rhodopsin are modified with palmitic acid.

Identification and sequence of a binding site peptide of the beta 2-adrenergic receptor

p-(Bromoacetamido)benzyl-1-[125I]iodocarazolol (125I-pBABC) is a potent derivative of the beta-adrenergic receptor antagonist p-aminobenzylcarazolol. Treatment of the receptor with 125I-pBABC results in efficient covalent incorporation of the ligand into the receptor binding site. Extensive degradation of 125I-pBABC-labeled beta 2-adrenergic receptor with either cyanogen bromide or Staphylococcus aureus V8 protease results in specifically labeled fragments having Mr's of about 1600 and 3500, respectively. Because the primary structure of the beta 2-adrenergic receptor is known, and these proteolytic reagents are highly sequence specific, the site of 125I-pBABC incorporation may be deduced from the sizes of the specifically labeled fragments. Thus the fragment generated by cyanogen bromide cleavage corresponds to residues 83-96, a region of 14 amino acids included in the second membrane spanning domain (helix II) of the beta 2-adrenergic receptor. This assignment was confirmed by direct amino acid sequencing of this labeled fragment, though the actual amino acid modified could not be determined. These data permit the assignment of a part of the hormone binding region of the beta 2-adrenergic receptor.

Sequence of the region coding for virion proteins C and E2 and the carboxy terminus of the nonstructural proteins of rubella virus: comparison with alphaviruses

The sequence of the 3' 4508 nucleotides (nt) of the genomic RNA of the Therien strain of rubella virus (RV) was determined for cDNA clones. The sequence contains a 3189-nt open reading frame (ORF) which codes for the structural proteins C, E2 and E1. C is predicted to have a length of 300 amino acids (aa). The N-terminal half of the C protein is highly basic and hydrophilic in nature, and is putatively the region of the protein which interacts with the virion RNA. At the C terminus of the C protein is a stretch of 20 hydrophobic aa which also serves as the signal sequence for E2, indicating that the cleavage of C from the polyprotein precursor may be catalyzed by signalase in the lumen of the endoplasmic reticulum. E2 is 282 aa in length and contains four potential N-linked glycosylation sites and a putative transmembrane domain near its C terminus. The sequence of E1 has been previously described [Frey et al., Virology 154 (1986) 228-232]. No homology could be detected between the amino acid sequence of the RV structural proteins and the amino acid sequence of the alphavirus structural proteins. From the position of a region of 30 nt in the RV genomic sequence which exhibited significant homology with the sequence in the alphavirus genome at which subgenomic RNA synthesis is initiated, the RV subgenomic RNA is predicted to be 3346 nt in length and the nontranslated region from the 5' end of the subgenomic RNA to the structural protein ORF is predicted to be 98 nt. In a different translation frame beginning at the 5' end of the RV nt sequence reported here is a 1407 nt ORF which is the C terminal region of the nonstructural protein ORF. This ORF overlaps the structural protein ORF by 149 nt. A low level of homology could be detected between the predicted amino acid sequence of the C-terminus of the RV nonstructural protein ORF and the replicase proteins of several positive RNA viruses of animals and plants, including nsp4 of the alphaviruses, the protein encoded by the C-terminal region of the alphavirus nonstructural ORF. However, the overall homology between RV and the alphaviruses in this region of the genome was only 18%, indicating that these two genera of the Togavirus family are only distantly related. Intriguingly, there is a 2844-nt ORF present in the negative polarity orientation of the RV sequence which could encode a 928-aa polyprotein.

The bacteriorhodopsin proton pump: effect of crosslinkings of lysine residues

All six available lysine residues in bacteriorhodopsin were amidinated with dimethyl-3,3'-dithiobispropionimidate, which is a crosslinking agent. The photocycle was studied by measuring light absorption and electric signals. The data show an essential change in the photocycle: instead of single components, the rise of the signal due to the M intermediate can be decomposed into two components, and the decay into three. The life-times and the intensities of these components and in general the proton pumping activity of bacteriorhodopsin depend only negligibly upon pH. Changes upon removing the crosslinks are not significantly different from those in the crosslinked samples. The lysine residues therefore may not be considered of primary importance in proton translocation.

A monoclonal antibody that binds to photoreceptors in the turtle retina

We have raised monoclonal antibodies to photoreceptor cells in the retina of the turtle (Pseudemys scripta elegans). One of these antibodies, 15-18 (an IgG1), was studied by immunoelectron microscopy using colloidal gold, and found to bind to the outer segments of all rods and some single cones, but did not stain turtle double cones. Immunoblotting and immunoprecipitation show that antibody 15-18 binds to an antigen of apparent Mr approximately 34,5000 which is probably turtle opsin. Antibody 15-18 binds visual pigments from several species, including bovine opsin. In order to determine the antigenic site bound by 15-18 in bovine opsin, synthetic peptides were used as competitors in an enzyme-linked immunoassay (ELISA). The antigenic site is located in the surface loop connecting rhodopsin helices IV-V, in the sequence 190-197. Antibody 15-18 binds to the external surface of rod cell outer segments, thus providing direct evidence for the predicted orientation of rhodopsin in the plasma membrane.

Isolation and sequence determination of the chicken rhodopsin gene

A chicken genomic library was screened with a bovine opsin cDNA probe. A clone isolated under high stringency hybridization conditions contained DNA sequences highly homologous to all of the five exons of bovine and human opsin genes. Sequence comparison of the putative open reading frame in the chicken DNA fragment of 4.3 kb with bovine opsin cDNA revealed 82% identity for the nucleotide and 87% for the deduced amino acid sequence, indicating that this DNA fragment contains the complete chicken opsin gene. The position of four introns and amino acid sequences at all putative cytoplasmic loops are exactly conserved in chicken and mammals.

Refolding of bacteriorhodopsin in lipid bilayers. A thermodynamically controlled two-stage process

Possible steps in the folding of bacteriorhodopsin are revealed by studying the refolding and interaction of two fragments of the molecule reconstituted in lipid vesicles. (1) Two denatured bacteriorhodopsin fragments have been purified starting from chymotryptically cleaved bacteriorhodopsin. Cleaved bacteriorhodopsin has been renatured from a mixture of the fragments in Halobacterium lipids/retinal/dodecyl sulfate solution following removal of dodecyl sulfate by precipitation with potassium. The renatured molecules have the same absorption spectrum and extinction coefficient as native cleaved bacteriorhodopsin. They are integrated into small lipid vesicles as a mixture of monomers and aggregates. Extended lattices form during the partial dehydration process used to orient samples for X-ray and neutron crystallography. (2) Correct refolding of cleaved bacterioopsin occurs upon renaturation in the absence of retinal. Regeneration of the chromophore and reformation of the purple membrane lattice are observed following subsequent addition of all-trans retinal. (3) The two chymotryptic fragments have been reinserted separately into lipid vesicles and refolded in the absence of retinal. Circular dichroism spectra of the polypeptide backbone transitions indicate that they have regained a highly alpha-helical structure. The kinetics of chromophore regeneration following reassociation have been studied by absorption spectroscopy. Upon vesicle fusion, the refolded fragments first reassociate, then bind retinal and finally regenerate cleaved bacteriorhodopsin. The complex formed in the absence of retinal is kinetically indistinguishable from cleaved bacterioopsin. The refolded fragments in lipid vesicles are stable for months, both as separate entities and after reassociation. These observations provide further evidence that the native folded structure of bacteriorhodopsin lies at a free energy minimum. They are interpreted in terms of a two-stage folding mechanism for membrane proteins in which stable transmembrane helices are first formed. They subsequently pack without major rearrangement to produce the tertiary structure.

Proline utilization in Saccharomyces cerevisiae: sequence, regulation, and mitochondrial localization of the PUT1 gene product

The PUT1 gene of Saccharomyces cerevisiae, believed to encode proline oxidase, has been completely sequenced and contains an open reading frame capable of encoding a polypeptide of 476 amino acids in length. The amino terminus of the protein deduced from the DNA sequence has a characteristic mitochondrial import signal; two PUT1-lacZ gene fusions were constructed that produced mitochondrially localized beta-galactosidase in vivo. The transcription initiation and termination sites of the PUT1 mRNA were determined. By using a PUT1-lacZ gene fusion that makes a cytoplasmic beta-galactosidase, the regulation of the PUT1 gene was studied. PUT1 is inducible by proline, responds only slightly to carbon catabolite repression, and is not regulated by the cytochrome activator proteins HAP1 and HAP2. The PUT1 gene is under oxygen regulation; expression in anaerobically grown cells is 10-fold lower than in aerobically grown cells. Oxygen regulation is abolished when cells are respiratory deficient. PUT1 expression in a [rho-] strain grown either aerobically or anaerobically is as high as that seen in a [rho+] strain grown aerobically. Studies on PUT1 promoter deletions define a region between positions -458 and -293 from the translation initiation site that is important for full expression of the PUT1 gene and required for oxygen regulation.

Cloning, sequencing, and expression of the gene coding for the human platelet alpha 2-adrenergic receptor

The gene for the human platelet alpha 2-adrenergic receptor has been cloned with oligonucleotides corresponding to the partial amino acid sequence of the purified receptor. The identity of this gene has been confirmed by the binding of alpha 2-adrenergic ligands to the cloned receptor expressed in Xenopus laevis oocytes. The deduced amino acid sequence is most similar to the recently cloned human beta 2- and beta 1-adrenergic receptors; however, similarities to the muscarinic cholinergic receptors are also evident. Two related genes have been identified by low stringency Southern blot analysis. These genes may represent additional alpha 2-adrenergic receptor subtypes.

cDNA cloning of bovine substance-K receptor through oocyte expression system

The neuropeptide receptors which are present in very small quantities in the cell and are embedded tightly in the plasma membrane have not been well characterized. Mammals contain three distinct tachykinin neuropeptides, substance P, substance K and neuromedin K, and it has been suggested that there are multiple tachykinin receptors. By electrophysiological measurement, we have previously shown that Xenopus oocytes injected with brain and stomach mRNAs faithfully express mammalian substance-P and substance-K receptors, respectively. Here we report the isolation of the cDNA clone for bovine substance-K receptor (SKR) by extending this method to develop a new cloning strategy. We constructed a stomach cDNA library with a cloning vector that allowed in vitro synthesis of mRNAs and then identified a particular cDNA clone by testing for receptor expression following injection of the mRNAs synthesized in vitro into the oocyte system. Because oocytes injected with exogenous mRNAs can express numerous receptors and channels, our new strategy will be applicable in the general molecular cloning of these proteins. The result provides the first indication that the neuropeptide receptor has sequence similarity with rhodopsin-type receptors (the G-protein-coupled receptor family) and thus possesses multiple membrane-spanning domains.

GPA1, a haploid-specific essential gene, encodes a yeast homolog of mammalian G protein which may be involved in mating factor signal transduction

GPA1 protein of Saccharomyces cerevisiae is homologous to the alpha subunit of mammalian G protein. GPA1 transcript was found in haploid cells but was not detected in diploid cells. Disruption of GPA1 resulted in a haploid-specific lethal phenotype, indicating that GPA1 is a haploid-specific essential gene for cell growth. Upon regulation of expression of GPA1 by the galactose-inducible GAL1 promoter, the loss of GPA1 function was found to lead to cell-cycle arrest at the late G1 phase. Mutants that suppress the lethality of the gpa1::HIS3 mutation showed a sterile phenotype that was not cell-type-specific. These results suggest that GPA1 protein may control the signal for mating-factor-mediated cell-cycle arrest.

Early genes that were oligomeric repeats generated a number of divergent domains on their own

One of the more popular concepts to emerge in recent years is that new proteins evolved by domain exchanges between preexisting proteins. The presence of introns within eukaryotic genes is thought to enhance such exchanges. Yet domain exchanges must necessarily be the secondarily developed process in evolution, for they would have been effective only after multitudes of domains came into being. Many of the proteins with functionally divergent domains were established before the division of prokaryotes from eukaryotes; i.e., soon after the creation of life on this earth. I attribute the extreme innovativeness of early coding sequences to their construction; i.e., being repeats of oligomeric units. The rhodopsin family of proteins--with seven hydrophobic, alpha-helical transmembrane domains, four extracellular domains, and four intracytoplasmic domains--indeed arose before the division of prokaryotes from eukaryotes and later gave rise to muscarinic acetylcholine receptor and beta-adrenergic receptor among others. In this paper, I show that the entire coding sequence for porcine muscarinic acetylcholine receptor is still replete with copies of three heptameric units that are very closely related to each other. Original heptameric units are more stringently conserved in parts encoding the seven transmembrane domains, whereas new repeating units are comingled with the old in parts encoding extracellular and intracytoplasmic domains.

On the disulphide bonds of rhodopsins

Carboxymethylation using 14C- or 3H-labelled iodoacetic acid has been used to identify the cysteine residues in bovine rhodopsin involved in the formation of the two intramolecular disulphide bridges. Iodo[2-14C]acetic acid was used to modify 5.8-5.9 residues of cysteine under non-reducing conditions. After dialysis and reduction of disulphide bridges by 2-mercaptoethanol, iodo[2-3H]acetic acid was employed to covalently modify 3.3-3.6 residues of cysteine. Peptide purification and sequencing has unambiguously shown that cysteine residues 322 and 323 are only carboxymethylated after reduction of disulphide bridges. Indirect evidence presented, now coupled with the earlier finding [Findlay & Pappin (1986) Biochem. J. 238, 625-642] suggests that the other disulphide bridge is formed between cysteine residues 110 and 187. A comparison is made of all the sequences of mammalian rhodopsins and colour pigments and attention is drawn to the fact that whereas Cys-322 and Cys-323 are conserved only in three rhodopsins (bovine, ovine and human), the residues corresponding to Cys-110 and Cys-187 are found in all the visual proteins (from rods as well as human cones).

Multiple topogenic sequences in bovine opsin

Bovine opsin, a polytopic integral membrane protein, contains seven transmembrane segments connecting eight hydrophilic domains alternating on each side of the membrane. To localize topogenic sequences that might specify the distinct topology of opsin in the membrane, we constructed various opsin mutants, each containing only one transmembrane segment. Messenger RNAs transcribed from these mutants were translated in a cell-free system supplemented with microsomal membranes. Among six of the seven transmembrane segments of opsin that were analyzed, five were able to function as signal sequences and also expressed stop-transfer sequences of variable strength. By the criteria of extractability at pH 11 and protease sensitivity, the presence of a signal sequence in combination with a "strong" stop-transfer sequence yielded integration into the lipid bilayer of the majority of chains. However, in combination with a "weak" stop-transfer sequence, we observed integration into the lipid bilayer of only some chains, with the others either completely translocated across the membrane or retained in a water-accessible space in the membrane.

Identification of a family of muscarinic acetylcholine receptor genes

Complementary DNAs for three different muscarinic acetylcholine receptors were isolated from a rat cerebral cortex library, and the cloned receptors were expressed in mammalian cells. Analysis of human and rat genomic clones indicates that there are at least four functional muscarinic receptor genes and that these genes lack introns in the coding sequence. This gene family provides a new basis for evaluating the diversity of muscarinic mechanisms in the nervous system.

Primary structure and biochemical properties of an M2 muscarinic receptor

A partial amino acid sequence obtained for porcine atrial muscarinic acetylcholine receptor was used to isolate complementary DNA clones containing the complete receptor coding region. The deduced 466-amino acid polypeptide exhibits extensive structural and sequence homology with other receptors coupled to guanine nucleotide binding (G) proteins (for example, the beta-adrenergic receptor and rhodopsins); this similarity predicts a structure of seven membrane-spanning regions distinguished by the disposition of a large cytoplasmic domain. Stable transfection of the Chinese hamster ovary cell line with the atrial receptor complementary DNA leads to the binding of muscarinic antagonists in these cells with affinities characteristic of the M2 receptor subtype. The atrial muscarinic receptor is encoded by a unique gene consisting of a single coding exon and multiple, alternatively spliced 5' noncoding regions. The atrial receptor is distinct from the cerebral muscarinic receptor gene product, sharing only 38% overall amino acid homology and possessing a completely nonhomologous large cytoplasmic domain, suggesting a role for the latter region in differential effector coupling.

Regulation of transmembrane signaling by receptor phosphorylation

At least two major effects of receptor phosphorylation have been identified--regulation of receptor function, and regulation of receptor distribution. In many cases where phosphorylation directly alters the functions of receptors, this appears to be in a negative direction. Such decreases in receptor activity may reflect reduced ability to interact with biochemical effectors (e.g., the beta-adrenergic receptor, rhodopsin), reduced affinity for binding agonist ligands (EGF,IGF-I, insulin receptors) or reduced enzymatic activity (e.g., tyrosine kinase activity of the insulin or EGF receptor). In all instances, these negative modulations are associated with phosphorylation of serine and/or threonine residues of the receptor proteins. In contrast, the tyrosine kinase receptors also appear to be susceptible to positive modulation by phosphorylation. With these receptors, autophosphorylation of tyrosine residues may lead to enhanced protein-tyrosine kinase activity of the receptors and increased receptor function. In addition, the subcellular distribution of a receptor may be regulated by its phosphorylation status (e.g., the beta-adrenergic receptor, receptors for insulin, EGF, IGF-II, and transferrin). The emerging paradigm is that receptor phosphorylation may in some way promote receptor internalization into sequestered compartments where dephosphorylation occurs. The molecular and cellular mechanisms involved in translating changes in receptor phosphorylation into changes in receptor distribution remain to be elucidated. Moreover, the biological role of receptor internalization may be quite varied. Thus, in the case of the beta-adrenergic receptor, it may serve primarily as a mechanism for bringing the phosphorylated receptors into contact with intracellular phosphatases that dephosphorylate and resensitize it. By contrast, for the transferrin receptor and other receptors involved in receptor-mediated endocytosis, the internalization presumably functions to carry some specific ligand or metabolite into the cell. The role of phosphorylation in regulating receptor function dramatically extends the range of regulatory control of this important covalent modification.

Fluorescent labeling of bacteriorhodopsin: implications for helix connections

Purple membrane from Halobacterium halobium was reacted with dansyl (5-dimethylamino-1-naphthalenyl fluorescent labels that have specificity for different protein side chains of bacteriorhodopsin. Dansyl chloride was found to react primarily with Lys-41. Dansyl hydrazine was coupled, with water-soluble carbodiimide, to Glu-74 and/or Asp-85, which was the major modified site after papain-cleavage of the carboxyl-terminal 17 amino acids. Fluorescence energy transfer was used to probe the proximity of the modified sites to the retinal chromophore of bacteriorhodopsin. The dansyl group on Lys-41 was greater than 2.99 nm from retinal, while the dansyl group on Glu-74/Asp-85 was greater than 2.10 nm from retinal. Information available on the location of retinal in the transmembrane profile and probable surface locations of the fluorescent labels was combined with the energy transfer results to calculate distances projected in the plane of the membrane. The projected distances to retinal were 1.64 nm (Lys-41) and 1.65 nm (Gly-74). These measurements, combined with many other labeling experiments that have been reported, restrict the number of likely helix-connection models to only three: EDCABGF, FEDCBAG and FGEABDC (in the nomenclature of Engelman et al. (1980) Proc. Natl. Acad. Sci. USA 77, 2023-2027).

High-resolution solid-state 13C-NMR study of carbons C-5 and C-12 of the chromophore of bovine rhodopsin. Evidence for a 6-S-cis conformation with negative-charge perturbation near C-12

Solid-state 13C magic-angle spinning NMR spectroscopy has been employed to study the conformation of the 11-cis-retinylidene Schiff base chromophore in bovine rhodopsin. Spectra were obtained from lyophilized samples of bovine rhodopsin selectively 13C-labeled at position C-5 or C-12 of the retinyl moiety, and reconstituted in the fully saturated branched-chain phospholipid diphytanoyl glycerophosphocholine. Comparison of the NMR parameters for carbon C-5 presented in this paper with those published for retinyl Schiff base model compounds and bacteriorhodopsin by Harbison and coworkers [Harbison et al. (1985) Biochemistry 24, 6955-6962], indicate that in bovine rhodopsin the C-6-C-7 single bond has the unperturbed cis conformation. This is in contrast to the 6-S-trans conformation found in bacteriorhodopsin. The NMR parameters for bovine [12-13C]rhodopsin present evidence for the presence of a negative charge interacting with the retinyl moiety near C-12, in agreement with the model for the opsin shift presented by Honig and Nakanishi and coworkers [Kakitani et al. (1985) Photochem. Photobiol. 41, 471-479].

Primary structure of porcine cardiac muscarinic acetylcholine receptor deduced from the cDNA sequence

The complete amino acid sequence of the porcine cardiac muscarinic acetylcholine receptor has been deduced by cloning and sequencing the cDNA. The tissue location of the RNA hybridizing with the cDNA suggests that this muscarinic receptor species represents the M2 subtype.

Evaluation of methods for the prediction of membrane protein secondary structures

With the advent of molecular cloning methods, the amino acid sequences for a number of membrane proteins have been determined. The relative paucity of detailed three-dimensional structural information available for these molecules has led to attempts to predict the secondary structures of membrane proteins based on folding motifs found in soluble proteins of known three-dimensional structure and sequence. In this study, we evaluated the accuracy of several of these methods in predicting the conformation of 15 integral membrane proteins and membrane-spanning polypeptides for which both primary and secondary structural information are available. chi 2 analyses indicated a less than 0.5% correlation between the net predicted secondary structures and the experimental results. A more stringent test of the accuracy of the methods, the index of prediction, was calculated for individual residues in four of the polypeptides for which the crystal structures were known; this criterion also indicated that the predicted assignments for the secondary structures of the residues were inaccurate. Thus, prediction schemes using soluble protein bases appear to be inappropriate for the prediction of membrane protein folding.

Multiple opsin mRNA species in bovine retina

Two retina specific cDNAs have been isolated by differential colony hybridization to retina and brain, and one of them, pCR-394, was identified as an opsin cDNA. By Northern hybridization experiment, the opsin cDNA hybridized to two species of bovine mRNA, one approximately 18 S (1800 bp) and the other 22 S (2600 bp). Using pCR-394 as a probe two opsin clones, R-5 (about 1200 bp) and LR-8 (about 2500 bp), were isolated from a cDNA library which was prepared by the method of Okayama-Berg. Each had a different length of 3'-untranslated DNA. The nucleotide sequences of R-5 and LR-8, as well as Northern and Southern hybridization experiments suggest that at least two species of opsin mRNA are expressed from a single gene. When the effects of illumination were examined by Northern hybridization and translation assays, the ratio of the two opsin mRNA species was changed between light- and dark-adapted eyes.

Cloning, sequencing and expression of complementary DNA encoding the muscarinic acetylcholine receptor

Cloning and sequence analysis of DNA complementary to porcine cerebral messenger RNA encoding the muscarinic acetylcholine receptor predict the complete amino-acid sequence of this protein. Expression of the complementary DNA produced functional muscarinic receptor in Xenopus oocytes. The muscarinic receptor is homologous with the beta-adrenergic receptor and rhodopsin in both amino-acid sequence and suggested transmembrane topography.

The opsin family of proteins

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Cyclic GMP phosphodiesterase from cattle retina. Amino acid sequence of the gamma-subunit and nucleotide sequence of the corresponding cDNA

The primary structure of the gamma-subunit of cyclic GMP phosphodiesterase was determined by parallel analysis of the amino acid sequence of the protein and nucleotide sequence of the corresponding cDNA. The enzyme gamma-subunit contains 87 amino acid residues, its N-terminal amino group being acetylated.

Light-dependent phosphorylation of rhodopsin by beta-adrenergic receptor kinase

The structural components involved in transduction of extracellular signals as diverse as a photon of light impinging on the retina or a hormone molecule impinging on a cell have been highly conserved. These components include a recognition unit or receptor (for example, the beta-adrenergic receptor (beta AR) for catecholamines or the 'light receptor' rhodopsin), a guanine nucleotide regulatory or transducing protein, and an effector enzyme (for example, adenylate cyclase or cyclic GMP phosphodiesterase). Molecular cloning has revealed that the beta AR shares significant sequence and three-dimensional homology with rhodopsin. The function of the beta AR is diminished by exposure to stimulatory agonists, leading to desensitization. Similarly, 'light adaptation' involves decreased coupling of photoactivated rhodopsin to cGMP phosphodiesterase activation. Both forms of desensitization involve receptor phosphorylation. The latter is mediated by a unique protein kinase, rhodopsin kinase, which phosphorylates only the light-bleached form of rhodopsin. An analogous enzyme (termed beta AR kinase or beta ARK) phosphorylates only the agonist-occupied beta AR. We report here that beta ARK is also capable of phosphorylating rhodopsin in a totally light-dependent fashion. Moreover, rhodopsin kinase can phosphorylate the agonist-occupied beta AR. Thus the mechanisms which regulate the function of these disparate signalling systems also appear to be similar.

Pig kidney Na+,K+-ATPase. Primary structure and spatial organization

cDNAs complementary to pig kidney mRNAs coding for alpha- and beta-subunits of Na+,K+-ATPase were cloned and sequenced. Selective tryptic hydrolysis of the alpha-subunit within the membrane-bound enzyme and tryptic hydrolysis of the immobilized isolated beta-subunit were also performed. The mature alpha- and beta-subunits contain 1016 and 302 amino acid residues, respectively. Structural data on the peptides from extramembrane regions of the alpha-subunit and on glycopeptides of the beta-subunit underlie a model for the transmembrane arrangement of Na+,K+-ATPase polypeptide chains.

Isolation and characterization of a new cellular oncogene encoding a protein with multiple potential transmembrane domains

We have cloned and sequenced a new human oncogene and have named it mas. This oncogene was detected by its tumorigenicity in nude mice using the cotransfection and tumorigenicity assay previously described. The mas oncogene has a weak focus-inducing activity in transfected NIH 3T3 cells. A DNA rearrangement in the 5' noncoding sequence, which occurred during transfection, is probably responsible for activation of the mas gene. The cDNA sequence of the mas oncogene reveals a long open reading frame that codes for a 325 amino acid protein. This protein is very hydrophobic and has seven potential transmembrane domains. In this respect, the structure of the mas protein is novel among cellular oncogene products and may reflect a new functional class of oncogenes.

Visual pigment homologies revealed by DNA hybridization

A bovine rhodopsin complementary DNA probe was used to detect homologous visual pigment genes in a variety of species. Under stringent DNA hybridization conditions, genomic DNA from most vertebrate species carried a single homologous fragment. Additional homologies were detected in some vertebrates by reducing the hybridization stringency. Homologous fragments were also detected in DNA isolated from invertebrate species, a unicellular alga, and an archaebacterium; many of these fragments were homologous to a Drosophila opsin probe. These results suggest that photosensory pigments in a wide variety of species arose from a common precursor.