Location of two sulfhydryl groups in the rhodopsin molecule by use of the spin label technique.

Sulfhydryl groups of membrane-bound rhodopsin are studied with the spin label technique by using five maleimide derivative probes of different lengths. Two sulfhydryl groups are titrated per molecule of rhodopsin, These groups are located in protected but probably different environments, less than 12 A away from the aqueous phase. A distance of about 37 A is measured between the two groups. These results are consistent with a model in which the two groups would be located close by the external surface of the protein but embedded within the membrane layer, the strong immobilization of the label molecules resulting from phosphlipid-protein interactions.     

A 12 Å resolution X-ray diffraction study of the profile structure of isolated bovine retinal rod outer segment disk membranes

Electron density profiles of disk membranes isolated from bovine retinal rod outer segments have been determined to 12 Å resolution by analysis of the X-ray diffraction from oriented multilayers, in the absence of lipid phase separation. Data were collected on both film and a two-dimensional TV-detector; both detectors yielded identical patterns consisting of relatively sharp lamellar reflections of small mosaic spread. The unit cell repeat was reversibly varied over the range of 143 to 183 Å. The diffraction patterns changed dramatically at 150 Å; consequently, the low (less than 150 Å) and high (greater than 150 Å) periodicity data were independently analyzed via a swelling algorithm. The high periodicity data yielded two statistically equivalent phase choices corresponding to two symmetric, but different membrane profiles. The low periodicity data yielded essentially one, characteristically asymmetric profile. These profiles have been modeled with regard to the separate profiles of rhodopsin, lipid and water, subject to the known composition of the isolated disk membranes.     

Transverse location of the retinal chromophore of rhodopsin in rod outer segment disc membranes

Diffusion-enhanced fluorescence energy transfer was used to study the structure of photoreceptor membranes from bovine retinal rod outer segments. The fluorescent energy donor was Tb³⁺ chelated to dipicolinate and the acceptor was the 11-cis retinal chromophore of rhodopsin in vesicles made from disc membranes. The rapid-diffusion limit for energy transfer was attained in these experiments because of the long excited state lifetime of the terbium donor (~2 ms). Under these conditions, energy transfer is very sensitive to a, the distance of closest approach between the donor and acceptor (Thomas et al., 1978). Vesicles containing terbium dipicolinate in their inner aqueous space were prepared by sonicating disc membranes in the presence of this chelate and chromatographing this mixture on a gel filtration column. The sidedness of rhodopsin in these vesicles was the same as in native disc membranes. The transfer efficiency from terbium to retinal in this sample was 43%. For an R₀ value of 46.7 Å and an average vesicle diameter of 650 Å, this corresponds to an a value of 22 Å from the inner aqueous space of the vesicle. The distance of closest approach from the external aqueous space, determined by adding terbium dipicolinate to a suspension of already formed vesicles, was found to be 28 Å. These values of a show that the retinal chromophore is far from both aqueous surfaces of the disc membrane. Hence, the transverse location of the retinal chromophore is near the center of the hydrophobic core of the disc membrane. These findings suggest that conformational changes induced by photoisomerization are transmitted through a distance of at least 20 Å within rhodopsin to trigger subsequent events in visual excitation.     

An ordered membrane-cytoskeleton network in squid photoreceptor microvilli

To study the organization of microvilli in the photoreceptor cells of an invertebrate. X-ray diffraction patterns were obtained from aldehyde-fixed squid retinas to a resolution of (40 Å)^?1 and correlated with results from electron microscopy and sodium dodecyl sulphate/polyacrylamide gel electrophoresis. Squid photoreceptor microvilli are packed in extensive hexagonal arrays; in addition each microvillus has a hexagonal substructure. Image reconstruction from thin section electron micrographs shows that the microvilli are linked together with specialized membrane junctions at their neighbour contacts, and phosphotungstic acid-stained sections show a central cytoskeleton connected to the membrane by side-arms.The X-ray patterns also reveal two axial periodicities in the microvilli. A weak and diffuse (50 Å)^?1 band is tentatively assigned to rhodopsin molecules ordered in the plane of the membrane. In addition, an arc at (85 Å)^?1 is attributed to a cytoplasmic or extracellular structure.Sodium dodecyl sulphate/polyacrylamide gel electrophoresis of the isolated microvilli shows that the major component, rhodopsin, comprises about 50% of the total protein. There are two major detergent-insoluble polypeptides with molecular weights of 145,000 and 42,000. The 42,000 component is identified as actin by papain digestion fragment mapping.Cephalopod photoreceptors are highly sensitive to the polarization vector of linearly polarized light. In consequence, the linear rhodopsin chromophores must be aligned relative to the microvillar axes. The membrane junctions and cytoskeleton described here may provide a mechanism for maintaining this rhodopsin alignment.     

Modeling of halorhodopsin and rhodopsin based on bacteriorhodopsin

Bacteriorhodopsin (BR), halorhodopsin (HR), and rhodopsin (Rh) all belong to the class of seven-helix membrane proteins. For BR, a structural model at atomic resolution is available; for HR, diffraction data are available only down to a resolution of 6 Å in the membrane plane, and for Rh, down to 9 Å. BR and HR are closely related proteins with a sequence homology of 34%, while Rh does not share any sequence homology with BR. An atomic model for HR is derived that is based on sequence alignment and the atomic model for BR and is improved by molecular dynamics simulations. The model structure obtained accounts well for the experimentally observed difference between HR and BR in the projection map, where HR exhibits a higher density in the region between helices D and E. The reason for this difference lies partially in the different side chains and partially in slightly different helix tilts. The scattering amplitudes and phases of the model structure are calculated and agree with the experimental data down to a resolution of about 8 Å. If the helix positions are adopted from the projection map for HR and used as input in the model, this number improves to 7 Å. Analogously, an atomic model for Rh is derived based on the atomic model for BR and subjected to molecular dynamics simulations. Optimal agreement with the experimental projection map for Rh is obtained when the entire model structure is rotated slightly about two axes in the membrane plane. The agreement with the experimental projection map is not as satisfactory as for HR, but the results indicate that even for a nonhomologous, but structurally related, protein such as Rh, an acceptable model structure can be derived from the structure of BR. © 1996 Wiley-Liss, Inc.     

Biochemical aspects of the visual process XXVIII. Classification of sulfhydryl groups in rhodopsin and other photoreceptor membrane proteins

Reaction of isolated bovine rod outer segment membrane with radioactiveN-ethylmaleimide, both in the presence and absence of 1% dodecyl sulfate followed by dodecyl sulfate-polyacrylamide gel electrophoresis, shows that six sulfhydryl groups (96% of total sulfhydryl in this membrane) are located on the rhodopsin molecule.On the basis of their reactivity towardsp-chloromercuribenzoate andp-chloromercuribenzene sulfonate in suspensions of outer segment membranes, the sulfhydryl groups of rhodopsin can be divided into three pairs. One pair is rapidly modified, both in light and darkness. This modification does not impair the recombination capacity of opsin with 11-cis retinaldehyde under regeneration of rhodopsin. A second pair is modified upon prolonged interaction with thep-chloromercuriderivatives in darkness. Modification of this pair leaves the typical rhodopsin absorbance at 500 nm intact, but a proportional loss of recombination capacity does occur. The third pair is only modified after illumination and is probably located in the vicinity of the chromophoric center.The difference between these results and those obtained by modification with dithiobis-(2-nitrobenzoic acid) orN-ethylmaleimide in suspension, where even upon prolonged exposure to light as well as in darkness only two sulfhydryl groups of rhodopsin are modified, is explained by the detergent-like character of thep-chloromercuri-derivatives.     

Biochemical aspects of the visual process. XXVIII. Classification of sulfhydryl groups in phodopsin and other photoreceptor membrane proteins.

Reaction of isolated bovine rod outer segment membrane with radioactive N-ethylmaleimide, both in the presence and absence of 1% dodecyl sulfate followed by dodecyl sulfate-polyacrylamide gel electrophoresis, shows that six sulfhydryl groups (96% of total sulfhydryl in this membrane) are located on the rhodopsin molecule. On the basis of their reactivity towards rho-chloromercuribenzoate and rho-chloromercuribenzene sulfonate in suspensions of outer segment membranes, the sulfhydryl groups of rhodopsin can be divided into three pairs. One pair is rapidly modified, both in light and darkness. This modification does not impair the recombination capacity of opsin with 11-cis retinaldehyde under regeneration of rhodopsin. A second pair is modified upon prolonged interaction with the rho-chloromercuriderivatives in darkness. Modification of this pair leaves the typical rhodopsin absorbance at 500 nm intact, but a proportional loss of recombination capacity does occur. The third pair is only modified after illumination and isprobably located in the vicinity of the chromophoric center. The differences between these results and those obtained by modification with dithiobis-(2-nitrobenzoic acid) or N-ethylmaleimide in suspension, where even upon prolonged exposure to light as well as in darkness only two sulfhydryl groups of rhodopsin are modified, is explained by the detergent-like character of the rho-chloromercuri-derivatives.     

Comparison of the transmembrane helices of bovine rhodopsin in the crystal structure and the C α template based on cryo-electron microscopy maps and sequence analysis of the G protein-coupled receptors

G protein-coupled receptors (GPCR) are activated by a diverse array of extracellular signals, ranging from light to polypeptide molecules. The receptors propagate these signals intracellularly using G protein secondary messenger pathways. A common feature in the architecture of these receptors is their seven transmembrane domains. The first crystal structure of a GPCR, bovine rhodopsin, has recently been solved at 2.8 Å. We compared the seven membrane-spanning helices (TMH) from the crystal structure of bovine rhodopsin with those from the low-resolution model of bovine rhodopsin based on the cryo-electron microscopy structure of frog rhodopsin developed by Dr Joyce Baldwin. The model developed by Baldwin used a consensus sequence approach to predict the rotational position of each helix with respect to the other six helices. Superposition of the entire helix bundle of the Baldwin model with the crystal structure gave a RMS difference (RMSD) of 3.2 Å for the 198 C f atoms which suggests a high level of similarity in the arrangement of the helices. Except for TMH IV (RMSD of 4.0 Å), the position of corresponding helices within the helix bundle overlapped well. The superposition of individual helices showed that the RMSD values over 3 Å in the global superposition were largely due to one or more of the following: (i) differences in the unraveling and kinks for these helices, (ii) translation of TMH perpendicular to the membrane and (iii) rotation of helices up to 31°, except for TMH IV in which an additional contribution to the RMSD came from the aforementioned observation. As other crystal structures of GPCRs become available, a comparison with the Baldwin consensus model may reveal larger differences than those observed here.     

Different rhodopsin monoclonal antibodies reveal different binding patterns on developing and adult rat retina

We used a battery of 10 monoclonal antibodies directed against different identified peptide sequences within the carboxyl, transmembrane loop, and amino terminal regions of rhodopsin to label retinas from early postnatal and adult rats. Intensity of label, age of initial appearance of staining, and distribution of label varied depending on the antibody. Most antibodies showed detectable labeling at postnatal day 1, and were eventually observed binding to the cell bodies and the inner and outer segments of the photoreceptors. One amino terminal and two carboxyl terminal antibodies, however, showed no detectable labeling until postnatal day 5 and were only transiently detectable in the cell body region. These patterns cannot be explained by accessibility of binding site, binding affinity, fixation artifact, or crossreactivity. The results indicate that physiological and experimental parameters can alter the apparent immunocytochemical localization of conformationally active molecules such as rhodopsin. The results also suggest that rhodopsin can undergo light-dependent conformational changes in several different compartments within rat retinal photoreceptors before the time of eye opening.     

Ordered membrane particles in rhabdomeric microvilli of the housefly (Musca domestica L.)

Rhabdomeric microvilli of the housefly were freeze-fractured (FF) and thin sectioned (TS) for ultrastructural examination. Ordered files of closely packed membrane particles (82 Å wide, 250 Å long) were seen (FF) on the microvillar membrane (usually E face). The long axis of each particle was canted about 45° to that of the microvillus. Occasionally particles in this array appeared on the P face. It is hypothesized that ordered particles may represent either a photopigment precursor stock, a second photolabile pigment, or the newly discovered sensitizing, UV-absorbing, photostable visual pigment. In the underlying membrane leaflet (P face) were found spherical (85 Å diameter) unoriented particles in a concentration of about 6,000/μm². The size, shape and density of these structures are compatible with those of rhodopsin particles. These particles also covered the basal area of each microvillus. The findings from TS material were difficult to correlate with those from FF replicas. At high magnification the former showed that the plasma membrane of the transected microvillus is composed of spherical, hollow subunits (averaging 43 Å diameter), sometimes fused to form double, 86 Å units. These substructures were closely packed and continuous around the microvillus. This beaded plasma membrane, in rare cases, was doubled around the microvillus. In other instances the plasma membranes were continuous between neighboring microvilli. The physiological implications of these ultrastructural features are discussed.     

Effect of phospholipid removal on the kinetics of the metarhodopsin I to metarhodopsin II reaction.

The kinetics of the metarhodopsin (meta) I → metarhodopsin II reaction have been studied by flash photolysis in two different types of preparations of bovine rhodopsin: (i) digitonin-solubilized rod outer segment (ROS) membranes with a molar ratio of phospholipid to rhodopsin of approximately 90, and (ii) digitonin-solubilized phospholipid-free rhodopsin with a molar ratio of phospholipid to rhodopsin of less than 0.2. At 20 °C the kinetics in both preparations are multiexponential, but four terms are required to fit the data with the solubilized membranes, whereas only two are required with the phospholipid-free preparation. Thus, phospholipid removal simplifies the kinetics of the meta I → meta II reaction, but the resulting preparation still does not show first-order kinetics. The ratio of the time constants of these two components with detergent-solubilized phospholipid-free rhodopsin was nearly equal to the values found with ROS particles, rhodopsin-phospholipid recombinants and intact rabbit eyes. This suggests a common origin for these two components in all these preparations and appears to exclude heterogeneity in bound phospholipid as the basis of these two-component kinetics.     

The positions of the N-terminus and residue 68 in tobacco mosaic virus

Specific chemical modifications of the tobacco mosaic virus coat protein lead to new heavy-atom derivatives. They can be used for the determination of phases in the isomorphous replacement method, but more important they are necessary as markers if one wants to trace the polypeptide chain through an electron density map of limited resolution (10 Å). In addition to the positions of two residues known from previous work, two more residues out of the 158 have now been located in three dimensions. The N-terminus is at the outside of the particle (r = 88 Å), and Lys-68 lies at a radius of 72 Å.     

Crystallization,crystal structure analysis and molecular model of the third domain of Japanese quail ovomucoid,a Kazal type inhibitor

The third domain of Japanese quail ovomucoid, a Kazal type inhibitor, has been crystallized and its crystal structure determined at 2.5 Å resolution using multiple isomorphous replacement techniques. The asymmetric unit contains four molecules. In the crystal the molecules are arranged in two slightly different octamers with approximate D4 symmetry. The molecules are held together mainly by interactions of the N-terminal residues, which form a novel secondary structural element, a β-channel.The molecule is globular with approximate dimensions 35 Å × 27 Å × 19 Å. The secondary structural elements are a double-stranded anti-parallel β-sheet of residues Pro22 to Gly32 and an α-helix from Asn33 to Ser44. The reactive site Lys18-Asp19 is located in an exposed loop. It is close to Asn33 at the N terminus of the helical segment. The polypeptide chain folding of ovomucoid bears some resemblance to other inhibitors in the existence of an anti-parallel double strand following the reactive site loop.     

Shape and size of bovine rhodopsin: A small-angle X-ray scattering study of a rhodopsin-detergent complex

Rhodopsin is extracted from rod outer segments of retinas with dodecyldimethylamine oxide (DDAO), a non-ionie detergent. The rhodopsin-DDAO complex is characterized by binding experiments, gel filtration, sedimentation, densimetry; its homogeneity, chemical composition, weight and partial specific volume are determined. The complex turns out to be a reasonably monodisperse association of one rhodopsin and 156 DDAO molecules. The rhodopsin-DDAO complex and the detergent micelles are studied by small-angle X-ray scattering techniques using a water/sucrose solvent of variable density. The experiments are performed on an absolute scale; mainly the value and curvature of the scattering curves at zero angle are exploited. The structure of the complex and of the micelles is shown to be independent of sucrose. Under these conditions the final result of the X-ray scattering study of each type of particle is the numerical value of a set of five parameters: molecular weight, volume and radius of gyration of the volume occupied by the particles, average electron density and second moment of the electron density fluctuations inside the particles. It is also shown that in the complex the centres of gravity of rhodopsin and of the detergent moiety are very near to each other. The analysis of these parameters leads to the determination of the size and shape of the detergent micelles and to an estimate of the size and shape of the volumes occupied by protein and by detergent in the complex. We find rhodopsin to be a very elongated molecule (maximum diameter ~95 Å) which spans a flat detergent micelle. These results suggest that in the rod outer segment discs the rhodopsin molecules span the membranes, that the rhodopsin molecules of the two opposite membranes of each disc come near to each other and that a high fraction of the intra-disc space is occupied by rhodopsin.     

Structural basis for acceptor‐substrate recognition of UDP‐glucose: anthocyanidin 3‐O‐glucosyltransferase from Clitoria ternatea

UDP‐glucose: anthocyanidin 3‐O‐glucosyltransferase (UGT78K6) from Clitoria ternatea catalyzes the transfer of glucose from UDP‐glucose to anthocyanidins such as delphinidin. After the acylation of the 3‐O‐glucosyl residue, the 3′‐ and 5′‐hydroxyl groups of the product are further glucosylated by a glucosyltransferase in the biosynthesis of ternatins, which are anthocyanin pigments. To understand the acceptor‐recognition scheme of UGT78K6, the crystal structure of UGT78K6 and its complex forms with anthocyanidin delphinidin and petunidin, and flavonol kaempferol were determined to resolutions of 1.85 Å, 2.55 Å, 2.70 Å, and 1.75 Å, respectively. The enzyme recognition of unstable anthocyanidin aglycones was initially observed in this structural determination. The anthocyanidin‐ and flavonol‐acceptor binding details are almost identical in each complex structure, although the glucosylation activities against each acceptor were significantly different. The 3‐hydroxyl groups of the acceptor substrates were located at hydrogen‐bonding distances to the Nε2 atom of the His17 catalytic residue, supporting a role for glucosyl transfer to the 3‐hydroxyl groups of anthocyanidins and flavonols. However, the molecular orientations of these three acceptors are different from those of the known flavonoid glycosyltransferases, VvGT1 and UGT78G1. The acceptor substrates in UGT78K6 are reversely bound to its binding site by a 180° rotation about the O1–O3 axis of the flavonoid backbones observed in VvGT1 and UGT78G1; consequently, the 5‐ and 7‐hydroxyl groups are protected from glucosylation. These substrate recognition schemes are useful to understand the unique reaction mechanism of UGT78K6 for the ternatin biosynthesis, and suggest the potential for controlled synthesis of natural pigments.     

Further characterization of the lipid-depleted bovine rhodopsin obtained by cholate-ammonium sulfate fractionation

The rhodopsin preparation obtained by the method of ammonium sulfate fractionation contained 3–6 mol phospholipid and about 18 mol cholate per mol rhodopsin. The purified rhodopsin had 74% helical structure and showed a visible CD spectrum different from that of rhodopsin in the membrane. The rhodopsin was stable below but denatured gradually above 20°C. The lifetime of metarhodopsin I was long in this preparation. Regeneration capacity was low and only 30% of the original rhodopsin was regenerable by addition of 11-cis-retinal after bleaching.50 mol of phosphatidylcholine were maximally bound to 1 mol rhodopsin when the purified rhodopsin was mixed with phosphatidylcholine in 0.5% cholate. The rhodopsin recombined with lipid had properties similar to those of the original rhodopsin in the membrane. Exchange of cholate for other detergents was easily performed by dialysis. The rhodopsin preparation in which cholate was exchanged for digitonin gave almost the same CD, thermal stability and regenerability as those of a native rhodopsin in the membrane but metarhodopsin I still retained its long lifetime.     

Study of the molecular organization of visual rhodopsin in photoreceptor membranes by limited proteolysis

Proteolysis of rhodopsin in disc membranes of right-side out orientation by thermolysin, papain and St. aureus V8 protease allowed to identify two highly exposed regions of polypeptide chain located on the cytoplasmic membrane surface: carboxyl terminal sequence 321-348 and the fragment 236-241. Incubation with chymotrypsin reveals the third site on the cytoplasmic surface, 146-147, accessible to proteolytic enzymes. Frozen-thawed membranes comprise a mixture of vesicles with normal and inverted orientation. Both thermolytic and chymotryptic digests of rhodopsin in these membranes contain the polypeptide which represents the amino terminal sequence lacking the first 30 amino acid residues. Thus at least 30 amino acids from the N-terminus must protrude into the intradiscal space. One additional site was located on the intradiscal surface: papain digests rhodopsin in the inverted membranes at the position 186-187. Localization of the proteolytic cleavage sites allowed to propose a model for rhodopsin topography in disc membrane: the polypeptide chain traverses the bilayer thickness seven times; each of seven transmembrane segments containing approximately 40 amino acid residues includes a sequence of approximately 30 hydrophobic amino acids; which are probably in close contact with hydrocarbon matrix of the membrane. Hydrophobic sequences are terminated with fragments containing clusters of hydrophilic amino acids, possibly interacting with lipid polar head groups and orienting each segment in the bilayer.     

Structure of the tubulin dimer in zinc-induced sheets

The structure of tubulin has been studied in projection by minimum beam electron microscopy and image processing of negatively stained zinc-induced sheets. The reconstructed images include data to 15 Å resolution.We report here a clear and reproducible 82 Å repeat arising from the arrangement of heterodimers in sheet aggregates of tubulin. This repeat is only observed in diffraction patterns from images recorded by minimum beam methods (10 to 20 e/Ų) and arises from small, but consistent, structural differences between two similar subunits believed to represent the two chemical species of tubulin monomer (M_r, 55,000). At higher electron doses (100 to 200 e/Ų), the additional information is lost or very much reduced, and only a repeat of 41 Å is observed, owing to the loss of distinction between monomers in the tubulin heterodimer.The sheets are composed of 49 Å wide, polar protofilaments, similar to those observed in microtubules; however, the interprotofilament packing is completely different in the two structures. In these sheets, adjacent protofilaments point and face in opposite directions; i.e. they are related by dyad-screw axes normal to the protofilament axes and in the plane of the sheet. Thus, the zinc-induced sheets are crystals of space group P2₁, with cell dimensions of about 97 Å × 82 Å, containing one tubulin heterodimer per asymmetric unit.Reconstructed images of four individual sheets, and their average, show the arrangement and shapes of the two heterodimers contained in each unit cell. The structure and packing of heterodimers in sheets are compared to those in opened out microtubules where all protofilaments point and face in the same direction.     

Three-dimensional image reconstruction of straight flagella from a mutant Salmonella typhimurium.

The structure of the straight flagella from a mutant Salmonella typhimurium was studied by electron microscopy using digital image processing, including three-dimensional reconstruction, to an effective resolution of about 14 Å.Three-dimensional studies suggest that there are two sets of intersubunit bonds, i.e. intraprotofilament bonds along the (n = 11, l = 1) helix at a radius of about 55 Å and interprotofilament bonds along the (n = ?5, l = 7) helix at radii of about 10 to 15 Å and 50 Å, and along the (n = 6, l = 8) helix at a radius of about 45 Å and along the (n = 1, l = 15) helix at a radius of about 20 Å. There are four high density regions in a morphological subunit. These regions are situated at radii of about 15 Å, 40 Å, 70 Å and 80 Å. Variation was seen in the position of the high density regions at radii of about 15 Å and 40 Å among the ten models that were reconstituted individually. The regions at radii of 40 Å and 70 Å are the highest in density. The radial distance between these two regions is consistent with the 32 Å feature of a cylindrically averaged Patterson function calculated using equatorial data from X-ray diffraction pattern (Champness, 1968,1971).At the outer radii of the flagellum the shape of the morphological subunit roughly corresponded to that of the “chevron” described by O'Brien &; Bennett (1972), but there was no corresponding structure at the inner radii; the appearance of chevrons in that region might arise from the superposition of the two sides of the helical lattice.The biological significance of the “beaded” submolecular structure of flagellin and the presence of two sets of intersubunit bonds at the different radii is discussed with reference to the waveform and polymorphic behaviour of flagellar filaments.