Orientation of Intermediates in the Bleaching of Shear-Oriented Rhodopsin

Cattle rhodopsin can be highly oriented by shearing a wet paste of digitonin micelles of this visual pigment between two quartz slides. This orients the rhodopsin micelles so that their chromophores lie mainly parallel to the direction of shear. In such preparations the orientation of rhodopsin and intermediates of its bleaching by light have been measured with plane-polarized light from -195°C to room temperature. The chromophore maintains essentially the same orientation as in rhodopsin in all the intermediates of bleaching: bathorhodopsin (prelumirhodopsin), lumirhodopsin, and metarhodopsins I and II. When, however, the retinaldehyde chromophore is hydrolyzed from opsin in the presence of hydroxylamine, the retinaldehyde oxime that results rotates so as to lie mainly across the direction of shear. That is, the retinal oxime, though free, orients itself upon the oriented matrix of the opsin-digitonin micelles. These experiments show the rhodopsin-digitonin micelle to be markedly asymmetric, with the chromophore lying parallel to its long axis. The asymmetry could originate in the formation of the micelle, in rhodopsin itself, or by its linear polymerization under the conditions of the experiment. If rhodopsin itself is markedly asymmetric, for which there is some evidence, then, since in the rod outer segments its chromophores lie parallel to the disk membranes, the molecules themselves must lie with their long axes parallel to the membranes.     

Orientations of the retinyl and the heme chromophores in the brown membrane of Halobacterium halobium

The orientations of the retinyl and heme chromophores of bacteriorhodopsin and cytochrome b-561 of the brown membrane of Halobacterium halobium have been determined by linear dichroic spectroscopy of oriented brown membrane films. Both chromophores exhibit cylindrical symmetry with respect to the membrane normal. However, the retinyl transition dipole moment is polarized at an angle of 20 to 24 ° with respect to the plane of the membrane while the plane of the heme is oriented nearly perpendicular to the membrane plane. Therefore, the orientation of retinal bound to bacterio-opsin in the brown membrane is approximately the same as in the purple membrane. This is supportive of our previous conclusions that the fine structures of the bacteriorhodopsins of these membranes are very similar in spite of differences in the composition and structure of the two membranes. The orientation of the heme plane of the membrane-bound cytochrome b-561 is very similar to orientations of several membrane-bound heme proteins that are involved in electron transfer processes and may be suggestive of its function in the brown membrane. Analysis of the linear dichroic spectrum over the entire bacteriorhodopsin band using an exciton formalism is in accord with the energy separation of the in-plane and out-of-plane excitonic transitions being less than 5 nm. Since a similar energy separation was reported for the purple membrane, the relative positions of the retinals must be approximately the same in both membranes. A similar analysis of the Soret region, based on the existence of two degenerate mutually perpendicular porphyrin transitions, indicates that the energy separation should be from 5 to 20 nm. However, the smaller value is unlikely for it would imply very large circular dichroic bands not yet encountered in any heme proteins.     

Studies on the orientations of the mitochondrial redox carriers. Orientation of the chromophores of cytochrome b--c1 complex with respect to the plane of a cytochrome b--c1 complex--lipid model membrane.

Orientations of the active site chromophores of the mitochondrial cytochrome b-c₁ complex incorporated into liposomes have been investigated in hydrated oriented multilayers of proteoliposome membranes using optical and epr spectroscopy. The hemes of cytochromes c₁ and b were found to be oriented with the normal to their heme planes lying approximately in the plane of the proteoliposome membrane. Rieske's iron-sulfur center was oriented with the z-axis of the g tensor parallel to the plane of the membranes. It is concluded that the cytochrome b-c₁ complex has a structural asymmetry which causes it to orient with respect to the lipid bilayer.     

Studies on the orientations of the mitochondrial redox carriers II. Orientation of the mitochondrial chromophores with respect to the plane of the membrane in hydrated,oriented mitochondrial multilayers

Orientations of the active site chromophores of the mitochondrial redox carriers have been investigated in hydrated, oriented multilayers of mitochondrial membranes using optical and EPR spectroscopy. The hemes of cytochrome c oxidase, cytochrome c₁, and cytochromes b were found to be oriented in a similar manner, with the normal to their heme planes lying approximately in the plane of the mitochondrial membrane. The heme of cytochrome c was either less oriented in general or was oriented at an angle closer to the plane of the mitochondrial membrane than were the hemes of the “tightly bound” mitochondrial cytochromes. EPR spectra of the azide, sulfide and formate complexes of cytochrome c oxidase in mitochondria in situ obtained as a function of the orientation of the applied magnetic field relative to the planes of the membrane multilayers showed that both hemes of the oxidase were oriented in such a way that the angle between the heme normal and the membrane normal was approx. 90°.     

Studies on the orientations of the mitochondrial redox carriers I. Orientation of the hemes of cytochrome c oxidase with respect to the plane of a cytochrome oxidase-lipid model membrane

The liganded derivatives of mitochondrial cytochrome c oxidase have been prepared in hydrated oriented multilayers of membranous cytochrome c oxidase. The optical spectra of the liganded derivatives recorded at an angle of 45° between the incident light beam and the normal to the planes of the membranes in the multilayers show dichroic ratios of almost 2 in the visible region and 1.2–1.4 in the Soret region. The dichroic ratios were found to be similar for both cytochromes a and a₃. Electron paramagnetic resonance spectra of the azide, sulfide, and formate complexes of cytochrome c oxidase obtained as a function of the orientation of the applied magnetic field relative to the planes of the membranes in the multilayer confirm the optical data and demonstrate that both hemes of cytochrome c oxidase are oriented such that the angle between the heme normal and the membrane normal is approximately 90°.     

Photothermal confocal spectromicroscopy of multiple cellular chromophores and fluorophores

Confocal fluorescence microscopy is a powerful biological tool providing high-resolution, three-dimensional (3D) imaging of fluorescent molecules. Many cellular components are weakly fluorescent, however, and thus their imaging requires additional labeling. As an alternative, label-free imaging can be performed by photothermal (PT) microscopy (PTM), based on nonradiative relaxation of absorbed energy into heat. Previously, little progress has been made in PT spectral identification of cellular chromophores at the 3D microscopic scale. Here, we introduce PTM integrating confocal thermal-lens scanning schematic, time-resolved detection, PT spectral identification, and nonlinear nanobubble-induced signal amplification with a tunable pulsed nanosecond laser. The capabilities of this confocal PTM were demonstrated for high-resolution 3D imaging and spectral identification of up to four chromophores and fluorophores in live cells and Caenorhabditis elegans. Examples include cytochrome c, green fluorescent protein, Mito-Tracker Red, Alexa-488, and natural drug-enhanced or genetically engineered melanin as a PT contrast agent. PTM was able to guide spectral burning of strong absorption background, which masked weakly absorbing chromophores (e.g., cytochromes in the melanin background). PTM provided label-free monitoring of stress-related changes to cytochrome c distribution, in C. elegans at the single-cell level. In nonlinear mode ultrasharp PT spectra from cyt c and the lateral resolution of 120 nm during calibration with 10-nm gold film were observed, suggesting a potential of PTM to break through the spectral and diffraction limits, respectively. Confocal PT spectromicroscopy could provide a valuable alternative or supplement to fluorescence microscopy for imaging of nonfluorescent chromophores and certain fluorophores.     

Spectroscopic identification of the catalytic intermediates of cytochrome c oxidase in respiring heart mitochondria

The catalytic cycle of cytochrome c oxidase (COX) couples the reduction of oxygen to the translocation of protons across the inner mitochondrial membrane and involves several intermediate states of the heme a₃-Cu_B binuclear center with distinct absorbance properties. The absorbance maximum close to 605 nm observed during respiration is commonly assigned to the fully reduced species of hemes a or a₃ (R). However, by analyzing the absorbance of isolated enzyme and mitochondria in the Soret (420–450 nm), alpha (560–630 nm) and red (630–700 nm) spectral regions, we demonstrate that the Peroxy (P) and Ferryl (F) intermediates of the binuclear center are observed during respiration, while the R form is only detectable under nearly anoxic conditions in which electrons also accumulate in the higher extinction coefficient low spin a heme. This implies that a large fraction of COX (>50 %) is active, in contrast with assumptions that assign spectral changes only to R and/or reduced heme a. The concentration dependence of the COX chromophores and reduced c-type cytochromes on the transmembrane potential (ΔΨ_m) was determined in isolated mitochondria during substrate or apyrase titration to hydrolyze ATP. The cytochrome c-type redox levels indicated that soluble cytochrome c is out of equilibrium with respect to both Complex III and COX. Thermodynamic analyses confirmed that reactions involving the chromophores we assign as the P and F species of COX are ΔΨ_m-dependent, out of equilibrium, and therefore much slower than the ΔΨ_m-insensitive oxidation of the R intermediate, which is undetectable due to rapid oxygen binding.     

All-trans retinal constitutes the functional chromophore in Chlamydomonas rhodopsin

Orientation of the green alga Chlamydomonas in light (phototaxis and stop responses) is controlled by a visual system with a rhodopsin as the functional photoreceptor. Here, we present evidence that in Chlamydomonas wild-type cells all-trans retinal is the predominant isomer and that it is present in amounts similar to that of the rhodopsin itself.

The ability of different retinal isomers and analog compounds to restore photosensitivity in blind Chlamydomonas cells (strain CC2359) was tested by means of flash-induced light scattering transients or by measuring phototaxis in a taxigraph. All-trans retinal reconstitutes behavioral light responses within one minute, whereas cis-isomers require at least 50 × longer incubation times, suggesting that the retinal binding site is specific for all-trans retinal. Experiments with 13-demethyl(dm)-retinal and short-chained analogs reveal that only chromophores with a β-methyl group and at least three double bonds in conjugation with the aldehyde mediate function. Because neither 13-dm-retinal, nor 9,12-phenylretinal restores a functional rhodopsin, a trans/13-cis isomerisation seems to take place in the course of the activation mechanism. We conclude that with respect to its chromophore, Chlamydomonas rhodopsin bears a closer resemblence to bacterial rhodopsins than to visual rhodopsins of higher animals.

     

Squid retinochrome

Retinochrome is a photosensitive pigment located primarily in the inner portions of the visual cells of cephalopods. Its absorption spectrum resembles that of rhodopsin, but its chromophore is all-trans retinal, which light isomerizes to 11-cis, the reverse of the situation in rhodopsin. The 11-cis photoproduct of retinochrome slowly reverts to retinochrome in the dark. The chromophoric site of retinochrome is more reactive than that of most visual pigments: (a) Hydroxylamine converts retinochrome in the dark to all-trans retinal oxime + retinochrome opsin. (by Sodium borohydride reduces it to N-retinyl opsin. (c) Lambda max of retinochrome shifts from 500 to 515 nm as the pH is raised from 6 to 10, with a loss of absorption above pH 8; meanwhile above this PH a second band appears at shorter wavelengths with lambda max 375 nm. These changes are reversible. (d) If retinochrome is incubated with all-trans 3-dehydroretinal (retinal2) in the dark, some 3-dehydroretinochrome (retinochrome2, lambda max about 515 nm) is formed. Conversely, when retinochrome2, made by adding all-trans retinal2 to bleached retinochrome or retinochrome opsin, is incubated in the dark with all-trans retinal some of it is converted to retinochrome. Retinal and 3-dehydroretinal therefore can replace each other as chromophores in the dark.     

Large Scale Global Structural Changes of the Purple Membrane during the Photocycle

Both the solution and the oriented film absorption and circular dichroic spectra of the bacteriorhodopsin (bR₅₆₈) and M₄₁₂ intermediate of the purple membrane photocycle were compared over the wavelength region 800-183 nm to assess structural changes during this photocycle. The main findings are (a) loss of the excitonic interaction among the chromophoric retinal transitions indicating disordering of the retinal orientations in the membrane and distortions of the membrane hexagonal crystal lattice, (b) structural change of the chromophoric retinal, (c) changes in the key interactions between the retinal and specific groups in the local environment of the apoprotein, (d) significant changes of the tertiary structure of the bR with negligible secondary structure involvement, and (e) a net tilting of the rodlike segments of the bR polypeptides away from the membrane normal. These findings are in accord with large scale global structural changes of the membrane during the photocycle and with structural metastability of the bR molecules. An important implication of these changes is the possibility of transmembrane retinal-regulated pulsating channels during the photocycle. The significance of this possibility in respect to models for the proton translocation function of this membrane is discussed.     

Cytochrome c-556, a di-heme protein from Pseudomonas aeruginosa

A procedure is described for the purification of cytochrome c-556 from Pseudomonas aeruginosa. The isolated hemoprotein exists as a dimer with a molecular weight of approximately 77 200. The dimer can be dissociated into a monomeric species (or single polypeptide chain) of 40 500 molecular weight by means of sodium dodecyl sulfate or 4 M urea. The amino acid composition demonstrates the presence of four half-cystine residues per 43 000 molecular weight. Heme and iron analyses indicate that two c-type hemes are covalently linked to each polypeptide chain. The absorption spectrum of ferrocytochrome c-556 has a double α-band with a peak at 556 nm and a shoulder at 552 nm; the β-band appears at 521 nm and the Soret band at 420 nm.The electron paramagnetic resonance spectrum of ferricytochrome c-556 contains the elements of two ferric iron species, one a low spin and the other a high spin form.The function of cytochrome c-556 is obscure. The purified cytochrome does not react with Pseudomonas cytochrome oxidase nor with the Pseudomonas cytochrome c-551 or copper protein.The properties of cytochrome c-556 indicate that it is probably not the same species as the cytochrome c-554 previously isolated from the same organism.     

Effects of detergent micelles on the recombination reaction of opsin and 11-cis-retinal

When detergent-solubilized proteins interact with hydrophobic or amphiphilic molecules in the presence of detergent micelles, the solubility of the latter species in the micelles must be included in both thermodynamic and kinetic treatments. In this paper, we derive equations which describe the distribution of species present at equilibrium for a system in which a detergent-solubilized protein binds a hydrophobic (or amphiphilic) ligand. We have applied the formalism developed in this paper to the reaction describing the formation of rhodopsin from its apoprotein and 11-cis-retinal. Qualitatively, the results demonstrate that a significant portion of the observed decrease in the extent of recombination for rhodopsin solubilized in either sodium cholate or Tween 80 may be attributed to the partition of retinal into detergent micelles and that a detergent-induced protein denaturation need not be invoked to explain the data. We also discuss results for rhodopsin solubilized in a nonionic detergent (octaethylene glycol n-dodecyl ether) in which the detergent is clearly causing irreversible loss of the capability to recombine with 11-cis-retinal.     

Spectral Characterization of the Photoreducible b-Type Cytochrome of Dictyostelium discoideum

Irradiation of a soluble extract from broken cells of Dictyostelium discoideum causes the photoreduction of a b-type cytochrome. The cytochrome b can be separated from cytochrome c, which is also present in the extract, by column chromatography on Brushite, but the cytochrome b is no longer sensitive to light after separation on the column. Low temperature spectroscopy shows that reduced form of the photoreducible cytochrome b has a Soret band at 423 nm and a split α band with maxima at 558 and 551 nm similar to the b-type cytochrome in complex II of beef heart mitochondria.     

Turnover and vectorial properties of cytochrome c oxidase in reconstituted vesicles

1. Proteoliposomes containing cytochrome c oxidase and phospholipid have been made by sonication and by the cholate dialysis procedure. In both methods of preparation, only about 50% of the enzyme molecules are oriented in the membrane with their cytochrome c reaction sites exposed to the outside of the vesicle.2. The activity of cytochrome c oxidase in the reconstituted vesicles is not increased by incubation in 1% Tween 80. Experiments on reconstituted vesicles containing internal (entrapped) cytochrome c indicate that turnover of enzyme oxidising entrapped cytochrome c in the presence of N,N,N′,N′-tetramethyl-p-phenylenediamine or 2,3,5,6-tetramethyl-p-phenylenediamine is at a very much lower rate than enzyme oxidising external ferrocytochrome c.3. Oxidation of ascorbate by externally added cytochrome c results in an electrogenic production of OH^? inside the vesicles, which can be monitored using entrapped phenol red. Polylysine inhibits, but does not abolish, the internal alkalinity change in reconstituted vesicles oxidising internal (entrapped) cytochrome c using externally added ascorbate plus N,N,N′,N′-tetramethyl-p-phenylenediamine. When 2,3,5,6-tetramethyl-p-phenylenediamine is used as the permeable redox mediator, an increase in internal acidity can be monitored under the same conditions.     

Characterization of some low spin complexes of ferric hemeoctapeptide from cytochrome-c

Complexes of hemeoctapeptide, derived from bovine cytochrome c, show similar magnetic properties to those of low spin complexes of cytochrome c and hemoglobin. The electronic properties of hemeoctapeptide and cytochrome complexes are also similar while the Soret and beta bands of these analogs are generally blue shifted from those of corresponding complexes of hemoglobin due largely to the differences in the type of heme. Electron spin resonance calculations were carried out using Taylor's method to elucidate d orbital splittings and structural differences in hemeoctapeptide, hemoglobin, and cytochrome c. A correlation between V, the rhombicity, and the position of the beta band was found to exist and was dependent on protein type. However, neither the electronic not magnetic data was largely dependent on protein bulk. A large rhombic splitting caused shifts to the blue, and showed a dependence of the porphyrin pi orbitals on the placement of the metal relative to the porphyrin plane. A structural basis for the degree of rhombic splitting and thermodynamic parameters for ligand binding is proposed.     

Solid-State H NMR spectroscopy of retinal proteins in aligned membranes

Solid-state ²H NMR spectroscopy gives a powerful avenue to investigating the structures of ligands and cofactors bound to integral membrane proteins. For bacteriorhodopsin (bR) and rhodopsin, retinal was site-specifically labeled by deuteration of the methyl groups followed by regeneration of the apoprotein. ²H NMR studies of aligned membrane samples were conducted under conditions where rotational and translational diffusion of the protein were absent on the NMR time scale. The theoretical lineshape treatment involved a static axial distribution of rotating C-C²H₃ groups about the local membrane frame, together with the static axial distribution of the local normal relative to the average normal. Simulation of solid-state ²H NMR lineshapes gave both the methyl group orientations and the alignment disorder (mosaic spread) of the membrane stack. The methyl bond orientations provided the angular restraints for structural analysis. In the case of bR the retinal chromophore is nearly planar in the dark- and all-trans light-adapted states, as well upon isomerization to 13-cis in the M state. The C13-methyl group at the “business end” of the chromophore changes its orientation to the membrane upon photon absorption, moving towards W182 and thus driving the proton pump in energy conservation. Moreover, rhodopsin was studied as a prototype for G protein-coupled receptors (GPCRs) implicated in many biological responses in humans. In contrast to bR, the retinal chromophore of rhodopsin has an 11-cis conformation and is highly twisted in the dark state. Three sites of interaction affect the torsional deformation of retinal, viz. the protonated Schiff base with its carboxylate counterion; the C9-methyl group of the polyene; and the β-ionone ring within its hydrophobic pocket. For rhodopsin, the strain energy and dynamics of retinal as established by ²H NMR are implicated in substituent control of activation. Retinal is locked in a conformation that is twisted in the direction of the photoisomerization, which explains the dark stability of rhodopsin and allows for ultra-fast isomerization upon absorption of a photon. Torsional strain is relaxed in the meta I state that precedes subsequent receptor activation. Comparison of the two retinal proteins using solid-state ²H NMR is thus illuminating in terms of their different biological functions.     

UV-Light Effects on Cytochrome C Modulated by the Aggregation State of Phenothiazines

The present study shows the factors that modulate the photodamage promoted by phenothiazines. Cytochrome c was irradiated with UV light for 120 min, over a pH range from 4.0 to 8.0, in the absence and in the presence of different concentrations of thioridazine (TR) and fluphenazine (FP). In the absence of phenothiazines, the maximal rate of a Soret band blue shift (nm/min) from 409 to 406 nm was obtained at pH 4.0 (0.028 nm/min). The presence of phenothiazines at the concentration range 10-25 µmol/L amplified and accelerated a cytochrome c blue shift (409 to 405 nm, at a rate = 0.041 nm/min). Above 25 µmol/L, crescent concentrations of phenothiazines contributed to cytochrome c protection with (maximal at 2500 µmol/L). Scanning electronic microscopy revealed the formation of nanostructures. The pH also influenced the effect of low phenothiazine concentrations on cytochrome c. Thus, the predominance of phenothiazine-promoted cytochrome c damage or protection depends on a balance of the following factors: the yield of photo-generated drug cation radicals, which is favored by acidic pH; the stability of the cation radicals, which is favored by the drug aggregation; and the cytochrome c structure, modulated by the pH.     

Studies on methemoglobin reductase. Immunochemical similarity of soluble methemoglobin reductase and cytochrome b5 of human erythrocytes with NADH-cytochrome b5 reductase and cytochrome b5 of rat liver microsomes.

An antibody preparation elicited against purified, lysosomal-solubilized NADH-cytochrome b₅ reductase from rat liver microsomes was shown to interact with methemoglobin reductase of human erythrocytes by inhibiting the rate of erythrocyte cytochrome b₅ reduction by NADH. The ferricyanide reductase activity of the enzyme was not inhibited by the antibody, suggesting that the inhibition of methemoglobin reductase activity may be due to interference with the binding of cytochrorme b₅ to the flavoprotein. Under conditions of limiting concentrations of flavoprotein, the antibody inhibited the rate of methemoglobin reduction in a reconstituted system consisting of homogeneous methemoglobin reductase and cytochrome b₅ from human erythrocytes. This inhibition was due to the decreased level of reduced cytochrome b₅ during the steady state of methemoglobin reduction while the rate of methemoglobin reduction per reduced cytochrome b₅ stayed constant, suggesting that the enzyme was not concerned with an electron transport between the reduced cytochrome b₅ and methemoglobin.An antibody to purified, trypsin-solubilized cytochrome b₅ from rat liver microsomes was shown to inhibit erythrocyte cytochrome b₅ reduction by methemoglobin reductase and NADH to a lesser extent than microsomal cytochrome b₅ preparations from rat liver (trypsin solubilized or detergent solubilized) and pig liver (trypsin solubilized). The results presented establish that soluble methemoglobin reductase and cytochrome b₅ of human erythrocytes are immunochemically similar to NADH-cytochrome b₅ reductase and cytochrome b₅ of liver microsomes, respectively.     

Studies of electron transport in dry and imbibed peanut embryos

The respiration of isolated peanut (Arachis hypogea) embryos has been studied with dry and wet embryos and mitochondria prepared after various times of imbibition. Dry seeds respire slowly, apparently via a respiratory chain which is deficient in cytochrome c. Cytochrome c-deficient mitochondria have been prepared from the embryos up to 16 hours following imbibition. These mitochondria can metabolize reduced nicotinamide adenine dinucleotide and succinate, without respiratory control by ADP, but they do phosphorylate. Added cytochrome c increases both respiration and phosphorylation of these embryonic mitochondria. When growth starts, mitochondria appear which are similar to those isolated from other mature plant tissues; they have respiratory control and can actively metabolize succinate, malate, and reduced nicotinamide adenine dinucleotide. These latter mitochondria contain a concentration of cytochrome c comparable to that found in mitochondria isolated from other mature plant tissues. It is suggested that the earliest type of mitochondria may be required to control respiration in the dry and the recently wetted embryo.     

Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin

Upon absorption of light, the retinal chromophore in rhodopsin isomerizes from the 11-cis to the trans configuration, initiating a photoreaction cycle. The primary photoreaction state, bathorhodopsin (BATHO), relaxes thermally through lumirhodopsin (LUMI) into a photoactive state, metarhodopsin (META), which stimulates the conjugated G-protein. Previous crystallographic studies of squid and bovine rhodopsins have shown that the structural change in the primary photoreaction of squid rhodopsin is considerably different from that observed in bovine rhodopsin. It would be expected that there is a fundamental difference in the subsequent thermal relaxation process between vertebrate and invertebrate rhodopsins. In this work, we performed crystallographic analyses of the LUMI state of squid rhodopsin using the P62 crystal. When the crystal was illuminated at 100 K with blue light, a half fraction of the protein was converted into BATHO. This reaction state relaxed into LUMI when the illuminated crystal was warmed in the dark to 170 K. It was found that, whereas trans retinal is largely twisted in BATHO, it takes on a more planar configuration in LUMI. This relaxation of retinal is accompanied by reorientation of the Schiff base NH bond, the hydrogen-bonding partner of which is switched to Asn185 in LUMI. Unlike bovine rhodopsin, the BATHO-to-LUMI transition in squid rhodopsin was accompanied by no significant change in the position/orientation of the beta-ionone ring of retinal.