Bacteriorhodopsin's L550 intermediate contains a C14-C15 s-trans-retinal chromophore

Conformational changes of the retinal chromophore about the C14-C15 bond in bacteriorhodopsin (BR) have been proposed in models for the mechanism of light-driven proton transport. To determine the C14-C15 conformation in BR's L550 intermediate, we have examined the resonance Raman spectra of BR derivatives regenerated with retinal deuterated at the 14 and 15 positions. Vibrational calculations show that the C14-2H and C15-2H rocking modes form symmetric (A) and antisymmetric (B) combinations in [14,15-2H]retinal chromophores. When there is a trans conformation about the single bond between C14 and C15 (14-s-trans), a small frequency separation or splitting is observed between the A and B modes, which are found at approximately equal to 970 cm-1. In 14-s-cis molecules, the splitting is large, and the Raman-active symmetric A mode is predicted at approximately equal to 850 cm-1. In addition, the monodeuterium rock should appear at an unusually low frequency (920-930 cm-1) in the 14-2H-labeled 14-s-cis molecules. These patterns are insensitive to computational details: similar results are predicted by a modified Urey-Bradley force field and by MNDO (modified neglect of differential overlap) calculations for twisted chromophores and for highly delocalized protonated Schiff base cations. Time-resolved resonance Raman spectra were obtained of BR's L550 intermediate regenerated with [14-2H]-, [15-2H]- and [14,15-2H]retinal. The symmetric A rock in L550 is found at 968 cm-1, within 4 cm-1 of the frequencies for the monodeuterio derivatives, and no scattering is observed between 800 and 940 cm-1. The rocking frequencies of deuterated L550 are within 5 cm-1 of those observed in BR568, which contains a 14-s-trans chromophore. These results show that L550 contains a 14-s-trans chromophore and suggest that only 14-s-trans structures are involved in the proton pumping photocycle of BR.

[Synthesis and properties of C13-substituted retinals]

Several analogues of all-trans-retinal were synthesised, containing, instead of CH3-group at C13, the following substituents: H, C[2H]3, C2H5, iso-C3H7, C4H9, C6H5 or alpha-C10H8. The compounds synthesised on coupling with bacterioopsin gave artificial chromoproteins, which retained the ability to participate in the cycle of photochemical transformations and H+-transport.

Structure-function studies on bacteriorhodopsin. V. Effects of amino acid substitutions in the putative helix F

To test structural and mechanistic proposals about bacteriorhodopsin, a series of analogues with single amino acid substitutions has been studied. Mutants in the proposed helix F of bacteriorhodopsin were chosen for investigation because of the probable interaction of this part of the protein with the retinal chromophore. Seven mutants of the bacteriorhodopsin gene were constructed by site-directed mutagenesis, and the gene products were expressed in Escherichia coli. The resulting mutant proteins were purified and assayed for their ability to interact with retinal in phospholipid/detergent micelles to form a bacteriorhodopsin-like chromophore. Four mutants, Ser-183----Ala, Tyr-185----Phe, Ser-193----Ala, and Glu-194----Gln, bound retinal to give pigments with absorption maxima approximately the same as the wild type. Three mutant opsins bound retinal to give chromophores that were blue-shifted relative to the wild type. Two Trp----Phe substitutions at positions 182 and 189 gave absorption maxima of 480 and 524 nm, respectively, and the mutant Pro-186----Leu gave a pigment with an absorption maximum of 470 nm. However, none of the amino acid substitutions eliminated the ability of the mutant bacteriorhodopsin to pump protons in response to illumination.

Photoactive retinal pigments in haloalkaliphilic bacteria

Light-induced fast transient absorbance changes were detected by time-resolved spectroscopy in 38 of 51 haloalkaliphilic isolates from alkaline salt lakes in Kenya and the Wadi Natrun in Egypt. They indicate the presence of two retinal pigments, Pf and Ps, which undergo cyclic photoreactions with half-times of 2 ms and 500 ms respectively. Pf absorbs maximally near 580 nm and Ps near 500 nm. The pigments differ in their sensitivity to hydroxylamine and detergent bleaching and the photoreactions of Pf are strongly dependent on chloride concentration. Of the 38 pigment-containing strains, 29 possess both Pf and Ps, 9 possess only Ps. Inhibition of retinal synthesis with nicotine blocks pigment formation and addition of retinal restores it. Hydroxylamine-bleached pigments can be reconstituted with retinal or retinal analogues. Their similarity to the retinal pigments of Halobacterium halobium strongly suggests that they are also rhodopsin-like retinyledene proteins. Pf in all properties tested is almost identical to halorhodopsin, the light-driven chloride pump of H. halobium, and may serve the same function in the haloalkaliphiles. Ps has photocycle kinetics similar to sensory rhodopsin and a far-blue-shifted long-lived photocycle intermediate, but its ground state absorption maximum is near 500 nm instead of 587 nm. We have not found a bacteriorhodopsin-like pigment in the haloalkaliphiles.

[Surface-enhanced Raman spectroscopy of biopolymers: membrane proteins, bacteriorhodopsin and rhodopsin adsorbed on silver electrodes and silver hydrosols]

Surface-enhanced Raman (SER) spectra of purple membranes of Halobacterium halobium and photoreceptor disks of the rod outer segments adsorbed on silver hydrosols were analysed. It has been shown that the intensity of SER spectra of bacterial and visual rhodopsins increases 5 X 10(4) times at adsorption. Concentration relationship of the signal intensity of SER spectra has the maximum at bacteriorhodopsin concentration about 2 X 10(-7) M. It has been shown that adsorption on silver hydrosol leads to fixation of light-induced photochemical transformations in bacterial and visual rhodopsins. Adsorption on the "smooth" electrodes at the potential of the zero charge of silver does not affect the photocycle of bacteriorhodopsin. An increase or decrease of the electrode potential relative to the zero charge point of silver leads to the accumulation of kinetic intermediate K610 and a decrease of the concentration of the form BRh570. It has been shown that on the "smooth" electrode primarily the long-range component of the SER mechanism is realized. Bands corresponding to the vibrations of the atom groups directly contacting with the metal are mainly intensified after redox cycle which increases the concentration of chemosorption centres. A conclusion is drawn that the method of SER spectroscopy of biomolecules adsorbed on "smooth" electrodes, permits obtaining information similar to that obtained from the analysis of Raman spectra of unadsorbed molecules, but at concentrations by two orders less. Adsorption on the electrodes treated with the help of redox cycle permits to obtain highly oriented preparations and to study topography of biopolymers in water solutions and suspensions.

Solid-state 13C NMR detection of a perturbed 6-s-trans chromophore in bacteriorhodopsin

Solid-state 13C magic angle sample spinning NMR spectroscopy has been used to study the ionone ring portion of the chromophore of bacteriorhodopsin. Spectra were obtained from fully hydrated samples regenerated with retinals 13C labeled at positions C-5, C-6, C-7, C-8, and C-18 and from lyophilized samples regenerated with retinals labeled at C-9 and C-13. C-15-labeled samples were studied in both lyophilized and hydrated forms. Three independent NMR parameters (the downfield element of the C-5 chemical shift tensor, the C-8 isotropic chemical shift, and the C-18 longitudinal relaxation time) indicate that the chromophore has a 6-s-trans conformation in the protein, in contrast to the 6-s-cis conformation that is energetically favored for retinoids in solution. We also observe an additional 27 ppm downfield shift in the middle element of the C-5 shift tensor, which provides support for the existence of a negatively charged protein residue near C-5. Evidence for a positive charge near C-7, possibly the counterion for the negative charge, is also discussed. On the basis of these results, we present a new model for the retinal binding site, which has important implications for the mechanism of the "opsin shift" observed in bacteriorhodopsin.

Stability of transmembrane regions in bacteriorhodopsin studied by progressive proteolysis

Proteinase K digestions of bacteriorhodopsin were carried out with the aim of characterizing the membrane-embedded regions of the protein. Products of digestions for two, eight or 24 hours were separated by high-pressure liquid chromotography. A computerized search procedure was used to compare the amino acid analyses of peptide-containing peaks with segments of the bacteriorhodopsin sequence. Molecular weight distributions of the products were determined by sodium dodecylsulfate-urea polyacrylamide gel electrophoresis. The structural integrity of the protein after digestion was monitored through the visible absorption spectrum, by X-ray diffraction of partially dried membranes, and by following release of biosynthetically-incorporated 3H leucine from the digested membranes. During mild proteolysis, bacteriorhodopsin was cleaved near the amino and carboxyl termini and at two internal regions previously identified as being accessible to the aqueous medium. Longer digestion resulted in cleavage at new sites. Under conditions where no fragments of bacteriorhodopsin larger than 9000 mol wt were observed, a significant proportion of the digested membranes retained diffraction patterns similar to those of native purple membranes. The harshest digestion conditions led to complete loss of the X-ray diffraction patterns and optical absorption and to release of half the hydrophobic segments of the protein from the membrane in the form of small soluble peptides. Upon cleavage of aqueous loop regions of the protein, isolated transmembrane segments may experience motion in a direction perpendicular to the plane of the membrane, allowing them access to protease.

The Rhodopseudomonas viridis photosynthetic membrane: arrangement in situ

The organization of photosynthetic membranes in the cytoplasm of the photosynthetic bacterium Rh. viridis has been examined by several techniques for electron microscopy. Thin sections of membrane stacks show that the regular lattice of membrane subunits reported in other studies can be observed in thin section. Tilting of sections in the electron microscope shows that the regular lattices of several membranes overlap in a way that suggests they are in register with each other. This observation can be confirmed by freeze-fracture images in which a regular arrangement of membrane lattices can be observed, each perfectly aligned. Analysis of the spacings of membrane pairs shows that the photosynthetic membranes of Rh. viridis are very closely apposed. The mean diameter of two membranes is 160A, and the average space between two such membranes is only 42A. When a recently developed atomic level model of Rh. viridis reaction center is superimposed against these spacings, each reaction center extends from the surface of its respective membrane far enough to make contact with an apposing membrane. The limited free space between membranes and regular alignment of lattices has a number of implications for how this membrane is organized to carry out the process of energy transfer.

Transient proton inflows during illumination of anaerobic Halobacterium halobium cells

In Halobacterium halobium strain R1 containing both bacteriorhodopsin (bR) and halorhodopsin (hR), the light-driven proton uptake has been experimentally resolved into three transient inflows which are superimposed on the larger proton outflow. Under anaerobic conditions the early proton uptake consists of two components: (i) an inflow which can be blocked using the ATPase inhibitor, Dio-9, and (ii) an inflow which can be abolished by low concentrations (less than 125 nM) of triphenyltin chloride (TPT) with no inhibition of ATP synthesis. At pH 6 these two inflows are approximately equal in magnitude and duration. Measurements of buffering capacity and internal pH indicate that Dio-9 does not alter the passive proton-hydroxyl permeability of the cell membrane and that TPT at these low concentrations slightly decreases it. At later times of illumination (iii) another transient light-driven proton inflow occurs. This inflow is most evident during the first illumination after cells have been stored for extended times in the dark. The internal potassium concentration is not changed by storage, but apparently sodium is taken up, and we attribute the third inflow to sodium extrusion in exchange for protons. These results demonstrate the existence of three distinct triggered secondary proton inflows through the cell membrane. The proton inflow, which can be inhibited by Dio-9, correlates with proton-dependent ATP synthesis. The second inflow, which disappears in the presence of low TPT concentrations, is a passive proton uptake through an otherwise unidentified channel in response to electrogenic chloride pumping by bacteriorhodopsin and/or halorhodopsin. The third system correlates with the Na+/H+ antiporter function that has been demonstrated in H. halobium cell envelope vesicles. In contrast to observations on hR-containing vesicles, which can develop substantial Cl- gradients, the electroneutral OH-/Cl- exchange function can be demonstrated in intact cells only at TPT concentrations greater than 500 nM.

Biochemical characterization of halorhodopsin in native membranes

Procedures are described for selectively radiolabeling the protein moiety (haloopsin) or the chromophoric prosthestic group (retinal) of the light-driven chloride pump halorhodopsin in intact cells of Halobacterium halobium. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autofluorography, two retinal-binding polypeptides are observed to band near the known molecular weight of the halorhodopsin chromophoric polypeptide (25,000). Synthesis of one of these polypeptides is controlled by retinal and is sufficient for generation of complete halorhodopsin function. The other is constitutively produced by the cells and differs chemically from the haloopsin protein as indicated by differences in their V8 protease digestion patterns. V8 protease cleavage of haloopsin in its native membrane is compared with that of the protein in denaturing and nondenaturing detergents. Protease cleavage sites available in the denatured haloopsin molecule are hidden in its native membrane-integrated conformation and in nondenaturing detergent micelles. Treatment with a variety of proteases indicates susceptibility of a short terminal region of the haloopsin chain in its native conformation.

Circular dichroism analyses of membrane proteins: an examination of differential light scattering and absorption flattening effects in large membrane vesicles and membrane sheets

The circular dichroism spectra of membrane suspensions are distorted by differential light scattering and absorption flattening effects, which arise as a consequence of the large size of the membrane particles relative to the wavelength of light and the high concentration of proteins in the membranes. In this paper, the consequences of these phenomena on the protein spectra of large membrane particles are discussed, and methods for eliminating them are examined. The distortions due to differential light scattering are relatively small in membrane systems, and can be compensated for by use of a large detector acceptance angle geometry. Several methods for correcting for differential flattening, which introduces a substantial distortion, have been evaluated, and a new method, the flattening quotient approach, which produces by far the best results, is described. Since the secondary structures calculated from circular dichroism spectra are highly dependent on accurate spectral shape and magnitude, this method for correcting the spectra may find general application in circular dichroism studies of membrane proteins.

Solid-state 13C NMR studies of retinal in bacteriorhodopsin

Solid-state 13C magic-angle sample spinning (MASS) NMR has been used to study lyophilized dark-adapted purple membrane containing 13C-labeled retinals. C-10-, C-11-, and C-12-labeled derivatives each showed two lines, assigned to the coexisting 13-cis and all-trans isomers. The isotropic chemical shifts, particularly of C-11, indicate that the Schiff base is protonated. Shift anisotropies are also similar to those of model compounds, indicating that this part of the chromophore is rigid and immobile and possesses the same degree of in-plane bending as crystalline retinal derivatives. Purple membrane samples labeled on the C-19- and C-20-methyl groups both give single lines from the retinal, upfield shifted by 2.1 and 1.0 ppm, respectively, from model compounds. In all cases, high-quality spectra were obtained from approximately 50-mg samples in modest signal-averaging times. These results suggest that it is now practical to exploit the enormous potential of MASS NMR for structural studies of 13C-labeled membrane proteins.

Photoacoustic spectroscopy of bacteriorhodopsin photocycle

Photoacoustic spectroscopy was applied to study the energetics and the kinetics of the slow intermediates of the bacteriorhodopsin photocycle. An analysis of the modulation frequency dependence of the photoacoustic signal allowed us to estimate the enthalpy changes and the kinetic parameters associated with those intermediates. The effects of pH, salt concentration, and protein aggregation were studied. Three photoacoustic transitions were found. The two low frequency transitions were attributed to O660 and M412, respectively. The third transition was interpreted as resulting from a protein conformational change undetected spectrophotometrically. The frequency spectra were simulated between 5 and 180 Hz at pH's 5.1, 7.0, and 8.9 assuming a branching in the bacteriorhodopsin photocycle at the M412 level. The enthalpy changes associated with M412 and O660 were computed and compared with the experimental values.

Effects of pressure and temperature on the M412 intermediate of the bacteriorhodopsin photocycle. Implications for the phase transition of the purple membrane

The effects of pressure and temperature on the decay kinetics of the M412 (M) intermediate in the photocycle of bacteriorhodopsin were studied to provide information about the phase transitions of the purple membrane lipids. The activation volume (delta V++) for the decay of M is expected to be different below and above a phase transition. However, no abrupt change in delta V++ was found from 3.5 degrees to 60 degrees C. But a sharp break was observed in a plot of the logarithm of the rate of M decay vs. pressure. Extrapolation of this break point to standard atmospheric pressure gives a temperature of -42 degrees C, which probably corresponds to the phase transition of the purple membrane lipids. This conclusion is supported by studies of the effect of pressure on the M kinetics of bacteriorhodopsin incorporated into dimyristoylphosphatidylcholine vesicles, whose phase transition has previously been characterized.

Regeneration of the native bacteriorhodopsin structure from two chymotryptic fragments

Chymotrypsin cleaves bacteriorhodopsin to two fragments: C-1, amino acids 72-248, and C-2, amino acids 1-71. Denaturation and renaturation of these fragments have been studied. Following denaturation in sodium dodecyl sulfate, both C-1 and C-2 regain secondary structure in phospholipid/cholate/sodium dodecyl sulfate mixed micelles. When combined, they form a complex with a secondary structure resembling that of bacterio-opsin. However, on further incubation in phospholipid/cholate/sodium dodecyl sulfate, separate fragments as well as the C-1 and C-2 complex denature again. Retinal binds tightly to the C-1 and C-2 complex (Kb greater than 10(7) M-1) and stabilizes the folded conformation. The formation of the complex of C-1, C-2, and retinal is maximal at pH 6.0. The ternary complex contains two species: one which absorbs similarly to the light-adapted purple membrane and a second with a lambda max between 450 and 500 nm. The formation of the latter species is favored at higher temperatures and is reversible. Vesicles formed from the ternary complex of C-1, C-2, and retinal translocate protons at a level close to that of intact bacteriorhodopsin.

Isolation and properties of the native chromoprotein halorhodopsin

The native chromoprotein of the light-driven chloride pump halorhodopsin (HR) was isolated from Halobacterium halobium strain L-33 which lacks bacteriorhodopsin but contains 'slow cycling rhodopsin-like pigment' (SR). A membrane fraction was prepared in low salt and dissolved in a high salt medium by the detergents Lubrol PX or octylglucoside. These conditions destroyed the chromophore of SR but not the HR pigment. Chromatography on phenyl-Sepharose and hydroxylapatite produced, in 60% yield, a 230-fold enriched monomeric chromoprotein with an apparent mol. wt. of 20,000. The chromoprotein was stable in 1 M NaCl and 1% octylglucoside and remained stable upon removal of detergent. It reacted with borohydride in the dark and with hydroxylamine in the light. The absorption maximum of the light-adapted state is at 580 + 2 nm and its molar extinction approximately 50,000/M/cm. Upon illumination in the presence of detergent it was converted into a 410 nm absorbing species with concomitant release of protons. A thermal reconversion to the 580 nm species occurred with a half time of 76 s at -6 degrees C. Blue light absorbed by the photoproduct accelerated the re-conversion as well as the re-uptake of protons. Removal of the detergent prevented the light-induced formation of the 410 nm species. Under these conditions a photochemical behaviour similar to that in intact cells and cell vesicles, i.e., a photocycle in the 10-20 ms range was observed. These findings form the basis for functional reconstitution of HR.

Pair distribution functions of bacteriorhodopsin and rhodopsin in model bilayers

The pair distribution functions have been measured from freeze-fracture pictures of bacteriorhodopsin and rhodopsin recombinants with diacyl phosphatidylcholines (PC) of various hydrocarbon chain lengths. Pictures were used of samples that had been frozen from above the phase transition temperature of the lipid. Measured functions were compared with those calculated from two model interparticle potential energy functions, (a) a hard-disk repulsion only, and (b) a hard-disk repulsion plus electrostatic repulsion for a point charge buried in the membrane. The measured functions for bacteriorhodopsin di 12:0 PC, di 14:0 PC, and di 16:0 PC recombinants can be simulated using an interparticle hard-disk repulsion only. Bleached rhodopsin di 12:0 PC and di 18:1 trans-PC recombinants, and dark-adapted rhodopsin di 10:0 PC recombinants yield functions that are better simulated by assuming an additional repulsive interaction. The measured functions resemble those calculated using the hard-disk plus electrostatic repulsion model. The picture of dark-adapted rhodopsin in di 18:1 trans-PC frozen from 20 degrees C shows partial aggregation that is apparent in the measured pair distribution function. This attractive interaction persists even at 37 degrees C, where the measured function shows deviations from the hard-disk repulsive model, indicative of an attractive interparticle interaction. Implications of these results are discussed in terms of protein-lipid interactions.

Photochemical cycle and light-dark adaptation of monomeric and aggregated bacteriorhodopsin in various lipid environments

Spectral changes of bacteriorhodopsin (BR) reflecting its photochemical cycle and light-dark adaptation were monitored in order to study the effect of protein-protein and protein-lipid interactions on these reactions. For this purpose, the light-driven proton pump BR was reconstituted with various lipids, i.e., dimyristoyl- and dipalmitoyl-phosphatidylcholine, soybean phospholipids, and diphytanoyllecithin. In these vesicle systems, BR is monomeric above the lipid phase transition and above molar lipid to BR ratios of about 80. Well below the phase transition, BR is aggregated in a hexagonal lattice as in the purple membrane. This allows, on the one hand, comparison of monomeric and aggregated BR in the respective vesicle systems and, on the other hand, comparison of reconstituted BR with BR in the native purple membrane. The photoreaction cycle of all-trans-BR accompanying proton translocation proceeds via the same intermediates in the monomeric and aggregated pigment. Furthermore, both the rate and the activation energy for the decay of the cycle intermediate M-410 are independent of the aggregation state. From the results, we conclude that the functional unit responsible for BR's photocycle is the monomer itself. This is in accordance with previous observations that BR monomers are able to translocate protons during illumination [Drencher, N. A., & Heyn, M.P. (1979) FEBS Lett. 108, 307-310]. The light-dark adaptation reaction, however, is affected by BR's aggregation state. In the case of the monomer, the extent of light adaptation, i.e., the fraction of BR molecules containing 13-cis-retinal as chromophore which is converted by illumination to the respective pigment with the all-trans isomer, is reduced by 50% or more, and the rate of dark adaptation is slowed down about 2.5 times. For these properties too, the monomer is functional, but with a reduced efficiency. This indicates regulatory control by neighboring BR molecules. The rate of the photocycle as well as of dark adaptation is strongly affected by the chemical nature of the lipids used for reconstitution but not by the physical state of the lipid phase.

Identification of a third rhodopsin-like pigment in phototactic Halobacterium halobium

Mutant Halobacterium halobium strains deficient in all previously reported rhodopsin-like pigments show phototaxis responses comparable to those of wild-type strains. Spectroscopic analysis reveals the presence of a third retinal-containing pigment in the cells and their membrane fractions. It undergoes a photoreaction cycle with a half-time of approximately equal to 1 sec at room temperature and at physiological light intensities the photostationary state of the pigment consists of two species, one absorbing in the 580- to 590-nm region and the other at 373 nm, both of which are photoactive. Illumination of the long-wavelength species generates the 373-nm intermediate, which upon photoexcitation reconverts to the long-wavelength form. Therefore, changes in the relative light intensities in the long- and short-wavelength regions of the visible spectrum cause opposing shifts in the photostationary state. The spectral sensitivity of this pigment correlates with the color-discriminating phototaxis sensitivities of this organism and strongly suggests that it is the sensory photoreceptor.

Box-shaped halophilic bacteria

Three morphologically similar strains of halophilic, box-shaped procaryotes have been isolated from brines collected in the Sinai, Baja California (Mexico), and southern California (United States). Although the isolates in their morphology resemble Walsby's square bacteria, which are a dominant morphological type in the Red Sea and Baja California brines, they are probably not identical to them. The cells show the general characteristics of extreme halophiles and archaebacteria. They contain pigments similar to bacteriorhodopsin which apparently mediate light-driven ion translocation and photophosphorylation.