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PubMed1991

Detergent delipidation and solubilization strategies for high-resolution NMR of the membrane protein bacteriorhodopsin.

High-resolution NMR studies of bacteriorhodopsin require the availability of the detergent-solubilized protein with both high concentration and small rotational correlation time. A procedure is described for the optimized preparation of such samples. Bacteriorhodopsin was first delipidated by detergent treatment of purple membrane under nonsolubilizing conditions for the protein. The delipidated aggregated protein could then be solubilized into monomers at concentration close to millimolar by selected detergents. The solubilizing detergent had an important effect on the rotational correlation time of the protein as shown by measuring in each case the temperature-dependent stability of the protein, the size of the detergent-protein complex, and the detergent viscosity. Consistently, a strong influence of the detergent was also found on spectral resolution in 13C NMR spectra of solubilized bacteriorhodopsin labeled with [1-13C]phenylalanine. Best resolution was obtained using n-dodecylmaltoside as detergent, with which relatively narrow well resolved 13C NMR resonances were observed at 50 degrees C. It is suggested that high-resolution NMR studies performed with this detergent may contribute to the structural resolution of bacteriorhodopsin.

Bacteriorhodopsins↗
PubMed1990

Ultraviolet-visible transient spectroscopy of bacteriorhodopsin mutants. Evidence for two forms of tyrosine-185----phenylalanine.

The photocycle kinetics of the bacteriorhodopsin mutant Tyr-185----Phe has been investigated by UV-visible transient spectroscopy. Flash-induced spectral changes were measured from 100 ns to 500 ms using a gated optical multichannel analyzer on protein samples that were reconstituted in vesicles with Halobacterium halobium lipids. Tyr-185----Phe exhibits a pH-dependent absorbance spectrum reflecting contributions from two different species. At pH 6, the dominant photocycling species has a lambda max near 610 nm although the absorption maximum of light-adapted Tyr-185----Phe is at 581 nm. This red-shifted species does not form any M-like intermediate and undergoes a photocycle similar to that observed for deionized blue membrane. At pH 8, the dominant photoactive form exhibits a lambda max near 550 nm. This purple species, which is blue shifted 20 nm relative to wild-type bacteriorhodopsin, exhibits a photocycle similar to the wild type. However, M formation occurs in 8 microseconds, approximately three times faster than wild-type bacteriorhodopsin at pH 8. In addition, an unusually long lived intermediate absorbing at 610 nm is observed at high pH. In the UV region, a broad band near 300-310 nm is absent in the mutant relative to wild type, consistent with earlier measurements made at low temperature which suggest that Tyr-185 undergoes a change in protonation. Steady-state proton pumping action spectra indicate that the 550 nm species does transport protons but that the blue species is inactive. These results are discussed in terms of a model that hypothesizes that Tyr-185 is located close to the bacteriorhodopsin chromophore and stabilizes the interaction of helices F and G through formation of a polarizable bond with Asp-212.

Amino Acid Sequence↗
PubMed1978

Bacteriorhodopsin: lipid environment and conformational changes.

The polar lipids of the purple membrane were exchanged for different phosphatidylcholine species. The resulting complexes had the same protein to lipid-phosphorus ratio as the natural membrane, but only about 0.5-1.0 mole of original lipid was still present per mole of bacteriorhodopsin. In such complexes the bacteriorhodopsin photocycle is slowed down 10-20 times, but the strong protein-protein interaction is not abolished. Due to the slow rate of the photocycle we were able to measure in the light the ratio between net proton release and net accumulation of the last intermediate of the photocycle, the unprotonated M412. This ratio was not constant and equal to 1.0, as expected for a single deprotonation reaction, but varied with pH from 1.5 to 0.4. The variable ratio suggests that light-induced conformational changes occur in the nonchromophore part of the protein, which shift the pKa values of unidentified groups so as to cause binding or release of additional protons. A similar conclusion was drawn from experiments on the kinetics of proton transfer by bacteriorhodopsin in subbacterial particles of Halobacterium halobium and in reconstituted bacteriorhodopsin proteoliposomes. However, in this case light-induced association and dissociation of additional protons occurs simultaneously on different sides of the membrane.

Bacteriorhodopsins↗
PubMed1982

Reversible inhibition of the proton pump bacteriorhodopsin by modification of tyrosine 64.

Five mol of lysine per mol of bacteriorhodopsin were modified with methylacetimidate. This treatment did not inactivate bacteriorhodopsin but prevented all lysines from subsequent reaction with diazotized sulfanilic acid. This reaction predominantly modified tyrosine 64 and light-induced proton translocation was abolished. Reduction of the mono(p-azobenzene sulfonic acid) tyrosine 64 to the corresponding 3-amino derivative with sodium dithionite led to complete reactivation of the proton translocation activity of bacteriorhodopsin. The relative location of tyrosines 26 and 64 and the COOH terminus on the two surfaces of the purple membrane was determined by incorporation into phospholipid vesicles, subsequent modification, and proteolytic treatment. The results obtained support the models proposed by Engelmann et al. (Engelman, D. M., Henderson, R. McLauchlan, A. D., and Wallace, B. A. (1980) Proc. Natl. Acad. Sci. U. S. A. 77, 2023-2027) and by Ovchinnikov et al. (Ovchinnikov, Yu. A., Abdulaev, N. G., Feigina M. Yu., Kiselev A. V., and Lobanov, N. A. (1979) FEBS Lett. 100, 219-224). Tyrosine 64 is located on the extracellular side of the membrane, whereas tyrosine 26 and the COOH terminus are located on the cytoplasmic side. Because specific nitration of tyrosine 26 also leads to inactivation of bacteriorhodopsin (Lemke, H. D., and Oesterhelt, D. (1981) Eur. J. Biochem. 115, 595-604), the results obtained demonstrate that amino acid residues located on both surfaces of the purple membrane are involved in proton translocation.

Amino Acid Sequence↗
PubMed1984

Bacteriorhodopsin precursor. Characterization and its integration into the purple membrane.

Halobacterium halobium spheroplasts synthesize and accumulate a bacteriorhodopsin precursor. By labeling of the precursor with [35S]Met and [3H]Leu followed by Edman degradation, we have confirmed the previous conclusion from the DNA sequencing that the precursor contains 13 additional amino acids at the NH2 terminus of bacteriorhodopsin. Although not processed in the spheroplasts, it integrates into the purple membrane in the correctly folded conformation. This was shown by the mode of cleavage by a number of proteolytic enzymes, the site of attachment of retinal, and the formation of oligomers on reaction with bifunctional cross-linking reagents. In all these respects, the behavior of the precursor was identical with that of native mature bacteriorhodopsin in the purple membrane. Finally, the precursor was not processed to bacteriorhodopsin even when the spheroplasts were subsequently allowed to revert to rod-shaped cells. This suggests that either the processing of the precursor is cotranslational or that the NH2 terminus of the precursor becomes inaccessible to the processing enzyme in the spheroplasts following integration into the membrane.

Amino Acid Sequence↗
PubMedDate not supplied

[Photochemical transformations of bacteriorhodopsin].

Results of experimental studies of bacteriorhodopsin photochemical transformations of purple membranes at low temperatures are presented. A scheme of reactions of light-adapted bacteriorhodopsin is proposed, some regularities of its phototransformations are considered. Relationships between quantum yields of direct and reverse photoreactions and absorption spectra of the states initiated during phototransformations of the pigment are determined. Proceeding from spectroscopic data the mechanisms of photochemical processes in bacteriorhodopsin are discussed. The author's and literature data point to the participation of retinal structural changes, of alterations in retinal interactions with opsin and of proton in bacteriorhodopsin photoreactions.

Bacteriorhodopsins↗
PubMed1981

[Phases of photoelectrical response of bacteriorhodopsin].

The generation of electrical potential difference by bacteriorhodopsin sheets incorporated into collodium film impregnated with a lecithine solution in decane was studied. The electrical response to a short light flash inducing a single turnover of bacteriorhodopsin consists of four phases. Phase I of photoresponse (tau less than 0.2 mks) has a small amplitude and is directed oppositely to the electrical response to continuous light. The negative phase is followed by positive phases, i.e. microsecond (II) and millisecond (III) ones, either of which can be decomposed at least into two exponents. Phase IV of the electrical response is a passive discharge of capacity of the "bacteriorhodopsin sheets--collodium film" system. Although phases II and III correspond to the generation and disappearance of the photochemical cycle intermediate with an absorption maximum at 412 nm, the parameters and activation energy of these two processes do not show complete coincidence. The effects of gramicidin A and the trifluoromethoxycarbonylcyanidephenylhydrazone uncoupler on the photoelectrical response were analyzed. The data obtained are discussed in terms of an equivalent electrical scheme, according to which the bacteriorhodopsin sheets form closed vesicles upon being incorporated into collodium film.

Bacteriorhodopsins↗
PubMed1981

Reconstitution of delipidated bacteriorhodopsin with endogenous polar lipids.

Delipidated bacteriorhodopsin has been reconstituted with endogenous polar lipids from Halobacterium halobium. The vesicle (diameter, 250-500 A) formed are very stable, relatively homogeneous in bacteriorhodopsin and lipid content, and almost optically clear; a minor turbid fraction can be separated by gel filtration. Bacteriorhodopsin in the reconstituted vesicles has an inside out orientation and, on illumination, translocates protons efficiently from the medium to the interior of the vesicles in the presence of the ionophore valinomycin. In the absence of the latter, both the rate and the extent of light-dependent proton uptake by the vesicles are decreased 3-6- and 5-15-fold, respectively, depending on the salt in the assay medium. Both the stimulation by valinomycin and the proton-translocating activity are higher in NaCl than in KCl. Bacteriorhodopsin in these vesicles as in purple membrane, undergoes light adaptation as indicated by a red shift (7-8 nm) of the absorption maximum. At low pH, the absorption maximum of reconstituted protein shows a 50-nm red shift, possibly due to protonation of an ionizable group which interacts with the chromophore. The latter group appears to be accessible only from the external medium.

Bacteriorhodopsins↗
PubMed1981

[Some features of photochemical conversions of bacteriorhodopsin at low pH values].

Association of bacteriorhodopsin sheets and proteoliposomes with collodium film impregnated with a lecithine solution in decane was carried out. The generation of electrical potential difference in response to a light flash within the pH range of 0-6 was studied. The amplitude of microsecond (II) and millisecond (III) phases of the photoelectrical response was shown to decline with a decrease in pH as in the case when the inhibition by acid is due to protonation of a group with a pK of 3,7. The photoelectrical response of the "acid" form of bacteriorhodopsin with a maximun at 605 nm is represented by a negative phase having a small amplitude. This phase is coupled with the formation of the photochemical cycle bathointermediate and is sharply increased in an acid medium simultaneously with the generation of bacteriorhodopsin form with an absorption maximum at 565 nm. The effects of KCl, phenyldicarbaundecaborane and fluoride on the spectral and photoelectrical responses of bacteriorhodopsin are described.

Bacteriorhodopsins↗
PubMed1993

Asp96 deprotonation and transmembrane alpha-helical structural changes in bacteriorhodopsin.

The M-->N transition in the photocycle of bacteriorhodopsin involves the transfer of a proton from Asp96 to the retinylidene Schiff base, possibly through a network of hydrogen-bonded amino acid residues and water molecules (Rothschild, K. J., He, Y. W., Sonar, S., Marti, T., and Khorana, H. G. (1992) J. Biol. Chem. 267, 1615-1622). A conformational change of the protein backbone is also observed during this transition. In this work, we have investigated the effects of replacing the residue Thr46, which might be part of this chain, with an aspartic acid. Both Fourier transform infrared and resonance Raman spectroscopy show that the chromophore structure of this mutant (T46D) is normal. However, N formation is accelerated and N decay is significantly slowed compared to wild-type bacteriorhodopsin. This effect causes the N intermediate to accumulate under steady-state illumination thereby facilitating spectroscopic studies under normal pH conditions. Fourier transform infrared difference spectroscopy reveals that like native bacteriorhodopsin, N formation in T46D involves deprotonation of Asp96, reprotonation of the Schiff base, and a change in the backbone secondary structure. However, in contrast to bacteriorhodopsin, bands assigned to the C = O stretch mode of the carboxylic acid group of Asp96 are upshifted by 10 cm-1 reflecting a change in the Asp96 environment and a drop in its effective pKa throughout the photocycle. This change in the pKa can directly account for changes in the photocycle kinetics and indicates that Asp96 deprotonation/protonation are the rate limiting steps in the formation and decay of the N intermediate. By studying the effects of H/D exchange, evidence is found that the backbone structural changes involve transmembrane alpha-helices. It is proposed that these structural changes serve to modulate the local environment and protonation state of Asp96 during the photocycle and are also essential for formation of the proton conducting hydrogen bonded network which functions during Schiff base reprotonation.

Aspartic Acid↗
PubMed1982

Characterization and crystal packing of three-dimensional bacteriorhodopsin crystals.

The three-dimensional crystals of the integral membrane protein bacteriorhodopsin have been characterized by X-ray diffraction and freeze-fracture electron microscopy: the needle-like form A crystals belong to space group P 1 (pseudohexagonal) with seven molecules per crystallographic unit cell forming one turn of a non-crystallographic helix. The probable arrangement of the bacteriorhodopsin molecules is derived from freeze-fracture electron micrographs and chromophore orientation. Membrane-like structures are not present. The same helices of bacteriorhodopsin molecules found in crystal form A also make up the cube-like crystal form B. They are now arranged in all three mutually perpendicular directions. These cubes are always highly disordered, since the unit cell length corresponds to 6.7 molecules of the 7-fold helix. Very often, conversion of bacteriorhodopsin from the three-dimensional crystals into filamentous material occurs.

Journal Article↗
PubMed1986

Dynamic properties of bacteriorhodopsin in purple membranes upon heat treatment.

Reversible temperature-dependent conformational changes in bacteriorhodopsin of the purple membranes from Halobacterium halobium have been studied by the method of deuterium exchange. A noticeable increase in the mobility of structured peptide groups in bacteriorhodopsin was revealed upon reorganization of the supermolecular structure at about 60 degrees C. In the supermolecular structure formed, bacteriorhodopsin molecules have no contacts with external medium at 75-80 degrees C. Membrane destruction results in a drastic increase in molecular mobility within the narrow temperature range 100-110 degrees C. The effects observed are induced by predenaturation changes in the bacteriorhodopsin structure and rearrangements in the structure of a protein-lipid complex. The temperature dependence of the number of peptide groups involved in reversible conformational rearrangements is in good agreement with the microcalorimetry data.

Journal Article↗
PubMedDate not supplied

Bacteriorhodopsin: the effect of bilayer thickness on 2D-array formation, and the structural re-alignment of retinal through the photocycle.

From our earlier extensive protein-lipid reconstitution studies, the conditions under which bacteriorhodopsin forms organised 2D arrays in large unilamellar vesicles have been established using freeze-fracture electron microscopy. In a background bilayer matrix of phosphatidylcholine (diC(14:0)), the protein can form arrays only when the anionic purple membrane lipid, phosphatidylglycerol phosphate (or the sulphate derivative) is present. Here we have now extended this work to investigate the effect of bilayer thickness on array formation. Phosphatidylcholines with various chain lengths (diC(12:0), diC(14:0) and diC(16:0)) and which form bilayers of well defined bilayer thickness, have been used as the matrix into which bacteriorhodopsin, together with minimal levels (c. 4-10 lipids per bacteriorhodopsin) of diphytanyl phosphatidyl-glycerol phosphate, has been reconstituted. Arrays are formed in all complexes and bhickness appears only to alter the type of array formed, either as an orthogonal or as an hexagonal array. Secondly, we have previously deduced the entire conformation of retinal within the bacteriorhodopsin binding pocket in oriented purple membrane fragments. Using solid state deuterium NMR of the specifically deutero-methylated retinal labelled at each of the methyl positions in the molecule, the C-CD(3) bond vectors of the chromophore have been resolved to +/- 2 degrees . The ring conformation is 6-S-trans, but the polyene chain is slightly curved when in the protein binding site. Here, we describe studies on the protein in both the ground state and the trapped M(412)-state of the photocycle, to show that the orientation of the central methyl group (C(19)) on the polyene chain, which is at 40 degrees +/- 1 degrees with respect to the membrane normal, only changes its orientation by approximately 4 degrees upon 13-cis-isomerization. Thus, it is the Schiff base end of the chromophore which moves upon light incidence acting as a local switch on the protein in the photocycle, whilst the ring end of the chromophore moves rather less.

Journal Article↗
PubMed1997

Evolutionary relationships among proteins probed by an iterative neighborhood cluster analysis (INCA). Alignment of bacteriorhodopsins with the yeast sequence YRO2.

PURPOSE: Searching the existing databases for homologous sequences is essential to understanding a protein's structure and function. For a query sequence, its nearest neighbors can be identified by BLAST (basic local alignment search tool). However, a single query sequence is sufficient to define the entire neighborhood of related sequences, and multiple BLAST queries are needed. We describe here a program which permits automated and iterative BLAST analysis of an entire neighborhood of sequences and apply this to search for homologs of the bacteriorhodopsins outside the archaea phylum. METHODS: We have developed a Java program, 'Iterative Neighborhood Cluster Analysis' (INCA), which performs iterative BLAST searches, beginning with a single starter sequence, and proceeding with any other sequence achieving a predefined minimum alignment score. This results in a cluster of sequences where each sequence is related to at least one other sequence by the cutoff score, additional lists of more distantly related sequences for each member of cluster. RESULTS: Bacteriorhodopsins had not been previously aligned with any other protein family with scores indicative of probable homology. Using INCA, we identified a probable homolog in yeast, YRO2_YEAST, also containing seven putative transmembrane domains. A finding of probable homology was supported by additional alignment strategies. CONCLUSIONS: INCA is a useful tool to assess complete protein neighborhoods. With an increasing database, INCA can serve to detect the emergence of evolutionary links between even the most distantly related protein families. Identifying a homolog of the bacteriorhodopsins in yeast illustrates this approach but at the same time highlights the vast evolutionary distances between polytopic membrane proteins, such as the bacteriorhodopsins.

Amino Acid Sequence↗
PubMed1974

Tunable laser resonance raman spectroscopy of bacteriorhodopsin.

Bacteriorhodopsin is a rhodopsin-like protein found in the cell membrane of Halobacterium halobium. It shows an absorption maximum at 570 nm and, in the light, undergoes cyclic spectral changes which include a relatively long-lived complex absorbing maximally at 412 nm. Excitation profiles have been obtained with several laser frequencies for two vibrations in the resonance Raman spectrum of bacteriorhodopsin. The results show that the Schiff base retinylidene lysine linkage is protonated in the 570 nm complex and that in the 412 nm complex it is unprotonated. The 412 nm complex must be present at appreciable concentrations when bacteriorhodopsin is exposed to high-energy argon ion laser light of the Raman spectrophotometer at room temperature. We conclude that the observed C=N stretch at 1622 cm(-1) in the room temperature spectra, which in an earlier study by Mendelsohn was interpreted as evidence for an unprotonated linkage in bacteriorhodopsin, results from the presence of the 412 nm complex.

Bacterial Proteins↗
PubMed1993

Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin.

Structural changes are central to the mechanism of light-driven proton transport by bacteriorhodopsin, a seven-helix membrane protein. The main intermediate formed upon light absorption is M, which occurs between the proton release and uptake steps of the photocycle. To investigate the structure of the M intermediate, we have carried out electron diffraction studies with two-dimensional crystals of wild-type bacteriorhodopsin and the Asp96-->Gly mutant. The M intermediate was trapped by rapidly freezing the crystals in liquid ethane following illumination with a xenon flash lamp at 5 and 25 degrees C. Here, we present 3.5 A resolution Fourier projection maps of the differences between the M intermediate and the ground state of bacteriorhodopsin. The most prominent structural changes are observed in the vicinity of helices F and G and are localized to the cytoplasmic half of the membrane.

Amino Acid Sequence↗
PubMed1992

An energy-based approach to packing the 7-helix bundle of bacteriorhodopsin.

Based on the heavy-atom coordinates determined by the electron microscopy for the seven main helical regions of bacteriorhodopsin with the all-trans retinal isomer, energy optimizations were carried out for helix bundles containing the all-trans retinal and 13-cis retinal chromophores, respectively. A combination of simulated annealing and energy minimization was utilized during the process of energy optimization. It was found that the 7-helix bundle containing the all-trans isomer is about 10 kcal/mol lower in conformational energy than that containing the 13-cis isomer. An energetic analysis indicates that such a difference in energy is consistent with the observation that absorption of a 570-nm proton is required for the conversion of a bacteriorhodopsin from its all-trans to 13-cis form. It was also found that the above conversion process is accompanied by a significant conformational perturbation around the chromophore, as reflected by the fact that the beta-ionone ring of retinal moves about 5.6 A along the direction perpendicular to the membrane plane. This is consistent with the observation by Fodor et al. (Fodor, S.P.A., Ames, J.B., Gebhard, R., van der Berg, E.M.M., Stoeckenius, W., Lugtenburg, J., & Mathies, R.A., 1988, Biochemistry 27, 7097-7101). Furthermore, it is interesting to observe that although the retinal chromophore undergoes a significant change in its spatial position, the orientation of its transition dipole changes only slightly, in accord with experimental observations. In other words, even though orientation of the retinal transition dipole is very restricted, there is sufficient room, and degrees of freedom, for the retinal chromophore to readjust its position considerably. This finding provides new insight into the subtle change of the retinal microenvironment, which may be important for revealing the proton-pumping mechanism of bacteriorhodopsin. The importance of electrostatic and nonbonded interactions in stabilizing the 7-helix bundle structure has also been analyzed. Electrostatic interactions favor an antiparallel arrangement among adjacent helices. Nonbonded interactions, however, drive most of the closely packed helices into an arrangement in which the packing angles lie around -160 degrees, a value very near the -154 degrees value computed earlier as the most favorable packing arrangement of two poly(Ala) alpha-helices (Chou, K.-C., Némethy, G., & Scheraga, H.A., 1983, J. Phys. Chem. 87, 2869-2881). The structural features of the 7-helix bundle and their relationship to those found in typical 4-helix bundle proteins are also discussed.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1993

Refolding and proton pumping activity of a polyethylene glycol-bacteriorhodopsin water-soluble conjugate.

Bacteriorhodopsin (BR), from the purple membrane (PM) of Halobacterium halobium, was chemically modified with methoxypolyethylene glycol (m-PEG; molecular weight = 5,000 Da) succinimidyl carbonate. The polyethylene glycol-bacteriorhodopsin (m-PEG-SC-BR33) conjugate, containing one polyethylene glycol chain, was water soluble. The secondary structure of the conjugate in water appeared partially denatured, but was shown to contain alpha-helical segments by circular dichroism spectroscopy. The isolated bacteriorhodopsin conjugate, with added retinal, was refolded in a mixed detergent-lipid micelle and had an absorption maximum at 555 nm. The refolded conjugate was transferred into vesicles that pumped protons, upon illumination, as efficiently as did native BR. Modification of the PM with m-PEG did not alter the native structure or inhibit proton pumping, and therefore it is suggested that the glycol polymer is present as a moiety covalently linked to residues unnecessary for proton pumping and proper folding. The site of attachment of m-PEG was determined to be at either Lys 129 or Lys 159, with position Lys 129 the most probable site of attachment. The m-PEG-SC-BR33 could be stepwise refolded to the native conformation by the addition of trifluoroethanol to lower the dielectric constant, simulating the insertion of the BR into the phospholipid bilayer.

Bacteriorhodopsins↗