Interpretations of the effects of pH on the spectra of purple membrane

Comparison of gamma irradiation and heating treatment on cytotoxicity, insulinotropic activity, and molecular structure change of mistletoe viscothionin

Mistletoe offers health-promoting effects; however, it has toxicity, requiring careful application. Viscothionin is a polypeptide of mistletoe that while contributing to toxicity also demonstrates anti-cancer and anti-diabetic activities. The aim of this study was to evaluate whether gamma irradiation or heating treatment could selectively reduce viscothionin-mediated cytotoxicity. Gamma irradiation effectively inhibited viscothionin-induced cytotoxicity to RIN5mF cells, but heating treatment did not affect its cytotoxicity. Both heating and gamma irradiation further increased the insulinotropic activity of viscothionin, whereas the effect of gamma irradiation was dose-dependent and diminished above 20 kGy. Structural analysis showed that gamma irradiation significantly altered the ordered structure of viscothionin, unlike heating treatment, resulting in a change of its molecular properties, which could be linked to the observed changes in the cytotoxicity and insulinotropic activity of the polypeptide. These results suggest gamma irradiation as an alternative method for minimizing viscothionin toxicity without interfering with anti-diabetic effect.

Independent photocycles of the spectrally distinct forms of bacteriorhodopsin

Time-resolved, flash-induced difference absorbance spectra (300-700 nm) at pH 10.5 and 5 degrees C for the bacteriorhodopsin photocycle fast and slow decaying forms of the M intermediate (M(f) and M(s), respectively) and R intermediate are reported. The main distinguishing features are as follows: For M(f), DeltaA(max) = 412 nm, a shoulder at 436 nm, no absorbance change at 350 nm; DeltaA(min) = 565 nm; DeltaA(412)/DeltaA(565) = 0.85. For M(s), DeltaA(max) = 412 nm, a shoulder at 386 nm; DeltaA(min) = 575 nm; DeltaA(412)/DeltaA(575) = 0.6. For R, DeltaA(max) = 336 and 350 nm (double peak), smaller peaks at 386 and 412 nm; DeltaA(min) = 585 nm; DeltaA(350)/DeltaA(585) = 0.2. The different difference spectra for M(f) and M(s) provide direct evidence that these species, initially identified by their kinetics, are physically distinct. With fast transient absorption spectroscopy, it was shown that R may form very fast, perhaps faster than the L intermediate decays. On the basis of the different bleaching peaks for M(f) and M(s), we propose that M(f) and M(s) are in independent photocycles formed from slightly different forms of bacteriorhodopsin. R may also be in a different photocycle. The different forms of bacteriorhodopsin are probably in dynamic equilibrium with their ratios, controlled by pH and temperature.

Importance of bound divalent cations to the tyrosine deprotonation during the photocycle of bacteriorhodopsin

The transient absorption changes occurring at 297 nm during the photocycles of the deionized and acidified bacteriorhodopsins (blue membranes) were studied. As opposed to what happens during the photocycle of the purple membrane, for the blue membranes only the fast absorption increase corresponding to trans-cis isomerization of the retinal chromophore is present; the slow rise attributed to the tyrosine deprotonation is not observed. The addition of different salts to the deionized membrane restores the original color and causes a tyrosine deprotonation during the photocycle. This suggests that the presence of cations is required for the deprotonation of tyrosine as it is for the deprotonation of the retinylidene Schiff base. These results are discussed in terms of the recently proposed cation model for the observed deprotonation processes in the photocycle of bacteriorhodopsin.

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 (bR(568)) and M(412) 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.

Correlation between absorption maxima and thermal isomerization rates in bacteriorhodopsin

The reported rates of thermal 13-cis to all-trans isomerization of the protonated Schiff base of retinal (PSBR) in solution and in bacteriorhodopsin (BR) are shown to be correlated with the red shift in the absorption maximum of the chromophore, though the linear fit is different for BR and for a model PSBR in solution. Because the red shift in the absorption has been previously shown to be correlated with pi-electron delocalization in the chromophore, this suggests that the thermal isomerization rate is largely regulated by the amount of double bond character in the chromophore. Because the linear fit of isomerization rates with absorption maxima is different for BR and the model PSBR, specific interactions of the protein with the chromophore must also be a factor in determining thermal isomerization rates in BR. A model of the later steps in the photocycle of BR is presented in which the 13-cis to all-trans thermal isomerization occurs during the O intermediate.

Redshift of the purple membrane absorption band and the deprotonation of tyrosine residues at high pH: Origin of the parallel photocycles of trans-bacteriorhodopsin

At high pH (> 8) the 570 nm absorption band of all-trans bacteriorhodopsin (bR) in purple membrane undergoes a small (1.5 nm) shift to longer wavelengths, which causes a maximal increase in absorption at 615 nm. The pK of the shift is 9.0 in the presence of 167 mM KCl, and its intrinsic pK is approximately 8.3. The red shift of the trans-bR absorption spectrum correlates with the appearance of the fast component in the light-induced L to M transition, and absorption increases at 238 and 297 nm which are apparently caused by the deprotonation of a tyrosine residue and red shift of the absorption of tryptophan residues. This suggests that the deprotonation of a tyrosine residue with an exceptionally low pK (pK(a) approximately 8.3) is responsible for the absorption shift of the chromophore band and fast M formation. The pH and salt dependent equilibrium between the two forms of bR, "neutral" and "alkaline," bR <--> bR(a), results in two parallel photocycles of trans-bR at high pH, differing in the rate of the L to M transition. In the pH range 10-11.8 deprotonation of two more tyrosine residues is observed with pK's approximately 10.3 and 11.3 (in 167 mM KCL). Two simple models discussing the role of the pH induced tyrosine deprotonation in the photocycle and proton pumping are presented.It is suggested that the shifts of the absorption bands at high pH are due to the appearance of a negatively charged group inside the protein (tyrosinate) which causes electrochromic shifts of the chromophore and protein absorption bands due to the interaction with the dipole moments in the ground and excited states of bR (Stark effect). This effect gives evidence for a significant change in the dipole moment of the chromophore of bR upon excitation.Under illumination alkaline bR forms, besides the usual photocycle intermediates, a long-lived species with absorption maximum at 500 nm (P500). P500 slowly converts into bR(a) in the dark. Upon illumination P500 is transformed into an intermediate having an absorption maximum at 380 nm (P380). P380 can be reconverted to P500 by blue light illumination or by incubation in the dark.

Nature of forces stabilizing the transmembrane protein bacteriorhodopsin in purple membrane

Analysis of the far-ultraviolet solution and the oriented-film circular dichroic (CD) spectra of the purple membrane (PM) has indicated that the alpha-helical segments of its sole protein bacteriorhodopsin (bR) can undergo a significant tilting from the normal to the membrane plane during light-dependent hydroxylamine-mediated bleaching of the bR. However, this drastic change in tertiary structure is free of any observable secondary structural changes. This phenomenon can provide an excellent means for studying the relative contributions of forces responsible for the stability of this transmembrane protein within the membrane bilayer. Perturbation of the PM by varying degrees of papain digestion (resulting in changes in the bR ranging from only an elimination of the long COOH-terminal tail to the additional eliminations of the short NH(2)-terminal tail and a number of linkage amino acids between the helical segments of the bR) and by chemical cross-linking with dimethyl adipimidate (resulting primarily in the formation of intramolecular cross-links) resulted in a significant increase in this bleaching-induced tilting in all cases except the one in which only the COOH-tail was eliminated. The most severe perturbation (2-wk papain digestion) increased the net tilt angle per segment from 24 to 39 degrees with no indication of any secondary structural changes. Although these perturbations drastically reduced the structural stability of the bR to bleaching, they caused virtually no observable changes in the intramolecular structure of the bR or the supramolecular structure of the PM based on analysis of extensive absorption, linear dichroic, and CD spectra. In addition, study of the bleaching rates for the perturbed PM samples indicated that a linear correlation exists between the calculated initial bleaching rates and the net tilt angles.Considering the forces generally assumed to account for the stability of transmembrane proteins in membranes, (a) intersegmental hydrogen bonding and electrostatic interactions, (b) electrostatic interactions between hydrophilic polypeptide segments extending outside the bilayer and the many charged lipid heads of the bilayer, and (c) hydrophobic interactions, it is clear that the results of the bleaching experiments eliminate all but perhaps the last as contributing significantly to the bR stability in the PM. Furthermore, they provide more compelling evidence than previously available that the bR is capable of undergoing relatively large retinyldiene-controlled tertiary structural changes and that the chromophoric retinal serves as the most important factor in the native bR structural stability. This dynamic view of the bR bears directly on models proposed for bR function, favoring those in which protein structural metastability, rather than rigidity, is an essential factor. The proteinquake or deformation wave model proposed by this laboratory falls into this category.

Dehydration-induced molecular structural changes of purple membrane of halobacterium halobium

The nature and extent of dehydration-induced molecular structural changes of the purple membrane of Halobacterium halobium have been studied by absorption and circular dichroism spectra in solution and in oriented membrane films. High glycerol concentrations, exhaustive dry nitrogen gas flushing, and exhaustive high-vacuum pumping were employed as dehydrants. The effect of these dehydrants on the spectra were reversible, similar, and additive. Analysis of the spectral changes observed at maximal dehydration revealed: (a) at least two additional optical states of the bacteriorhodopsin, one at higher energy and another at lower energy than the characteristic dark- and light-adapted states; (b) no change in the dichroic ratio at the visible absorption maximum within experimental error; (c) no change in the polarity of the visible monomeric retinylidene circular dichroic bands; (d) pronounced reduction in the characteristic excitonic interactions among the retinals in the hexagonal crystalline lattice of the membrane; (e) no changes in the native structural anisotropism of the membrane in respect to the orientation of the amino acid aromatic rings of the bacteriorhodopsin; (f) no changes in the secondary structure of the bacteriorhodopsin; and (g) a net tilting of approximately 20.5 degrees per segment of the helical polypeptide segments of the bacteriorhodopsin away from the membrane normal. A molecular model of the structural changes of the membrane resulting from water removal consistent with these findings can be constructed. Dehydration results in only subtle localized tertiary structural changes of the protein which do not significantly alter its shape or size. However, there are pronounced global supramolecular structural changes of the membrane. Water removal, which is most likely to be from the lipid headgroups of the membrane, disrupts the interactions responsible for maintaining the native crystalline lattice of the membrane resulting in pronounced randomization of the positions of the proteins in the membrane.

Unique biphasic band shape of the visible circular dichroism of bacteriorhodopsin in purple membrane: Excitons, multiple transitions or protein heterogeneity?

OVER A DECADE AND A HALF AGO, WHEN THE FIRST VISIBLE MEMBRANE SUSPENSION CIRCULAR DICHROIC (CD) SPECTRUM OF THE PURPLE MEMBRANE (PM) WAS PRESENTED, TWO MECHANISMS WERE PROPOSED TO ACCOUNT FOR THE OBSERVED BIPHASIC SHAPED CD BAND: (a) excitonic interactions among the retinals of the sole protein bacteriorhodopsin (bR) in the crystalline structure of the PM, and (b) combination of CD bands with opposite rotational strengths due to a retinal-apoprotein heterogeneity of the bR molecules or due to two possible close-lying long-wavelength transitions of the retinal of the bR with opposite rotational strengths. Since that time, an impressive body of experimental and theoretical evidence has been accumulated, mostly consistent with an exciton model but many at serious odds with any heterogeneity or multiple transition model. Recently, a number of articles have appeared reporting analyses of new experimental observations which are proposed to cast serious doubts on the viability of the exciton model, and therefore, may revive the heterogeneity or multiple transition model as an explanation for the unique shape of the CD band of the PM. The intent of this article is to demonstrate that if all observations found in literature baring on this question are considered in toto and in a consistent manner, they can be interpreted without exception by excitons, and furthermore, that there is no plausible evidence available to warrant the revival of the heterogeneity or multiple transition model as an explanation for the unique shape of the biphasic CD band of the PM.

Circular dichroism and cross-linking studies of bacteriorhodopsin mutants

Circular dichroism (CD) spectroscopy was employed for native (wild type, WT) bacteriorhodopsin (bR) and several mutant derivatives: R134K, R134H, R82Q, S35C, L66C, and R134C/E194C. Comparative analysis of the CD spectra in visible range shows that only R134C/E194C exhibits biphasic CD, typical for native bR, the other mutants demonstrate CD spectra with significantly smaller or absent negative band. Since the biphasic CD is a feature of hexagonal lattice structure composed by bR trimers in the purple membrane, these mutants and WT were examined by cross-linking studies, which confirmed the same trend towards trimeric organization. Therefore, a single amino acid substitution may lead to drastically different CD spectra without disruption of bR trimeric organization. Thus, although disruption of bR trimeric crystalline lattice structure (e.g., solubilization with detergents) directly results in the disappearance of characteristic bilobe in visible CD, the lack of the bilobe in the CD alone does not predict the absence of trimers.

Structural Changes of Purple Membrane and Bacteriorhodopsin during Its Denaturation Induced by High pH

Bacteriorhodopsin (bR) trimers naturally form two-dimensional hexagonal crystals in purple membrane (PM), which make it very stable. However, the dnaturation of bR was found to occur during a very narrow pH range when the pH was increased above 12.0, as indicated by inactivation of the photochemical cycle observed by flash photolysis kinetic spectra. Here, atomic force microscopy was used to study the surface structural changes of PM during the denaturation process induced by high pH. Together with the absorption and fluorescence spectra, it was found that the structural changes could be divided into three steps. First, some hydrophobic amino acids of bR become exposed to the aqueous environment and PM loses its 2D crystalline structure, transforming into the so-called "nonisland" structure. Second, bR molecules are extracted out of membrane and form protrusions on the surface like islands in the sea; therefore, the "nonisland" structure transforms into the "island" structure. Finally, most bRs break off from the membrane and form large depositions.

Circular dichroism of heterochromophoric and partially regenerated purple membrane: Search for exciton coupling

In order to determine the origin of the bisignate CD spectra of native purple membrane, heterochromophoric analogues containing bacteriorhodopsin regenerated with native all-trans-retinal and retinal analogues were investigated. The data collected for the purple membrane samples containing two different chromophores suggest the additive character of the CD spectra. This conclusion was supported by a series of spectra using 5,6-dihydroretinal and 3-dehydroretinal and by using 33% regenerated PM in buffer and in presence of osmolytes. Our results support the idea of conformational heterogeneity of the chromophores in the bR in the trimer, suggesting that the three bR subunits in the trimer are not conformationally equal, and therefore, the bisignate CD spectrum of bR in the purple membrane occurs rather due to a superposition of the CD spectra from variously distorted bR subunits in the trimer than interchromophoric exciton-coupling interactions.

Effects of pH and acetylation on Hg(2+)-induced purple to blue transition in bacteriorhodopsin

Effects of Hg(2+) ions on the absorption spectrum of bacteriorhodopsin have been measured at different pH values and after acetylation. UV-difference spectroscopy and CD spectra show that Hg(2+)-induced color change is essentially similar to that caused by removal of cations or acidification. The ability of Hg(2+)-induced purple-to-blue transition is pH-dependent and exhibits a maximum at pH 5.5. Acetylation influences the absorption in the same way as Hg(2+) ions and accelerates Hg(2+)-induced purple to blue transition. All these results strongly suggest that the Hg(2+) effect is not a specific binding but just a replacement of intrinsic cations on the membrane surface, where they form a double layer. The composition of the double layer determines the surface pH on the membrane, which affects the color of the bacteriorhodopsin.

Thermal denaturing of bacteriorhodopsin by X-Ray scattering from oriented purple membranes

We present a temperature-dependent x-ray diffraction study of thin films of purple membranes (PMs) with the native membrane protein bacteriorhodopsin (BR). The high degree of alignment with respect to the silicon substrates allows for the application of modern interface-sensitive scattering techniques. Here we focus on the structural changes of BR in PMs at the thermal denaturing transition. A partial unfolding of the helices is observed rather than the complete unfolding process known from helix to coil transitions. While BR remains threaded into the lipid bilayer in the denatured state, changes in the short-range lateral structures are associated with the partial unfolding of the transmembrane helices.

Fourier transform Raman spectroscopy of the bacteriorhodopsin mutant Tyr-185-->Phe: formation of a stable O-like species during light adaptation and detection of its transient N-like photoproduct

Near-infrared FT-Raman spectroscopy can be used to measure the vibrations of the bacteriorhodopsin (bR) chromophore without the disadvantage of conventional visible resonance Raman spectroscopy, where the visible excitation drives the bR photoreactions. We utilized this technique to investigate the light-dark adaptation of bacteriorhodopsin and the mutant Tyr-185-->Phe (Y185F) at room temperature in solution. Compared to wild-type bR, both the FT-Raman and resonance Raman spectra of the light-adapted Y185F displayed new features characteristic of the vibrations of the O intermediate. Light adaptation of Y185F was found to involve a 13-cis, C=N syn-->all-trans isomerization of the retinal chromophore which produces a species similar to bR570 and a second O-like species. Dark adaptation, which was much slower in Y185F compared to wild-type bR, involved a parallel decay of the bR570 and O-like species and resulted in a decreased all-trans:13-cis ratio compared to wild type. Further evidence for the existence of an O-like species in Y185F comes from pump-probe Raman difference spectroscopy, where a red pump beam is found to produce a species very similar to the N intermediate in the photocycle. This species is shown by stroboscopic Raman measurements to exist transiently even at high pH. We postulate that when the Y185F chromophore has an all-trans structure the effective pKa of Asp-85 and Asp-212 is elevated in Y185F due to the disruption of the Asp-212/Tyr-185 hydrogen bond, thereby accounting for the increased protonation of these residues in the O-like species.

Protein-chromophore interactions in bacteriorhodopsin: the effects of a change in surface potential

The chromophore retinal is bound to bacteriorhodopsin via a protonated Schiff base linkage. The retinal binding site is reported to be buried in the transmembrane portion of the protein, distant from the membrane surfaces. When bound to bacteriorhodopsin, the absorption maximum of retinal is red-shifted from 366 nm to 568 nm producing a purple color. This color persists across a wide pH range. However, when the pH is raised above 12.0, the membranes become pink in color, while at pH values of 3.0 or below, a blue color is produced. The blue color can also be obtained by removing the divalent cations bound to the surface of the protein. In this study, bacteriorhodopsin was examined by circular dichroism and absorption spectroscopy to determine if protein conformational changes were associated with the color shifts. It was found that although the retinal chromophore can be completely removed by bleaching with hydroxylamine with no significant influence on the secondary structure of the protein, a change in the surface charge of bacteriorhodopsin results in measurable conformational change in the protein, which apparently affects the nature of the retinal binding site.

Dramatic in situ conformational dynamics of the transmembrane protein bacteriorhodopsin

The conformational dynamic capabilities of the in situ bacteriorhodopsin (bR) can be studied by determination of the changes of the bR net helical segmental tilt angle (the angle between the polypeptide segments and the membrane normal) induced by various perturbations of the purple membrane (PM). The analysis of the far-UV oriented circular dichroism (CD) of the PM provides one means of achieving this. Previous CD studies have indicated that the tilt angle can change from approximately 10 degrees to 39 degrees depending on the perturbants used with no changes in the secondary structure of the bR. A recent study has indicated that the bleaching-induced tilt angle can be enhanced from approximately 24 degrees to 39 degrees by cross-linkage and papain-digestion perturbations which by themselves do not alter the tilt angle. To add further credence, this study has been repeated using midinfrared (IR) linear dichroic spectral analysis. In contrast to the CD method, analysis by the IR method depends on the orientation of the amide plane of the helix assumed. Excellent consistency is achieved between the two methods only when it is assumed that the structural characteristics of the alpha-helices of the bR are equally alpha I and alpha II in nature. Furthermore, the analysis of the IR data becomes essentially independent of the three amide transitions utilized. The net tilt angle of segments completely randomized relative to the incident light must be 54.736 in view of helix symmetry. A value of 54.735 degrees +/- 0.001 degree was achieved by the IR method for the ethanol-treated PM film, establishing this kind of film as an ideal random state standard and demonstrating the accuracy potential of the IR method.

Effects of detergent environments on the photocycle of purified monomeric bacteriorhodopsin

Time-resolved difference spectra have been obtained for the photocycle of delipidated bacteriorhodopsin monomers (d-BR) in six different detergent micelle environments that were prepared by two new detergent-exchange techniques. A global kinetic analysis of the photocycle spectra for d-BR in each detergent environment was performed. Comparison of these results with those obtained for the photocycle of bacteriorhodopsin in purple membrane (PM) shows that there is one fewer kinetically distinguishable process for monomeric BR between the decay of the K intermediate and the rise of the M intermediate. Assuming a sequential pathway occurs in the photocycle, it appears that the equilibrium between the L and M intermediates is reached much more rapidly in the detergent micelles. This is attributed to a more direct interaction between Asp-85 and the proton on the nitrogen of the Schiff base of retinal for BR in the detergents. Equilibrium concentrations of late photocycle intermediates are also altered in detergents. The later steps of the photocycle, including the decay of the M intermediate, are slowed in detergents with rings in their hydrocarbon region. This is attributed to effects on conformational changes occurring during the decay of M and/or other later photocycle intermediates. The lifetime of dark adaptation of light-adapted d-BR in different detergent environments increases in environments where the lifetime of the M intermediate increases. These results suggest that the high percentage of either unsaturated or methyl-branched lipids in PM and the membranes of other retinal proteins may be important for their effective functioning.

Binding of a single divalent cation directly correlates with the blue-to-purple transition in bacteriorhodopsin

We have characterized a unique divalent cation binding site on bacteriorhodopsin which controls the blue-to-purple transition in the purple membrane of Halobacterium halobium. To identify this site we first showed the correlation between the binding of one Ca2+ per bacteriorhodopsin and the amount of blue membrane converted to purple membrane. When the free Ca2+ was reduced below 1 microM, and the pH was set below 5.0 with 0.5 mM citrate, only binding to this high-affinity site was observed, and we could separate its effect from the effect of other divalent cations binding to the membrane under other conditions. Second, the titration of purple membrane showed that protons are taken up in two distinct steps, about 13 with a pKa of 4-5 and an additional 2 protons with a pKa of 2.75, in 5 mM MgSO4. The latter is identical to the pKa for the purple-to-blue transition in 5 mM MgSO4. Taken together, these observations strongly suggest a direct role for cations in the regulation of the bacteriorhodopsin color under normal conditions. We have also found that the intrinsic pKa for the purple-to-blue transition is about 2.05, suggesting this is the pKa of the group or groups that, when protonated, lead to the blue membrane. Previously published data can now be interpreted to suggest that the cation regulates an active site near the retinal chromophore. A binding site for the divalent cation that includes Asp-212 and interactions with the protonated Schiff base, Asp-85, Tyr-57, Tyr-185, and Arg-82 is proposed.

Effect of genetic modification of tyrosine-185 on the proton pump and the blue-to-purple transition in bacteriorhodopsin

The retinylidene chromophore mutant (Y185F) of bacteriorhodopsin, in which Tyr-185 is substituted by phenylalanine, is examined and compared with wild-type bacteriorhodopsin expressed in Escherichia coli; both were reinstituted similarly in vesicles. The Y185F mutant shows (at least) two distinct spectra at neutral pH. Upon light absorption, the blue species (which absorbs in the red) behaves as if "dead"--i.e., neither its tyrosine nor its protonated Schiff base undergoes deprotonation nor does its tryptophan fluorescence undergo quenching. This result is unlike either the purple species (which absorbs in the blue) or wild-type bacteriorhodopsin expressed in E. coli. As the pH increases, both the color changes and the protonated Schiff base deprotonation efficiency suggest a blue-to-purple transition of the Y185F mutant near pH 9. If this blue-to-purple transition of Y185F corresponds to the blue-to-purple transition of purple-membrane (native) bacteriorhodopsin (occurring at pH 2.6) and of wild-type bacteriorhodopsin expressed in E. coli (occurring at pH 5), the protein-conformation changes of this transition as well as the protonated Schiff base deprotonation may be controlled not by surface pH alone, but rather by the coupling between surface potential and the general protein internal structure around the active site. The results also suggest that Tyr-185 does not deprotonate during the photocycle in purple-membrane bacteriorhodopsin.

Structure and thermal stability of monomeric bacteriorhodopsin in mixed phospholipid/detergent micelles

Thermal unfolding experiments on bacteriorhodopsin in mixed phospholipid/detergent micelles were performed. Bacteriorhodopsin was extracted from the purple membrane in a denatured state and then renatured in the micellar system. The purpose of this study was to compare the changes, if any, in the structure and stability of a membrane protein that has folded in a nonnative environment with results obtained on the native system, i.e., the purple membrane. The purple membrane crystalline lattice is an added factor that may influence the structural stability of bacteriorhodopsin. Micelles containing bacteriorhodopsin are uniformly sized disks 105 +/- 13 A in diameter (by electron microscopy) and have an estimated molecular mass of 210 kDa (by gel filtration HPLC). The near-UV CD spectra (which is indicative of tertiary structure) for micellar bacteriorhodopsin and the purple membrane are very similar. In the visible CD region of retinal absorption, the double band seen in the spectrum of the purple membrane is replaced with a broad positive band for micellar bacteriorhodopsin, indicating that in micelles, bacteriorhodopsin is monomeric. The plot of denaturational temperature vs. pH for micellar bacteriorhodopsin is displaced downward on the temperature axis, illustrating the lower thermal stability of micellar bacteriorhodopsin when compared to the purple membrane at the same pH. Even though micellar bacteriorhodopsin is less stable, similar changes in response to pH and temperature are seen in the visible absorption spectra of micellar bacteriorhodopsin and the purple membrane. This demonstrates that changes in the protonation state or temperature have a similar affect on the local environment of the chromophore and the protein conformation.(ABSTRACT TRUNCATED AT 250 WORDS)

Purple-to-blue transition of bacteriorhodopsin in a neutral lipid environment

The red shift in the absorption maximum of native purple membrane suspensions caused by deionization is missing in lipid-depleted purple membrane, and the pK of the acid-induced transition is down-shifted to pH approximately 1.4 and has become independent of cation concentration (Szundi, I., and W. Stoeckenius. 1987. Proc. Natl. Acad. Sci. USA. 84:3681-3684). However, the proton pumping function cannot be demonstrated in these membranes. When native acidic lipids of purple membrane are exchanged for egg phosphatidylcholine or digalactosyldiglyceride, bacteriorhodopsin is functionally active in the modified membrane. It shows spectral shifts upon light-dark adaptation, a photocycle with M-intermediate and complex decay kinetics; when reconstituted into vesicles with the same neutral lipids, it pumps protons. Unlike native purple membrane, lipid-substituted modified membranes do not show a shift of the absorption maximum to longer wavelength upon deionization. A partial shift can be induced by titration with HCl; it has a pK near 1.5 and no significant salt dependence. Titration with HNO3 and H2SO4, which causes a complete transition in the lipid-depleted membranes, i.e., it changes their colors from purple to blue, does not cause the complete transition in the lipid-substituted preparations. These results show that the purple color of bacteriorhodopsin is independent of cations and their role in the purple-to-blue transition of native membranes is indirect. The purple and blue colors of bacteriorhodopsin are interpreted as two conformational states of the protein, rather than different protonation states of a counterion to the protonated Schiff base.

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

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

Resonance Raman spectra of the acidified and deionized forms of bacteriorhodopsin

The 568-nm absorption band of light-adapted bacteriorhodopsin (BR) shifts to 605 nm at pH 2, forming BR605A, and it shifts back to 565 nm at pH 0, forming BR565A. We have obtained resonance Raman spectra of BR605A and BR565A using purple membrane samples that have been suspended in a rotating Raman cell with a polyacrylamide gel. Raman spectra were also obtained of purple membrane in deionized solutions (BR605D). The spectra of BR605A and BR605D are very similar, and they correspond closely with the Raman spectrum of dark-adapted BR, which contains an approximately equal mixture of 13-cis and all-trans retinal protonated Schiff-base chromophores. This shows that BR605A and BR605D are not homogeneous molecular species but contain a mixture of pigment molecules with both 13-cis and all-trans retinal isomers. The Raman spectrum of BR565A is nearly identical to that of light-adapted BR, demonstrating that BR565A contains an all-trans protonated Schiff-base chromophore. These data provide constraints on the possible structural changes that can be invoked to explain the spectral shifts induced in the acid and deionized species.

On the protein (tyrosine)-chromophore (protonated Schiff base) coupling in bacteriorhodopsin

The kinetics of formation of both the tyrosinate ion (from its absorption at 296 nm) and the deprotonated Schiff base (M412) (from its absorption at 404 nm) are studied simultaneously at different pH values (7-11) and temperatures (5-25 degrees C). Two formation rates are observed for M412 in agreement with previous observations. The slow one is dominant under physiological conditions and is found to be slightly faster than that for the tyrosinate formation. This is in disagreement with the proposal that the tyrosinate formation is a prerequisite to the deprotonation of the Schiff base (M412). The ratio of the amplitudes of the fast and slow components is found to be sensitive to pH and, at any pH, it can be used to calculate an amino acid pKa value of 9.6. This is explained by proposing the existence of two sites for the protonated Schiff base within the protein. In one site, the Schiff base is near the neutral form of an amino acid residue with a pKa value of 9.6 (giving rise to the slow component), while in the other, it is near its conjugate base. The formation of the tyrosinate ion as well as the formation of the slow and fast components of M412 all have activation energies that are comparable to H-bond energies. A model is suggested to account for this and the comparable deprotonation rates of tyrosine and the slow component of the protonated Schiff base. It involves the reduction of their pKa by their exposure to a positively charged species.

Effect of specific carboxyl modifications on the blue acid species and O650 photocycle intermediate of bacteriorhodopsin

Carboxyl groups were specifically modified in purple membranes using hydrophobic or hydrophilic activating reagents and endogenous or exogenous nucleophiles. Modification of surface residues using a negatively charged nucleophile had no effect on blue-species formation, whereas surface or internal carboxyl modification using an uncharged nucleophile prevented blue-species formation. The carboxyl-modified samples showed poor correlation between blue-species and O650 intermediate. These results indicate that formation of the blue-species requires negative surface charge and is not associated with the O650 intermediate of bacteriorhodopsin, as had been previously postulated.

Retinal migration during dark reduction of bacteriorhodopsin

When the retinal Schiff base in chymotryptically cleaved bacteriorhodopsin is reduced to a secondary retinylamine by prolonged exposure to 10% (wt/vol) sodium cyanoborohydride, at pH 10, in the absence of light, approximately 45% of the retinal is found linked to Lys-41 and 22% to Lys-40, and the remainder is scattered over various sites on the large chymotryptic fragment, including the physiological site at Lys-216. The retinal-binding site is destroyed or blocked by the reduction conditions, but the bacteriorhodopsin lattice remains intact. The results demonstrate that artifactual linkage to Lys-40/41 is possible under special conditions. Under these conditions, the epsilon-amino groups of Lys-40/41 show an enhanced ability to form retinylidene linkages with the retinal released by the physiological linkage site at Lys-216, due to some combination of close proximity to the normal linkage site, and increased reactivity with respect to other lysine epsilon-amino groups. The results are of interest for the characterization of the two newly discovered rhodopsin-like proteins, halorhodopsin and slow rhodopsin.

Induction of the blue form of bacteriorhodopsin by low concentrations of sodium dodecyl sulfate

The effects produced on bacteriorhodopsin by low concentrations of several detergents have been studied by absorption and fourth-derivative spectrophotometry. Sodium dodecyl sulfate induces the appearance of the blue form of bacteriorhodopsin (lambda max = 600 nm) at pH values up to 7.0 in a reversible manner. The apparent pK of the purple-to-blue transition raised with increasing concentration of SDS. Of the other detergents tested, only sodium dodecyl-N-sarcosinate showed a slight red-shift of the absorption band to 580 nm, whereas sodium taurocholate, Triton X-100 and cetyltrimethylammonium bromide did not favour the appearance of the blue form. The effect of SDS was found to be consistent with a localized conformational change that moves away the counter-ion of the protonated Schiff base.

Evidence for a carboxyl group in the vicinity of the retinal chromophore of bacteriorhodopsin

Carboxyl groups of bacteriorhodopsin in purple membranes were activated using a hydrophobic reagent and then covalently labeled with a pH-sensitive reporter group, nitrotyrosine methyl ester. The membrane-bound reporter group had different spectral properties, and a pK 3 units higher than in solution. In purple membranes, an isosbestic point between the 428nm absorption peak of nitrotyrosine methyl ester, and the bacteriorhodopsin 570nm chromophore seen in alkaline titration, indicated interactions between the reporter group and retinal. Modification of white membranes (bacterioopsin from R1mW strain) revealed similar, unusual spectral and ionization properties. Thus, the hydrophobic environment, not retinal interactions per se, are responsible for the ionization behavior of the reporter group. These results indicate that a carboxyl group is near the retinal chromophore of bacteriorhodopsin.

Multiple isoelectric forms of detergent-solubilized bovine rhodopsin. II. Spectral analysis

The absorption and circular dichroic spectra of three stable isoelectric forms of purified rhodopsin (in Emulphogene BC 720) with isoelectric points of 5.19, 5.58 and 6.14 were analysed over the accessible wavelength region of 190-800 nm. It was found from the spectral analysis of the 5.58 and 6.14 forms that the tertiary structure of these isoelectric forms was different, without any change being observed in the secondary structure of these proteins. The difference in structure was removed by denaturation with SDS. Specifically, the aromatic amino acid residues of the 6.14 isoelectric form were suggested to be in a more polar environment as compared to those for the 5.58 isoelectric form. The changes of structure in the microenvironment of retinal in these proteins were minor in comparison to the tertiary changes observed in the proteins. This indicated that the site of charge perturbation is not localized in the retinylidene microenvironment. Furthermore, the spectral features of these isoelectric forms were features common to the spectra of both purified unfocused rhodopsin and crude rhodopsin, suggesting that the isoelectric forms are not a consequence of purification. Spectral analysis of the 5.19 isoelectric form indicated that this form of rhodopsin had an increased tendency to aggregate after focusing. Based on the denaturation properties of these isoelectric forms, it was shown that the 5.19 and 5.58 isoelectric forms had different conformations. It was concluded from this study that preparations of 'purified' rhodopsin are a heterogeneous mixture of stable proteins with different tertiary structures and different isoelectric points.