The photochemical cycle of halorhodopsin: absolute spectra of intermediates obtained by flash photolysis and fast difference spectra measurements

The Crystal Structure of the L1 Intermediate of Halorhodopsin at 1.9 Å Resolution†

The mutant T203V of the light driven chloride pump halorhodopsin from Halobacterium salinarum was crystallized and the X-ray structure was solved at 1.6 angstroms resolution. The T203V structure turned out to be nearly identical to the wild type protein with a root mean square deviation of 0.43 angstroms for the carbon alpha atoms of the protein backbone. Two chloride binding (CB) sites were demonstrated by a substitution of chloride with bromide and an analysis of anomalous difference Fourier maps. The CB1 site was found at the same position as in the wild type structure. In addition, a second chloride binding site CB2 was identified around Q105 due to higher resolution in the mutant crystal. As T203V showed a 10 times slower decay of its photocycle intermediate L, this intermediate could be trapped with an occupancy of 60% upon illumination at room temperature and subsequent cooling to 120 degrees K. Fourier transform infrared spectroscopy clearly identified the crystal to be trapped in the L1 intermediate state and the X-ray structure was solved to 1.9 angstroms resolution. In this intermediate, the chloride moved by 0.3 angstroms within binding site CB1 as indicated by peaks in difference Fourier density maps. The chloride in the second binding site CB2 remained unchanged. Thus, intraproteinous chloride translocation from the extracellular to the cytoplasmic part of the protein must occur in reaction steps following the L1 intermediate in the catalytic cycle of halorhodopsin.

Metabolism of chloride in halophilic prokaryotes

While much understanding has been achieved on the intracellular sodium and potassium concentrations of halophilic and halotolerant microorganisms and on their regulation, we know little on the metabolism of anions. Archaea of the family Halobacteriaceae contain molar concentrations of chloride, which is pumped into the cells by cotransport with sodium ions and/or using the light-driven primary chloride pump halorhodopsin. Most halophilic and halotolerant representatives of the bacterial domain contain low intracellular ion concentrations, with organic osmotic solutes providing osmotic balance. However, some species show a specific requirement for chloride. In Halobacillus halophilus certain functions, such as growth, endospore germination, motility and flagellar synthesis, and glycine betaine transport are chloride dependent. In this organism the expression of a large number of proteins is chloride regulated. Other moderately halophilic Bacteria such as Halomonas elongata do not show a specific demand for chloride. A very high requirement for chloride was demonstrated in two groups of Bacteria that accumulate inorganic salts intracellularly rather than using organic osmotic solutes: the anaerobic Halanaerobiales and the aerobic extremely halophilic Salinibacter ruber. It is thus becoming increasingly clear that chloride has specific functions in haloadaptation in different groups of halophilic microorganisms.

Proton translocation by bacteriorhodopsin in the absence of substantial conformational changes

Unlike wild-type bacteriorhodopsin (BR), the BR triple mutant D96G/F171C/F219L has been shown to undergo only minor structural rearrangements during its photocycle. Nonetheless, the mutant is capable of transporting protons at a rate of 125(+/-40) H+/BR per minute under light-saturating conditions. Light adaptation of the triple mutant's retinal proceeds in a pH-dependent manner up to a maximum of 63% all-trans. These two findings imply that the transport activity of the triple mutant comprises 66% of the wild-type activity. Time-resolved spectroscopy reveals that the identity and sequence of intermediates in the photocycle of the triple mutant in the all-trans configuration correspond to that of wild-type BR. The only differences relate to a slower rise and decay of the M and O intermediates, and a significant spectral contribution from a 13-cis component. No indication for accumulation of the N intermediate is found under a variety of conditions that normally favor the formation of this species in wild-type BR. The Fourier transform infrared (FTIR) spectrum of the M intermediate in the triple mutant resembles that of wild type. Minor changes in the amide I region during the photocycle suggest that only small movements of the protein backbone occur. Electron microscopy reveals large differences in conformation between the unilluminated state of the mutant protein and wild-type but no light-induced changes in time-resolved measurements. Evidently, proton transport by the triple mutant does not require the major conformational rearrangements that occur on the same time-scale with wild-type. Thus, we conclude that large conformational changes observed in the photocycle of the wild-type and many BR mutants are not a prerequisite for the change in accessibility of the Schiff base nitrogen atom that must occur during vectorial catalysis to allow proton transport.

Temperature and halide dependence of the photocycle of halorhodopsin from Natronobacterium pharaonis

The photocycle kinetics of halorhodopsin from Natronobacterium pharaonis (pHR(575)) was analyzed at different temperatures and chloride concentrations as well as various halides. Over the whole range of modified parameters the kinetics can be adequately modeled with six apparent rate constants. Assuming a model in which the observed rates are assigned to irreversible transitions of a single relaxation chain, six kinetically distinguishable states (P(1-6)) are discernible that are formed from four chromophore states (spectral archetypes S(j): K(570), L(N)(520), O(600), pHR'(575)). Whereas P(1) coincides with K(570) (S(1)), both P(2) and P(3) have identical spectra resembling L(520) (S(2)), thus representing a true spectral silent transition between them. P(4) constitutes a fast temperature-dependent equilibrium between the chromophore states S(2) and S(3) (L(520) and O(600), respectively). The subsequent equilibrium (P(5)) of the same spectral archetypes is only moderately temperature dependent but shows sensitivity toward the type of anion and the chloride concentration. Therefore, S(2) and S(3) occurring in P(4) as well as in P(5) have to be distinguished and are assigned to L(520)<--> O(1)(600) and O(2)(600)<--> N(520) equilibrium, respectively. It is proposed that P(4) and P(5) represent the anion release and uptake steps. Based on the experimental data affinities of the halide binding sites are estimated.

Roles of cytoplasmic arginine and threonine in chloride transport by the bacteriorhodopsin mutant D85T

In the light-driven anion pump halorhodopsin (HR), the residues arginine 200 and threonine 203 are involved in anion release at the cytoplasmic side of the membrane. Because of large sequence homology and great structural similarities between HR and bacteriorhodopsin (BR), it has been suggested that anion translocation by HR and by the chloride-pumping BR mutant BR-D85T occurs by the same mechanism. Consequently, the functions of the R200/T203 pair in HR should be the same as those of the corresponding pair in BR-D85T (R175/T178). We have put this hypothesis to a test by creating two mutants of BR-D85T in which R175 and T178 were replaced by glutamine and valine, respectively. Chloride transport activities were essentially the same for all three mutants, whereas chloride binding and the kinetics of parts of the photocycle were markedly affected by the replacement of T178. In contrast, the consequences of mutating R175 proved to be less significant. These findings are consistent with evidence obtained on HR and therefore support the idea that the respective mechanistic roles of the cytoplasmic arginine/threonine pairs in HR and BR-D85T are equal.

Nano- and microsecond time-resolved FTIR spectroscopy of the halorhodopsin photocycle

Step-scan Fourier transform infrared spectroscopy with 50 ns time resolution was applied to the early stages of the photocycle of halorhodopsin (hR) for the temperature range 3-42 degrees C. Kinetic data analysis with global fitting revealed two distinct kinetic processes associated with relaxations of the early red-shifted photoproduct hK; these processes have time constants tau 1 approximately equal to 280 ns and tau 2 approximately equal to 360 microns at 20 degrees C. Spectral features demonstrate that the tau 1 process corresponds to a transition between two distinct bathointermediates, hKE and hKL. The vibrational difference bands associated with both tau 1 and tau 2 transitions are spread throughout the whole 1800-900 cm-1 range. However, the largest bands correspond to ethylenic C=C stretches, fingerprint C-C stretches and hydrogen out-of-plane (HOOP) wags of the retinal chromophore. The time evolution of these difference bands indicate that both the tau 1 and tau 2 decay processes involve principally a relaxation of the chromophore and its immediate environment. The decay of the intense HOOP vibrations is nearly equally divided between the tau 1 and tau 2 processes, indicating a complex chromophore relaxation from a twisted nonrelaxed conformation in the primary (hKE) bathointermediate, to a less-twisted structure in hKL, and finally to a roughly planar structure in the hypsochromically shifted hL intermediate. This conclusion is also supported by the unexpectedly large positive entropy of activation observed for the tau 1 process. The two relaxations from hKE to hL are largely analogous to corresponding relaxations (KE-->KL-->L) in the bacteriorhodopsin photocycle, except that the second step is slowed down by over 200-fold in hR.

Evaluation of intrinsic chemical kinetics and transient product spectra from time-resolved spectroscopic data

This communication is devoted to the evaluation of true spectra and intrinsic (microscopic) rate constants from apparent kinetics measured in time-resolved spectroscopic experiments monitoring complex relaxation dynamics of multi-intermediate systems. Retinal proteins, cytochrom c oxidase, phytochrome, hemoglobin, and photoactive yellow protein are examples of natural systems in which several transient states (intermediates) overlap so strongly, both in time and spectral domains, that their isolation and full characterization by classical biochemical methods is impossible, and mathematical evaluation of their true spectra and microscopic kinetic constants is required. Most of the popular methods for analysis of kinetic data, global fitting (GF), singular value decomposition (SVD), principal component analysis (PCA) and factor analysis (FA), are applicable to two-dimensional (2D, in time and spectral domains) arrays of data. All these methods produce only a phenomenological description of data, that approximates the measured data only with apparent kinetics. A fundamental limitation, namely, insufficient information in 2D data, does not allow any of these methods to reach the final goal: to recalculate from apparent to intrinsic values in any but the most trivial cases. A strategy was proposed (J.F. Nagle, Biophys. J.. 59 (1991) 476-487) to include an additional (third) information-rich dimension, temperature, into the simultaneous computer analysis. A simultaneous direct fitting of 3D data arrays to systems of differential rate equations allows recalculation of apparent kinetics into true spectra and intrinsic rate constants. In spite of its evident theoretical advantages, this strategy has not been successful on real data. Here we describe another custom-built program, SCHEMEFIT, developed for the same purpose: to fit measured kinetics directly to the system of coupled differential rate equations describing the photochrome's relaxation dynamics. Though sharing the main strategy with the previous approach, SCHEMEFIT is based on a different set of numeric algorithms, and its application requires different tactics. Its performance is illustrated on synthetic data, and compared with GF and SVD. An example of applying SCHEMEFIT to the photocycle of halorhodopsin is also reported.

Catalysis of the retinal subpicosecond photoisomerization process in acid purple bacteriorhodopsin and some bacteriorhodopsin mutants by chloride ions

The dynamics and the spectra of the excited state of the retinal in bacteriorhodopsin (bR) and its K-intermediate at pH 0 was compared with that of bR and halorhodopsin at pH 6.5. The quantum yield of photoisomerization in acid purple bR was estimated to be at least 0.5. The change of pH from 6.5 to 2 causes a shift of the absorption maximum from 568 to 600 nm (acid blue bR) and decreases the rate of photoisomerization. A further decrease in pH from 2 to 0 shifts the absorption maximum back to 575 nm when HCl is used (acid purple bR). We found that the rate of photoisomerization increases when the pH decreases from 2 to 0. The effect of chloride anions on the dynamics of the retinal photoisomerization of acid bR (pH 2 and 0) and some mutants (D85N, D212N, and R82Q) was also studied. The addition of 1 M HCl (to make acid purple bR, pH 0) or 1 M NaCl to acid blue bR (pH 2) was found to catalyze the rate of the retinal photoisomerization process. Similarly, the addition of 1 M NaCl to the solution of some bR mutants that have a reduced rate of retinal photoisomerization (D85N, D212N, and R82Q) was found to catalyze the rate of their retinal photoisomerization process up to the value observed in wild-type bR. These results are explained by proposing that the bound Cl- compensates for the loss of the negative charges of the COO- groups of Asp85 and/or Asp212 either by neutralization at low pH or by residue replacement in D85N and D212N mutants.

Shuttling between two protein conformations: the common mechanism for sensory transduction and ion transport

It has recently become known that light-dependent interconversions between two protein conformations underlie both ion transport in bacteriorhodopsin and halorhodopsin and phototaxis signaling by the sensory rhodopsins of halobacteria. In the transport proteins, the two conformations facilitate alternating access of an occluded ion-binding site to the two surfaces of the membrane, and in the sensory receptors the conformations modulate signal-transducer activity. In sensory rhodopsin I, the same conformational equilibrium is implicated in providing both sensory signaling when bound to its transducer and proton transport when free.

Influence exercised by histidine-95 on chloride transport and the photocycle in halorhodopsin

The anion pumping mechanism of halorhodopsin was studied using site-directed mutagenesis. Comparison of the amino acid sequence revealed that the B-C interhelix loop segment was highly homologous in all known halorhodopsins. Especially a basic residue, histidine-95, was conserved in all halorhodopsins. Using the expression-vector plasmid carrying the bop promoter, two His-95 mutants (H95R, H95A) were successfully expressed in Halobacterium salinarium. The expression levels of these halorhodopsin mutants were slightly lower than that for the wild-type halorhodopsin. In addition, these mutants were unstable under illumination compared with the wild-type. It suggested that His-95 is probably important for stabilizing the structure of halorhodopsin. The absorption maxima of these mutants are approximately 15 nm blue-shifted compared with the wild-type, suggesting that His-95 interacts with the retinal Schiff base. At low chloride concentrations, the light-induced chloride pumping activity of these mutants was more than 20 times lower than that for the wild-type. Only under physiological conditions, the chloride pumping activity was detected. Even at a high chloride concentration (1 M NaCl), the HR520 intermediate could not be detected for these mutants. These results clearly indicate that His-95 has a crucial role in the chloride transport of halorhodopsin.

Over-expression of a new photo-active halorhodopsin in Halobacterium salinarium

The gene of haloopsin (hop) from halobacterial strain shark was cloned and its nucleotide sequence was determined. The deduced amino acid sequence of shark halorhodopsin (HR) showed that its homology with halobium HR was 62%. The gene product seems to be HR having several positively charged residues that are conserved in all known HRs. The gene encoding shark hop as well as that encoding halobium hop were successfully expressed in Halobacterium salinarium (halobium) by using a plasmid shuttle vector containing the bacterioopsin (bop) promoter. The expression level of shark HR is almost the same as that for halobium HR with the same shuttle vector containing the bop promoter. Under the physiological conditions, the anion pumping activity of the shark HR expressed in H. salinarium was almost the same as that for halobium HR; however, the anion selectivity and half-maximal anion transport were different. Furthermore, its absorption maximum in the absence of chloride shifted to approx. 596 nm in contrast to that for halobium HR. The half-lifetimes of HR520 formation for shark HR and halobium HR were almost the same; however, the half-lifetime of its decay was approx. 6-times faster for shark HR than it was for halobium HR at a high chloride concentration (1000 mM). Even at a low chloride concentration (50 mM), HR520 and HR640 intermediates could be detected for shark HR, and the half-lifetime of HR640 decay was found to be approx. 25 ms. In the presence of nitrate, the half-lifetime of HR565 recovery for shark HR was approx. 10-times slower than that for halobium HR. Some of amino acid substitutions between shark HR and halobium HR may affect the anion selectivity and the photoreaction of HR.

Conversion of bacteriorhodopsin into a chloride ion pump

In the light-driven proton pump bacteriorhodopsin, proton transfer from the retinal Schiff base to aspartate-85 is the crucial reaction of the transport cycle. In halorhodopsin, a light-driven chloride ion pump, the equivalent of residue 85 is threonine. When aspartate-85 was replaced with threonine, the mutated bacteriorhodopsin became a chloride ion pump when expressed in Halobacterium salinarium and, like halorhodopsin, actively transported chloride ions in the direction opposite from the proton pump. Chloride was bound to it, as revealed by large shifts of the absorption maximum of the chromophore, and its photointermediates included a red-shifted state in the millisecond time domain, with its amplitude and decay rate dependent on chloride concentration. Bacteriorhodopsin and halorhodopsin thus share a common transport mechanism, and the interaction of residue 85 with the retinal Schiff base determines the ionic specificity.

Photocycle of halorhodopsin from Halobacterium salinarium

The light-driven chloride pump, halorhodopsin, is a mixture containing all-trans and 13-cis retinal chromophores under both light and dark-adapted conditions and can exist in chloride-free and chloride-binding forms. To describe the photochemical cycle of the all-trans, chloride-binding state that is associated with the transport, and thereby initiate study of the chloride translocation mechanism, one must first dissect the contributions of these species to the measured spectral changes. We resolved the multiple photochemical reactions by determining flash-induced difference spectra and photocycle kinetics in halorhodopsin-containing membranes prepared from Halobacterium salinarium, with light- and dark-adapted samples at various chloride concentrations. The high expression of cloned halorhodopsin made it possible to do these measurements with unfractionated cell envelope membranes in which the chromophore is photostable not only in the presence of NaCl but also in the Na2SO4 solution used for reference. Careful examination of the flash-induced changes at selected wavelengths allowed separating the spectral changes into components and assigning them to the individual photocycles. According to the results, a substantial revision of the photocycle model for H. salinarium halorhodopsin, and its dependence on chloride, is required. The cycle of the all-trans chloride-binding form is described by the scheme, HR-hv-->K<==>L1<==>L2<==>N-->HR, where HR, K, L, and N designate halorhodopsin and its photointermediates. Unlike the earlier models, this is very similar to the photoreaction of bacteriorhodopsin when deprotonation of the Schiff base is prevented (e.g., at low pH or in the D85N mutant). Also unlike in the earlier models, no step in this photocycle was noticeably affected when the chloride concentration was varied between 20 mM and 2 M in an attempt to identify a chloride-binding reaction.

Charge transport of ion pumps on lipid bilayer membranes

Ion pumps create ion gradients across cell membranes while consuming light energy or chemical energy. The ion gradients are used by the corresponding cell types for passive-ion transport via ion channels or carriers or for accumulation of nutrients like sugar or amino acids via cotransport systems or antiporters.

Light-driven proton or chloride pumping by halorhodopsin

Halorhodopsin from Halobacterium halobium was purified and reconstituted with lipids from purple membranes. The resulting protein-containing membrane sheets were adsorbed to a planar lipid membrane and photoelectric properties were analyzed. Depending on light conditions, halorhodopsin acted either as a light-driven chloride pump or as a proton pump: green light caused chloride transport and additional blue light induced proton pumping. In the living cell, both to these vectorial processes would be directed toward the cytoplasm and, compared to ion transport by bacteriorhodopsin, this is an inversed proton flow. Azide, a catalyst for reversible deprotonation of halorhodopsin, enhanced proton transport, and the deprotonated Schiff base in the 13-cis configuration (H410) was identified as the key intermediate of this alternative catalytic cycle in halorhodopsin. While chloride transport in halorhodopsin is mediated by a one-photon process, proton transport requires the absorption of two photons: one photon for formation of H410 and release of a proton, and one photon for photoisomerization of H410 and re-formation of H578 with concomitant uptake of a proton by the Schiff base.

The two consecutive M substates in the photocycle of bacteriorhodopsin are affected specifically by the D85N and D96N residue replacements

The photocycle of the proton pump bacteriorhodopsin contains two consecutive intermediates in which the retinal Schiff base is unprotonated; the reaction between these states, termed M1 and M2, was suggested to be the switch in the proton transport which reorients the Schiff base from D85 on the extracellular side to D96 on the cytoplasmic side (Váró and Lanyi, Biochemistry 30, 5016-5022, 1991). At pH 10 the absorption maxima of both M1 and M2 could be determined in the recombinant D96N protein. We find that M1 absorbs at 411 nm as do M1 and M2 in wild-type bacteriorhodopsin, but M2 absorbs at 404 nm. Thus, in M2 but not M1 the unprotonated Schiff base is affected by the D96N residue replacement. The connectivity of the Schiff base to D96 in the detected M2 state, but not in M1, is thereby established. On the other hand, the photostationary state which develops during illumination of D85N bacteriorhodopsin contains an M state corresponding to M1 with an absorption maximum shifted to 400 nm, suggesting that this species in turn is affected by D85. These results are consistent with the suggestion that M1 and M2 are pre-switch and post-switch states, respectively.

Anion binding to the chloride pump, halorhodopsin, and its implications for the transport mechanism

The light-driven chloride pump, halorhodopsin, binds and transports chloride across the membrane, and to a lesser extent nitrate. Binding and transport kinetics, and resonance Raman spectra of the retinal Schiff base, with these anions suggest the existence of two mutually exclusive binding sites. One of these may be the uptake site, and the other the release site during the transport. Plausible locations can be suggested for these sites, because halorhodopsin is a small protein with few buried positively charged residues, and the primary structure of a second pigment with similar function has recently become available for comparison.

Activation parameters for the halorhodopsin photocycle: a phase lifetime spectroscopic study of the 520- and 640-nanometer intermediates

Phase lifetime spectroscopy is used to investigate the kinetics of the 520- and 640-nm intermediates in the halorhodopsin photocycle. These intermediates decay on the millisecond time scale and are strongly implicated in the chloride transport steps. The temperature dependence of the 520 and 640 relaxations was measured for chloride and nitrate buffers at pH 6, 7, and 8 and for iodide buffer at pH 6. The 640 relaxations have small activation energies but large entropy barriers. The two relaxation times observed for the 640 intermediate were interpreted by using a mechanism in which two 640 species exist in equilibrium. The second 640 species is not along the main decay path for the photocycle. A quantitative analysis of the data allowed rate constants and activation parameters to be calculated for the elementary steps of this isomerization process. These parameters are similar for both chloride and nitrate buffers but differ somewhat in iodide. The derived calculated rate constants were consistent with the relaxation times observed for the 520 intermediate. These results indicate that the 520 and two 640 intermediates have very similar free energies as well as similar free energies of activation for the various interconversion processes.

Low-temperature photoreactions of halorhodopsin. 1. Detection of conformational substates of the chromoprotein

Absorption spectra of halorhodopsin (HR), a retinal protein in the halobacterial membrane, and its photostationary states were determined at 80 K. The absorption lines appear to narrow upon cooling, thereby revealing complex spectral fine structure of the main absorption band in the visible region, characteristic of conformational substates of HR. Illumination causes (1) the redistribution of these substrates and consequent changing of the fine structure ("hole-burning") and (2) the appearance of a hypsoproduct of undefined nature, in addition to the previously described bathoproduct HR600. Bacteriorhodopsin, a related retinal pigment, gives rise only to the bathointermediate (i.e., K590) under these conditions. After warming of illuminated HR to 110 K, and recooling to 80 K, relaxation of the illumination-induced change in spectral fine structure, and decay of the hypsoproduct but not the bathoproduct, was observed. The results are explained with a model in which one ensemble of HR conformational substates at 80 K is converted to another in a photoequilibrium via the excited state, which also produces the batho- and hypsoproducts. The original ensemble can be regained through thermal pathways at a somewhat higher temperature, and only the bathoproduct will decay thermally into the next intermediate of the HR photocycle.

Two pumps, one principle: light-driven ion transport in halobacteria

Comparison of the primary structure of the chloride pump halorhodopsin with that of the proton pump bacteriorhodopsin provides insight into light-driven ion transport by retinal proteins. Several conserved amino acid residues in the membrane-spanning region of both proteins and their interaction with different isomerization states of retinal are suggested to be the key element for ion transport in both proteins.