ESR - a retinal protein with unusual properties from Exiguobacterium sibiricum.

This review covers the properties of a retinal protein (ESR) from the psychrotrophic bacterium Exiguobacterium sibiricum that functions as a light-driven proton pump. The presence of a lysine residue at the position corresponding to intramolecular proton donor for the Schiff base represents a unique structural feature of ESR. We have shown that Lys96 successfully facilitates delivery of protons from the cytoplasmic surface to the Schiff base, thus acting as a proton donor in ESR. Since proton uptake during the photocycle precedes Schiff base reprotonation, we conclude that this residue is initially in the uncharged state and acquires a proton for a short time after Schiff base deprotonation and M intermediate formation. Involvement of Lys as a proton donor distinguishes ESR from the related retinal proteins - bacteriorhodopsin (BR), proteorhodopsin (PR), and xanthorhodopsin (XR), in which the donor function is performed by residues with a carboxyl side chain. Like other eubacterial proton pumps (PR and XR), ESR contains a histidine residue interacting with the proton acceptor Asp85. In contrast to PR, this interaction leads to shift of the acceptor's pKa to more acidic pH, thus providing its ability to function over a wide pH range. The presence of a strong H-bond between Asp85 and His57, the structure of the proton-conducting pathways from cytoplasmic surface to the Schiff base and to extracellular surface, and other properties of ESR were demonstrated by solving its three-dimensional structure, which revealed several differences from known structures of BR and XR. The structure of ESR, its photocycle, and proton transfer reactions are discussed in comparison with homologous retinal proteins.

Aspartate-histidine interaction in the retinal schiff base counterion of the light-driven proton pump of Exiguobacterium sibiricum.

One of the distinctive features of eubacterial retinal-based proton pumps, proteorhodopsins, xanthorhodopsin, and others, is hydrogen bonding of the key aspartate residue, the counterion to the retinal Schiff base, to a histidine. We describe properties of the recently found eubacterium proton pump from Exiguobacterium sibiricum (named ESR) expressed in Escherichia coli, especially features that depend on Asp-His interaction, the protonation state of the key aspartate, Asp85, and its ability to accept a proton from the Schiff base during the photocycle. Proton pumping by liposomes and E. coli cells containing ESR occurs in a broad pH range above pH 4.5. Large light-induced pH changes indicate that ESR is a potent proton pump. Replacement of His57 with methionine or asparagine strongly affects the pH-dependent properties of ESR. In the H57M mutant, a dramatic decrease in the quantum yield of chromophore fluorescence emission and a 45 nm blue shift of the absorption maximum with an increase in the pH from 5 to 8 indicate deprotonation of the counterion with a pK(a) of 6.3, which is also the pK(a) at which the M intermediate is observed in the photocycle of the protein solubilized in detergent [dodecyl maltoside (DDM)]. This is in contrast with the case for the wild-type protein, for which the same experiments show that the major fraction of Asp85 is deprotonated at pH >3 and that it protonates only at low pH, with a pK(a) of 2.3. The M intermediate in the wild-type photocycle accumulates only at high pH, with an apparent pK(a) of 9, via deprotonation of a residue interacting with Asp85, presumably His57. In liposomes reconstituted with ESR, the pK(a) values for M formation and spectral shifts are 2-3 pH units lower than in DDM. The distinctively different pH dependencies of the protonation of Asp85 and the accumulation of the M intermediate in the wild-type protein versus the H57M mutant indicate that there is strong Asp-His interaction, which substantially lowers the pK(a) of Asp85 by stabilizing its deprotonated state.

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.

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.

Infrared methods for monitoring the protonation state of carboxylic amino acids in the photocycle of bacteriorhodopsin.

This review deals with the role of carboxylic amino acids in the proton-transport activity of bacteriorhodopsin. The main focus is on the infrared data, which allow direct monitoring of the protonation/deprotonation of specific residues during the proton movement in the course of the photocycle. Additional attention is paid to the potential use of carboxylic acids in proteins as internal sensors, based on the sensitivity of their IR frequencies to the immediate environment.

Low temperature restriction of charge shift in the primary reaction of the bacteriorhodopsin photocycle.

Fast electrical signals associated with the primary photoreaction of the bacteriorhodopsin photocycle were studied on dried oriented samples in the temperature range from 77 to 300 K. The rise of the electrical signal, associated with bathointermediate formation, was faster than 5 ns even at 77 K; no slow rising component was detected at any temperature in the nano- to microsecond time range. The amplitude of the signal associated with bathointermediate formation was not affected by cooling from 300 to 210 K, but decreased by a factor of two when the sample was further cooled from 210 to 190 K. At 77 K the amplitude from the first excitation flash is 25-30 per cent of that at 260 K. Our data suggest that low temperature restricts the size of the charge shift during the bathointermediate formation, resulting in creation of a "low temperature bathointermediate" distinct from the "room temperature bathointermediate".

A large photolysis-induced pKa increase of the chromophore counterion in bacteriorhodopsin: implications for ion transport mechanisms of retinal proteins.

The proton-pumping mechanism of bacteriorhodopsin is dependent on a photolysis-induced transfer of a proton from the retinylidene Schiff base chromophore to the aspartate-85 counterion. Up until now, this transfer was ascribed to a > 7-unit decrease in the pKa of the protonated Schiff base caused by photoisomerization of the retinal. However, a comparably large increase in the pKa of the Asp-85 acceptor also plays a role, as we show here with infrared measurements. Furthermore, the shifted vibrational frequency of the Asp-85 COOH group indicates a transient drop in the effective dielectric constant around Asp-85 to approximately 2 in the M photointermediate. This dielectric decrease would cause a > 40 kJ-mol-1 increase in free energy of the anionic form of Asp-85, fully explaining the observed pK alpha increase. An analogous photolysis-induced destabilization of the Schiff base counterion could initiate anion transport in the related protein, halorhodopsin, in which aspartate-85 is replaced by Cl- and the Schiff base proton is consequently never transferred.

Kinetics of the fast electric signal from oriented purple membrane.

The photoinduced electric response of oriented purple membranes associated with processes before the K-intermediate decay of bacteriorhodopsin was measured in the 180-300 K temperature range. These response signals consist of two kinetically distinct components (both temperature dependent). The experimental data show a correlation between the time constants of the rise of the signal and solution resistance. A model is proposed to assign these components to two diffusion-limited processes of charge displacement in the solution. The displacement is caused by the electric field of the photoinduced transient dipole which is formed in the primary act of the bacteriorhodopsin photocycle. The two processes are assigned as: (a) the conduction of electrical current through H-bonds (time resolved only in the temperature range 180-200 K) and (b) the diffusion of charges through the interfacial layer.

Fourier transform infrared spectra of a late intermediate of the bacteriorhodopsin photocycle suggest transient protonation of Asp-212.

We measured time-resolved difference spectra, in the visible and the infrared, for the Glu-194 and Glu-204 mutants of bacteriorhodopsin and detected an anomalous O state, labeled O', in addition to the authentic O intermediate, before recovery of the initial state in the photocycle. The O' intermediate exhibits prominent bands at 1712 cm(-1) (positive) and 1387 cm(-1) (negative). These bands arise with the same time constant as the deprotonation of Asp-85. Both bands are shifted to lower frequency upon labeling of the protein with [4-(13)C]aspartic acid. The former band, but not the latter, is shifted in D2O. These shifts identify the two bands as the carboxyl stretch of a protonated aspartic acid and the symmetric carbonyl stretch of an unprotonated aspartate, respectively, and suggest that in O' an initially anionic aspartate enters into protonation equilibrium with Asp-85. Elimination of the few other candidates, on various grounds, identifies Asp-212 as the unknown residue. It is possible, therefore, that in the last step of the photocycle of the mutants studied the proton released from Asp-85 is conducted to the extracellular surface via Asp-212. An earlier report of a weak band at 1712 cm(-1) late in the wild-type photocycle [Zscherp and Heberle (1997) J. Phys. Chem. B 101, 10542-10547] suggests that Asp-212 might play this role in the wild-type protein also.

Connectivity of the retinal Schiff base to Asp85 and Asp96 during the bacteriorhodopsin photocycle: the local-access model.

In the recently proposed local-access model for proton transfers in the bacteriorhodopsin transport cycle (Brown et al. 1998. Biochemistry. 37:3982-3993), connection between the retinal Schiff base and Asp85 (in the extracellular direction) and Asp96 (in the cytoplasmic direction)is maintained as long as the retinal is in its photoisomerized state. The directionality of the proton translocation is determined by influences in the protein that make Asp85 a proton acceptor and, subsequently, Asp96 a proton donor. The idea of concurrent local access of the Schiff base in the two directions is now put to a test in the photocycle of the D115N/D96N mutant. The kinetics had suggested that there is a single sequence of intermediates, L<-->M1<-->M2<-->N, and the M2-->M1 reaction depends on whether a proton is released to the extracellular surface. This is now confirmed. We find that at pH 5, where proton release does not occur, but not at higher pH, the photostationary state created by illumination with yellow light contains not only the M1 and M2 states, but also the L and the N intermediates. Because the L and M1 states decay rapidly, they can be present only if they are in equilibrium with later intermediates of the photocycle. Perturbation of this mixture with a blue flash caused depletion of the M intermediate, followed by its partial recovery at the expense of the L state. The change in the amplitude of the C=O stretch band at 1759 cm-1 demonstrated protonation of Asp85 in this process. Thus, during the reequilibration the Schiff base lost its proton to Asp85. Because the N state, also present in the mixture, arises by protonation of the Schiff base from the cytoplasmic surface, these results fulfill the expectation that under the conditions tested the extracellular access of the Schiff base would not be lost at the time when there is access in the cytoplasmic direction. Instead, the connectivity of the Schiff base flickers rapidly (with the time constant of the M1<-->M2 equilibration) between the two directions during the entire L-to-N segment of the photocycle.

Local-access model for proton transfer in bacteriorhodopsin.

The accessibility of the retinal Schiff base in bacteriorhodopsin was studied in the D85N/D96N mutant where the proton acceptor and donor are absent. Protonation and deprotonation of the Schiff base after pH jump without illumination and in the photocycle of the unprotonated Schiff base were measured in the visible and the infrared. Whether access is extracellular (EC) or cytoplasmic (CP) was decided from the effect of millimolar concentrations of azide on the rates of proton transfers. The results, together with earlier work on the wild-type protein, suggest a new hypothesis for the proton-transfer switch: (i) In the metastable 13-cis, 15-anti and all-trans, 15-syn photoproducts, but not in the stable isomeric states, access flickers between the EC and CP directions. (ii) The direction of proton transfer is decided both by this local access and by the presence of a suitable donor or acceptor group (in the wild type), or the proton conductivity in the EC and CP half-channels (in D85N/D96N). (iii) Thermal reisomerization of the retinal can occur only when the Schiff base is protonated, as is well-known. In the wild-type transport cycle, the concurrent local EC and CP access during the lifetime of the metastable 13-cis, 15-anti state enables the changing pKa's of the proton acceptor and donor to determine the direction of proton transfer. Proton transfer from the Schiff base to Asp-85 in the EC direction is followed by reprotonation by Asp-96 from the CP direction because proton release to the EC surface raises the pKa of Asp-85 and a large-scale protein conformation change lowers the pKa of Asp-96. The unexpected finding we report here for D85N/D96N, that when the retinal is in the stable all-trans, 15-anti and 13-cis, 15-syn isomeric forms access of the Schiff base is locked (in the EC and CP directions, respectively), suggests that in this protein reisomerization, rather than changes in the proton conductivities of the EC and CP half-channels, provides the switch function. With this mechanism, the various modes of transport reported for Asp-85 mutants (CP to EC direction with blue light, and EC to CP direction with blue plus green light) are understood also in terms of rules i-iii.

Partitioning of free energy gain between the photoisomerized retinal and the protein in bacteriorhodopsin.

Photoisomerization of the all-trans-retinal of bacteriorhodopsin to 13-cis,15-anti initiates a sequence of thermal reactions in which relaxation of the polyene chain back to all-trans is coupled to various changes in the protein and the translocation of a proton across the membrane. We investigated the nature of this high-energy state in a genetically modified bacteriorhodopsin. When the electric charges of residues 85 and 96, the two aspartic acids critical for proton transport, are both changed to what they become after photoexcitation of the wild-type protein, i.e., neutral and anionic, respectively, the retinal assumes a thermally stable 13-cis,15-anti configuration. Thus, we have reversed cause and effect in the photocycle. It follows that when the 13-cis,15-anti isomeric state is produced by illumination, in the wild type it is unstable initially only because of conflicts with the retinal binding pocket. Later in the photocycle, the free energy gain is transferred from the chromophore to the protein. Before recovery of the initial state, it will come to be represented entirely by the free energy of the changed protonation states of aspartic acids 85 and 96.

Coupling of the reisomerization of the retinal, proton uptake, and reprotonation of Asp-96 in the N photointermediate of bacteriorhodopsin.

In the N to O reaction of the bacteriorhodopsin photocycle, Asp-96 is protonated from the cytoplasmic surface, and coupled to this, the retinal isomerizes from 13-cis,15-anti back to the initial all-trans configuration. To dissect the two steps, and to better understand how and why they occur, we describe the properties of two groups of site-specific mutants in which the N intermediate has greatly increased lifetime. In the first group, with the mutations near the retinal, an unusual N state is produced in which the retinal is 13-cis,15-anti but Asp-96 has a protonated carboxyl group. The apparent pK(a) for the protonation is 7.5, as in the wild-type. It is likely that here the interference with N decay is the result of steric conflict of side-chains with the retinal or with the side-chain of Lys-216 connected to the retinal, which delays the reisomerization after protonation of Asp-96. In the second group, with the mutations located near Asp-96 or between Asp-96 and the cytoplasmic surface, reprotonation of Asp-96 is strongly perturbed. The reisomerization of the retinal occurs only after recovery from a long-living protein conformation in which reprotonation of Asp-96 is either entirely blocked or blocked at low pH.

Photochemical reaction cycle and proton transfers in Neurospora rhodopsin.

It was recently found that NOP-1, a membrane protein of Neurospora crassa, shows homology to haloarchaeal rhodopsins and binds retinal after heterologous expression in Pichia pastoris. We report on spectroscopic properties of the Neurospora rhodopsin (NR). The photocycle was studied with flash photolysis and time-resolved Fourier-transform infrared spectroscopy in the pH range 5-8. Proton release and uptake during the photocycle were monitored with the pH-sensitive dye, pyranine. Kinetic and spectral analysis revealed six distinct states in the NR photocycle, and we describe their spectral properties and pH-dependent kinetics in the visible and infrared ranges. The phenotypes of the mutant NR proteins, D131E and E142Q, in which the homologues of the key carboxylic acids of the light-driven proton pump bacteriorhodopsin, Asp-85 and Asp-96, were replaced, show that Glu-142 is not involved in reprotonation of the Schiff base but Asp-131 may be. This implies that, if the NR photocycle is associated with proton transport, it has a low efficiency, similar to that of haloarchaeal sensory rhodopsin II. Fourier-transform Raman spectroscopy revealed unexpected differences between NR and bacteriorhodopsin in the configuration of the retinal chromophore, which may contribute to the less effective reprotonation switch of NR.

Existence of a proton transfer chain in bacteriorhodopsin: participation of Glu-194 in the release of protons to the extracellular surface.

Glu-194 near the extracellular surface of bacteriorhodopsin is indispensable for proton release to the medium upon protonation of Asp-85 during light-driven transport. As for Glu-204, its replacement with glutamine (but not aspartate) abolishes both proton release and the anomalous titration of Asp-85 that originates from coupling between the pKa of this buried aspartate and those of the other acidic groups. Unlike the case of Glu-204, however, replacement of Glu-194 with aspartate raises the pKa for proton release. In Fourier transform infrared spectra of the E194D mutant a prominent positive band is observed at 1720 cm-1. It can be assigned from [4-13C]aspartate and D2O isotope shifts to the C&dbd;O stretch of protonated Asp-194. Its rise correlates with proton transfer from the retinal Schiff base to Asp-85. Its decay coincides with the appearance of a proton at the surface, detected under similar conditions with fluorescein covalently bound to Lys-129 and with pyranine. Its amplitude decreases with increasing pH, with a pKa of about 9. We show that this pKa is likely to be that of the internal proton donor to Asp-194, the Glu-204 site, before photoexcitation, while 13C NMR titration indicates that Asp-194 has an initial pKa of about 3. We propose that there is a chain of interacting residues between the retinal Schiff base and the extracellular surface. After photoisomerization of the retinal the pKa's change so as to allow (i) Asp-85 to become protonated by the Schiff base, (ii) the Glu-204 site to transfer its proton to Asp-194 in E194D, and therefore to Glu-194 in the wild type, and (iii) residue 194 to release the proton to the medium.