Protein structural change at the cytoplasmic surface as the cause of cooperativity in the bacteriorhodopsin photocycle

Nanosecond Transient IR Spectroscopy of Halorhodopsin in Living Cells

The ability to track minute changes of a single amino acid residue in a cellular environment is causing a paradigm shift in the attempt to fully understand the responses of biomolecules that are highly sensitive to their environment. Detecting early protein dynamics in living cells is crucial to understanding their mechanisms, such as those of photosynthetic proteins. Here, we elucidate the light response of the microbial chloride pump NmHR from the marine bacterium Nonlabens marinus, located in the membrane of living Escherichia coli cells, using nanosecond time-resolved UV/vis and IR absorption spectroscopy over the time range from nanoseconds to seconds. Transient structural changes of the retinal cofactor and the surrounding apoprotein are recorded using light-induced time-resolved UV/vis and IR difference spectroscopy. Of particular note, we have resolved the kinetics of the transient deprotonation of a single cysteine residue during the photocycle of NmHR out of the manifold of molecular vibrations of the cells. These findings are of high general relevance, given the successful development of optogenetic tools from photoreceptors to interfere with enzymatic and neuronal pathways in living organisms using light pulses as a noninvasive trigger.

A conserved Trp residue in HwBR contributes to its unique tolerance toward acidic environments

Bacteriorhodopsin (BR) is a light-driven outward proton pump found mainly in halophilic archaea. A BR from an archaeon Haloquadratum walsbyi (HwBR) was found to pump protons under more acidic conditions compared with most known BR proteins. The atomic structural study on HwBR unveiled that a pair of hydrogen bonds between the BC and FG loop in its periplasmic region may be a factor in such improved pumping capability. Here, we further investigated the retinal-binding pocket of HwBR and found that Trp94 contributes to the higher acid tolerance. Through single mutations in a BR from Halobacterium salinarum and HwBR, we examined the conserved tryptophan residues in the retinal-binding pocket. Among these residues of HwBR, mutagenesis at Trp94 facing the periplasmic region caused the most significant disruption to optical stability and proton-pumping capability under acidic conditions. The other tryptophan residues of HwBR exerted little impact on both maximum absorption wavelength and pH-dependent proton pumping. Our findings suggest that the residues from Trp94 to the hydrogen bonds at the BC loop confer both optical stability and functionality on the overall protein in low-pH environments.

Mechanisms of long-distance allosteric couplings in proton-binding membrane transporters

Membrane transporters that use proton binding and proton transfer for function couple local protonation change with changes in protein conformation and water dynamics. Changes of protein conformation might be required to allow transient formation of hydrogen-bond networks that bridge proton donor and acceptor pairs separated by long distances. Inter-helical hydrogen-bond networks adjust rapidly to protonation change, and ensure rapid response of the protein structure and dynamics. Membrane transporters with known three-dimensional structures and proton-binding groups inform on general principles of protonation-coupled protein conformational dynamics. Inter-helical hydrogen bond motifs between proton-binding carboxylate groups and a polar sidechain are observed in unrelated membrane transporters, suggesting common principles of coupling protonation change with protein conformational dynamics.

Membrane Independence of Ultrafast Photochemistry in Pharaonis Halorhodopsin: Testing the Role of Bacterioruberin

Ultrafast photochemistry of pharaonis halorhodopsin (p-HR) in the intact membrane of Natronomonas pharaonis has been studied by photoselective femtosecond pump-hyperspectral probe spectroscopy with high time resolution. Two variants of this sample were studied, one with wild-type retinal prosthetic groups and another after shifting the retinal absorption deep into the blue range by reducing the Schiff base linkage, and the results were compared to a previous study on detergent-solubilized p-HR. This comparison shows that retinal photoisomerization dynamics is identical in the membrane and in the solubilized sample. Selective photoexcitation of bacterioruberin, which is associated with the protein in the native membrane, in wild-type and reduced samples, demonstrates conclusively that unlike the carotenoids associated with some bacterial retinal proteins the carrotenoid in p-HR does not act as a light-harvesting antenna.

Tuning the Photocycle Kinetics of Bacteriorhodopsin in Lipid Nanodiscs

Monodisperse lipid nanodiscs are particularly suitable for characterizing membrane protein in near-native environment. To study the lipid-composition dependence of photocycle kinetics of bacteriorhodopsin (bR), transient absorption spectroscopy was utilized to monitor the evolution of the photocycle intermediates of bR reconstituted in nanodiscs composed of different ratios of the zwitterionic lipid (DMPC, dimyristoyl phosphatidylcholine; DOPC, dioleoyl phosphatidylcholine) to the negatively charged lipid (DOPG, dioleoyl phosphatidylglycerol; DMPG, dimyristoyl phosphatidylglycerol). The characterization of ion-exchange chromatography showed that the negative surface charge of nanodiscs increased as the content of DOPG or DMPG was increased. The steady-state absorption contours of the light-adapted monomeric bR in nanodiscs composed of different lipid ratios exhibited highly similar absorption features of the retinal moiety at 560 nm, referring to the conservation of the tertiary structure of bR in nanodiscs of different lipid compositions. In addition, transient absorption contours showed that the photocycle kinetics of bR was significantly retarded and the transient populations of intermediates N and O were decreased as the content of DMPG or DOPG was reduced. This observation could be attributed to the negatively charged lipid heads of DMPG and DOPG, exhibiting similar proton relay capability as the native phosphatidylglycerol (PG) analog lipids in the purple membrane. In this work, we not only demonstrated the usefulness of nanodiscs as a membrane-mimicking system, but also showed that the surrounding lipids play a crucial role in altering the biological functions, e.g., the ion translocation kinetics of the transmembrane proteins.

Modeling of photocurrent kinetics upon pulsed photoexcitation of photosynthetic proteins: a case of bacteriorhodopsin

The proton pump of bacteriorhodopsin in an aqueous solution at varied pH upon pulsed excitation was monitored using a solution-based electrochemical module. The photocurrent action spectrum agreed with the absorption contour at 495-645 nm. Diminishing the photocurrent amplitude by adding a protonophore, carbonyl cyanide m-chlorophenyl hydrazone, revealed that protons were the charge carriers of the photocurrent. The evolution of the conventional proton pump is proposed to occur in three elementary steps consecutively: first, the proton relay from the protonated Schiff base to the purple membrane (PM) surface (k1), then the proton exchange between PM surface and bulk (k2), and finally, the proton uptake (k3). The fitted temporal profiles of the photocurrent agreed with observations in the pH range 5.8-9.5. At pH 7.3, k1, k2, and k3 were 2098 s(-1), 412 s(-1), and 44 s(-1), respectively. The rate coefficients at pH 9.5 were smaller than those at pH 6.3 by a factor of approximately 2, consistent with the differences in the intrinsic mobilities of the charge carriers proton and hydroxide ion. The combination of the electrochemical detection module and the concomitant model provides a promising tool for quantitative and qualitative characterization of the light-driven ion pumps.

The EF loop in green proteorhodopsin affects conformation and photocycle dynamics

The proteorhodopsin family consists of retinal proteins of marine bacterial origin with optical properties adjusted to their local environments. For green proteorhodopsin, a highly specific mutation in the EF loop, A178R, has been found to cause a surprisingly large redshift of 20 nm despite its distance from the chromophore. Here, we analyze structural and functional consequences of this EF loop mutation by time-resolved optical spectroscopy and solid-state NMR. We found that the primary photoreaction and the formation of the K-like photo intermediate is almost pH-independent and slower compared to the wild-type, whereas the decay of the K-intermediate is accelerated, suggesting structural changes within the counterion complex upon mutation. The photocycle is significantly elongated mainly due to an enlarged lifetime of late photo intermediates. Multidimensional MAS-NMR reveals mutation-induced chemical shift changes propagating from the EF loop to the chromophore binding pocket, whereas dynamic nuclear polarization-enhanced (13)C-double quantum MAS-NMR has been used to probe directly the retinylidene conformation. Our data show a modified interaction network between chromophore, Schiff base, and counterion complex explaining the altered optical and kinetic properties. In particular, the mutation-induced distorted structure in the EF loop weakens interactions, which help reorienting helix F during the reprotonation step explaining the slower photocycle. These data lead to the conclusion that the EF loop plays an important role in proton uptake from the cytoplasm but our data also reveal a clear interaction pathway between the EF loop and retinal binding pocket, which might be an evolutionary conserved communication pathway in retinal proteins.

Role of trimer-trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy

Bacteriorhodopsin (bR) trimers form a two-dimensional hexagonal lattice in the purple membrane of Halobacterium salinarum. However, the physiological significance of forming the lattice has long been elusive. Here, we study this issue by comparing properties of assembled and non-assembled bR trimers using directed mutagenesis, high-speed atomic force microscopy (HS-AFM), optical spectroscopy, and a proton pumping assay. First, we show that the bonds formed between W12 and F135 amino acid residues are responsible for trimer-trimer association that leads to lattice assembly; the lattice is completely disrupted in both W12I and F135I mutants. HS-AFM imaging reveals that both crystallized D96N and non-crystallized D96N/W12I mutants undergo a large conformational change (i.e., outward E-F loop displacement) upon light-activation. However, lattice disruption significantly reduces the rate of conformational change under continuous light illumination. Nevertheless, the quantum yield of M-state formation, measured by low-temperature UV-visible spectroscopy, and proton pumping efficiency are unaffected by lattice disruption. From these results, we conclude that trimer-trimer association plays essential roles in providing bound retinal with an appropriate environment to maintain its full photo-reactivity and in maintaining the natural photo-reaction pathway.

High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin

Dynamic changes in protein conformation in response to external stimuli are important in biological processes, but it has proved difficult to directly visualize such structural changes under physiological conditions. Here, we show that high-speed atomic force microscopy can be used to visualize dynamic changes in stimulated proteins. High-resolution movies of a light-driven proton pump, bacteriorhodopsin, reveal that, upon illumination, a cytoplasmic portion of each bacteriorhodopsin monomer is brought into contact with adjacent trimers. The bacteriorhodopsin-bacteriorhodopsin interaction in the transiently formed assembly engenders both positive and negative cooperative effects in the decay kinetics as the initial bacteriorhodopsin recovers and, as a consequence, the turnover rate of the photocycle is maintained constant, on average, irrespective of the light intensity. These results confirm that high-resolution visualization is a powerful approach for studying elaborate biomolecular processes under realistic conditions.

The ability of actinic light to modify the bacteriorhodopsin photocycle revisited: heterogeneity vs photocooperativity

In 1995, evidence both for photocooperativity and for heterogeneity as possible explanations for the ability of actinic light to modify the kinetics and pathways of the bacteriorhodopsin (BR) photocycle was reviewed ( Shrager, R. I., Hendler, R. W., and Bose, S. (1995) Eur. J. Biochem. 229, 589-595 ). Because both concepts could be successfully modeled to experimental data and there was suggestive published evidence for both, it was concluded that both photocooperativity and heterogeneity may be involved in the adaptation of the BR photocycle to different levels of actinic light. Since that time, more information has become available and it seemed appropriate to revisit the original question. In addition to the traditional models based on all intermediates in strict linear sequences, we have considered both homogeneous and heterogeneous models with branches. It is concluded that an explanation based on heterogeneity is more likely to be the true basis for the variation of the properties of the photocycle caused by changes in actinic light intensity. On the basis of new information presented here, it seems that a heterogeneous branched model is more likely than one with separate linear sequences.

An apparent general solution for the kinetic models of the bacteriorhodopsin photocycles

For the past decade, the field of Bacteriorhodopsin (BR) research has been influenced by a kinetic view of the photocycle as a reversible, homogeneous, model (RHM) with a linear sequence of intermediates. More recently, we proposed a much different model which consists of essentially unidirectional, parallel (i.e., heterogeneous) cycles (UPM) (Hendler, R. W.; Shrager, R. I.; Bose, S. J. Phys. Chem. B 2001, 105, 3319-3328). It is important to try to resolve which of the two models is more likely to be correct, because models influence and provide a basis for further experimentation. Therefore, in this communication, we reexamine the basis for the RHM with a focus on the most recent and complete description of this model (van Stokkum, I., H., M.; Lozier, R. J. Phys. Chem. B 2002, 106, 3477-3485) vis a vis the UPM in an in-depth study. We show that (i) the tested RHM does not really work for the data of van Stokkum and Lozier nor ours; (ii) no previously published RHM model has been shown to work for data under any conditions; (iii) there are many published observations that are difficult if not impossible to explain by RHM, but are readily explained by parallel cycles. It is also shown that either a UPM or a parallel cycle model with limited reversibility correctly describes photocycle data collected at pH 5, 7, and 9 and at 10, 20, and 30 degrees and is consistent with all known experimental observations.

Bacteriorhodopsin photocycle at cryogenic temperatures reveals distributed barriers of conformational substates

The time course of thermal reactions after illumination of 100% humidified bacteriorhodopsin films was followed with FTIR spectroscopy between 125 and 195 K. We monitored the conversion of the initial photoproduct, K, to the next, L intermediate, and a shunt reaction of the L state directly back to the initial BR state. Both reactions can be described by either multiexponential kinetics, which would lead to apparent end-state mixtures that contain increasing amounts of the product, i.e., L or BR, with increasing temperature, or distributed kinetics. Conventional kinetic schemes that could account for the partial conversion require reversible reactions, branching, or parallel cycles. These possibilities were tested by producing K or L and monitoring their interconversion at a single temperature and by shifting the temperature upward or downward after an initial incubation and after their redistribution. The results are inconsistent with any conventional scheme. Instead, we attribute the partial conversions to the other alternative, distributed kinetics, observed previously in myoglobin, which arise from an ensemble of frozen conformational substates at the cryogenic temperatures. In this case, the time course of the reactions reflects the progressive depletion of distinct microscopic substates in the order of their increasing activation barriers, with a distribution width for K to L reaction of approximately 7 kJ/mol.

Actinic light-energy dependence of proton release from bacteriorhodopsin

Measuring the light-density (fluence) dependence of proton release from flash excited bacteriorhodopsin with two independent methods we found that the lifetime of proton release increases and the proton pumping activity, defined as a number of protons per number of photocycle, decreases with increasing fluence. An interpretation of these results, based on bending of purple membrane and electrical interaction among the proton release groups of bacteriorhodopsin trimer, is presented.

Interconversions among four M-intermediates in the bacteriorhodopsin photocycle

Halobacterium salinarum displays four distinct kinetic forms of M-intermediate in its bacteriorhodopsin photocycle. In wild-type, there are mainly two species with time constants near 2 and 5 ms. Under various kinds of stress, two other species arise with time constants near 10 and 70 ms. We show that these four species are interconvertible. Increases in membrane hydrophobicity convert the slower to faster forms. Perturbations caused by Triton X-100 or mutations convert faster to slower forms. The fastest form requires a hydrophobic membrane environment near a ring of four charged aspartate residues in the trimer, namely Asp36, Asp38, Asp102, and Asp104 in the cytoplasmic loop regions. Interconversions of the 2-ms and 5-ms species of the wild-type are accomplished by pH-changes. The potential significance of these findings is discussed.

The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin

The last phase of the proton transfer cycle of bacteriorhodopsin calls for a passage of a proton from D38 to D96. This reaction utilizes a narrow shaft approximately 10-A long that connects the two carboxylates that cross through a very hydrophobic domain. As the shaft is too narrow to be permanently hydrated, there are two alternatives for the proton propagation into the channel. The proton may propagate through the shaft without solvation at the expense of a high electrostatic barrier; alternatively, the shaft will expand to accommodate some water molecules, thus lowering the Born energy for the insertion of the charge into the protein (B. Schätzler, N. A. Dencher, J. Tittor, D. Oesterhelt, S. Yaniv-Checover, E. Nachliel, and G. Gutman, 2003, BIOPHYS: J. 84:671-686). A comparative study of nine published crystal-structures of bacteriorhodopsin identified, next to the shaft, microcavities in the protein whose position and surrounding atoms are common to the reported structures. Some of the cavities either shrink or expand during the photocycle. It is argued that the plasticity of the cavities provides a working space needed for the transient solvation of the shaft, thus reducing the activation energy necessary for the solvation of the shaft. This suggestion is corroborated by the recent observations of Klink et al. (B. U. Klink, R. Winter, M. Engelhard, and I. Chizhov, 2002, BIOPHYS: J. 83:3490-3498) that the late phases of the photocycle (tau >/=1 ms) are strongly inhibited by external pressure.

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.

Electrogenic processes and protein conformational changes accompanying the bacteriorhodopsin photocycle

The possible mechanisms of electrogenic processes accompanying proton transport in bacteriorhodopsin are discussed on the basis of recent structural data of the protein. Apparent inconsistencies between experimental data and their interpretation are considered. Special emphasis is placed on the protein conformational changes accompanying the reprotonation of chromophore and proton uptake stage in the bacteriorhodopsin photocycle.

Structure of the bacteriorhodopsin mutant F219L N intermediate revealed by electron crystallography

Bacteriorhodopsin is a light-driven proton pump in halobacteria that forms crystalline patches in the cell membrane. Isomerization of the bound retinal initiates a photocycle resulting in the extrusion of a proton. An electron crystallographic analysis of the N intermediate from the mutant F219L gives a three-dimensional view of the large conformational change that occurs on the cytoplasmic side after deprotonation of the retinal Schiff base. Helix F, together with helix E, tilts away from the center of the molecule, causing a shift of approximately 3 A at the EF loop. The top of helix G moves slightly toward the ground state location of helix F. These movements open a water-accessible channel in the protein, enabling the transfer of a proton from an aspartate residue to the Schiff base. The movement of helix F toward neighbors in the crystal lattice is so large that it would not allow all molecules to change conformation simultaneously, limiting the occupancy of this state in the membrane to 33%. This explains photocooperative phenomena in the purple membrane.

Structure of bacteriorhodopsin at 1.55 A resolution

Th?e atomic structure of the light-driven ion pump bacteriorhodopsin and the surrounding lipid matrix was determined by X-ray diffraction of crystals grown in cubic lipid phase. In the extracellular region, an extensive three-dimensional hydrogen-bonded network of protein residues and seven water molecules leads from the buried retinal Schiff base and the proton acceptor Asp85 to the membrane surface. Near Lys216 where the retinal binds, transmembrane helix G contains a pi-bulge that causes a non-proline? kink. The bulge is stabilized by hydrogen-bonding of the main-chain carbonyl groups of Ala215 and Lys216 with two buried water molecules located between the Schiff base and the proton donor Asp96 in the cytoplasmic region. The results indicate extensive involvement of bound water molecules in both the structure and the function of this seven-helical membrane protein. A bilayer of 18 tightly bound lipid chains forms an annulus around the protein in the crystal. Contacts between the trimers in the membrane plane are mediated almost exclusively by lipids.

Functional roles of aspartic acid residues at the cytoplasmic surface of bacteriorhodopsin

The functions of the four aspartic acid residues in interhelical loops at the cytoplasmic surface of bacteriorhodopsin, Asp-36, Asp-38, Asp-102, and Asp-104, were investigated by studying single and multiple aspartic acid to asparagine mutants. The same mutants were examined also with the additional D96N residue replacement. The kinetics of the M and N intermediates of the photochemical cycles of these recombinant proteins were affected only in a minor, although self-consistent, way. When residue 38 is an aspartate and anionic, it makes the internal proton exchange between the retinal Schiff base and Asp-96 about 3 times more rapid, and events associated with the reisomerization of retinal to all-trans about 3 times slower. Asp-36 has the opposite effect on these processes, but to a smaller extent. Asp-102 and Asp-104 have even less or none of these effects. Of the four aspartates, only Asp-36 could play a direct role in proton uptake at the cytoplasmic surface. In the 13 bacterioopsin sequences now available, only this surface aspartate is conserved.

Two forms of N intermediate (N(open) and N(closed)) in the bacteriorhodopsin photocycle

Glutaraldehyde, aluminum ions and glycerol (that inhibit the M intermediate decay in the wild-type bacteriorhodopsin and azide-induced M decay in the D96N mutant by stabilization of the M(closed)) accelerate the N decay in the D96N mutant. The aluminum ions, the most potent activator of the N decay, induce a blue shift of the N difference spectrum by approximately 10 nm. Protonated azide as well as acetate and formate inhibit the N decay in both the D96N mutant and the wild-type protein. It is concluded that the N intermediate represents, in fact, an equilibrium mixture of the two ('open' and 'closed') forms. These two forms, like M(closed) and M(open), come to an equilibrium in the microseconds range. The absorption spectrum of the N(open) is slightly shifted to red in comparison to that of the N(closed). Again, this resembles the M forms. 13-cis-all-trans re-isomerization is assumed to occur in the N(closed) form only. Binding of 1-2 molecules of protonated azide stabilizes the N(open) form. Existence of the 'open' and 'closed' forms of the M and N intermediates provides the appropriate explanation of the cooperative phenomenon as well as some other effects on the bacteriorhodopsin photocycle. Summarizing the available data, we suggest that M(open) is identical to the M(N) form, whereas M1 and M2 are different substates of M(closed).

Bacteriorhodopsin

Bacteriorhodopsin is a seven-transmembrane helical protein that contains all-trans retinal. In this light-driven pump, a reaction cycle initiated by photoisomerization to 13-cis causes translocation of a proton across the membrane. Local changes in the geometry of the protonated Schiff base and the proton acceptor Asp85, and the proton conductivities of the half channels that lead from this active site to the two membrane surfaces, interact so as to allow timely proton transfers that result in proton release on the extracellular side and proton uptake on the cytoplasmic one. The details of the steps in this photocycle, and the underlying principles that ensure unidirectionality of the movement of a proton across the protein, provide strong clues to how ion pumps function.

Kinetic and thermodynamic study of the bacteriorhodopsin photocycle over a wide pH range

The photocycle of bacteriorhodopsin and its thermodynamic parameters were studied in the pH range of 4.5-9. Measurements were performed at five different wavelengths (410, 500, 570, 610, and 650 nm), in the time interval 300 ns to 0.5 s, at six temperatures between 5 and 30 degreesC. Data were fitted to different photocycle models. The sequential model with reversible reactions gave a good fit, and the linear character of the Eyring plots was fulfilled. The parallel model with unidirectional reactions gave a poor fit, and the Eyring plot of the rate constants did not follow the expected linear behavior. When a parallel model with reversible reactions, which has twice as many free parameters as the sequential model, was considered, the quality of the fit did not improve and the Eyring plots were not linear. The sequential model was used to determine the thermodynamic activation parameters (activation enthalpy, entropy, and free energy) of the transitions and the free energy levels of the intermediates. pH dependence of the parameters revealed details of the transitions between the intermediates: the transitions M1 to M2 and N to O disclosed a large entropy increase, which could be interpreted as a loosening of the protein structure. The pH dependence of the energy levels explains the disappearance of intermediate O at high pH. A hypothesis is proposed to interpret the relation between the observed pKa of the photocycle energetics and the role of several amino acids in the protein.

Actinic light and pH effect on the proton pumping of bacteriorhodopsin

The actinic light effect on the bacteriorhodopsin (BR) photocycle kinetics led to the assumption of a cooperative interaction between the photocycling BR molecules. In this paper we report the results of the actinic light effect and pH on the proton release and uptake kinetics. An electrical method is applied to detect proton release and uptake during the photocycle [E. Papp, G. Fricsovszky, J. Photochem. Photobiol. B: Biol. 5 (1990) 321]. The BR photocycle kinetics was also studied by absorption kinetics measurements at 410 nm and the data were analyzed by the local analysis of the M state kinetics [E. Papp, V.H. Ha, Biophys. Chem. 57 (1996) 155]. While at high pH and ionic strength, we found a similar behavior as reported earlier, at low ionic strength the light effect proved to be more complex. The main conclusions are the following: Though the number of BR excited to the photocycle (fraction cycling, fc) goes to saturation with increasing laser pulse energy, the absorbed energy by BR increases linearly with pulse energy. From the local analysis we conclude that the light effect changes the kinetics much earlier, already at the L intermediate state decay. The transient electric signal, caused by proton release and uptake, can be decomposed into two components similarly to the absorption kinetic data of the M intermediate state. The actinic light energy affects mainly the ratio of the two components and the proton movements inside BR while pH has an effect on the kinetics of the proton release and uptake groups at the membrane surface.

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.

Quantitative model for the cooperative interaction of the bacteriorhodopsin molecules in purple membranes

The trimeric, asymmetric and sequential model for the cooperative interaction of the bacteriorhodopsin molecules in purple membranes [Zs. Tokaji, Biophys. J. 65 (1993) 1130-11341 is being extended in the paper. Analyses of data from absorption kinetic measurements with preexcitation and green background illumination, and photoselection measurements on oriented samples confirm the main features of this cooperative interaction and support the validity of the extended model. This model includes the observed heterogeneity of the non-excited state of the bacteriorhodopsin molecules in purple membranes, and the agreement with the data suggests that molecules in any other state than the bacteriorhodopsin ground state can alter the photocycle of their neighbors. The presented results seem to contradict other models for the cooperation of the bacteriorhodopsin molecules.

Transient channel-opening in bacteriorhodopsin: an EPR study

Active translocation of ions across membranes requires alternating access of the ion binding site inside the pump to the two membrane surfaces. Proton translocation by bacteriorhodopsin (bR), the light-driven proton pump in Halobacterium salinarium, involves this kind of a change in the accessibility of the centrally located retinal Schiff base. This key event in bR's photocycle ensures that proton release occurs to the extracellular side and proton uptake from the cytoplasmic side. To study the role of protein conformational changes in this reprotonation switch, spin labels were attached to pairs of engineered cysteine residues in the cytoplasmic interhelical loops of bR. Light-induced changes in the distance between a spin label on the EF interhelical loop and a label on either the AB or the CD interhelical loop were observed, and the changes were monitored following photoactivation with time-resolved electron paramagnetic resonance (EPR) spectroscopy. Both distances increase transiently by about 5 A during the photocycle. This opening occurs between proton release and uptake, and may be the conformational switch that changes the accessibility of the retinal Schiff base to the cytoplasmic surface after proton release to the extracellular side.

Restricted motion of photoexcited bacteriorhodopsin in purple membrane containing ethanol

The molecular motion of retinal within the purple membrane was investigated by flash-induced absorption anisotropies with or without ethanol. In the absence of ethanol, the measured anisotropies at several wavelengths exhibited almost the same slow decay. This slow decay was attributed to only the rotation of purple membrane sheet itself in the aqueous suspension. In the presence of ethanol, however, we observed the wavelength-dependent anisotropies. The fluidity of the purple membrane, investigated with a fluorescence anisotropy method, was increased by the addition of ethanol. These facts indicated that the characteristic motion of bacteriorhodopsin is induced in perturbed purple membrane with ethanol. The data analysis was performed, taking account of the overlapping of absorption from ground-state bacteriorhodopsin and photointermediates. The results showed that the rotational motion of photointermediates within the membrane was more restricted than that of nonexcited bacteriorhodopsin. The addition of ethanol facilitated the rotation of nonexcited protein, whereas it did not significantly affect the motion of photointermediates. The restricted motion of photointermediates is probably caused by a conformational change in them, which may hinder the rotation of monomer protein and/or induce the interaction between photointermediate and neighboring proteins.

A local electrostatic change is the cause of the large-scale protein conformation shift in bacteriorhodopsin

During light-driven proton transport bacteriorhodopsin shuttles between two protein conformations. A large-scale structural change similar to that in the photochemical cycle is produced in the D85N mutant upon raising the pH, even without illumination. We report here that (i) the pKa values for the change in crystallographic parameters and for deprotonation of the retinal Schiff base are the same, (ii) the retinal isomeric configuration is nearly unaffected by the protein conformation, and (iii) preventing rotation of the C13-C14 double bond by replacing the retinal with an all-trans locked analogue makes little difference to the Schiff base pKa. We conclude that the direct cause of the conformational shift is destabilization of the structure upon loss of interaction of the positively charged Schiff base with anionic residues that form its counter-ion.

Cooperativity-induced optical anisotropy changes during the photocycle of bacteriorhodopsin

Previous photoselection measurements showed that if the excitation is weak no optical anisotropy changes appear in immobilized purple membranes during the photocycle. The present study demonstrates that surprisingly at stronger excitations the anisotropy changes versus time. At 412 nm the dichroic ratio decreases after a few milliseconds, while at 570 nm the similar decrease is followed by an increase. The phenomenon cannot be described by tiltings of the retinal chromophore. It is the consequence of the cooperative interaction among the photocycling bacteriorhodopsin molecules that regulates the yields of more than one (expectedly two main) parallel pathways existing in the millisecond time domain of the photocycle.

Complicated character of the M decay pH dependence in the D96N mutant is due to the two pathways of the M conversion

At high ionic strength, the pH dependence of the M intermediate decay in a photocycle of the D96N mutant bacteriorhodopsin shows a complicated behavior which is found to be due to the coexistence of two pathways of the M conversion. The M decay which dominates at pH < 5 is coupled to the proton uptake from the cytoplasmic surface and proceeds probably through the N intermediate. This pathway is inhibited by glutaraldehyde, the potent inhibitor of M decay in the wild-type bacteriorhodopsin and of the azide-facilitated M decay in the D96N mutant. Another pathway of the M decay is predominant at pH > 5. This pathway is insensitive to glutaraldehyde and some other similar inhibitors (lutetium ions, sucrose and glycerol). On the other hand, it is sensitive to the pK changes of the group X (Glu-204) in the outward proton pathway. Possibly, the M decay through this pathway represents a reverse H+ transport process (the proton uptake from the external surface) and proceeds via the L intermediate.

Perturbed interaction between residues 85 and 204 in Tyr-185-->Phe and Asp-85-->Glu bacteriorhodopsins

According to earlier reports, residue 85 in the bacteriorhodopsin mutants D85E and Y185F deprotonates with two apparent pKa values. Additionally, in Y185F, Asp-85 becomes significantly more protonated during light adaptation. We provide a new explanation for these findings. It is based on the scheme that links the protonation state of residue 85 to the protonation state of residue 204 (S.P. Balashov, E.S. Imasheva, R. Govindjee, and T.G. Ebrey. 1996. Biophys. J. 70:473-481; H.T. Richter, L.S. Brown, R. Needleman, and J.K. Lanyi. 1996. Biochemistry. 35:4054-4062) and justified by the observation that the biphasic titration curves of D85E and Y185F are converted to monophasic when the E204Q residue change is introduced as a second mutation. Accordingly, the D85E and Y 185F mutations are not the cause of the biphasic titration, as that is a property of the wild-type protein. By perturbing the extracellular region of the protein, the mutations increase the pKa of residue 85. This increases the amplitude of the second titration component and makes the biphasic character of the curves more obvious. Likewise, a small rise in the pKa of Asp-85 when the retinal isomerizes from 13-cis, 15-syn to all-trans accounts for the changed titration behavior of Y185F after light adaptation. This mechanism simplifies and unites the interpretation of what had appeared to be complex and unrelated phenomena.

Two bacteriorhodopsin M intermediates differing in accesibility of the Schiff base for azide

Glutaraldehyde treatment leads to the inhibition (i) of the M intermediate decay in wild-type bacteriorhodopsin (bR) and (ii) of the azide-facilitated M decay in the D96N mutant bR. LuCl3 is shown to be a more potent inhibitor of both processes. Glycerol and sucrose are also inhibitors. None of these agents change the linearity of the azide concentration dependency of the M decay in the D96N mutant but they do shift this dependency to higher azide concentrations. It is concluded that the two M forms are in equilibrium. These M forms differ in the accessibility of the Schiff base for azide and, probably, also for water molecules. The above-mentioned agents shift the equilibrium toward the less accessible M form. The data obtained are in line with the model of azide action as the penetrating proton donor and can hardly be realized within the framework of the model of Le Coutre et al. [(1995) Proc. Natl. Acad. Sci. USA 92, 4962-4966] which assumes that a bound anionic form of azide catalyzes proton transfer to the Schiff base.

Actinic light density dependence of the O intermediate of the photocycle of bacteriorhodopsin

The O intermediate of the photocycle of bacteriorhodopsin (BR) was studied by absorption kinetic measurements at different actinic light densities. With increasing exciting flash intensity, the relative yield of O slightly increases, while that of Mf strongly decreases at the expense of Ms. Kinetic calculations and the optical anisotropy of O show that O can be formed only from Mf although Mf and O have different light intensity dependences. In order to resolve the apparent contradiction, a phenomenologically new cooperative regulatory mechanism seems to be necessary.